5.0 (#65)

* feat: Add Bioxel asset catalog and layer management functionality

- Introduced a new asset catalog definition file for Blender to manage Bioxel assets.
- Implemented layer caching and snapshot functionality in `layer.py`, allowing for VDB file generation and low-resolution snapshots.
- Created node management functions in `node.py` for handling Bioxel nodes within Blender's Geometry Node Editor.
- Added an operator to extract mesh data from selected nodes in `structure.py`.
- Developed UI panels in `panels.py` for layer management, including import options and layer library display.

* Add unit tests for bioxel module and documentation

- Created README.md for test instructions and categories.
- Implemented comprehensive unit tests for the Data, Layer, and utility functions in the bioxel module.
- Added tests for reading NRRD and DICOM formats, data properties, and edge cases.
- Included tests for real data files to ensure functionality with actual datasets.

* feat: Update .gitattributes and .gitignore for improved asset management and ignore patterns

chore: Add app.json and omoolab.css for Obsidian integration

refactor: Clean up AGENTS.md and remove outdated test files

* feat: Update .gitignore to include scipy_ndimage directory

* feat: Update release workflow and manifest for improved dependency management and layer handling

* feat: Update .gitignore and add binary files for scipy_ndimage across multiple platforms

* feat: Add OPSX commands for archiving, exploring, and proposing changes

* feat: Refactor asset library management and update manifest for improved organization

* feat: Downgrade h5py version to 3.14.0 in requirements and manifest

* feat: Update Help operator and panel labels to use English terminology

* Translate documentation to Chinese, add support format details, and enhance styling with new fonts. Update mkdocs configuration for multilingual support and improve package dependencies.

* feat: Remove default version setting from extra configuration in mkdocs.yml

* fix: Update documentation links to point to the correct URLs for Chinese and English versions

* Add documentation for basic usage, supported formats, and performance tips

- Created English and Chinese documentation for basic usage of the add-on, including data download, import, extraction, and rendering steps.
- Added support format documentation listing compatible file types for the add-on.
- Included links to open databases for volumetric data.
- Provided performance improvement tips for voxel reconstruction and rendering, including settings for low-resolution previews and balanced rendering configurations.

* Add OpenSpec skills for change management and exploration

- Implement openspec-apply-change skill for applying tasks from OpenSpec changes.
- Create openspec-archive-change skill for archiving completed changes.
- Introduce openspec-explore skill for exploring ideas and clarifying requirements.
- Add openspec-propose skill for proposing new changes with generated artifacts.
- Migrate source command skills: source-command-opsx-apply, source-command-opsx-archive, source-command-opsx-explore, and source-command-opsx-propose for improved command handling.

* feat: Update version to 2.0.1, refactor asset library handling, and enhance layer import process

* fix: downgrade scipy version to 1.16.3 in build.py and pyproject.toml

* Remove deprecated modules and functions from bioxel package

- Deleted _ni_support.py, _utils.py, and dtype.py as they contained unused or redundant functions.
- Removed the resize function and related utilities from _warps.py to streamline image processing.
- Cleaned up the skimage module by removing unnecessary imports and functions.

* feat: Add SKIP_MODULE_NAMES to exclude specific modules during import and refactor io_worker import logic

* refactor: Remove known limitations section from documentation for EEVEE NEXT support

* feat: Implement CLI command registration for bioxelnodes_import_worker and refactor io_worker for improved module handling

* chore: Update version to 2.0.2 in project files and dependencies

* feat: Enhance volumetric data parsing by adding progress updates and refactoring worker processes

* feat: Enhance asset library management with status checks and error handling

* feat: Update version to 2.0.3 and adjust dependencies in project files

* feat: Remove unused asset library removal function

* feat: Expand documentation with project overview, build instructions, and architecture details

.agents/skills/openspec-apply-change/SKILL.md

@@ -0,0 +1,156 @@
+---
+name: openspec-apply-change
+description: Implement tasks from an OpenSpec change. Use when the user wants to start implementing, continue implementation, or work through tasks.
+license: MIT
+compatibility: Requires openspec CLI.
+metadata:
+  author: openspec
+  version: "1.0"
+  generatedBy: "1.3.1"
+---
+
+Implement tasks from an OpenSpec change.
+
+**Input**: Optionally specify a change name. If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes.
+
+**Steps**
+
+1. **Select the change**
+
+   If a name is provided, use it. Otherwise:
+   - Infer from conversation context if the user mentioned a change
+   - Auto-select if only one active change exists
+   - If ambiguous, run `openspec list --json` to get available changes and use the **AskUserQuestion tool** to let the user select
+
+   Always announce: "Using change: <name>" and how to override (e.g., `/opsx:apply <other>`).
+
+2. **Check status to understand the schema**
+   ```bash
+   openspec status --change "<name>" --json
+   ```
+   Parse the JSON to understand:
+   - `schemaName`: The workflow being used (e.g., "spec-driven")
+   - Which artifact contains the tasks (typically "tasks" for spec-driven, check status for others)
+
+3. **Get apply instructions**
+
+   ```bash
+   openspec instructions apply --change "<name>" --json
+   ```
+
+   This returns:
+   - `contextFiles`: artifact ID -> array of concrete file paths (varies by schema - could be proposal/specs/design/tasks or spec/tests/implementation/docs)
+   - Progress (total, complete, remaining)
+   - Task list with status
+   - Dynamic instruction based on current state
+
+   **Handle states:**
+   - If `state: "blocked"` (missing artifacts): show message, suggest using openspec-continue-change
+   - If `state: "all_done"`: congratulate, suggest archive
+   - Otherwise: proceed to implementation
+
+4. **Read context files**
+
+   Read every file path listed under `contextFiles` from the apply instructions output.
+   The files depend on the schema being used:
+   - **spec-driven**: proposal, specs, design, tasks
+   - Other schemas: follow the contextFiles from CLI output
+
+5. **Show current progress**
+
+   Display:
+   - Schema being used
+   - Progress: "N/M tasks complete"
+   - Remaining tasks overview
+   - Dynamic instruction from CLI
+
+6. **Implement tasks (loop until done or blocked)**
+
+   For each pending task:
+   - Show which task is being worked on
+   - Make the code changes required
+   - Keep changes minimal and focused
+   - Mark task complete in the tasks file: `- [ ]` → `- [x]`
+   - Continue to next task
+
+   **Pause if:**
+   - Task is unclear → ask for clarification
+   - Implementation reveals a design issue → suggest updating artifacts
+   - Error or blocker encountered → report and wait for guidance
+   - User interrupts
+
+7. **On completion or pause, show status**
+
+   Display:
+   - Tasks completed this session
+   - Overall progress: "N/M tasks complete"
+   - If all done: suggest archive
+   - If paused: explain why and wait for guidance
+
+**Output During Implementation**
+
+```
+## Implementing: <change-name> (schema: <schema-name>)
+
+Working on task 3/7: <task description>
+[...implementation happening...]
+✓ Task complete
+
+Working on task 4/7: <task description>
+[...implementation happening...]
+✓ Task complete
+```
+
+**Output On Completion**
+
+```
+## Implementation Complete
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Progress:** 7/7 tasks complete ✓
+
+### Completed This Session
+- [x] Task 1
+- [x] Task 2
+...
+
+All tasks complete! Ready to archive this change.
+```
+
+**Output On Pause (Issue Encountered)**
+
+```
+## Implementation Paused
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Progress:** 4/7 tasks complete
+
+### Issue Encountered
+<description of the issue>
+
+**Options:**
+1. <option 1>
+2. <option 2>
+3. Other approach
+
+What would you like to do?
+```
+
+**Guardrails**
+- Keep going through tasks until done or blocked
+- Always read context files before starting (from the apply instructions output)
+- If task is ambiguous, pause and ask before implementing
+- If implementation reveals issues, pause and suggest artifact updates
+- Keep code changes minimal and scoped to each task
+- Update task checkbox immediately after completing each task
+- Pause on errors, blockers, or unclear requirements - don't guess
+- Use contextFiles from CLI output, don't assume specific file names
+
+**Fluid Workflow Integration**
+
+This skill supports the "actions on a change" model:
+
+- **Can be invoked anytime**: Before all artifacts are done (if tasks exist), after partial implementation, interleaved with other actions
+- **Allows artifact updates**: If implementation reveals design issues, suggest updating artifacts - not phase-locked, work fluidly

.agents/skills/openspec-archive-change/SKILL.md

@@ -0,0 +1,114 @@
+---
+name: openspec-archive-change
+description: Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.
+license: MIT
+compatibility: Requires openspec CLI.
+metadata:
+  author: openspec
+  version: "1.0"
+  generatedBy: "1.3.1"
+---
+
+Archive a completed change in the experimental workflow.
+
+**Input**: Optionally specify a change name. If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes.
+
+**Steps**
+
+1. **If no change name provided, prompt for selection**
+
+   Run `openspec list --json` to get available changes. Use the **AskUserQuestion tool** to let the user select.
+
+   Show only active changes (not already archived).
+   Include the schema used for each change if available.
+
+   **IMPORTANT**: Do NOT guess or auto-select a change. Always let the user choose.
+
+2. **Check artifact completion status**
+
+   Run `openspec status --change "<name>" --json` to check artifact completion.
+
+   Parse the JSON to understand:
+   - `schemaName`: The workflow being used
+   - `artifacts`: List of artifacts with their status (`done` or other)
+
+   **If any artifacts are not `done`:**
+   - Display warning listing incomplete artifacts
+   - Use **AskUserQuestion tool** to confirm user wants to proceed
+   - Proceed if user confirms
+
+3. **Check task completion status**
+
+   Read the tasks file (typically `tasks.md`) to check for incomplete tasks.
+
+   Count tasks marked with `- [ ]` (incomplete) vs `- [x]` (complete).
+
+   **If incomplete tasks found:**
+   - Display warning showing count of incomplete tasks
+   - Use **AskUserQuestion tool** to confirm user wants to proceed
+   - Proceed if user confirms
+
+   **If no tasks file exists:** Proceed without task-related warning.
+
+4. **Assess delta spec sync state**
+
+   Check for delta specs at `openspec/changes/<name>/specs/`. If none exist, proceed without sync prompt.
+
+   **If delta specs exist:**
+   - Compare each delta spec with its corresponding main spec at `openspec/specs/<capability>/spec.md`
+   - Determine what changes would be applied (adds, modifications, removals, renames)
+   - Show a combined summary before prompting
+
+   **Prompt options:**
+   - If changes needed: "Sync now (recommended)", "Archive without syncing"
+   - If already synced: "Archive now", "Sync anyway", "Cancel"
+
+   If user chooses sync, use Task tool (subagent_type: "general-purpose", prompt: "Use Skill tool to invoke openspec-sync-specs for change '<name>'. Delta spec analysis: <include the analyzed delta spec summary>"). Proceed to archive regardless of choice.
+
+5. **Perform the archive**
+
+   Create the archive directory if it doesn't exist:
+   ```bash
+   mkdir -p openspec/changes/archive
+   ```
+
+   Generate target name using current date: `YYYY-MM-DD-<change-name>`
+
+   **Check if target already exists:**
+   - If yes: Fail with error, suggest renaming existing archive or using different date
+   - If no: Move the change directory to archive
+
+   ```bash
+   mv openspec/changes/<name> openspec/changes/archive/YYYY-MM-DD-<name>
+   ```
+
+6. **Display summary**
+
+   Show archive completion summary including:
+   - Change name
+   - Schema that was used
+   - Archive location
+   - Whether specs were synced (if applicable)
+   - Note about any warnings (incomplete artifacts/tasks)
+
+**Output On Success**
+
+```
+## Archive Complete
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Archived to:** openspec/changes/archive/YYYY-MM-DD-<name>/
+**Specs:** ✓ Synced to main specs (or "No delta specs" or "Sync skipped")
+
+All artifacts complete. All tasks complete.
+```
+
+**Guardrails**
+- Always prompt for change selection if not provided
+- Use artifact graph (openspec status --json) for completion checking
+- Don't block archive on warnings - just inform and confirm
+- Preserve .openspec.yaml when moving to archive (it moves with the directory)
+- Show clear summary of what happened
+- If sync is requested, use openspec-sync-specs approach (agent-driven)
+- If delta specs exist, always run the sync assessment and show the combined summary before prompting

.agents/skills/openspec-explore/SKILL.md

@@ -0,0 +1,288 @@
+---
+name: openspec-explore
+description: Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change.
+license: MIT
+compatibility: Requires openspec CLI.
+metadata:
+  author: openspec
+  version: "1.0"
+  generatedBy: "1.3.1"
+---
+
+Enter explore mode. Think deeply. Visualize freely. Follow the conversation wherever it goes.
+
+**IMPORTANT: Explore mode is for thinking, not implementing.** You may read files, search code, and investigate the codebase, but you must NEVER write code or implement features. If the user asks you to implement something, remind them to exit explore mode first and create a change proposal. You MAY create OpenSpec artifacts (proposals, designs, specs) if the user asks—that's capturing thinking, not implementing.
+
+**This is a stance, not a workflow.** There are no fixed steps, no required sequence, no mandatory outputs. You're a thinking partner helping the user explore.
+
+---
+
+## The Stance
+
+- **Curious, not prescriptive** - Ask questions that emerge naturally, don't follow a script
+- **Open threads, not interrogations** - Surface multiple interesting directions and let the user follow what resonates. Don't funnel them through a single path of questions.
+- **Visual** - Use ASCII diagrams liberally when they'd help clarify thinking
+- **Adaptive** - Follow interesting threads, pivot when new information emerges
+- **Patient** - Don't rush to conclusions, let the shape of the problem emerge
+- **Grounded** - Explore the actual codebase when relevant, don't just theorize
+
+---
+
+## What You Might Do
+
+Depending on what the user brings, you might:
+
+**Explore the problem space**
+- Ask clarifying questions that emerge from what they said
+- Challenge assumptions
+- Reframe the problem
+- Find analogies
+
+**Investigate the codebase**
+- Map existing architecture relevant to the discussion
+- Find integration points
+- Identify patterns already in use
+- Surface hidden complexity
+
+**Compare options**
+- Brainstorm multiple approaches
+- Build comparison tables
+- Sketch tradeoffs
+- Recommend a path (if asked)
+
+**Visualize**
+```
+┌─────────────────────────────────────────┐
+│     Use ASCII diagrams liberally        │
+├─────────────────────────────────────────┤
+│                                         │
+│      ┌────────┐         ┌────────┐      │
+│      │ State  │────────▶│ State  │      │
+│      │   A    │         │   B    │      │
+│      └────────┘         └────────┘      │
+│                                         │
+│   System diagrams, state machines,      │
+│   data flows, architecture sketches,    │
+│   dependency graphs, comparison tables  │
+│                                         │
+└─────────────────────────────────────────┘
+```
+
+**Surface risks and unknowns**
+- Identify what could go wrong
+- Find gaps in understanding
+- Suggest spikes or investigations
+
+---
+
+## OpenSpec Awareness
+
+You have full context of the OpenSpec system. Use it naturally, don't force it.
+
+### Check for context
+
+At the start, quickly check what exists:
+```bash
+openspec list --json
+```
+
+This tells you:
+- If there are active changes
+- Their names, schemas, and status
+- What the user might be working on
+
+### When no change exists
+
+Think freely. When insights crystallize, you might offer:
+
+- "This feels solid enough to start a change. Want me to create a proposal?"
+- Or keep exploring - no pressure to formalize
+
+### When a change exists
+
+If the user mentions a change or you detect one is relevant:
+
+1. **Read existing artifacts for context**
+   - `openspec/changes/<name>/proposal.md`
+   - `openspec/changes/<name>/design.md`
+   - `openspec/changes/<name>/tasks.md`
+   - etc.
+
+2. **Reference them naturally in conversation**
+   - "Your design mentions using Redis, but we just realized SQLite fits better..."
+   - "The proposal scopes this to premium users, but we're now thinking everyone..."
+
+3. **Offer to capture when decisions are made**
+
+    | Insight Type               | Where to Capture               |
+    |----------------------------|--------------------------------|
+    | New requirement discovered | `specs/<capability>/spec.md` |
+    | Requirement changed        | `specs/<capability>/spec.md` |
+    | Design decision made       | `design.md`                  |
+    | Scope changed              | `proposal.md`                |
+    | New work identified        | `tasks.md`                   |
+    | Assumption invalidated     | Relevant artifact              |
+
+   Example offers:
+   - "That's a design decision. Capture it in design.md?"
+   - "This is a new requirement. Add it to specs?"
+   - "This changes scope. Update the proposal?"
+
+4. **The user decides** - Offer and move on. Don't pressure. Don't auto-capture.
+
+---
+
+## What You Don't Have To Do
+
+- Follow a script
+- Ask the same questions every time
+- Produce a specific artifact
+- Reach a conclusion
+- Stay on topic if a tangent is valuable
+- Be brief (this is thinking time)
+
+---
+
+## Handling Different Entry Points
+
+**User brings a vague idea:**
+```
+User: I'm thinking about adding real-time collaboration
+
+You: Real-time collab is a big space. Let me think about this...
+
+      COLLABORATION SPECTRUM
+      ════════════════════════════════════════════
+
+      Awareness          Coordination         Sync
+          │                   │                 │
+          ▼                   ▼                 ▼
+      ┌────────┐         ┌────────┐        ┌────────┐
+      │Presence│         │Cursors │        │  CRDT  │
+      │  "3    │         │ Multi  │        │Conflict│
+      │online" │         │ select │        │  free  │
+      └────────┘         └────────┘        └────────┘
+          │                   │                 │
+       trivial            moderate           complex
+
+      Where's your head at?
+```
+
+**User brings a specific problem:**
+```
+User: The auth system is a mess
+
+You: [reads codebase]
+
+     ┌─────────────────────────────────────────────┐
+     │              CURRENT AUTH FLOW              │
+     └─────────────────────────────────────────────┘
+                        │
+          ┌─────────────┼─────────────┐
+          ▼             ▼             ▼
+     ┌─────────┐  ┌─────────┐  ┌─────────┐
+     │ Google  │  │  GitHub │  │  Email  │
+     │  OAuth  │  │  OAuth  │  │  Magic  │
+     └────┬────┘  └────┬────┘  └────┬────┘
+          │             │             │
+          └─────────────┼─────────────┘
+                        ▼
+                  ┌───────────┐
+                  │  Session  │
+                  └─────┬─────┘
+                        │
+                        ▼
+                  ┌───────────┐
+                  │   Perms   │
+                  └───────────┘
+
+     I see three tangles. Which one's burning?
+```
+
+**User is stuck mid-implementation:**
+```
+User: /opsx:explore add-auth-system
+      The OAuth integration is more complex than expected
+
+You: [reads change artifacts]
+
+     You're on task 4: "Implement OAuth flow"
+
+     Let me trace what's involved...
+
+     [draws diagram, explores options, suggests paths]
+
+     Want to update the design to reflect this?
+     Or add a spike task to investigate?
+```
+
+**User wants to compare options:**
+```
+User: Should we use Postgres or SQLite?
+
+You: Generic answer is boring. What's the context?
+
+User: A CLI tool that tracks local dev environments
+
+You: That changes everything.
+
+     ┌─────────────────────────────────────────────────┐
+     │          CLI TOOL DATA STORAGE                  │
+     └─────────────────────────────────────────────────┘
+
+     Key constraints:
+     • No daemon running
+     • Must work offline
+     • Single user
+
+                  SQLite          Postgres
+     Deployment   embedded ✓      needs server ✗
+     Offline      yes ✓           no ✗
+     Single file  yes ✓           no ✗
+
+     SQLite. Not even close.
+
+     Unless... is there a sync component?
+```
+
+---
+
+## Ending Discovery
+
+There's no required ending. Discovery might:
+
+- **Flow into a proposal**: "Ready to start? I can create a change proposal."
+- **Result in artifact updates**: "Updated design.md with these decisions"
+- **Just provide clarity**: User has what they need, moves on
+- **Continue later**: "We can pick this up anytime"
+
+When it feels like things are crystallizing, you might summarize:
+
+```
+## What We Figured Out
+
+**The problem**: [crystallized understanding]
+
+**The approach**: [if one emerged]
+
+**Open questions**: [if any remain]
+
+**Next steps** (if ready):
+- Create a change proposal
+- Keep exploring: just keep talking
+```
+
+But this summary is optional. Sometimes the thinking IS the value.
+
+---
+
+## Guardrails
+
+- **Don't implement** - Never write code or implement features. Creating OpenSpec artifacts is fine, writing application code is not.
+- **Don't fake understanding** - If something is unclear, dig deeper
+- **Don't rush** - Discovery is thinking time, not task time
+- **Don't force structure** - Let patterns emerge naturally
+- **Don't auto-capture** - Offer to save insights, don't just do it
+- **Do visualize** - A good diagram is worth many paragraphs
+- **Do explore the codebase** - Ground discussions in reality
+- **Do question assumptions** - Including the user's and your own

.agents/skills/openspec-propose/SKILL.md

@@ -0,0 +1,110 @@
+---
+name: openspec-propose
+description: Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation.
+license: MIT
+compatibility: Requires openspec CLI.
+metadata:
+  author: openspec
+  version: "1.0"
+  generatedBy: "1.3.1"
+---
+
+Propose a new change - create the change and generate all artifacts in one step.
+
+I'll create a change with artifacts:
+- proposal.md (what & why)
+- design.md (how)
+- tasks.md (implementation steps)
+
+When ready to implement, run /opsx:apply
+
+---
+
+**Input**: The user's request should include a change name (kebab-case) OR a description of what they want to build.
+
+**Steps**
+
+1. **If no clear input provided, ask what they want to build**
+
+   Use the **AskUserQuestion tool** (open-ended, no preset options) to ask:
+   > "What change do you want to work on? Describe what you want to build or fix."
+
+   From their description, derive a kebab-case name (e.g., "add user authentication" → `add-user-auth`).
+
+   **IMPORTANT**: Do NOT proceed without understanding what the user wants to build.
+
+2. **Create the change directory**
+   ```bash
+   openspec new change "<name>"
+   ```
+   This creates a scaffolded change at `openspec/changes/<name>/` with `.openspec.yaml`.
+
+3. **Get the artifact build order**
+   ```bash
+   openspec status --change "<name>" --json
+   ```
+   Parse the JSON to get:
+   - `applyRequires`: array of artifact IDs needed before implementation (e.g., `["tasks"]`)
+   - `artifacts`: list of all artifacts with their status and dependencies
+
+4. **Create artifacts in sequence until apply-ready**
+
+   Use the **TodoWrite tool** to track progress through the artifacts.
+
+   Loop through artifacts in dependency order (artifacts with no pending dependencies first):
+
+   a. **For each artifact that is `ready` (dependencies satisfied)**:
+      - Get instructions:
+        ```bash
+        openspec instructions <artifact-id> --change "<name>" --json
+        ```
+      - The instructions JSON includes:
+        - `context`: Project background (constraints for you - do NOT include in output)
+        - `rules`: Artifact-specific rules (constraints for you - do NOT include in output)
+        - `template`: The structure to use for your output file
+        - `instruction`: Schema-specific guidance for this artifact type
+        - `outputPath`: Where to write the artifact
+        - `dependencies`: Completed artifacts to read for context
+      - Read any completed dependency files for context
+      - Create the artifact file using `template` as the structure
+      - Apply `context` and `rules` as constraints - but do NOT copy them into the file
+      - Show brief progress: "Created <artifact-id>"
+
+   b. **Continue until all `applyRequires` artifacts are complete**
+      - After creating each artifact, re-run `openspec status --change "<name>" --json`
+      - Check if every artifact ID in `applyRequires` has `status: "done"` in the artifacts array
+      - Stop when all `applyRequires` artifacts are done
+
+   c. **If an artifact requires user input** (unclear context):
+      - Use **AskUserQuestion tool** to clarify
+      - Then continue with creation
+
+5. **Show final status**
+   ```bash
+   openspec status --change "<name>"
+   ```
+
+**Output**
+
+After completing all artifacts, summarize:
+- Change name and location
+- List of artifacts created with brief descriptions
+- What's ready: "All artifacts created! Ready for implementation."
+- Prompt: "Run `/opsx:apply` or ask me to implement to start working on the tasks."
+
+**Artifact Creation Guidelines**
+
+- Follow the `instruction` field from `openspec instructions` for each artifact type
+- The schema defines what each artifact should contain - follow it
+- Read dependency artifacts for context before creating new ones
+- Use `template` as the structure for your output file - fill in its sections
+- **IMPORTANT**: `context` and `rules` are constraints for YOU, not content for the file
+  - Do NOT copy `<context>`, `<rules>`, `<project_context>` blocks into the artifact
+  - These guide what you write, but should never appear in the output
+
+**Guardrails**
+- Create ALL artifacts needed for implementation (as defined by schema's `apply.requires`)
+- Always read dependency artifacts before creating a new one
+- If context is critically unclear, ask the user - but prefer making reasonable decisions to keep momentum
+- If a change with that name already exists, ask if user wants to continue it or create a new one
+- Verify each artifact file exists after writing before proceeding to next

.agents/skills/source-command-opsx-apply/SKILL.md

@@ -0,0 +1,156 @@
+---
+name: "source-command-opsx-apply"
+description: "Implement tasks from an OpenSpec change (Experimental)"
+---
+
+# source-command-opsx-apply
+
+Use this skill when the user asks to run the migrated source command `opsx-apply`.
+
+## Command Template
+
+Implement tasks from an OpenSpec change.
+
+**Input**: Optionally specify a change name (e.g., `/opsx:apply add-auth`). If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes.
+
+**Steps**
+
+1. **Select the change**
+
+   If a name is provided, use it. Otherwise:
+   - Infer from conversation context if the user mentioned a change
+   - Auto-select if only one active change exists
+   - If ambiguous, run `openspec list --json` to get available changes and use the **AskUserQuestion tool** to let the user select
+
+   Always announce: "Using change: <name>" and how to override (e.g., `/opsx:apply <other>`).
+
+2. **Check status to understand the schema**
+   ```bash
+   openspec status --change "<name>" --json
+   ```
+   Parse the JSON to understand:
+   - `schemaName`: The workflow being used (e.g., "spec-driven")
+   - Which artifact contains the tasks (typically "tasks" for spec-driven, check status for others)
+
+3. **Get apply instructions**
+
+   ```bash
+   openspec instructions apply --change "<name>" --json
+   ```
+
+   This returns:
+   - `contextFiles`: artifact ID -> array of concrete file paths (varies by schema)
+   - Progress (total, complete, remaining)
+   - Task list with status
+   - Dynamic instruction based on current state
+
+   **Handle states:**
+   - If `state: "blocked"` (missing artifacts): show message, suggest using `/opsx:continue`
+   - If `state: "all_done"`: congratulate, suggest archive
+   - Otherwise: proceed to implementation
+
+4. **Read context files**
+
+   Read every file path listed under `contextFiles` from the apply instructions output.
+   The files depend on the schema being used:
+   - **spec-driven**: proposal, specs, design, tasks
+   - Other schemas: follow the contextFiles from CLI output
+
+5. **Show current progress**
+
+   Display:
+   - Schema being used
+   - Progress: "N/M tasks complete"
+   - Remaining tasks overview
+   - Dynamic instruction from CLI
+
+6. **Implement tasks (loop until done or blocked)**
+
+   For each pending task:
+   - Show which task is being worked on
+   - Make the code changes required
+   - Keep changes minimal and focused
+   - Mark task complete in the tasks file: `- [ ]` → `- [x]`
+   - Continue to next task
+
+   **Pause if:**
+   - Task is unclear → ask for clarification
+   - Implementation reveals a design issue → suggest updating artifacts
+   - Error or blocker encountered → report and wait for guidance
+   - User interrupts
+
+7. **On completion or pause, show status**
+
+   Display:
+   - Tasks completed this session
+   - Overall progress: "N/M tasks complete"
+   - If all done: suggest archive
+   - If paused: explain why and wait for guidance
+
+**Output During Implementation**
+
+```
+## Implementing: <change-name> (schema: <schema-name>)
+
+Working on task 3/7: <task description>
+[...implementation happening...]
+✓ Task complete
+
+Working on task 4/7: <task description>
+[...implementation happening...]
+✓ Task complete
+```
+
+**Output On Completion**
+
+```
+## Implementation Complete
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Progress:** 7/7 tasks complete ✓
+
+### Completed This Session
+- [x] Task 1
+- [x] Task 2
+...
+
+All tasks complete! You can archive this change with `/opsx:archive`.
+```
+
+**Output On Pause (Issue Encountered)**
+
+```
+## Implementation Paused
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Progress:** 4/7 tasks complete
+
+### Issue Encountered
+<description of the issue>
+
+**Options:**
+1. <option 1>
+2. <option 2>
+3. Other approach
+
+What would you like to do?
+```
+
+**Guardrails**
+- Keep going through tasks until done or blocked
+- Always read context files before starting (from the apply instructions output)
+- If task is ambiguous, pause and ask before implementing
+- If implementation reveals issues, pause and suggest artifact updates
+- Keep code changes minimal and scoped to each task
+- Update task checkbox immediately after completing each task
+- Pause on errors, blockers, or unclear requirements - don't guess
+- Use contextFiles from CLI output, don't assume specific file names
+
+**Fluid Workflow Integration**
+
+This skill supports the "actions on a change" model:
+
+- **Can be invoked anytime**: Before all artifacts are done (if tasks exist), after partial implementation, interleaved with other actions
+- **Allows artifact updates**: If implementation reveals design issues, suggest updating artifacts - not phase-locked, work fluidly

.agents/skills/source-command-opsx-archive/SKILL.md

@@ -0,0 +1,161 @@
+---
+name: "source-command-opsx-archive"
+description: "Archive a completed change in the experimental workflow"
+---
+
+# source-command-opsx-archive
+
+Use this skill when the user asks to run the migrated source command `opsx-archive`.
+
+## Command Template
+
+Archive a completed change in the experimental workflow.
+
+**Input**: Optionally specify a change name after `/opsx:archive` (e.g., `/opsx:archive add-auth`). If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes.
+
+**Steps**
+
+1. **If no change name provided, prompt for selection**
+
+   Run `openspec list --json` to get available changes. Use the **AskUserQuestion tool** to let the user select.
+
+   Show only active changes (not already archived).
+   Include the schema used for each change if available.
+
+   **IMPORTANT**: Do NOT guess or auto-select a change. Always let the user choose.
+
+2. **Check artifact completion status**
+
+   Run `openspec status --change "<name>" --json` to check artifact completion.
+
+   Parse the JSON to understand:
+   - `schemaName`: The workflow being used
+   - `artifacts`: List of artifacts with their status (`done` or other)
+
+   **If any artifacts are not `done`:**
+   - Display warning listing incomplete artifacts
+   - Prompt user for confirmation to continue
+   - Proceed if user confirms
+
+3. **Check task completion status**
+
+   Read the tasks file (typically `tasks.md`) to check for incomplete tasks.
+
+   Count tasks marked with `- [ ]` (incomplete) vs `- [x]` (complete).
+
+   **If incomplete tasks found:**
+   - Display warning showing count of incomplete tasks
+   - Prompt user for confirmation to continue
+   - Proceed if user confirms
+
+   **If no tasks file exists:** Proceed without task-related warning.
+
+4. **Assess delta spec sync state**
+
+   Check for delta specs at `openspec/changes/<name>/specs/`. If none exist, proceed without sync prompt.
+
+   **If delta specs exist:**
+   - Compare each delta spec with its corresponding main spec at `openspec/specs/<capability>/spec.md`
+   - Determine what changes would be applied (adds, modifications, removals, renames)
+   - Show a combined summary before prompting
+
+   **Prompt options:**
+   - If changes needed: "Sync now (recommended)", "Archive without syncing"
+   - If already synced: "Archive now", "Sync anyway", "Cancel"
+
+   If user chooses sync, use Task tool (subagent_type: "general-purpose", prompt: "Use Skill tool to invoke openspec-sync-specs for change '<name>'. Delta spec analysis: <include the analyzed delta spec summary>"). Proceed to archive regardless of choice.
+
+5. **Perform the archive**
+
+   Create the archive directory if it doesn't exist:
+   ```bash
+   mkdir -p openspec/changes/archive
+   ```
+
+   Generate target name using current date: `YYYY-MM-DD-<change-name>`
+
+   **Check if target already exists:**
+   - If yes: Fail with error, suggest renaming existing archive or using different date
+   - If no: Move the change directory to archive
+
+   ```bash
+   mv openspec/changes/<name> openspec/changes/archive/YYYY-MM-DD-<name>
+   ```
+
+6. **Display summary**
+
+   Show archive completion summary including:
+   - Change name
+   - Schema that was used
+   - Archive location
+   - Spec sync status (synced / sync skipped / no delta specs)
+   - Note about any warnings (incomplete artifacts/tasks)
+
+**Output On Success**
+
+```
+## Archive Complete
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Archived to:** openspec/changes/archive/YYYY-MM-DD-<name>/
+**Specs:** ✓ Synced to main specs
+
+All artifacts complete. All tasks complete.
+```
+
+**Output On Success (No Delta Specs)**
+
+```
+## Archive Complete
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Archived to:** openspec/changes/archive/YYYY-MM-DD-<name>/
+**Specs:** No delta specs
+
+All artifacts complete. All tasks complete.
+```
+
+**Output On Success With Warnings**
+
+```
+## Archive Complete (with warnings)
+
+**Change:** <change-name>
+**Schema:** <schema-name>
+**Archived to:** openspec/changes/archive/YYYY-MM-DD-<name>/
+**Specs:** Sync skipped (user chose to skip)
+
+**Warnings:**
+- Archived with 2 incomplete artifacts
+- Archived with 3 incomplete tasks
+- Delta spec sync was skipped (user chose to skip)
+
+Review the archive if this was not intentional.
+```
+
+**Output On Error (Archive Exists)**
+
+```
+## Archive Failed
+
+**Change:** <change-name>
+**Target:** openspec/changes/archive/YYYY-MM-DD-<name>/
+
+Target archive directory already exists.
+
+**Options:**
+1. Rename the existing archive
+2. Delete the existing archive if it's a duplicate
+3. Wait until a different date to archive
+```
+
+**Guardrails**
+- Always prompt for change selection if not provided
+- Use artifact graph (openspec status --json) for completion checking
+- Don't block archive on warnings - just inform and confirm
+- Preserve .openspec.yaml when moving to archive (it moves with the directory)
+- Show clear summary of what happened
+- If sync is requested, use the Skill tool to invoke `openspec-sync-specs` (agent-driven)
+- If delta specs exist, always run the sync assessment and show the combined summary before prompting

.agents/skills/source-command-opsx-explore/SKILL.md

@@ -0,0 +1,177 @@
+---
+name: "source-command-opsx-explore"
+description: "Enter explore mode - think through ideas, investigate problems, clarify requirements"
+---
+
+# source-command-opsx-explore
+
+Use this skill when the user asks to run the migrated source command `opsx-explore`.
+
+## Command Template
+
+Enter explore mode. Think deeply. Visualize freely. Follow the conversation wherever it goes.
+
+**IMPORTANT: Explore mode is for thinking, not implementing.** You may read files, search code, and investigate the codebase, but you must NEVER write code or implement features. If the user asks you to implement something, remind them to exit explore mode first and create a change proposal. You MAY create OpenSpec artifacts (proposals, designs, specs) if the user asks—that's capturing thinking, not implementing.
+
+**This is a stance, not a workflow.** There are no fixed steps, no required sequence, no mandatory outputs. You're a thinking partner helping the user explore.
+
+**Input**: The argument after `/opsx:explore` is whatever the user wants to think about. Could be:
+- A vague idea: "real-time collaboration"
+- A specific problem: "the auth system is getting unwieldy"
+- A change name: "add-dark-mode" (to explore in context of that change)
+- A comparison: "postgres vs sqlite for this"
+- Nothing (just enter explore mode)
+
+---
+
+## The Stance
+
+- **Curious, not prescriptive** - Ask questions that emerge naturally, don't follow a script
+- **Open threads, not interrogations** - Surface multiple interesting directions and let the user follow what resonates. Don't funnel them through a single path of questions.
+- **Visual** - Use ASCII diagrams liberally when they'd help clarify thinking
+- **Adaptive** - Follow interesting threads, pivot when new information emerges
+- **Patient** - Don't rush to conclusions, let the shape of the problem emerge
+- **Grounded** - Explore the actual codebase when relevant, don't just theorize
+
+---
+
+## What You Might Do
+
+Depending on what the user brings, you might:
+
+**Explore the problem space**
+- Ask clarifying questions that emerge from what they said
+- Challenge assumptions
+- Reframe the problem
+- Find analogies
+
+**Investigate the codebase**
+- Map existing architecture relevant to the discussion
+- Find integration points
+- Identify patterns already in use
+- Surface hidden complexity
+
+**Compare options**
+- Brainstorm multiple approaches
+- Build comparison tables
+- Sketch tradeoffs
+- Recommend a path (if asked)
+
+**Visualize**
+```
+┌─────────────────────────────────────────┐
+│     Use ASCII diagrams liberally        │
+├─────────────────────────────────────────┤
+│                                         │
+│      ┌────────┐         ┌────────┐      │
+│      │ State  │────────▶│ State  │      │
+│      │   A    │         │   B    │      │
+│      └────────┘         └────────┘      │
+│                                         │
+│   System diagrams, state machines,      │
+│   data flows, architecture sketches,    │
+│   dependency graphs, comparison tables  │
+│                                         │
+└─────────────────────────────────────────┘
+```
+
+**Surface risks and unknowns**
+- Identify what could go wrong
+- Find gaps in understanding
+- Suggest spikes or investigations
+
+---
+
+## OpenSpec Awareness
+
+You have full context of the OpenSpec system. Use it naturally, don't force it.
+
+### Check for context
+
+At the start, quickly check what exists:
+```bash
+openspec list --json
+```
+
+This tells you:
+- If there are active changes
+- Their names, schemas, and status
+- What the user might be working on
+
+If the user mentioned a specific change name, read its artifacts for context.
+
+### When no change exists
+
+Think freely. When insights crystallize, you might offer:
+
+- "This feels solid enough to start a change. Want me to create a proposal?"
+- Or keep exploring - no pressure to formalize
+
+### When a change exists
+
+If the user mentions a change or you detect one is relevant:
+
+1. **Read existing artifacts for context**
+   - `openspec/changes/<name>/proposal.md`
+   - `openspec/changes/<name>/design.md`
+   - `openspec/changes/<name>/tasks.md`
+   - etc.
+
+2. **Reference them naturally in conversation**
+   - "Your design mentions using Redis, but we just realized SQLite fits better..."
+   - "The proposal scopes this to premium users, but we're now thinking everyone..."
+
+3. **Offer to capture when decisions are made**
+
+    | Insight Type               | Where to Capture               |
+    |----------------------------|--------------------------------|
+    | New requirement discovered | `specs/<capability>/spec.md` |
+    | Requirement changed        | `specs/<capability>/spec.md` |
+    | Design decision made       | `design.md`                  |
+    | Scope changed              | `proposal.md`                |
+    | New work identified        | `tasks.md`                   |
+    | Assumption invalidated     | Relevant artifact              |
+
+   Example offers:
+   - "That's a design decision. Capture it in design.md?"
+   - "This is a new requirement. Add it to specs?"
+   - "This changes scope. Update the proposal?"
+
+4. **The user decides** - Offer and move on. Don't pressure. Don't auto-capture.
+
+---
+
+## What You Don't Have To Do
+
+- Follow a script
+- Ask the same questions every time
+- Produce a specific artifact
+- Reach a conclusion
+- Stay on topic if a tangent is valuable
+- Be brief (this is thinking time)
+
+---
+
+## Ending Discovery
+
+There's no required ending. Discovery might:
+
+- **Flow into a proposal**: "Ready to start? I can create a change proposal."
+- **Result in artifact updates**: "Updated design.md with these decisions"
+- **Just provide clarity**: User has what they need, moves on
+- **Continue later**: "We can pick this up anytime"
+
+When things crystallize, you might offer a summary - but it's optional. Sometimes the thinking IS the value.
+
+---
+
+## Guardrails
+
+- **Don't implement** - Never write code or implement features. Creating OpenSpec artifacts is fine, writing application code is not.
+- **Don't fake understanding** - If something is unclear, dig deeper
+- **Don't rush** - Discovery is thinking time, not task time
+- **Don't force structure** - Let patterns emerge naturally
+- **Don't auto-capture** - Offer to save insights, don't just do it
+- **Do visualize** - A good diagram is worth many paragraphs
+- **Do explore the codebase** - Ground discussions in reality
+- **Do question assumptions** - Including the user's and your own

.agents/skills/source-command-opsx-propose/SKILL.md

@@ -0,0 +1,110 @@
+---
+name: "source-command-opsx-propose"
+description: "Propose a new change - create it and generate all artifacts in one step"
+---
+
+# source-command-opsx-propose
+
+Use this skill when the user asks to run the migrated source command `opsx-propose`.
+
+## Command Template
+
+Propose a new change - create the change and generate all artifacts in one step.
+
+I'll create a change with artifacts:
+- proposal.md (what & why)
+- design.md (how)
+- tasks.md (implementation steps)
+
+When ready to implement, run /opsx:apply
+
+---
+
+**Input**: The argument after `/opsx:propose` is the change name (kebab-case), OR a description of what the user wants to build.
+
+**Steps**
+
+1. **If no input provided, ask what they want to build**
+
+   Use the **AskUserQuestion tool** (open-ended, no preset options) to ask:
+   > "What change do you want to work on? Describe what you want to build or fix."
+
+   From their description, derive a kebab-case name (e.g., "add user authentication" → `add-user-auth`).
+
+   **IMPORTANT**: Do NOT proceed without understanding what the user wants to build.
+
+2. **Create the change directory**
+   ```bash
+   openspec new change "<name>"
+   ```
+   This creates a scaffolded change at `openspec/changes/<name>/` with `.openspec.yaml`.
+
+3. **Get the artifact build order**
+   ```bash
+   openspec status --change "<name>" --json
+   ```
+   Parse the JSON to get:
+   - `applyRequires`: array of artifact IDs needed before implementation (e.g., `["tasks"]`)
+   - `artifacts`: list of all artifacts with their status and dependencies
+
+4. **Create artifacts in sequence until apply-ready**
+
+   Use the **TodoWrite tool** to track progress through the artifacts.
+
+   Loop through artifacts in dependency order (artifacts with no pending dependencies first):
+
+   a. **For each artifact that is `ready` (dependencies satisfied)**:
+      - Get instructions:
+        ```bash
+        openspec instructions <artifact-id> --change "<name>" --json
+        ```
+      - The instructions JSON includes:
+        - `context`: Project background (constraints for you - do NOT include in output)
+        - `rules`: Artifact-specific rules (constraints for you - do NOT include in output)
+        - `template`: The structure to use for your output file
+        - `instruction`: Schema-specific guidance for this artifact type
+        - `outputPath`: Where to write the artifact
+        - `dependencies`: Completed artifacts to read for context
+      - Read any completed dependency files for context
+      - Create the artifact file using `template` as the structure
+      - Apply `context` and `rules` as constraints - but do NOT copy them into the file
+      - Show brief progress: "Created <artifact-id>"
+
+   b. **Continue until all `applyRequires` artifacts are complete**
+      - After creating each artifact, re-run `openspec status --change "<name>" --json`
+      - Check if every artifact ID in `applyRequires` has `status: "done"` in the artifacts array
+      - Stop when all `applyRequires` artifacts are done
+
+   c. **If an artifact requires user input** (unclear context):
+      - Use **AskUserQuestion tool** to clarify
+      - Then continue with creation
+
+5. **Show final status**
+   ```bash
+   openspec status --change "<name>"
+   ```
+
+**Output**
+
+After completing all artifacts, summarize:
+- Change name and location
+- List of artifacts created with brief descriptions
+- What's ready: "All artifacts created! Ready for implementation."
+- Prompt: "Run `/opsx:apply` to start implementing."
+
+**Artifact Creation Guidelines**
+
+- Follow the `instruction` field from `openspec instructions` for each artifact type
+- The schema defines what each artifact should contain - follow it
+- Read dependency artifacts for context before creating new ones
+- Use `template` as the structure for your output file - fill in its sections
+- **IMPORTANT**: `context` and `rules` are constraints for YOU, not content for the file
+  - Do NOT copy `<context>`, `<rules>`, `<project_context>` blocks into the artifact
+  - These guide what you write, but should never appear in the output
+
+**Guardrails**
+- Create ALL artifacts needed for implementation (as defined by schema's `apply.requires`)
+- Always read dependency artifacts before creating a new one
+- If context is critically unclear, ask the user - but prefer making reasonable decisions to keep momentum
+- If a change with that name already exists, ask if user wants to continue it or create a new one
+- Verify each artifact file exists after writing before proceeding to next

.gitattributes

@@ -1 +1,131 @@
-*.blend filter=lfs diff=lfs merge=lfs -text
+# Define macros (only works in top-level gitattributes files)
+[attr]lfs               filter=lfs diff=lfs merge=lfs -text
+
+# 3D models
+*.collada               lfs
+*.dae                   lfs
+*.dxf                   lfs
+*.FBX                   lfs
+*.fbx                   lfs
+*.jas                   lfs
+*.lws                   lfs
+*.lxo                   lfs
+*.obj                   lfs
+*.ply                   lfs
+*.skp                   lfs
+*.stl                   lfs
+*.stp                   lfs
+*.usd                   lfs
+*.usda                  lfs
+*.usdc                  lfs
+*.usdz                  lfs
+*.glb                   lfs
+*.gltf                  lfs
+
+# Audio
+*.aif                   lfs
+*.aiff                  lfs
+*.it                    lfs
+*.mod                   lfs
+*.mp3                   lfs
+*.ogg                   lfs
+*.s3m                   lfs
+*.wav                   lfs
+*.xm                    lfs
+
+# Video
+*.asf                   lfs
+*.avi                   lfs
+*.flv                   lfs
+*.mov                   lfs
+*.mp4                   lfs
+*.mpeg                  lfs
+*.mpg                   lfs
+*.ogv                   lfs
+*.wmv                   lfs
+*.mkv                   lfs
+
+# Images
+*.bmp                   lfs
+*.exr                   lfs
+*.gif                   lfs
+*.hdr                   lfs
+*.iff                   lfs
+*.jpeg                  lfs
+*.jpg                   lfs
+*.pict                  lfs
+*.png                   lfs
+*.psd                   lfs
+*.tga                   lfs
+*.tif                   lfs
+*.tiff                  lfs
+*.webp                  lfs
+
+# Compressed Archive
+*.7z                    lfs
+*.bz2                   lfs
+*.gz                    lfs
+*.rar                   lfs
+*.tar                   lfs
+*.zip                   lfs
+
+# Compiled Dynamic Library
+*.dll                   lfs
+*.pdb                   lfs
+*.so                    lfs
+
+# Fonts
+*.otf                   lfs
+*.ttf                   lfs
+*.woff                  lfs
+*.woff2                 lfs
+
+# Executable/Installer
+*.apk                   lfs
+*.exe                   lfs
+
+# Documents
+*.pdf                   lfs
+*.doc                   lfs
+*.xls                   lfs
+*.ppt                   lfs
+*.docx                  lfs
+*.xlsx                  lfs
+*.pptx                  lfs
+
+# Adobe
+*.psd                   lfs
+*.ai                    lfs
+*.aep                   lfs
+*.prproj                lfs
+*.spp                   lfs
+
+# Zbrush
+*.zbr                   lfs
+*.zpr                   lfs
+*.ztl                   lfs
+*.c4d                   lfs
+
+# Autodesk
+*.max                   lfs
+*.ma                    lfs
+*.mb                    lfs
+*.3dm                   lfs
+*.3ds                   lfs
+
+# Blender
+*.blend                 lfs
+*.blend1                lfs
+*.c4d                   lfs
+
+# Imaging
+*.dicom                 lfs
+*.dcm                   lfs
+*.nii                   lfs
+*.ome                   lfs
+*.map                   lfs
+*.mrc                   lfs
+
+# Others
+*.abr                   lfs
+*.tpl                   lfs

.github/workflows/release.yml

@@ -1,31 +1,12 @@
-name: Upload Assets to Release
+name: Release Version
 
 on:
   push:
-    branches:
-      - "release/*"
+    tags:
+      # Publish on any tag starting with a `v`, e.g., v0.1.0
+      - 'v*'
 
 jobs:
-  # draft_release:
-  #   name: Draft Release
-  #   runs-on: ubuntu-latest
-  #   outputs:
-  #     upload_url: ${{ steps.draft_release.outputs.upload_url }}
-  #     version: ${{ steps.set_env.outputs.version }}
-  #   steps:
-  #     - name: Set Version Env
-  #       id: set_env
-  #       run: |
-  #         ref_name=${{ github.ref_name }}
-  #         echo "version=${ref_name#release/}" >> "$GITHUB_OUTPUT"
-  #     - name: Get release
-  #       id: draft_release
-  #       uses: cardinalby/git-get-release-action@1.2.4
-  #       with:
-  #         releaseName: Upload
-  #       env:
-  #         GITHUB_TOKEN: ${{ github.token }}
-
   draft_release:
     name: Draft Release
     permissions:
@@ -50,7 +31,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  build_blender_add-on:
+  build_extension:
     name: Build Blender Extension
     needs: draft_release
     runs-on: ubuntu-latest
@@ -62,16 +43,20 @@ jobs:
         uses: actions/checkout@v4
         with:
           lfs: "true"
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-      - name: Build Add-on
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Dependencies
         run: |
-          pip install tomlkit
-          python build.py ${{ matrix.platform }}
-          zip -r package.zip bioxelnodes
-      - name: Upload Release Asset
+          uv python install 3.11
+          uv python pin 3.11
+          uv sync
+      - name: Build Extension
+        run: | # build.py need tomlkit to edit blender_manifest.toml
+          uv run build.py ${{ matrix.platform }} 3.11
+          uv run build.py ${{ matrix.platform }} 3.13
+          cd src/bioxelnodes
+          zip -r ../../package.zip .
+      - name: Upload Extension
         id: upload-release-asset
         uses: actions/upload-release-asset@v1
         env:
@@ -79,5 +64,5 @@ jobs:
         with:
           upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
           asset_path: ./package.zip
-          asset_name: BioxelNodes_${{ needs.draft_release.outputs.version }}_${{ matrix.platform }}.zip
+          asset_name: BioxelNodes.${{ needs.draft_release.outputs.version }}.${{ matrix.platform }}.zip
           asset_content_type: application/zip

.gitignore

@@ -1,6 +1,51 @@
+# Tempary files
+temp
+sandbox.*
+/notes/
+
+# Environments
+.env
+.envrc
+.venv
+.env.*
+!.env.example
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+.secrets
+.secrets.*
+!.secrets.example
+secrets/
+SECRETS/
+secrets.bak/
+
+# Claude Code
+.claude/settings.local.json
+.claudian
+
+# Obsidian
+.obsidian/*
+!.obsidian/snippets
+!.obsidian/app.json
+
+*.canvas
+
+# Keep odox for extract to openwiki
+!.obsidian/plugins
+.obsidian/plugins/*
+!.obsidian/plugins/odox
+
+# Blender
+*.blend1
+blender_assets.cats.txt~
+blendcache_*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -20,7 +65,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -28,8 +72,8 @@ share/python-wheels/
 MANIFEST
 
 # PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
 
@@ -47,8 +91,10 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
+*.py.cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -71,6 +117,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -81,30 +128,70 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies
 #   having no cross-platform support, pipenv may install dependencies that don't work, or not
 #   install all needed dependencies.
-#Pipfile.lock
+# Pipfile.lock
 
-# celery beat schedule file
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
 celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
 
 # SageMath parsed files
 *.sage.py
 
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
 # Spyder project settings
 .spyderproject
 .spyproject
@@ -123,16 +210,183 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-pythonlib*
+# pytype static type analyzer
+.pytype/
 
-*.blend1
+# Cython debug symbols
+cython_debug/
 
-blendcache_*
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
 
-*.ipynb
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
 
-.secrets
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
 
-.vdb
+# Ruff stuff:
+.ruff_cache/
 
-!scipy_ndimage/*/**
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Snowpack dependency directory (https://snowpack.dev/)
+web_modules/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional stylelint cache
+.stylelintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+.parcel-cache
+
+# Next.js build output
+.next
+out
+
+# Nuxt.js build / generate output
+.nuxt
+dist
+.output
+
+# Gatsby files
+.cache/
+# Comment in the public line in if your project uses Gatsby and not Next.js
+# https://nextjs.org/blog/next-9-1#public-directory-support
+# public
+
+# vuepress build output
+.vuepress/dist
+
+# vuepress v2.x temp and cache directory
+.temp
+.cache
+
+# Sveltekit cache directory
+.svelte-kit/
+
+# vitepress build output
+**/.vitepress/dist
+
+# vitepress cache directory
+**/.vitepress/cache
+
+# Docusaurus cache and generated files
+.docusaurus
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+# Firebase cache directory
+.firebase/
+
+# TernJS port file
+.tern-port
+
+# Stores VSCode versions used for testing VSCode extensions
+.vscode-test
+
+# pnpm
+.pnpm-store
+
+# yarn v3
+.pnp.*
+.yarn/*
+!.yarn/patches
+!.yarn/plugins
+!.yarn/releases
+!.yarn/sdks
+!.yarn/versions
+
+# Vite files
+vite.config.js.timestamp-*
+vite.config.ts.timestamp-*
+.vite/

.obsidian/app.json

@@ -0,0 +1,22 @@
+{
+  "showInlineTitle": false,
+  "useMarkdownLinks": true,
+  "pdfExportSettings": {
+    "pageSize": "Letter",
+    "landscape": false,
+    "margin": "0",
+    "downscalePercent": 100
+  },
+  "userIgnoreFilters": [
+    "notes/assets/"
+  ],
+  "showUnsupportedFiles": false,
+  "attachmentFolderPath": "notes/assets",
+  "livePreview": true,
+  "showIndentGuide": false,
+  "alwaysUpdateLinks": true,
+  "openBehavior": "file:README",
+  "newFileLocation": "folder",
+  "newFileFolderPath": "notes",
+  "newLinkFormat": "relative"
+}

.obsidian/snippets/omoolab.css

@@ -0,0 +1,30 @@
+/* not show label in canvas */
+.canvas-node-label {
+    display: none;
+}
+
+.canvas-node-container:hover + .canvas-node-label {
+    display: inherit;
+}
+
+/* image caption */
+.image-embed {
+    flex-wrap: wrap;
+}
+
+.image-embed[alt]:after {
+    content: attr(alt);
+    display: block;
+    padding-bottom: 12px;
+    line-height: 2.0;
+    font-style: italic;
+    color: var(--text-faint);
+    text-align: center;
+    width: 100%;
+}
+
+
+/* fix image in canvas */
+.image-embed {
+    padding: 0;
+}

.python-version

@@ -0,0 +1 @@
+3.11

.vscode/BioxelNodes.code-workspace

@@ -0,0 +1,11 @@
+{
+	"folders": [
+		{
+			"path": ".."
+		},
+		{
+			"path": "../src/bioxelnodes"
+		}
+	],
+	"settings": {}
+}

AGENTS.md

@@ -0,0 +1,92 @@
+# Bioxel Nodes
+
+## 项目概览
+
+Bioxel Nodes 是一个基于 Blender 的科学体数据可视化插件，利用 Blender 自带的 Geometry Nodes 与 Cycles（同时支持 EEVEE NEXT）处理并渲染体数据。
+
+- 支持格式：`.dcm`、`.tif`/`.tiff`、`.nii`/`.nii.gz`、`.nrrd`、`.ome.tiff`、`.mrc`、`.h5` 等，完整列表见 `src/bioxelnodes/bioxel/data.py` 的 `SUPPORT_EXTS`
+- 支持 4D 体数据（多帧 / 多通道 / 时间序列）
+- v2.0.x 仅支持 Blender 5.0+
+- 核心依赖：SimpleITK、pyometiff、mrcfile、h5py、numpy、scipy、transforms3d、matplotlib
+
+## 构建、测试与开发命令
+
+- 环境：Python 3.11，依赖由 uv 管理（`uv.lock`）
+- `uv sync` 安装 / 同步依赖
+- `uv run pytest` 运行测试（当前暂无测试用例）
+- `uv run mkdocs serve` 本地预览文档；`uv run mkdocs build` 构建到 `site/`
+- `uv run mike deploy <version> -p` 发布版本化文档
+- `uv run build.py <platform> 3.11` 下载第三方 wheel 并更新 `src/bioxelnodes/blender_manifest.toml`，`platform` 取 `windows-x64` / `linux-x64` / `macos-arm64` / `macos-x64`
+- `python pack.py <platform> [output.zip]` 将 `src/bioxelnodes` 打包为 zip
+- 发布：推送 `v*` 标签触发 `.github/workflows/release.yml`，产物命名 `BioxelNodes.<version>.<platform>.zip`
+
+## 架构
+
+```text
+src/bioxelnodes/            插件包根目录
+├── __init__.py             入口：register/unregister、CLI 命令与 WindowManager 属性
+├── auto_load.py            自动发现并按拓扑排序注册 bpy 类
+├── constants.py            常量（节点库路径等）
+├── preferences.py          AddonPreferences（缓存目录）
+├── props.py                PropertyGroup / UIList / 属性更新回调
+├── menus.py                菜单与右键菜单
+├── panels.py               面板
+├── asset_library.py        "O Bioxel" 资产库管理
+├── node.py                 节点组加载与添加
+├── layer.py                VDB 缓存、快照、图层元数据（text datablock JSON）
+├── utils.py                通用工具（进度、对象查找、驱动等）
+├── exceptions.py           向后兼容占位（自定义异常已改用内置异常）
+├── blender_manifest.toml   Blender 扩展清单
+├── assets/O_Bioxel/        节点库 .blend 与资产目录
+├── wheels/                 随扩展分发的第三方 wheel
+├── bioxel/                 核心数据模型（不依赖 Blender）
+│   ├── data.py             Data 类与解析（read / read_meta）
+│   ├── parse.py            解析函数（parse_volumetric_data 等）
+│   ├── layer.py            Layer：TXYZC 顺序 ndarray + affine 变换
+│   ├── container.py        Container：name + layers
+│   └── io.py               HDF5 读写 Container
+└── operators/              Operator 实现
+    ├── io.py               导入 / 导出算子，启动后台导入进程
+    ├── io_worker.py        后台 CLI 导入 worker（bioxelnodes_import_worker）
+    ├── layer.py            图层管理算子
+    ├── node.py             AddNode
+    ├── structure.py        ExtractMesh
+    └── misc.py             杂项算子
+```
+
+数据流：导入时主进程通过 `operators/io.py` 启动一个后台 Blender 子进程（`blender --background --command bioxelnodes_import_worker`），由 `io_worker.py` 解析数据、生成 `Layer`，写为 VDB 缓存，并通过 JSON 文件（`progress.json` / `result.json` / `cancel`）回传进度与结果，避免阻塞 UI。
+
+仓库根目录另有 `docs/`（mkdocs-material 文档，中英双语）、`openspec/`（spec-driven 变更流程）、`.agents/`（技能定义）。
+
+## 总规范
+
+- 说明性内容（例如提交说明、文档、注释、mermaid），以中文为主，专有名词、约定俗称可用英文
+
+## Markdown 规范
+
+- 不使用`---`分割器
+- `# Heading` 一级标题仅用于开头
+- mermaid 节点名用英文字符
+
+## 代码规范
+
+- 避免嵌套结构
+- 特殊的、非常规的需要写注释
+- 变量、函数名、Docstring 用全英文
+- 同一事物用统一表达
+- 使用的依赖越少越好
+- 选用简单直接的方式实现
+- 代码、执行方式改变，调整已有的文档、计划，而非新建
+
+## Shell 规范
+
+- 优先使用、提供 Git Bash 执行所有 Shell 命令
+- Windows 路径在 Bash 命令中优先使用正斜杠形式
+
+## Blender 开发规范
+
+- 插件、资产库压缩包名用大驼峰，如果需要，用`b45`来表示适用blender版本。比如`OmooLab.v0.1.0.b45.zip`
+- Operator、Menu、Panel、AddonPreferences... Class 用大驼峰命名，不加任何前缀。Operator 动宾结构，比如`RenderImage`。Menu、Panel 以它们本身为后缀，比如`RenderPanel`
+- 根据项目名提炼项目缩写，作为 bl_idname 和 自定义 Property 的前缀以区分其他功能和属性，以`Omoo`为例
+  - bl_idname 用下划线小写命名，Operator 的 bl_idname 以`omoo.*`为前缀，比如`omoo.render_panel`；Menu 的以`OMOO_MT_*`为前缀；Panel 的以`OMOO_PT_*`为前缀。比如`OMOO_PT_render_panel`
+  - 自定义 Property 用下划线小写命名，以`omoo_*`为前缀。比如`omoo_progress_factor`

LICENSE

@@ -1,21 +1,674 @@
-MIT License
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
 
-Copyright (c) 2024 OmooLab
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+                            Preamble
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
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+
+  "Additional permissions" are terms that supplement the terms of this
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+Additional permissions that are applicable to the entire Program shall
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+  When you convey a copy of a covered work, you may at your option
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+  10. Automatic Licensing of Downstream Recipients.
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+
+  11. Patents.
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+  A "contributor" is a copyright holder who authorizes use under this
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+
+  Nothing in this License shall be construed as excluding or limiting
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+  12. No Surrender of Others' Freedom.
+
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+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
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+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
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+be similar in spirit to the present version, but may differ in detail to
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+  If the Program specifies that a proxy can decide which future
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+  Later license versions may give you additional or different
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+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
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+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
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+  To do so, attach the following notices to the program.  It is safest
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+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
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+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -1,4 +1,6 @@
-[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/LPKEwjooSivxjskWHlCcQznjnNf?from=from_copylink)
+**v2.0.x has been released, supporting only Blender 5.0+. The usage is completely different from before and is not compatible with old version files. See  http://docs.omoolab.xyz/bioxelnodes/2.0.x/en/basics/**
+
+[中文文档](https://docs.omoolab.xyz/bioxelnodes/latest/)
 
 # Bioxel Nodes
 
@@ -13,51 +15,29 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 
 ![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
+## Features
+
 -   Realistic rendering result, also support EEVEE NEXT.
--   Support multiple formats.
+-   Support many formats：.dcm, .jpg, .tif, .nii, .nrrd, .ome, .mrc...
 -   Support 4D volumetric data.
--   All kinds of cutters.
+-   Many kinds of cutters.
 -   Simple and powerful nodes.
 -   Based on blender natively, can work without addon.
 
-**Read the [getting started](https://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
+| ![4D](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif) | ![EEVEE](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif) |
+| :--------------------------------------------------------------------: | :---------------------------------------------------------------------: |
+|                       Support 4D volumetric data                       |                       Real-time render with eevee                       |
+
+**Read the [getting started](https://docs.omoolab.xyz/bioxelnodes/latest/en/installation) to begin your journey into visualizing volumetric data!**
 
 Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
-## Support Multiple Formats
+## Citation
 
-| Format | EXT                                      |
-| ------ | ---------------------------------------- |
-| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
-| BMP    | .bmp, .BMP                               |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
-| PNG    | .png, .PNG                               |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
-| Nrrd   | .nrrd, .nhdr                             |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
-| OME    | .ome.tiff, .ome.tif                      |
-| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
+If you want to cite this work, you can cite it from Zenodo:
 
-## Support 4D volumetric data
+[![DOI](https://zenodo.org/badge/786623459.svg)](https://zenodo.org/badge/latestdoi/786623459)
 
-![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif)
-
-🥰 4D volumetric data can also be imported into Blender.
-
-## Support EEVEE NEXT
-
-![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
-
-👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:
-
-1. Only one cutter supported.
-2. EEVEE result is not that great as Cycles does.
-
-## Known Limitations
-
--   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
--   Section surface cannot be generated when convert to mesh (will be supported soon)
 
 ## Roadmap
 

bioxelnodes/__init__.py

@@ -1,26 +0,0 @@
-import bpy
-
-from .props import BIOXELNODES_LayerListUL
-from . import auto_load
-from . import menus
-
-
-auto_load.init()
-
-
-def register():
-    auto_load.register()
-    bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty(
-        default=1.0)
-    bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
-    bpy.types.WindowManager.bioxelnodes_layer_list_UL = bpy.props.PointerProperty(
-        type=BIOXELNODES_LayerListUL)
-    menus.add()
-
-
-def unregister():
-    menus.remove()
-    del bpy.types.WindowManager.bioxelnodes_progress_factor
-    del bpy.types.WindowManager.bioxelnodes_progress_text
-    del bpy.types.WindowManager.bioxelnodes_layer_list_UL
-    auto_load.unregister()

bioxelnodes/bioxel/scipy/__init__.py

@@ -1,5 +0,0 @@
-from ._interpolation import zoom
-from ._filters import (gaussian_filter,
-                       median_filter,
-                       maximum_filter,
-                       minimum_filter)

bioxelnodes/bioxel/scipy/_interpolation.py

@@ -1,313 +0,0 @@
-import numpy as np
-import warnings
-
-from . import _ni_support
-from . import _nd_image
-from ._utils import normalize_axis_index
-
-
-def _prepad_for_spline_filter(input, mode, cval):
-    if mode in ['nearest', 'grid-constant']:
-        npad = 12
-        if mode == 'grid-constant':
-            padded = np.pad(input, npad, mode='constant',
-                               constant_values=cval)
-        elif mode == 'nearest':
-            padded = np.pad(input, npad, mode='edge')
-    else:
-        # other modes have exact boundary conditions implemented so
-        # no prepadding is needed
-        npad = 0
-        padded = input
-    return padded, npad
-
-def spline_filter1d(input, order=3, axis=-1, output=np.float64,
-                    mode='mirror'):
-    """
-    Calculate a 1-D spline filter along the given axis.
-
-    The lines of the array along the given axis are filtered by a
-    spline filter. The order of the spline must be >= 2 and <= 5.
-
-    Parameters
-    ----------
-    %(input)s
-    order : int, optional
-        The order of the spline, default is 3.
-    axis : int, optional
-        The axis along which the spline filter is applied. Default is the last
-        axis.
-    output : ndarray or dtype, optional
-        The array in which to place the output, or the dtype of the returned
-        array. Default is ``numpy.float64``.
-    %(mode_interp_mirror)s
-
-    Returns
-    -------
-    spline_filter1d : ndarray
-        The filtered input.
-
-    See Also
-    --------
-    spline_filter : Multidimensional spline filter.
-
-    Notes
-    -----
-    All of the interpolation functions in `ndimage` do spline interpolation of
-    the input image. If using B-splines of `order > 1`, the input image
-    values have to be converted to B-spline coefficients first, which is
-    done by applying this 1-D filter sequentially along all
-    axes of the input. All functions that require B-spline coefficients
-    will automatically filter their inputs, a behavior controllable with
-    the `prefilter` keyword argument. For functions that accept a `mode`
-    parameter, the result will only be correct if it matches the `mode`
-    used when filtering.
-
-    For complex-valued `input`, this function processes the real and imaginary
-    components independently.
-
-    .. versionadded:: 1.6.0
-        Complex-valued support added.
-
-    Examples
-    --------
-    We can filter an image using 1-D spline along the given axis:
-
-    >>> from scipy.ndimage import spline_filter1d
-    >>> import numpy as np
-    >>> import matplotlib.pyplot as plt
-    >>> orig_img = np.eye(20)  # create an image
-    >>> orig_img[10, :] = 1.0
-    >>> sp_filter_axis_0 = spline_filter1d(orig_img, axis=0)
-    >>> sp_filter_axis_1 = spline_filter1d(orig_img, axis=1)
-    >>> f, ax = plt.subplots(1, 3, sharex=True)
-    >>> for ind, data in enumerate([[orig_img, "original image"],
-    ...             [sp_filter_axis_0, "spline filter (axis=0)"],
-    ...             [sp_filter_axis_1, "spline filter (axis=1)"]]):
-    ...     ax[ind].imshow(data[0], cmap='gray_r')
-    ...     ax[ind].set_title(data[1])
-    >>> plt.tight_layout()
-    >>> plt.show()
-
-    """
-    if order < 0 or order > 5:
-        raise RuntimeError('spline order not supported')
-    input = np.asarray(input)
-    complex_output = np.iscomplexobj(input)
-    output = _ni_support._get_output(output, input,
-                                     complex_output=complex_output)
-    if complex_output:
-        spline_filter1d(input.real, order, axis, output.real, mode)
-        spline_filter1d(input.imag, order, axis, output.imag, mode)
-        return output
-    if order in [0, 1]:
-        output[...] = np.array(input)
-    else:
-        mode = _ni_support._extend_mode_to_code(mode)
-        axis = normalize_axis_index(axis, input.ndim)
-        _nd_image.spline_filter1d(input, order, axis, output, mode)
-    return output
-
-
-def spline_filter(input, order=3, output=np.float64, mode='mirror'):
-    """
-    Multidimensional spline filter.
-
-    Parameters
-    ----------
-    %(input)s
-    order : int, optional
-        The order of the spline, default is 3.
-    output : ndarray or dtype, optional
-        The array in which to place the output, or the dtype of the returned
-        array. Default is ``numpy.float64``.
-    %(mode_interp_mirror)s
-
-    Returns
-    -------
-    spline_filter : ndarray
-        Filtered array. Has the same shape as `input`.
-
-    See Also
-    --------
-    spline_filter1d : Calculate a 1-D spline filter along the given axis.
-
-    Notes
-    -----
-    The multidimensional filter is implemented as a sequence of
-    1-D spline filters. The intermediate arrays are stored
-    in the same data type as the output. Therefore, for output types
-    with a limited precision, the results may be imprecise because
-    intermediate results may be stored with insufficient precision.
-
-    For complex-valued `input`, this function processes the real and imaginary
-    components independently.
-
-    .. versionadded:: 1.6.0
-        Complex-valued support added.
-
-    Examples
-    --------
-    We can filter an image using multidimentional splines:
-
-    >>> from scipy.ndimage import spline_filter
-    >>> import numpy as np
-    >>> import matplotlib.pyplot as plt
-    >>> orig_img = np.eye(20)  # create an image
-    >>> orig_img[10, :] = 1.0
-    >>> sp_filter = spline_filter(orig_img, order=3)
-    >>> f, ax = plt.subplots(1, 2, sharex=True)
-    >>> for ind, data in enumerate([[orig_img, "original image"],
-    ...                             [sp_filter, "spline filter"]]):
-    ...     ax[ind].imshow(data[0], cmap='gray_r')
-    ...     ax[ind].set_title(data[1])
-    >>> plt.tight_layout()
-    >>> plt.show()
-
-    """
-    if order < 2 or order > 5:
-        raise RuntimeError('spline order not supported')
-    input = np.asarray(input)
-    complex_output = np.iscomplexobj(input)
-    output = _ni_support._get_output(output, input,
-                                     complex_output=complex_output)
-    if complex_output:
-        spline_filter(input.real, order, output.real, mode)
-        spline_filter(input.imag, order, output.imag, mode)
-        return output
-    if order not in [0, 1] and input.ndim > 0:
-        for axis in range(input.ndim):
-            spline_filter1d(input, order, axis, output=output, mode=mode)
-            input = output
-    else:
-        output[...] = input[...]
-    return output
-
-
-def zoom(input, zoom, output=None, order=3, mode='constant', cval=0.0,
-         prefilter=True, *, grid_mode=False):
-    """
-    Zoom an array.
-
-    The array is zoomed using spline interpolation of the requested order.
-
-    Parameters
-    ----------
-    %(input)s
-    zoom : float or sequence
-        The zoom factor along the axes. If a float, `zoom` is the same for each
-        axis. If a sequence, `zoom` should contain one value for each axis.
-    %(output)s
-    order : int, optional
-        The order of the spline interpolation, default is 3.
-        The order has to be in the range 0-5.
-    %(mode_interp_constant)s
-    %(cval)s
-    %(prefilter)s
-    grid_mode : bool, optional
-        If False, the distance from the pixel centers is zoomed. Otherwise, the
-        distance including the full pixel extent is used. For example, a 1d
-        signal of length 5 is considered to have length 4 when `grid_mode` is
-        False, but length 5 when `grid_mode` is True. See the following
-        visual illustration:
-
-        .. code-block:: text
-
-                | pixel 1 | pixel 2 | pixel 3 | pixel 4 | pixel 5 |
-                     |<-------------------------------------->|
-                                        vs.
-                |<----------------------------------------------->|
-
-        The starting point of the arrow in the diagram above corresponds to
-        coordinate location 0 in each mode.
-
-    Returns
-    -------
-    zoom : ndarray
-        The zoomed input.
-
-    Notes
-    -----
-    For complex-valued `input`, this function zooms the real and imaginary
-    components independently.
-
-    .. versionadded:: 1.6.0
-        Complex-valued support added.
-
-    Examples
-    --------
-    >>> from scipy import ndimage, datasets
-    >>> import matplotlib.pyplot as plt
-
-    >>> fig = plt.figure()
-    >>> ax1 = fig.add_subplot(121)  # left side
-    >>> ax2 = fig.add_subplot(122)  # right side
-    >>> ascent = datasets.ascent()
-    >>> result = ndimage.zoom(ascent, 3.0)
-    >>> ax1.imshow(ascent, vmin=0, vmax=255)
-    >>> ax2.imshow(result, vmin=0, vmax=255)
-    >>> plt.show()
-
-    >>> print(ascent.shape)
-    (512, 512)
-
-    >>> print(result.shape)
-    (1536, 1536)
-    """
-    if order < 0 or order > 5:
-        raise RuntimeError('spline order not supported')
-    input = np.asarray(input)
-    if input.ndim < 1:
-        raise RuntimeError('input and output rank must be > 0')
-    zoom = _ni_support._normalize_sequence(zoom, input.ndim)
-    output_shape = tuple(
-        [int(round(ii * jj)) for ii, jj in zip(input.shape, zoom)])
-    complex_output = np.iscomplexobj(input)
-    output = _ni_support._get_output(output, input, shape=output_shape,
-                                     complex_output=complex_output)
-    if complex_output:
-        # import under different name to avoid confusion with zoom parameter
-        from scipy.ndimage._interpolation import zoom as _zoom
-
-        kwargs = dict(order=order, mode=mode, prefilter=prefilter)
-        _zoom(input.real, zoom, output=output.real,
-              cval=np.real(cval), **kwargs)
-        _zoom(input.imag, zoom, output=output.imag,
-              cval=np.imag(cval), **kwargs)
-        return output
-    if prefilter and order > 1:
-        padded, npad = _prepad_for_spline_filter(input, mode, cval)
-        filtered = spline_filter(padded, order, output=np.float64, mode=mode)
-    else:
-        npad = 0
-        filtered = input
-    if grid_mode:
-        # warn about modes that may have surprising behavior
-        suggest_mode = None
-        if mode == 'constant':
-            suggest_mode = 'grid-constant'
-        elif mode == 'wrap':
-            suggest_mode = 'grid-wrap'
-        if suggest_mode is not None:
-            warnings.warn(
-                (f"It is recommended to use mode = {suggest_mode} instead of {mode} "
-                 f"when grid_mode is True."),
-                stacklevel=2
-            )
-    mode = _ni_support._extend_mode_to_code(mode)
-
-    zoom_div = np.array(output_shape)
-    zoom_nominator = np.array(input.shape)
-    if not grid_mode:
-        zoom_div -= 1
-        zoom_nominator -= 1
-
-    # Zooming to infinite values is unpredictable, so just choose
-    # zoom factor 1 instead
-    zoom = np.divide(zoom_nominator, zoom_div,
-                     out=np.ones_like(input.shape, dtype=np.float64),
-                     where=zoom_div != 0)
-    zoom = np.ascontiguousarray(zoom)
-    _nd_image.zoom_shift(filtered, zoom, None, output, order, mode, cval, npad,
-                         grid_mode)
-    return output

bioxelnodes/bioxel/scipy/_ni_support.py

@@ -1,119 +0,0 @@
-# Copyright (C) 2003-2005 Peter J. Verveer
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-#
-# 1. Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#
-# 2. Redistributions in binary form must reproduce the above
-#    copyright notice, this list of conditions and the following
-#    disclaimer in the documentation and/or other materials provided
-#    with the distribution.
-#
-# 3. The name of the author may not be used to endorse or promote
-#    products derived from this software without specific prior
-#    written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
-# OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
-# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
-# GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-from collections.abc import Iterable
-import operator
-import warnings
-import numpy as np
-
-
-def _extend_mode_to_code(mode):
-    """Convert an extension mode to the corresponding integer code.
-    """
-    if mode == 'nearest':
-        return 0
-    elif mode == 'wrap':
-        return 1
-    elif mode in ['reflect', 'grid-mirror']:
-        return 2
-    elif mode == 'mirror':
-        return 3
-    elif mode == 'constant':
-        return 4
-    elif mode == 'grid-wrap':
-        return 5
-    elif mode == 'grid-constant':
-        return 6
-    else:
-        raise RuntimeError('boundary mode not supported')
-
-
-def _normalize_sequence(input, rank):
-    """If input is a scalar, create a sequence of length equal to the
-    rank by duplicating the input. If input is a sequence,
-    check if its length is equal to the length of array.
-    """
-    is_str = isinstance(input, str)
-    if not is_str and isinstance(input, Iterable):
-        normalized = list(input)
-        if len(normalized) != rank:
-            err = "sequence argument must have length equal to input rank"
-            raise RuntimeError(err)
-    else:
-        normalized = [input] * rank
-    return normalized
-
-
-def _get_output(output, input, shape=None, complex_output=False):
-    if shape is None:
-        shape = input.shape
-    if output is None:
-        if not complex_output:
-            output = np.zeros(shape, dtype=input.dtype.name)
-        else:
-            complex_type = np.promote_types(input.dtype, np.complex64)
-            output = np.zeros(shape, dtype=complex_type)
-    elif isinstance(output, (type, np.dtype)):
-        # Classes (like `np.float32`) and dtypes are interpreted as dtype
-        if complex_output and np.dtype(output).kind != 'c':
-            warnings.warn("promoting specified output dtype to complex", stacklevel=3)
-            output = np.promote_types(output, np.complex64)
-        output = np.zeros(shape, dtype=output)
-    elif isinstance(output, str):
-        output = np.dtype(output)
-        if complex_output and output.kind != 'c':
-            raise RuntimeError("output must have complex dtype")
-        elif not issubclass(output.type, np.number):
-            raise RuntimeError("output must have numeric dtype")
-        output = np.zeros(shape, dtype=output)
-    elif output.shape != shape:
-        raise RuntimeError("output shape not correct")
-    elif complex_output and output.dtype.kind != 'c':
-        raise RuntimeError("output must have complex dtype")
-    return output
-
-
-def _check_axes(axes, ndim):
-    if axes is None:
-        return tuple(range(ndim))
-    elif np.isscalar(axes):
-        axes = (operator.index(axes),)
-    elif isinstance(axes, Iterable):
-        for ax in axes:
-            axes = tuple(operator.index(ax) for ax in axes)
-            if ax < -ndim or ax > ndim - 1:
-                raise ValueError(f"specified axis: {ax} is out of range")
-        axes = tuple(ax % ndim if ax < 0 else ax for ax in axes)
-    else:
-        message = "axes must be an integer, iterable of integers, or None"
-        raise ValueError(message)
-    if len(tuple(set(axes))) != len(axes):
-        raise ValueError("axes must be unique")
-    return axes

bioxelnodes/bioxel/scipy/_utils.py

@@ -1,10 +0,0 @@
-
-def normalize_axis_index(axis, ndim):
-    # Check if `axis` is in the correct range and normalize it
-    if axis < -ndim or axis >= ndim:
-        msg = f"axis {axis} is out of bounds for array of dimension {ndim}"
-        raise Exception(msg)
-
-    if axis < 0:
-        axis = axis + ndim
-    return axis

bioxelnodes/bioxel/skimage/__init__.py

@@ -1 +0,0 @@
-from ._warps import resize

bioxelnodes/bioxel/skimage/_utils.py

@@ -1,37 +0,0 @@
-import numpy as np
-
-
-def convert_to_float(image, preserve_range):
-    """Convert input image to float image with the appropriate range.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    preserve_range : bool
-        Determines if the range of the image should be kept or transformed
-        using img_as_float. Also see
-        https://scikit-image.org/docs/dev/user_guide/data_types.html
-
-    Notes
-    -----
-    * Input images with `float32` data type are not upcast.
-
-    Returns
-    -------
-    image : ndarray
-        Transformed version of the input.
-
-    """
-    if image.dtype == np.float16:
-        return image.astype(np.float32)
-    if preserve_range:
-        # Convert image to double only if it is not single or double
-        # precision float
-        if image.dtype.char not in 'df':
-            image = image.astype(float)
-    else:
-        from .dtype import img_as_float
-
-        image = img_as_float(image)
-    return image

bioxelnodes/bioxel/skimage/_warps.py

@@ -1,318 +0,0 @@
-import warnings
-import numpy as np
-from .. import scipy as ndi
-from ._utils import convert_to_float
-
-def _clip_warp_output(input_image, output_image, mode, cval, clip):
-    """Clip output image to range of values of input image.
-
-    Note that this function modifies the values of `output_image` in-place
-    and it is only modified if ``clip=True``.
-
-    Parameters
-    ----------
-    input_image : ndarray
-        Input image.
-    output_image : ndarray
-        Output image, which is modified in-place.
-
-    Other parameters
-    ----------------
-    mode : {'constant', 'edge', 'symmetric', 'reflect', 'wrap'}
-        Points outside the boundaries of the input are filled according
-        to the given mode.  Modes match the behaviour of `numpy.pad`.
-    cval : float
-        Used in conjunction with mode 'constant', the value outside
-        the image boundaries.
-    clip : bool
-        Whether to clip the output to the range of values of the input image.
-        This is enabled by default, since higher order interpolation may
-        produce values outside the given input range.
-
-    """
-    if clip:
-        min_val = np.min(input_image)
-        if np.isnan(min_val):
-            # NaNs detected, use NaN-safe min/max
-            min_func = np.nanmin
-            max_func = np.nanmax
-            min_val = min_func(input_image)
-        else:
-            min_func = np.min
-            max_func = np.max
-        max_val = max_func(input_image)
-
-        # Check if cval has been used such that it expands the effective input
-        # range
-        preserve_cval = (
-            mode == 'constant'
-            and not min_val <= cval <= max_val
-            and min_func(output_image) <= cval <= max_func(output_image)
-        )
-
-        # expand min/max range to account for cval
-        if preserve_cval:
-            # cast cval to the same dtype as the input image
-            cval = input_image.dtype.type(cval)
-            min_val = min(min_val, cval)
-            max_val = max(max_val, cval)
-
-        # Convert array-like types to ndarrays (gh-7159)
-        min_val, max_val = np.asarray(min_val), np.asarray(max_val)
-        np.clip(output_image, min_val, max_val, out=output_image)
-
-
-def _validate_interpolation_order(image_dtype, order):
-    """Validate and return spline interpolation's order.
-
-    Parameters
-    ----------
-    image_dtype : dtype
-        Image dtype.
-    order : int, optional
-        The order of the spline interpolation. The order has to be in
-        the range 0-5. See `skimage.transform.warp` for detail.
-
-    Returns
-    -------
-    order : int
-        if input order is None, returns 0 if image_dtype is bool and 1
-        otherwise. Otherwise, image_dtype is checked and input order
-        is validated accordingly (order > 0 is not supported for bool
-        image dtype)
-
-    """
-
-    if order is None:
-        return 0 if image_dtype == bool else 1
-
-    if order < 0 or order > 5:
-        raise ValueError(
-            "Spline interpolation order has to be in the " "range 0-5.")
-
-    if image_dtype == bool and order != 0:
-        raise ValueError(
-            "Input image dtype is bool. Interpolation is not defined "
-            "with bool data type. Please set order to 0 or explicitly "
-            "cast input image to another data type."
-        )
-
-    return order
-
-
-def _preprocess_resize_output_shape(image, output_shape):
-    """Validate resize output shape according to input image.
-
-    Parameters
-    ----------
-    image: ndarray
-        Image to be resized.
-    output_shape: iterable
-        Size of the generated output image `(rows, cols[, ...][, dim])`. If
-        `dim` is not provided, the number of channels is preserved.
-
-    Returns
-    -------
-    image: ndarray
-        The input image, but with additional singleton dimensions appended in
-        the case where ``len(output_shape) > input.ndim``.
-    output_shape: tuple
-        The output image converted to tuple.
-
-    Raises
-    ------
-    ValueError:
-        If output_shape length is smaller than the image number of
-        dimensions
-
-    Notes
-    -----
-    The input image is reshaped if its number of dimensions is not
-    equal to output_shape_length.
-
-    """
-    output_shape = tuple(output_shape)
-    output_ndim = len(output_shape)
-    input_shape = image.shape
-    if output_ndim > image.ndim:
-        # append dimensions to input_shape
-        input_shape += (1,) * (output_ndim - image.ndim)
-        image = np.reshape(image, input_shape)
-    elif output_ndim == image.ndim - 1:
-        # multichannel case: append shape of last axis
-        output_shape = output_shape + (image.shape[-1],)
-    elif output_ndim < image.ndim:
-        raise ValueError(
-            "output_shape length cannot be smaller than the "
-            "image number of dimensions"
-        )
-
-    return image, output_shape
-
-
-def _to_ndimage_mode(mode):
-    """Convert from `numpy.pad` mode name to the corresponding ndimage mode."""
-    mode_translation_dict = dict(
-        constant='constant',
-        edge='nearest',
-        symmetric='reflect',
-        reflect='mirror',
-        wrap='wrap',
-    )
-    if mode not in mode_translation_dict:
-        raise ValueError(
-            f"Unknown mode: '{mode}', or cannot translate mode. The "
-            f"mode should be one of 'constant', 'edge', 'symmetric', "
-            f"'reflect', or 'wrap'. See the documentation of numpy.pad for "
-            f"more info."
-        )
-    return _fix_ndimage_mode(mode_translation_dict[mode])
-
-
-def _fix_ndimage_mode(mode):
-    # SciPy 1.6.0 introduced grid variants of constant and wrap which
-    # have less surprising behavior for images. Use these when available
-    grid_modes = {'constant': 'grid-constant', 'wrap': 'grid-wrap'}
-    return grid_modes.get(mode, mode)
-
-
-def resize(
-    image,
-    output_shape,
-    order=None,
-    mode='reflect',
-    cval=0,
-    clip=True,
-    preserve_range=False,
-    anti_aliasing=None,
-    anti_aliasing_sigma=None,
-):
-    """Resize image to match a certain size.
-
-    Performs interpolation to up-size or down-size N-dimensional images. Note
-    that anti-aliasing should be enabled when down-sizing images to avoid
-    aliasing artifacts. For downsampling with an integer factor also see
-    `skimage.transform.downscale_local_mean`.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    output_shape : iterable
-        Size of the generated output image `(rows, cols[, ...][, dim])`. If
-        `dim` is not provided, the number of channels is preserved. In case the
-        number of input channels does not equal the number of output channels a
-        n-dimensional interpolation is applied.
-
-    Returns
-    -------
-    resized : ndarray
-        Resized version of the input.
-
-    Other parameters
-    ----------------
-    order : int, optional
-        The order of the spline interpolation, default is 0 if
-        image.dtype is bool and 1 otherwise. The order has to be in
-        the range 0-5. See `skimage.transform.warp` for detail.
-    mode : {'constant', 'edge', 'symmetric', 'reflect', 'wrap'}, optional
-        Points outside the boundaries of the input are filled according
-        to the given mode.  Modes match the behaviour of `numpy.pad`.
-    cval : float, optional
-        Used in conjunction with mode 'constant', the value outside
-        the image boundaries.
-    clip : bool, optional
-        Whether to clip the output to the range of values of the input image.
-        This is enabled by default, since higher order interpolation may
-        produce values outside the given input range.
-    preserve_range : bool, optional
-        Whether to keep the original range of values. Otherwise, the input
-        image is converted according to the conventions of `img_as_float`.
-        Also see https://scikit-image.org/docs/dev/user_guide/data_types.html
-    anti_aliasing : bool, optional
-        Whether to apply a Gaussian filter to smooth the image prior
-        to downsampling. It is crucial to filter when downsampling
-        the image to avoid aliasing artifacts. If not specified, it is set to
-        True when downsampling an image whose data type is not bool.
-        It is also set to False when using nearest neighbor interpolation
-        (``order`` == 0) with integer input data type.
-    anti_aliasing_sigma : {float, tuple of floats}, optional
-        Standard deviation for Gaussian filtering used when anti-aliasing.
-        By default, this value is chosen as (s - 1) / 2 where s is the
-        downsampling factor, where s > 1. For the up-size case, s < 1, no
-        anti-aliasing is performed prior to rescaling.
-
-    Notes
-    -----
-    Modes 'reflect' and 'symmetric' are similar, but differ in whether the edge
-    pixels are duplicated during the reflection.  As an example, if an array
-    has values [0, 1, 2] and was padded to the right by four values using
-    symmetric, the result would be [0, 1, 2, 2, 1, 0, 0], while for reflect it
-    would be [0, 1, 2, 1, 0, 1, 2].
-
-    Examples
-    --------
-    >>> from skimage import data
-    >>> from skimage.transform import resize
-    >>> image = data.camera()
-    >>> resize(image, (100, 100)).shape
-    (100, 100)
-
-    """
-
-    image, output_shape = _preprocess_resize_output_shape(image, output_shape)
-    input_shape = image.shape
-    input_type = image.dtype
-
-    if input_type == np.float16:
-        image = image.astype(np.float32)
-
-    if anti_aliasing is None:
-        anti_aliasing = (
-            not input_type == bool
-            and not (np.issubdtype(input_type, np.integer) and order == 0)
-            and any(x < y for x, y in zip(output_shape, input_shape))
-        )
-
-    if input_type == bool and anti_aliasing:
-        raise ValueError("anti_aliasing must be False for boolean images")
-
-    factors = np.divide(input_shape, output_shape)
-    order = _validate_interpolation_order(input_type, order)
-    if order > 0:
-        image = convert_to_float(image, preserve_range)
-
-    # Translate modes used by np.pad to those used by scipy.ndimage
-    ndi_mode = _to_ndimage_mode(mode)
-    if anti_aliasing:
-        if anti_aliasing_sigma is None:
-            anti_aliasing_sigma = np.maximum(0, (factors - 1) / 2)
-        else:
-            anti_aliasing_sigma = np.atleast_1d(anti_aliasing_sigma) * np.ones_like(
-                factors
-            )
-            if np.any(anti_aliasing_sigma < 0):
-                raise ValueError(
-                    "Anti-aliasing standard deviation must be "
-                    "greater than or equal to zero"
-                )
-            elif np.any((anti_aliasing_sigma > 0) & (factors <= 1)):
-                warnings.warn(
-                    "Anti-aliasing standard deviation greater than zero but "
-                    "not down-sampling along all axes",
-                    stacklevel=2
-                )
-        filtered = ndi.gaussian_filter(
-            image, anti_aliasing_sigma, cval=cval, mode=ndi_mode
-        )
-    else:
-        filtered = image
-
-    zoom_factors = [1 / f for f in factors]
-    out = ndi.zoom(
-        filtered, zoom_factors, order=order, mode=ndi_mode, cval=cval, grid_mode=True
-    )
-
-    _clip_warp_output(image, out, mode, cval, clip)
-
-    return out

bioxelnodes/bioxel/skimage/dtype.py

@@ -1,600 +0,0 @@
-import warnings
-from warnings import warn
-
-import numpy as np
-
-
-__all__ = [
-    'img_as_float32',
-    'img_as_float64',
-    'img_as_float',
-    'img_as_int',
-    'img_as_uint',
-    'img_as_ubyte',
-    'img_as_bool',
-    'dtype_limits',
-]
-
-# Some of these may or may not be aliases depending on architecture & platform
-_integer_types = (
-    np.int8,
-    np.byte,
-    np.int16,
-    np.short,
-    np.int32,
-    np.int64,
-    np.longlong,
-    np.int_,
-    np.intp,
-    np.intc,
-    int,
-    np.uint8,
-    np.ubyte,
-    np.uint16,
-    np.ushort,
-    np.uint32,
-    np.uint64,
-    np.ulonglong,
-    np.uint,
-    np.uintp,
-    np.uintc,
-)
-_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max) for t in _integer_types}
-dtype_range = {
-    bool: (False, True),
-    np.bool_: (False, True),
-    float: (-1, 1),
-    np.float16: (-1, 1),
-    np.float32: (-1, 1),
-    np.float64: (-1, 1),
-}
-
-with warnings.catch_warnings():
-    warnings.filterwarnings('ignore', category=DeprecationWarning)
-
-    # np.bool8 is a deprecated alias of np.bool_
-    if hasattr(np, 'bool8'):
-        dtype_range[np.bool8] = (False, True)
-
-dtype_range.update(_integer_ranges)
-
-_supported_types = list(dtype_range.keys())
-
-
-def dtype_limits(image, clip_negative=False):
-    """Return intensity limits, i.e. (min, max) tuple, of the image's dtype.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    clip_negative : bool, optional
-        If True, clip the negative range (i.e. return 0 for min intensity)
-        even if the image dtype allows negative values.
-
-    Returns
-    -------
-    imin, imax : tuple
-        Lower and upper intensity limits.
-    """
-    imin, imax = dtype_range[image.dtype.type]
-    if clip_negative:
-        imin = 0
-    return imin, imax
-
-
-def _dtype_itemsize(itemsize, *dtypes):
-    """Return first of `dtypes` with itemsize greater than `itemsize`
-
-    Parameters
-    ----------
-    itemsize: int
-        The data type object element size.
-
-    Other Parameters
-    ----------------
-    *dtypes:
-        Any Object accepted by `np.dtype` to be converted to a data
-        type object
-
-    Returns
-    -------
-    dtype: data type object
-        First of `dtypes` with itemsize greater than `itemsize`.
-
-    """
-    return next(dt for dt in dtypes if np.dtype(dt).itemsize >= itemsize)
-
-
-def _dtype_bits(kind, bits, itemsize=1):
-    """Return dtype of `kind` that can store a `bits` wide unsigned int
-
-    Parameters:
-    kind: str
-        Data type kind.
-    bits: int
-        Desired number of bits.
-    itemsize: int
-        The data type object element size.
-
-    Returns
-    -------
-    dtype: data type object
-        Data type of `kind` that can store a `bits` wide unsigned int
-
-    """
-
-    s = next(
-        i
-        for i in (itemsize,) + (2, 4, 8)
-        if bits < (i * 8) or (bits == (i * 8) and kind == 'u')
-    )
-
-    return np.dtype(kind + str(s))
-
-
-def _scale(a, n, m, copy=True):
-    """Scale an array of unsigned/positive integers from `n` to `m` bits.
-
-    Numbers can be represented exactly only if `m` is a multiple of `n`.
-
-    Parameters
-    ----------
-    a : ndarray
-        Input image array.
-    n : int
-        Number of bits currently used to encode the values in `a`.
-    m : int
-        Desired number of bits to encode the values in `out`.
-    copy : bool, optional
-        If True, allocates and returns new array. Otherwise, modifies
-        `a` in place.
-
-    Returns
-    -------
-    out : array
-        Output image array. Has the same kind as `a`.
-    """
-    kind = a.dtype.kind
-    if n > m and a.max() < 2**m:
-        mnew = int(np.ceil(m / 2) * 2)
-        if mnew > m:
-            dtype = f'int{mnew}'
-        else:
-            dtype = f'uint{mnew}'
-        n = int(np.ceil(n / 2) * 2)
-        warn(
-            f'Downcasting {a.dtype} to {dtype} without scaling because max '
-            f'value {a.max()} fits in {dtype}',
-            stacklevel=3,
-        )
-        return a.astype(_dtype_bits(kind, m))
-    elif n == m:
-        return a.copy() if copy else a
-    elif n > m:
-        # downscale with precision loss
-        if copy:
-            b = np.empty(a.shape, _dtype_bits(kind, m))
-            np.floor_divide(a, 2 ** (n - m), out=b, dtype=a.dtype, casting='unsafe')
-            return b
-        else:
-            a //= 2 ** (n - m)
-            return a
-    elif m % n == 0:
-        # exact upscale to a multiple of `n` bits
-        if copy:
-            b = np.empty(a.shape, _dtype_bits(kind, m))
-            np.multiply(a, (2**m - 1) // (2**n - 1), out=b, dtype=b.dtype)
-            return b
-        else:
-            a = a.astype(_dtype_bits(kind, m, a.dtype.itemsize), copy=False)
-            a *= (2**m - 1) // (2**n - 1)
-            return a
-    else:
-        # upscale to a multiple of `n` bits,
-        # then downscale with precision loss
-        o = (m // n + 1) * n
-        if copy:
-            b = np.empty(a.shape, _dtype_bits(kind, o))
-            np.multiply(a, (2**o - 1) // (2**n - 1), out=b, dtype=b.dtype)
-            b //= 2 ** (o - m)
-            return b
-        else:
-            a = a.astype(_dtype_bits(kind, o, a.dtype.itemsize), copy=False)
-            a *= (2**o - 1) // (2**n - 1)
-            a //= 2 ** (o - m)
-            return a
-
-
-def _convert(image, dtype, force_copy=False, uniform=False):
-    """
-    Convert an image to the requested data-type.
-
-    Warnings are issued in case of precision loss, or when negative values
-    are clipped during conversion to unsigned integer types (sign loss).
-
-    Floating point values are expected to be normalized and will be clipped
-    to the range [0.0, 1.0] or [-1.0, 1.0] when converting to unsigned or
-    signed integers respectively.
-
-    Numbers are not shifted to the negative side when converting from
-    unsigned to signed integer types. Negative values will be clipped when
-    converting to unsigned integers.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    dtype : dtype
-        Target data-type.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-    uniform : bool, optional
-        Uniformly quantize the floating point range to the integer range.
-        By default (uniform=False) floating point values are scaled and
-        rounded to the nearest integers, which minimizes back and forth
-        conversion errors.
-
-    .. versionchanged:: 0.15
-        ``_convert`` no longer warns about possible precision or sign
-        information loss. See discussions on these warnings at:
-        https://github.com/scikit-image/scikit-image/issues/2602
-        https://github.com/scikit-image/scikit-image/issues/543#issuecomment-208202228
-        https://github.com/scikit-image/scikit-image/pull/3575
-
-    References
-    ----------
-    .. [1] DirectX data conversion rules.
-           https://msdn.microsoft.com/en-us/library/windows/desktop/dd607323%28v=vs.85%29.aspx
-    .. [2] Data Conversions. In "OpenGL ES 2.0 Specification v2.0.25",
-           pp 7-8. Khronos Group, 2010.
-    .. [3] Proper treatment of pixels as integers. A.W. Paeth.
-           In "Graphics Gems I", pp 249-256. Morgan Kaufmann, 1990.
-    .. [4] Dirty Pixels. J. Blinn. In "Jim Blinn's corner: Dirty Pixels",
-           pp 47-57. Morgan Kaufmann, 1998.
-
-    """
-    image = np.asarray(image)
-    dtypeobj_in = image.dtype
-    if dtype is np.floating:
-        dtypeobj_out = np.dtype('float64')
-    else:
-        dtypeobj_out = np.dtype(dtype)
-    dtype_in = dtypeobj_in.type
-    dtype_out = dtypeobj_out.type
-    kind_in = dtypeobj_in.kind
-    kind_out = dtypeobj_out.kind
-    itemsize_in = dtypeobj_in.itemsize
-    itemsize_out = dtypeobj_out.itemsize
-
-    # Below, we do an `issubdtype` check.  Its purpose is to find out
-    # whether we can get away without doing any image conversion.  This happens
-    # when:
-    #
-    # - the output and input dtypes are the same or
-    # - when the output is specified as a type, and the input dtype
-    #   is a subclass of that type (e.g. `np.floating` will allow
-    #   `float32` and `float64` arrays through)
-
-    if np.issubdtype(dtype_in, dtype):
-        if force_copy:
-            image = image.copy()
-        return image
-
-    if not (dtype_in in _supported_types and dtype_out in _supported_types):
-        raise ValueError(f'Cannot convert from {dtypeobj_in} to ' f'{dtypeobj_out}.')
-
-    if kind_in in 'ui':
-        imin_in = np.iinfo(dtype_in).min
-        imax_in = np.iinfo(dtype_in).max
-    if kind_out in 'ui':
-        imin_out = np.iinfo(dtype_out).min
-        imax_out = np.iinfo(dtype_out).max
-
-    # any -> binary
-    if kind_out == 'b':
-        return image > dtype_in(dtype_range[dtype_in][1] / 2)
-
-    # binary -> any
-    if kind_in == 'b':
-        result = image.astype(dtype_out)
-        if kind_out != 'f':
-            result *= dtype_out(dtype_range[dtype_out][1])
-        return result
-
-    # float -> any
-    if kind_in == 'f':
-        if kind_out == 'f':
-            # float -> float
-            return image.astype(dtype_out)
-
-        if np.min(image) < -1.0 or np.max(image) > 1.0:
-            raise ValueError("Images of type float must be between -1 and 1.")
-        # floating point -> integer
-        # use float type that can represent output integer type
-        computation_type = _dtype_itemsize(
-            itemsize_out, dtype_in, np.float32, np.float64
-        )
-
-        if not uniform:
-            if kind_out == 'u':
-                image_out = np.multiply(image, imax_out, dtype=computation_type)
-            else:
-                image_out = np.multiply(
-                    image, (imax_out - imin_out) / 2, dtype=computation_type
-                )
-                image_out -= 1.0 / 2.0
-            np.rint(image_out, out=image_out)
-            np.clip(image_out, imin_out, imax_out, out=image_out)
-        elif kind_out == 'u':
-            image_out = np.multiply(image, imax_out + 1, dtype=computation_type)
-            np.clip(image_out, 0, imax_out, out=image_out)
-        else:
-            image_out = np.multiply(
-                image, (imax_out - imin_out + 1.0) / 2.0, dtype=computation_type
-            )
-            np.floor(image_out, out=image_out)
-            np.clip(image_out, imin_out, imax_out, out=image_out)
-        return image_out.astype(dtype_out)
-
-    # signed/unsigned int -> float
-    if kind_out == 'f':
-        # use float type that can exactly represent input integers
-        computation_type = _dtype_itemsize(
-            itemsize_in, dtype_out, np.float32, np.float64
-        )
-
-        if kind_in == 'u':
-            # using np.divide or np.multiply doesn't copy the data
-            # until the computation time
-            image = np.multiply(image, 1.0 / imax_in, dtype=computation_type)
-            # DirectX uses this conversion also for signed ints
-            # if imin_in:
-            #     np.maximum(image, -1.0, out=image)
-        elif kind_in == 'i':
-            # From DirectX conversions:
-            # The most negative value maps to -1.0f
-            # Every other value is converted to a float (call it c)
-            # and then result = c * (1.0f / (2⁽ⁿ⁻¹⁾-1)).
-
-            image = np.multiply(image, 1.0 / imax_in, dtype=computation_type)
-            np.maximum(image, -1.0, out=image)
-
-        else:
-            image = np.add(image, 0.5, dtype=computation_type)
-            image *= 2 / (imax_in - imin_in)
-
-        return np.asarray(image, dtype_out)
-
-    # unsigned int -> signed/unsigned int
-    if kind_in == 'u':
-        if kind_out == 'i':
-            # unsigned int -> signed int
-            image = _scale(image, 8 * itemsize_in, 8 * itemsize_out - 1)
-            return image.view(dtype_out)
-        else:
-            # unsigned int -> unsigned int
-            return _scale(image, 8 * itemsize_in, 8 * itemsize_out)
-
-    # signed int -> unsigned int
-    if kind_out == 'u':
-        image = _scale(image, 8 * itemsize_in - 1, 8 * itemsize_out)
-        result = np.empty(image.shape, dtype_out)
-        np.maximum(image, 0, out=result, dtype=image.dtype, casting='unsafe')
-        return result
-
-    # signed int -> signed int
-    if itemsize_in > itemsize_out:
-        return _scale(image, 8 * itemsize_in - 1, 8 * itemsize_out - 1)
-
-    image = image.astype(_dtype_bits('i', itemsize_out * 8))
-    image -= imin_in
-    image = _scale(image, 8 * itemsize_in, 8 * itemsize_out, copy=False)
-    image += imin_out
-    return image.astype(dtype_out)
-
-
-def convert(image, dtype, force_copy=False, uniform=False):
-    warn(
-        "The use of this function is discouraged as its behavior may change "
-        "dramatically in scikit-image 1.0. This function will be removed "
-        "in scikit-image 1.0.",
-        FutureWarning,
-        stacklevel=2,
-    )
-    return _convert(image=image, dtype=dtype, force_copy=force_copy, uniform=uniform)
-
-
-if _convert.__doc__ is not None:
-    convert.__doc__ = (
-        _convert.__doc__
-        + """
-
-    Warns
-    -----
-    FutureWarning:
-        .. versionadded:: 0.17
-
-        The use of this function is discouraged as its behavior may change
-        dramatically in scikit-image 1.0. This function will be removed
-        in scikit-image 1.0.
-    """
-    )
-
-
-def img_as_float32(image, force_copy=False):
-    """Convert an image to single-precision (32-bit) floating point format.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of float32
-        Output image.
-
-    Notes
-    -----
-    The range of a floating point image is [0.0, 1.0] or [-1.0, 1.0] when
-    converting from unsigned or signed datatypes, respectively.
-    If the input image has a float type, intensity values are not modified
-    and can be outside the ranges [0.0, 1.0] or [-1.0, 1.0].
-
-    """
-    return _convert(image, np.float32, force_copy)
-
-
-def img_as_float64(image, force_copy=False):
-    """Convert an image to double-precision (64-bit) floating point format.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of float64
-        Output image.
-
-    Notes
-    -----
-    The range of a floating point image is [0.0, 1.0] or [-1.0, 1.0] when
-    converting from unsigned or signed datatypes, respectively.
-    If the input image has a float type, intensity values are not modified
-    and can be outside the ranges [0.0, 1.0] or [-1.0, 1.0].
-
-    """
-    return _convert(image, np.float64, force_copy)
-
-
-def img_as_float(image, force_copy=False):
-    """Convert an image to floating point format.
-
-    This function is similar to `img_as_float64`, but will not convert
-    lower-precision floating point arrays to `float64`.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of float
-        Output image.
-
-    Notes
-    -----
-    The range of a floating point image is [0.0, 1.0] or [-1.0, 1.0] when
-    converting from unsigned or signed datatypes, respectively.
-    If the input image has a float type, intensity values are not modified
-    and can be outside the ranges [0.0, 1.0] or [-1.0, 1.0].
-
-    """
-    return _convert(image, np.floating, force_copy)
-
-
-def img_as_uint(image, force_copy=False):
-    """Convert an image to 16-bit unsigned integer format.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of uint16
-        Output image.
-
-    Notes
-    -----
-    Negative input values will be clipped.
-    Positive values are scaled between 0 and 65535.
-
-    """
-    return _convert(image, np.uint16, force_copy)
-
-
-def img_as_int(image, force_copy=False):
-    """Convert an image to 16-bit signed integer format.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of int16
-        Output image.
-
-    Notes
-    -----
-    The values are scaled between -32768 and 32767.
-    If the input data-type is positive-only (e.g., uint8), then
-    the output image will still only have positive values.
-
-    """
-    return _convert(image, np.int16, force_copy)
-
-
-def img_as_ubyte(image, force_copy=False):
-    """Convert an image to 8-bit unsigned integer format.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of ubyte (uint8)
-        Output image.
-
-    Notes
-    -----
-    Negative input values will be clipped.
-    Positive values are scaled between 0 and 255.
-
-    """
-    return _convert(image, np.uint8, force_copy)
-
-
-def img_as_bool(image, force_copy=False):
-    """Convert an image to boolean format.
-
-    Parameters
-    ----------
-    image : ndarray
-        Input image.
-    force_copy : bool, optional
-        Force a copy of the data, irrespective of its current dtype.
-
-    Returns
-    -------
-    out : ndarray of bool (`bool_`)
-        Output image.
-
-    Notes
-    -----
-    The upper half of the input dtype's positive range is True, and the lower
-    half is False. All negative values (if present) are False.
-
-    """
-    return _convert(image, bool, force_copy)

bioxelnodes/bioxelutils/common.py

@@ -1,270 +0,0 @@
-from ast import literal_eval
-from pathlib import Path
-import bpy
-
-from ..constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, VERSIONS
-from ..utils import get_cache_dir
-
-
-def move_node_to_node(node, target_node, offset=(0, 0)):
-    node.location.x = target_node.location.x + offset[0]
-    node.location.y = target_node.location.y + offset[1]
-
-
-def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
-    xs = []
-    ys = []
-    for target_node in target_nodes:
-        xs.append(target_node.location.x)
-        ys.append(target_node.location.y)
-
-    node.location.x = sum(xs) / len(xs) + offset[0]
-    node.location.y = sum(ys) / len(ys) + offset[1]
-
-
-def get_node_type(node):
-    node_type = type(node).__name__
-    if node_type == "GeometryNodeGroup":
-        node_type = node.node_tree.name
-
-    return node_type
-
-
-def get_nodes_by_type(node_group, type_name: str):
-    return [node for node in node_group.nodes if get_node_type(node) == type_name]
-
-
-def get_container_objs_from_selection():
-    container_objs = []
-    for obj in bpy.context.selected_objects:
-        if get_container_obj(obj):
-            container_objs.append(obj)
-
-    return list(set(container_objs))
-
-
-def get_container_obj(current_obj):
-    if current_obj:
-        if current_obj.get('bioxel_container'):
-            return current_obj
-        elif current_obj.get('bioxel_layer'):
-            parent = current_obj.parent
-            return parent if parent.get('bioxel_container') else None
-    return None
-
-
-def get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str):
-    node_group = layer_obj.modifiers[0].node_group
-    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
-    prop = layer_node.inputs.get(prop_name)
-    if prop is None:
-        return None
-
-    value = prop.default_value
-
-    if type(value).__name__ == "bpy_prop_array":
-        value = tuple(value)
-        return tuple([int(v) for v in value]) \
-            if prop in ["shape"] else value
-    elif type(value).__name__ == "str":
-        return str(value)
-    elif type(value).__name__ == "float":
-        value = float(value)
-        return round(value, 2) \
-            if prop in ["bioxel_size"] else value
-    elif type(value).__name__ == "int":
-        value = int(value)
-        return value
-    else:
-        return value
-
-
-def get_layer_name(layer_obj):
-    return get_layer_prop_value(layer_obj, "name")
-
-
-def get_layer_kind(layer_obj):
-    return get_layer_prop_value(layer_obj, "kind")
-
-
-def get_layer_label(layer_obj):
-    name = get_layer_name(layer_obj)
-    # kind = get_layer_kind(layer_obj)
-
-    label = f"{name}"
-
-    if is_missing_layer(layer_obj):
-        return "**MISSING**" + label
-    elif is_temp_layer(layer_obj):
-        return "* " + label
-    else:
-        return label
-
-
-def is_missing_layer(layer_obj):
-    cache_filepath = Path(bpy.path.abspath(
-        layer_obj.data.filepath)).resolve()
-    return not cache_filepath.is_file()
-
-
-def is_temp_layer(layer_obj):
-    cache_filepath = Path(bpy.path.abspath(
-        layer_obj.data.filepath)).resolve()
-    cache_dirpath = Path(get_cache_dir())
-    return cache_dirpath in cache_filepath.parents
-
-
-def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value):
-    node_group = layer_obj.modifiers[0].node_group
-    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
-    layer_node.inputs[prop].default_value = value
-
-
-def get_layer_obj(current_obj: bpy.types.Object):
-    if current_obj:
-        if current_obj.get('bioxel_layer') and current_obj.parent:
-            if current_obj.parent.get('bioxel_container'):
-                return current_obj
-    return None
-
-
-def get_container_layer_objs(container_obj: bpy.types.Object):
-    layer_objs = []
-    for obj in bpy.data.objects:
-        if obj.parent == container_obj and get_layer_obj(obj):
-            layer_objs.append(obj)
-
-    return layer_objs
-
-
-def get_all_layer_objs():
-    layer_objs = []
-    for obj in bpy.data.objects:
-        if get_layer_obj(obj):
-            layer_objs.append(obj)
-
-    return layer_objs
-
-
-def add_driver(target, target_prop, var_sources, expression):
-    driver = target.driver_add(target_prop)
-    is_vector = isinstance(driver, list)
-    drivers = driver if is_vector else [driver]
-
-    for i, driver in enumerate(drivers):
-        for j, var_source in enumerate(var_sources):
-
-            source = var_source['source']
-            prop = var_source['prop']
-
-            var = driver.driver.variables.new()
-            var.name = f"var{j}"
-
-            var.targets[0].id_type = source.id_type
-            var.targets[0].id = source
-            var.targets[0].data_path = f'["{prop}"][{i}]'\
-                if is_vector else f'["{prop}"]'
-
-        driver.driver.expression = expression
-
-
-def add_direct_driver(target, target_prop, source, source_prop):
-    drivers = [
-        {
-            "source": source,
-            "prop": source_prop
-        }
-    ]
-    expression = "var0"
-    add_driver(target, target_prop, drivers, expression)
-
-
-def read_file_prop(content: str):
-    props = {}
-    for line in content.split("\n"):
-        line = line.replace(" ", "")
-        p = line.split("=")[0]
-        if p != "":
-            v = line.split("=")[-1]
-            props[p] = v
-    return props
-
-
-def write_file_prop(props: dict):
-    lines = []
-    for p, v in props.items():
-        lines.append(f"{p} = {v}")
-    return "\n".join(lines)
-
-
-def set_file_prop(prop, value):
-    if bpy.data.texts.get("BioxelNodes") is None:
-        bpy.data.texts.new("BioxelNodes")
-
-    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
-    props[prop] = value
-    bpy.data.texts["BioxelNodes"].clear()
-    bpy.data.texts["BioxelNodes"].write(write_file_prop(props))
-
-
-def get_file_prop(prop):
-    if bpy.data.texts.get("BioxelNodes") is None:
-        bpy.data.texts.new("BioxelNodes")
-
-    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
-    return props.get(prop)
-
-
-def get_node_version():
-    node_version = get_file_prop("node_version")
-    return literal_eval(node_version) if node_version else None
-
-
-def is_incompatible():
-    node_version = get_node_version()
-    if node_version is None:
-        for node_group in bpy.data.node_groups:
-            if node_group.name.startswith("BioxelNodes"):
-                return True
-    else:
-        addon_version = VERSIONS[0]["node_version"]
-        if node_version[0] != addon_version[0]\
-                or node_version[1] != addon_version[1]:
-            return True
-
-    return False
-
-
-def get_node_lib_path(node_version):
-    version_str = "v"+".".join([str(i) for i in list(node_version)])
-    lib_filename = f"BioxelNodes_{version_str}.blend"
-    return Path(NODE_LIB_DIRPATH,
-                lib_filename).resolve()
-
-
-def local_lib_not_updated():
-    addon_version = VERSIONS[0]["node_version"]
-    addon_lib_path = LATEST_NODE_LIB_PATH
-
-    use_local = False
-    for node_group in bpy.data.node_groups:
-        if node_group.name.startswith("BioxelNodes"):
-            lib = node_group.library
-            if lib:
-                lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-                if lib_path != addon_lib_path:
-                    use_local = True
-                    break
-
-    not_update = get_node_version() != addon_version
-    return use_local and not_update
-
-
-def get_output_node(node_group):
-    try:
-        output_node = get_nodes_by_type(node_group,
-                                        'NodeGroupOutput')[0]
-    except:
-        output_node = node_group.nodes.new("NodeGroupOutput")
-
-    return output_node

bioxelnodes/bioxelutils/container.py

@@ -1,167 +0,0 @@
-import bpy
-
-from ..bioxel.container import Container
-from bpy_extras.io_utils import axis_conversion
-from mathutils import Matrix, Vector
-
-
-from .layer import Layer, layer_to_obj, obj_to_layer
-from .common import (get_container_layer_objs,
-                     get_layer_prop_value,
-                     get_nodes_by_type, get_output_node,
-                     move_node_to_node)
-from .node import add_node_to_graph
-from ..utils import get_use_link
-
-NODE_TYPE = {
-    "label": "BioxelNodes_MaskByLabel",
-    "scalar": "BioxelNodes_MaskByThreshold"
-}
-
-
-def calc_bbox_verts(origin: tuple, size: tuple):
-    bbox_origin = Vector(
-        (origin[0], origin[1], origin[2]))
-    bbox_size = Vector(
-        (size[0], size[1], size[2]))
-    bbox_verts = [
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + 0,
-            bbox_origin[2] + 0
-        ),
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + 0,
-            bbox_origin[2] + bbox_size[2]
-        ),
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + 0
-        ),
-        (
-            bbox_origin[0] + 0,
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + bbox_size[2]
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + 0,
-            bbox_origin[2] + 0
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + 0,
-            bbox_origin[2] + bbox_size[2],
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + 0,
-        ),
-        (
-            bbox_origin[0] + bbox_size[0],
-            bbox_origin[1] + bbox_size[1],
-            bbox_origin[2] + bbox_size[2],
-        ),
-    ]
-    return bbox_verts
-
-
-def obj_to_container(container_obj: bpy.types.Object):
-    layer_objs = get_container_layer_objs(container_obj)
-    layers = [obj_to_layer(obj) for obj in layer_objs]
-    container = Container(name=container_obj.name,
-                          layers=layers)
-    return container
-
-
-def add_layers(layers: list[Layer],
-               container_obj: bpy.types.Object,
-               cache_dir: str):
-
-    node_group = container_obj.modifiers[0].node_group
-    output_node = get_output_node(node_group)
-
-    for i, layer in enumerate(layers):
-        layer_obj = layer_to_obj(layer, container_obj, cache_dir)
-        fetch_node = add_node_to_graph("FetchLayer",
-                                       node_group,
-                                       use_link=get_use_link())
-        fetch_node.label = get_layer_prop_value(layer_obj, "name")
-        fetch_node.inputs[0].default_value = layer_obj
-
-        if len(output_node.inputs[0].links) == 0:
-            node_group.links.new(fetch_node.outputs[0],
-                                 output_node.inputs[0])
-            move_node_to_node(fetch_node, output_node, (-600, 0))
-        else:
-            move_node_to_node(fetch_node, output_node, (0, -100 * (i+1)))
-
-    return container_obj
-
-
-def container_to_obj(container: Container,
-                     scene_scale: float,
-                     step_size: float,
-                     cache_dir: str):
-    # Wrapper a Container
-
-    # Make transformation
-    # (S)uperior  -Z -> Y
-    # (A)osterior  Y -> Z
-    mat_ras2blender = axis_conversion(from_forward='-Z',
-                                      from_up='Y',
-                                      to_forward='Y',
-                                      to_up='Z').to_4x4()
-
-    mat_scene_scale = Matrix.Scale(scene_scale,
-                                   4)
-
-    bpy.ops.mesh.primitive_cube_add(enter_editmode=False,
-                                    align='WORLD',
-                                    location=(0, 0, 0),
-                                    scale=(1, 1, 1))
-
-    container_obj = bpy.context.active_object
-
-    bbox_verts = calc_bbox_verts((0, 0, 0), container.layers[0].shape)
-    for i, vert in enumerate(container_obj.data.vertices):
-        transform = Matrix(container.layers[0].affine)
-        vert.co = transform @ Vector(bbox_verts[i])
-
-    container_obj.matrix_world = mat_ras2blender @ mat_scene_scale
-    container_obj.name = container.name
-    container_obj.data.name = container.name
-    container_obj.show_in_front = True
-
-    container_obj.lock_location[0] = True
-    container_obj.lock_location[1] = True
-    container_obj.lock_location[2] = True
-
-    container_obj.lock_rotation[0] = True
-    container_obj.lock_rotation[1] = True
-    container_obj.lock_rotation[2] = True
-
-    container_obj.lock_scale[0] = True
-    container_obj.lock_scale[1] = True
-    container_obj.lock_scale[2] = True
-
-    container_obj['bioxel_container'] = True
-    container_obj["scene_scale"] = scene_scale
-    container_obj["step_size"] = step_size
-
-    modifier = container_obj.modifiers.new("GeometryNodes", 'NODES')
-    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
-    node_group.interface.new_socket(name="Output",
-                                    in_out="OUTPUT",
-                                    socket_type="NodeSocketGeometry")
-    modifier.node_group = node_group
-    node_group.nodes.new("NodeGroupOutput")
-
-    container_obj = add_layers(container.layers,
-                               container_obj=container_obj,
-                               cache_dir=cache_dir)
-
-    return container_obj

bioxelnodes/bioxelutils/layer.py

@@ -1,211 +0,0 @@
-import random
-import re
-import bpy
-import numpy as np
-
-import pyopenvdb as vdb
-from pathlib import Path
-from uuid import uuid4
-
-from ..bioxel.layer import Layer
-from ..utils import get_use_link
-from .node import add_node_to_graph
-from .common import (get_layer_prop_value,
-                     move_node_between_nodes)
-
-
-def obj_to_layer(layer_obj: bpy.types.Object):
-    cache_filepath = Path(bpy.path.abspath(layer_obj.data.filepath)).resolve()
-    is_sequence = re.search(r'\.\d{4}\.',
-                            cache_filepath.name) is not None
-    if is_sequence:
-        cache_path = cache_filepath.parent
-        data_frames = ()
-        for f in cache_path.iterdir():
-            if not f.is_file() or f.suffix != ".vdb":
-                continue
-            grids, base_metadata = vdb.readAll(str(f))
-            grid = grids[0]
-            metadata = grid.metadata
-            if grid["layer_kind"] in ['label', 'scalar']:
-                data_shape = grid["data_shape"]
-            else:
-                data_shape = tuple(list(grid["data_shape"]) + [3])
-            data_frame = np.ndarray(data_shape, np.float32)
-            grid.copyToArray(data_frame)
-            data_frames += (data_frame,)
-        data = np.stack(data_frames)
-    else:
-        grids, base_metadata = vdb.readAll(str(cache_filepath))
-        grid = grids[0]
-        metadata = grid.metadata
-        if grid["layer_kind"] in ['label', 'scalar']:
-            data_shape = grid["data_shape"]
-        else:
-            data_shape = tuple(list(grid["data_shape"]) + [3])
-        data = np.ndarray(data_shape, np.float32)
-        grid.copyToArray(data)
-        data = np.expand_dims(data, axis=0)  # expend frame
-
-    name = get_layer_prop_value(layer_obj, "name") \
-        or metadata["layer_name"]
-    kind = get_layer_prop_value(layer_obj, "kind") \
-        or metadata["layer_kind"]
-    affine = metadata["layer_affine"]
-    dtype = get_layer_prop_value(layer_obj, "dtype") \
-        or metadata.get("data_dtype") or "float32"
-    offset = get_layer_prop_value(layer_obj, "offset") \
-        or metadata.get("data_offset") or 0
-
-    data = data - np.full_like(data, offset)
-    data = data.astype(dtype)
-
-    if kind in ["scalar", "label"]:
-        data = np.expand_dims(data, axis=-1)  # expend channel
-
-    layer = Layer(data=data,
-                  name=name,
-                  kind=kind,
-                  affine=affine)
-
-    return layer
-
-
-def layer_to_obj(layer: Layer,
-                 container_obj: bpy.types.Object,
-                 cache_dir: str):
-
-    data = layer.data
-
-    # TXYZC > TXYZ
-    if layer.kind in ['label', 'scalar']:
-        data = np.amax(data, -1)
-
-    offset = 0
-    if layer.kind in ['scalar']:
-        data = data.astype(np.float32)
-        orig_min = float(np.min(data))
-        if orig_min < 0:
-            offset = -orig_min
-
-        data = data + np.full_like(data, offset)
-
-    metadata = {
-        "layer_name": layer.name,
-        "layer_kind": layer.kind,
-        "layer_affine": layer.affine.tolist(),
-        "data_shape": layer.shape,
-        "data_dtype": layer.data.dtype.str,
-        "data_offset": offset
-    }
-
-    layer_display_name = f"{container_obj.name}_{layer.name}"
-    if layer.frame_count > 1:
-        print(f"Saving the Cache of {layer.name}...")
-        vdb_name = str(uuid4())
-        sequence_path = Path(cache_dir, vdb_name)
-        sequence_path.mkdir(parents=True, exist_ok=True)
-
-        cache_filepaths = []
-        for f in range(layer.frame_count):
-            if layer.kind in ['label', 'scalar']:
-                grid = vdb.FloatGrid()
-                grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32))
-            else:
-                # color
-                grid = vdb.Vec3SGrid()
-                grid.copyFromArray(
-                    data[f, :, :, :, :].copy().astype(np.float32))
-            grid.transform = vdb.createLinearTransform(
-                layer.affine.transpose())
-            grid.metadata = metadata
-            grid.name = layer.kind
-
-            cache_filepath = Path(sequence_path,
-                                  f"{vdb_name}.{str(f+1).zfill(4)}.vdb")
-            vdb.write(str(cache_filepath), grids=[grid])
-            cache_filepaths.append(cache_filepath)
-
-    else:
-        if layer.kind in ['label', 'scalar']:
-            grid = vdb.FloatGrid()
-            grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32))
-        else:
-            # color
-            grid = vdb.Vec3SGrid()
-            grid.copyFromArray(data[0, :, :, :, :].copy().astype(np.float32))
-        grid.transform = vdb.createLinearTransform(
-            layer.affine.transpose())
-        grid.metadata = metadata
-        grid.name = layer.kind
-
-        print(f"Saving the Cache of {layer.name}...")
-        cache_filepath = Path(cache_dir, f"{uuid4()}.vdb")
-        vdb.write(str(cache_filepath), grids=[grid])
-        cache_filepaths = [cache_filepath]
-
-    layer_data = bpy.data.volumes.new(layer_display_name)
-    layer_data.render.space = 'WORLD'
-    scene_scale = container_obj.get("scene_scale") or 0.01
-    step_size = container_obj.get("step_size") or 1
-    layer_data.render.step_size = scene_scale * step_size
-    layer_data.sequence_mode = 'REPEAT'
-    layer_data.filepath = str(cache_filepaths[0])
-
-    if layer.frame_count > 1:
-        layer_data.is_sequence = True
-        layer_data.frame_duration = layer.frame_count
-    else:
-        layer_data.is_sequence = False
-
-    layer_obj = bpy.data.objects.new(layer_display_name, layer_data)
-    layer_obj['bioxel_layer'] = True
-
-    print(f"Creating Node for {layer.name}...")
-    modifier = layer_obj.modifiers.new("GeometryNodes", 'NODES')
-    node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree')
-    node_group.interface.new_socket(name="Cache",
-                                    in_out="INPUT",
-                                    socket_type="NodeSocketGeometry")
-    node_group.interface.new_socket(name="Layer",
-                                    in_out="OUTPUT",
-                                    socket_type="NodeSocketGeometry")
-    modifier.node_group = node_group
-
-    layer_node = add_node_to_graph("_Layer",
-                                   node_group,
-                                   use_link=get_use_link())
-
-    layer_node.inputs['name'].default_value = layer.name
-    layer_node.inputs['shape'].default_value = layer.shape
-    layer_node.inputs['kind'].default_value = layer.kind
-
-    for i in range(layer.affine.shape[1]):
-        for j in range(layer.affine.shape[0]):
-            affine_key = f"affine{i}{j}"
-            layer_node.inputs[affine_key].default_value = layer.affine[j, i]
-
-    layer_node.inputs['unique'].default_value = random.uniform(0, 1)
-    layer_node.inputs['bioxel_size'].default_value = layer.bioxel_size[0]
-    layer_node.inputs['dtype'].default_value = layer.dtype.str
-    layer_node.inputs['dtype_num'].default_value = layer.dtype.num
-    layer_node.inputs['frame_count'].default_value = layer.frame_count
-    layer_node.inputs['channel_count'].default_value = layer.channel_count
-    layer_node.inputs['offset'].default_value = max(0, -layer.min)
-    layer_node.inputs['min'].default_value = layer.min
-    layer_node.inputs['max'].default_value = layer.max
-
-    input_node = node_group.nodes.new("NodeGroupInput")
-    output_node = node_group.nodes.new("NodeGroupOutput")
-
-    node_group.links.new(input_node.outputs[0],
-                         layer_node.inputs[0])
-    node_group.links.new(layer_node.outputs[0],
-                         output_node.inputs[0])
-
-    move_node_between_nodes(
-        layer_node, [input_node, output_node])
-
-    layer_obj.parent = container_obj
-
-    return layer_obj

bioxelnodes/bioxelutils/node.py

@@ -1,71 +0,0 @@
-from pathlib import Path
-import bpy
-
-from .common import get_file_prop, set_file_prop
-from ..exceptions import NoFound
-
-from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
-
-
-def get_node_tree(node_type: str, use_link=True):
-    # unannotate below for local debug in node lib file.
-    # node_group = bpy.data.node_groups[node_type]
-    # return node_group
-
-    # added node is always from latest node version
-    addon_version = VERSIONS[0]["node_version"]
-    addon_lib_path = LATEST_NODE_LIB_PATH
-
-    if get_file_prop("node_version") is None:
-        set_file_prop("node_version", addon_version)
-
-    local_lib = None
-    for node_group in bpy.data.node_groups:
-        if node_group.name.startswith("BioxelNodes"):
-            lib = node_group.library
-            if lib:
-                lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-                if lib_path != addon_lib_path:
-                    local_lib = lib.filepath
-                    break
-
-    # local lib first
-    lib_path_str = local_lib or str(addon_lib_path)
-
-    with bpy.data.libraries.load(lib_path_str,
-                                 link=use_link,
-                                 relative=True) as (data_from, data_to):
-        data_to.node_groups = [n for n in data_from.node_groups
-                               if n == node_type]
-
-    node_tree = data_to.node_groups[0]
-
-    if node_tree is None:
-        raise NoFound('No custom node found')
-
-    return node_tree
-
-
-def assign_node_tree(node, node_tree):
-    node.node_tree = node_tree
-    node.width = 200.0
-    node.name = node_tree.name
-    return node
-
-
-def add_node_to_graph(node_name: str, node_group, node_label=None, use_link=True):
-    node_type = f"BioxelNodes_{node_name}"
-    node_label = node_label or node_name
-
-    # Deselect all nodes first
-    for node in node_group.nodes:
-        if node.select:
-            node.select = False
-
-    node_tree = get_node_tree(node_type, use_link)
-    node = node_group.nodes.new("GeometryNodeGroup")
-    assign_node_tree(node, node_tree)
-
-    node.label = node_label
-    node.show_options = False
-    return node

bioxelnodes/blender_manifest.toml

@@ -1,37 +0,0 @@
-schema_version = "1.0.0"
-
-id = "bioxelnodes"
-version = "1.0.3"
-name = "Bioxel Nodes"
-tagline = "For scientific volumetric data visualization in Blender"
-maintainer = "Ma Nan <icrdr2010@outlook.com>"
-type = "add-on"
-website = "https://omoolab.github.io/BioxelNodes/latest"
-
-tags = ["Geometry Nodes", "Render", "Import-Export"]
-blender_version_min = "4.2.0"
-license = ['SPDX:GPL-3.0-or-later']
-copyright = ["2024 OmooLab"]
-platforms = ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
-
-wheels = [
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl",
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_11_0_arm64.whl",
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-win_amd64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_arm64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-macosx_11_0_arm64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/tifffile-2024.7.24-py3-none-any.whl",
-  "./wheels/pyometiff-1.0.0-py3-none-any.whl",
-  "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
-  "./wheels/transforms3d-0.4.2-py3-none-any.whl"
-]
-
-[permissions]
-files = "Import/export volume data from/to disk"

bioxelnodes/constants.py

@@ -1,251 +0,0 @@
-from pathlib import Path
-
-VERSIONS = [{"label": "Latest", "node_version": (1, 0, 3)},
-            {"label": "v0.3.x", "node_version": (0, 3, 3)},
-            {"label": "v0.2.x", "node_version": (0, 2, 9)}]
-
-NODE_LIB_DIRPATH = Path(Path(__file__).parent,
-                        "assets/Nodes").resolve()
-
-LATEST_NODE_LIB_PATH = lib_path = Path(NODE_LIB_DIRPATH,
-                                  "BioxelNodes_latest.blend").resolve()
-
-COMPONENT_OUTPUT_NODES = [
-    "CutoutByThreshold",
-    "CutoutByRange",
-    "CutoutByHue",
-    "JoinComponent",
-    "SetProperties",
-    "SetColor",
-    "SetColorByColor",
-    "SetColorByColor",
-    "SetColorByRamp2",
-    "SetColorByRamp3",
-    "SetColorByRamp4",
-    "SetColorByRamp5",
-    "Cut",
-]
-
-MENU_ITEMS = [
-    {
-        'label': 'Component',
-        'icon': 'OUTLINER_DATA_VOLUME',
-        'items': [
-            {
-                'label': 'Cutout by Threshold',
-                'icon': 'EMPTY_SINGLE_ARROW',
-                'name': 'CutoutByThreshold',
-                'description': ''
-            },
-            {
-                'label': 'Cutout by Range',
-                'icon': 'IPO_CONSTANT',
-                'name': 'CutoutByRange',
-                'description': ''
-            },
-            {
-                'label': 'Cutout by Hue',
-                'icon': 'COLOR',
-                'name': 'CutoutByHue',
-                'description': ''
-            },
-            "separator",
-            {
-                'label': 'To Surface',
-                'icon': 'MESH_DATA',
-                'name': 'ToSurface',
-                'description': ''
-            },
-            {
-                'label': 'Join Component',
-                'icon': 'CONSTRAINT_BONE',
-                'name': 'JoinComponent',
-                'description': ''
-            },
-            {
-                'label': 'Slice',
-                'icon': 'TEXTURE',
-                'name': 'Slice',
-                'description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Property',
-        'icon': 'PROPERTIES',
-        'items': [
-            {
-                'label': 'Set Properties',
-                'icon': 'PROPERTIES',
-                'name': 'SetProperties',
-                'description': ''
-            },
-            "separator",
-            {
-                'label': 'Set Color',
-                'icon': 'IPO_SINE',
-                'name': 'SetColor',
-                'description': ''
-            },
-            {
-                'label': 'Set Color by Color',
-                'icon': 'IPO_QUINT',
-                'name': 'SetColorByColor',
-                'description': ''
-            },
-            {
-                'label': 'Set Color by Ramp 2',
-                'icon': 'IPO_QUAD',
-                'name': 'SetColorByRamp2',
-                'description': ''
-            },
-            {
-                'label': 'Set Color by Ramp 3',
-                'icon': 'IPO_CUBIC',
-                'name': 'SetColorByRamp3',
-                'description': ''
-            },
-            {
-                'label': 'Set Color by Ramp 4',
-                'icon': 'IPO_QUART',
-                'name': 'SetColorByRamp4',
-                'description': ''
-            },
-            {
-                'label': 'Set Color by Ramp 5',
-                'icon': 'IPO_QUINT',
-                'name': 'SetColorByRamp5',
-                'description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Surface',
-        'icon': 'MESH_DATA',
-        'items': [
-            {
-                'label': 'Membrane Shader',
-                'icon': 'NODE_MATERIAL',
-                'name': 'AssignMembraneShader',
-                'description': ''
-            },
-            {
-                'label': 'Solid Shader',
-                'icon': 'SHADING_SOLID',
-                'name': 'AssignSolidShader',
-                'description': ''
-            },
-            {
-                'label': 'Slime Shader',
-                'icon': 'OUTLINER_DATA_META',
-                'name': 'AssignSlimeShader',
-                'description': ''
-            },
-
-        ]
-    },
-    {
-        'label': 'Transform',
-        'icon': 'EMPTY_AXIS',
-        'items': [
-            {
-                'label': 'Transform',
-                'icon': 'EMPTY_AXIS',
-                'name': 'Transform',
-                'description': ''
-            },
-            {
-                'label': 'Transform Parent',
-                'icon': 'ORIENTATION_PARENT',
-                'name': 'TransformParent',
-                'description': ''
-            },
-            {
-                'label': 'ReCenter',
-                'icon': 'PROP_CON',
-                'name': 'ReCenter',
-                'description': ''
-            },
-            {
-                'label': 'Extract Transform',
-                'icon': 'EMPTY_AXIS',
-                'name': 'ExtractTransform',
-                'description': ''
-            },
-        ]
-    },
-    {
-        'label': 'Cut',
-        'icon': 'MOD_BEVEL',
-        'items': [
-            {
-                'label': 'Cut',
-                'icon': 'MOD_BEVEL',
-                'name': 'Cut',
-                'description': ''
-            },
-            "separator",
-            {
-                'label': 'Primitive Cutter',
-                'icon': 'MOD_LINEART',
-                'name': 'PrimitiveCutter',
-                'description': ''
-            },
-            {
-                'label': 'Object Cutter',
-                'icon': 'MESH_PLANE',
-                'name': 'ObjectCutter',
-                'description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Extra',
-        'icon': 'MODIFIER',
-        'items': [
-            {
-                'label': 'Fetch Mesh',
-                'icon': 'OUTLINER_OB_MESH',
-                'name': 'FetchMesh',
-                'description': ''
-            },
-            {
-                'label': 'Fetch Volume',
-                'icon': 'OUTLINER_OB_VOLUME',
-                'name': 'FetchVolume',
-                'description': ''
-            },
-            {
-                'label': 'Fetch Shape Wire',
-                'icon': 'FILE_VOLUME',
-                'name': 'FetchShapeWire',
-                'description': ''
-            },
-            {
-                'label': 'Fetch Bbox Wire',
-                'icon': 'MESH_CUBE',
-                'name': 'FetchBboxWire',
-                'description': ''
-            },
-            "separator",
-            {
-                'label': 'Inflate',
-                'icon': 'OUTLINER_OB_META',
-                'name': 'Inflate',
-                'description': ''
-            },
-            {
-                'label': 'Smooth',
-                'icon': 'MOD_SMOOTH',
-                'name': 'Smooth',
-                'description': ''
-            },
-            {
-                'label': 'Remove Small Island',
-                'icon': 'FORCE_LENNARDJONES',
-                'name': 'RemoveSmallIsland',
-                'description': ''
-            }
-        ]
-    }
-]

bioxelnodes/exceptions.py

@@ -1,22 +0,0 @@
-class CancelledByUser(Exception):
-    def __init__(self):
-        message = 'Cancelled by user'
-        super().__init__(message)
-
-
-class NoContent(Exception):
-    def __init__(self, message):
-        super().__init__(message)
-        self.message = message
-
-
-class NoFound(Exception):
-    def __init__(self, message):
-        super().__init__(message)
-        self.message = message
-
-
-class Incompatible(Exception):
-    def __init__(self, message):
-        super().__init__(message)
-        self.message = message

bioxelnodes/menus.py

@@ -1,426 +0,0 @@
-import bpy
-
-from .constants import MENU_ITEMS, VERSIONS
-from .node_menu import NodeMenu
-
-from .bioxelutils.common import (get_container_obj,
-                                 get_container_layer_objs, get_layer_label,
-                                 get_layer_prop_value, get_node_version, is_incompatible)
-from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer,
-                              RemoveSelectedLayers, SaveSelectedLayersCache,
-                              ResampleLayer, SignScalar, CombineLabels,
-                              FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (AddLocator, AddSlicer, ContainerProps,
-                                  SaveContainerLayersCache, RemoveContainerMissingLayers,
-                                  SaveContainer, LoadContainer,
-                                  AddPieCutter, AddPlaneCutter,
-                                  AddCylinderCutter, AddCubeCutter, AddSphereCutter,
-                                  ExtractBboxWire, ExtractMesh, ExtractShapeWire,
-                                  ExtractNodeMesh, ExtractNodeBboxWire, ExtractNodeShapeWire)
-
-from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor)
-from .operators.misc import (CleanTemp,
-                             ReLinkNodeLib, RemoveAllMissingLayers,
-                             RenderSettingPreset, SaveAllLayersCache,
-                             SaveNodeLib, SliceViewer)
-
-
-class IncompatibleMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_INCOMPATIBLE"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        tip_text = "please downgrade addon version."
-        node_version = get_node_version()
-        if node_version:
-            version_str = "v"+".".join([str(i) for i in list(node_version)])
-            tip_text = f"please downgrade addon version to {version_str}."
-
-        layout = self.layout
-        layout.label(text="Incompatible node version detected.")
-        layout.separator()
-        layout.label(
-            text="If you still want to edit this file with bioxel nodes, ")
-        layout.label(text=tip_text)
-        layout.separator()
-        layout.label(text="If this file is archived, "
-                     "please relink node library, ")
-        layout.label(text="check if it still works, "
-                     "then save node library.")
-        layout.separator()
-        layout.menu(ReLinkNodeLibMenu.bl_idname)
-        layout.operator(SaveNodeLib.bl_idname)
-
-        layout.separator()
-        layout.menu(DangerZoneMenu.bl_idname)
-
-        layout.separator()
-        layout.menu(RenderSettingMenu.bl_idname)
-
-
-class FetchLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_ADD_LAYER"
-    bl_label = "Fetch Layer"
-
-    def draw(self, context):
-        container_obj = get_container_obj(bpy.context.active_object)
-        layer_objs = get_container_layer_objs(container_obj)
-        layout = self.layout
-
-        for layer_obj in layer_objs:
-            op = layout.operator(FetchLayer.bl_idname,
-                                 text=get_layer_label(layer_obj))
-            op.layer_obj_name = layer_obj.name
-
-
-class ExtractFromContainerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_PICK"
-    bl_label = "Extract from Container"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ExtractMesh.bl_idname)
-        layout.operator(ExtractShapeWire.bl_idname)
-        layout.operator(ExtractBboxWire.bl_idname)
-
-
-class AddCutterMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_CUTTERS"
-    bl_label = "Add a Cutter"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(AddPlaneCutter.bl_idname,
-                        icon=AddPlaneCutter.bl_icon, text="Plane Cutter")
-        layout.operator(AddCylinderCutter.bl_idname,
-                        icon=AddCylinderCutter.bl_icon, text="Cylinder Cutter")
-        layout.operator(AddCubeCutter.bl_idname,
-                        icon=AddCubeCutter.bl_icon, text="Cube Cutter")
-        layout.operator(AddSphereCutter.bl_idname,
-                        icon=AddSphereCutter.bl_icon, text="Sphere Cutter")
-        layout.operator(AddPieCutter.bl_idname,
-                        icon=AddPieCutter.bl_icon, text="Pie Cutter")
-
-
-class ImportLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_IMPORTLAYER"
-    bl_label = "Import Volumetric Data (Init)"
-    bl_icon = "FILE_NEW"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ImportAsScalar.bl_idname,
-                        text="as Scalar")
-        layout.operator(ImportAsLabel.bl_idname,
-                        text="as Label")
-        layout.operator(ImportAsColor.bl_idname,
-                        text="as Color")
-
-
-class AddLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_ADDLAYER"
-    bl_label = "Import Volumetric Data (Add)"
-    bl_icon = "FILE_NEW"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ImportAsScalar.bl_idname,
-                        text="as Scalar")
-        layout.operator(ImportAsLabel.bl_idname,
-                        text="as Label")
-        layout.operator(ImportAsColor.bl_idname,
-                        text="as Color")
-
-
-class ModifyLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_MODIFYLAYER"
-    bl_label = "Modify Layer"
-    bl_icon = "FILE_NEW"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(SignScalar.bl_idname,
-                        icon=SignScalar.bl_icon)
-        layout.operator(FillByThreshold.bl_idname,
-                        icon=FillByThreshold.bl_icon)
-        layout.operator(FillByRange.bl_idname,
-                        icon=FillByRange.bl_icon)
-        layout.operator(FillByLabel.bl_idname,
-                        icon=FillByLabel.bl_icon)
-        layout.operator(CombineLabels.bl_idname,
-                        icon=CombineLabels.bl_icon)
-
-
-class ReLinkNodeLibMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_RELINK"
-    bl_label = "Relink Node Library"
-
-    def draw(self, context):
-        layout = self.layout
-
-        for index, version in enumerate(VERSIONS):
-            op = layout.operator(ReLinkNodeLib.bl_idname,
-                                 text=version["label"])
-            op.index = index
-
-
-class RenderSettingMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_RENDER"
-    bl_label = "Render Setting Presets"
-
-    def draw(self, context):
-        layout = self.layout
-        for k, v in RenderSettingPreset.PRESETS.items():
-            op = layout.operator(RenderSettingPreset.bl_idname,
-                                 text=v)
-            op.preset = k
-
-
-class DangerZoneMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_DANGER"
-    bl_label = "Danger Zone"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(CleanTemp.bl_idname)
-
-
-class BioxelNodesTopbarMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_TOPBAR"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        layout = self.layout
-
-        layout.menu(ImportLayerMenu.bl_idname,
-                    icon=ImportLayerMenu.bl_icon)
-        layout.operator(LoadContainer.bl_idname)
-
-        layout.separator()
-        layout.operator(SaveAllLayersCache.bl_idname)
-        layout.operator(RemoveAllMissingLayers.bl_idname)
-
-        layout.separator()
-        layout.menu(ReLinkNodeLibMenu.bl_idname)
-        layout.operator(SaveNodeLib.bl_idname)
-
-        layout.separator()
-        layout.menu(DangerZoneMenu.bl_idname)
-
-        layout.separator()
-        layout.menu(RenderSettingMenu.bl_idname)
-
-
-def TOPBAR(self, context):
-    layout = self.layout
-
-    if is_incompatible():
-        layout.menu(IncompatibleMenu.bl_idname)
-    else:
-        layout.menu(BioxelNodesTopbarMenu.bl_idname)
-
-
-class NodeHeadMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_NODE_HEAD"
-    bl_label = "Bioxel Nodes"
-    bl_icon = "FILE_VOLUME"
-
-    def draw(self, context):
-
-        layout = self.layout
-        layout.menu(AddLayerMenu.bl_idname,
-                    icon=AddLayerMenu.bl_icon)
-        layout.operator(SaveContainer.bl_idname)
-
-        layout.separator()
-        layout.operator(ContainerProps.bl_idname)
-        layout.menu(ExtractFromContainerMenu.bl_idname)
-
-        layout.separator()
-        layout.operator(SaveContainerLayersCache.bl_idname,
-                        icon=SaveContainerLayersCache.bl_icon)
-        layout.operator(RemoveContainerMissingLayers.bl_idname)
-
-        layout.separator()
-        layout.operator(AddLocator.bl_idname,
-                        icon=AddLocator.bl_icon)
-        layout.operator(AddSlicer.bl_idname,
-                        icon=AddSlicer.bl_icon)
-        layout.menu(AddCutterMenu.bl_idname)
-
-        layout.separator()
-        layout.menu(FetchLayerMenu.bl_idname)
-
-
-class NodeContextMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_NODE_CONTEXT"
-    bl_label = "Bioxel Nodes"
-    bl_icon = "FILE_VOLUME"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ExtractNodeMesh.bl_idname)
-        layout.operator(ExtractNodeShapeWire.bl_idname)
-        layout.operator(ExtractNodeBboxWire.bl_idname)
-
-        layout.separator()
-        layout.operator(SaveSelectedLayersCache.bl_idname,
-                        icon=SaveSelectedLayersCache.bl_icon)
-        layout.operator(RemoveSelectedLayers.bl_idname)
-
-        layout.separator()
-        layout.operator(RenameLayer.bl_idname,
-                        icon=RenameLayer.bl_icon)
-        layout.operator(RetimeLayer.bl_idname)
-        layout.operator(RelocateLayer.bl_idname)
-
-        layout.separator()
-        layout.operator(ResampleLayer.bl_idname,
-                        icon=ResampleLayer.bl_icon)
-        layout.operator(SignScalar.bl_idname)
-        layout.operator(FillByThreshold.bl_idname)
-        layout.operator(FillByRange.bl_idname)
-        layout.operator(FillByLabel.bl_idname)
-        layout.operator(CombineLabels.bl_idname)
-
-
-def NODE_CONTEXT(self, context):
-    if is_incompatible():
-        return
-
-    container_obj = context.object
-    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
-    is_container = get_container_obj(container_obj)
-
-    if not is_geo_nodes or not is_container:
-        return
-
-    layout = self.layout
-    layout.separator()
-    layout.menu(NodeContextMenu.bl_idname)
-
-
-def NODE_HEAD(self, context):
-    if is_incompatible():
-        return
-
-    container_obj = context.object
-    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
-    is_container = get_container_obj(container_obj)
-
-    if not is_geo_nodes or not is_container:
-        return
-
-    layout = self.layout
-    layout.separator()
-    layout.menu(NodeHeadMenu.bl_idname)
-
-
-def NODE_PROP(self, context):
-    if is_incompatible():
-        return
-
-    container_obj = context.object
-    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
-    is_container = get_container_obj(container_obj)
-    self.bl_label = "Group"
-
-    if not is_geo_nodes or not is_container:
-        return
-
-    if container_obj.modifiers[0].node_group != context.space_data.edit_tree:
-        return
-
-    self.bl_label = "Bioxel Nodes"
-
-    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
-    layer_list = layer_list_UL.layer_list
-    layer_list.clear()
-
-    for layer_obj in get_container_layer_objs(container_obj):
-        layer_item = layer_list.add()
-        layer_item.label = get_layer_label(layer_obj)
-        layer_item.obj_name = layer_obj.name
-        layer_item.info_text = "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
-                                          for prop in ["kind",
-                                                       "bioxel_size",
-                                                       "shape",
-                                                       "frame_count",
-                                                       "channel_count",
-                                                       "min", "max"]])
-
-    layout = self.layout
-    layout.label(text="Layer List")
-    split = layout.row()
-    split.template_list(listtype_name="BIOXELNODES_UL_layer_list",
-                        list_id="layer_list",
-                        dataptr=layer_list_UL,
-                        propname="layer_list",
-                        active_dataptr=layer_list_UL,
-                        active_propname="layer_list_active",
-                        item_dyntip_propname="info_text",
-                        rows=20)
-
-    # sidebar = split.column(align=True)
-    # sidebar.menu(AddLayerMenu.bl_idname,
-    #              icon=AddLayerMenu.bl_icon, text="")
-
-    # sidebar.operator(SaveContainerLayersCache.bl_idname,
-    #                  icon=SaveContainerLayersCache.bl_icon, text="")
-    # sidebar.operator(RemoveContainerMissingLayers.bl_idname,
-    #                  icon=RemoveContainerMissingLayers.bl_icon, text="")
-
-    # sidebar.separator()
-    # sidebar.operator(SaveSelectedLayersCache.bl_idname,
-    #                  icon=SaveSelectedLayersCache.bl_icon, text="")
-    # sidebar.operator(RemoveSelectedLayers.bl_idname,
-    #                  icon=RemoveSelectedLayers.bl_icon, text="")
-
-    # sidebar.separator()
-    # sidebar.operator(RenameLayer.bl_idname,
-    #                  icon=RenameLayer.bl_icon, text="")
-    # sidebar.operator(ResampleLayer.bl_idname,
-    #                  icon=ResampleLayer.bl_icon, text="")
-    # sidebar.operator(RetimeLayer.bl_idname,
-    #                  icon=RetimeLayer.bl_icon, text="")
-
-    # sidebar.separator()
-    # sidebar.operator(SignScalar.bl_idname,
-    #                  icon=SignScalar.bl_icon, text="")
-    # sidebar.operator(FillByThreshold.bl_idname,
-    #                  icon=FillByThreshold.bl_icon, text="")
-    # sidebar.operator(FillByRange.bl_idname,
-    #                  icon=FillByRange.bl_icon, text="")
-    # sidebar.operator(FillByLabel.bl_idname,
-    #                  icon=FillByLabel.bl_icon, text="")
-
-    # sidebar.separator()
-    # layout.separator()
-
-
-def VIEW3D_TOPBAR(self, context):
-    layout = self.layout
-    layout.operator(SliceViewer.bl_idname)
-
-
-node_menu = NodeMenu(
-    menu_items=MENU_ITEMS
-)
-
-
-def add():
-    node_menu.register()
-    bpy.types.VIEW3D_HT_header.append(VIEW3D_TOPBAR)
-    bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR)
-    bpy.types.NODE_PT_node_tree_properties.prepend(NODE_PROP)
-    bpy.types.NODE_MT_editor_menus.append(NODE_HEAD)
-    bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT)
-
-
-def remove():
-    bpy.types.VIEW3D_HT_header.remove(VIEW3D_TOPBAR)
-    bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR)
-    bpy.types.NODE_PT_node_tree_properties.remove(NODE_PROP)
-    bpy.types.NODE_MT_editor_menus.remove(NODE_HEAD)
-    bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT)
-    node_menu.unregister()

bioxelnodes/node_menu.py

@@ -1,87 +0,0 @@
-import bpy
-from .operators.node import AddNode
-
-
-class NodeMenu():
-    def __init__(
-        self,
-        menu_items,
-    ) -> None:
-
-        self.menu_items = menu_items
-        self.class_prefix = f"BIOXELNODES_MT"
-        root_label = "Bioxel Nodes"
-        menu_classes = []
-        self._create_menu_class(
-            items=menu_items,
-            label=root_label,
-            menu_classes=menu_classes
-        )
-        self.menu_classes = menu_classes
-
-        idname = f"{self.class_prefix}_{root_label.replace(' ', '').upper()}"
-        icon = "FILE_VOLUME"
-
-        def drew_menu(self, context):
-            if (bpy.context.area.spaces[0].tree_type == 'GeometryNodeTree'):
-                layout = self.layout
-                layout.separator()
-                layout.menu(idname,
-                            icon=icon)
-        self.drew_menu = drew_menu
-
-    def _create_menu_class(self, menu_classes, items, label='CustomNodes', icon=0, idname_namespace=None):
-        idname_namespace = idname_namespace or self.class_prefix
-        idname = f"{idname_namespace}_{label.replace(' ', '').upper()}"
-
-        # create submenu class if item is menu.
-        for item in items:
-            item_items = item.get('items') if item != 'separator' else None
-            if item_items:
-                menu_class = self._create_menu_class(
-                    menu_classes=menu_classes,
-                    items=item_items,
-                    label=item.get('label') or 'CustomNodes',
-                    icon=item.get('icon') or 0,
-                    idname_namespace=idname
-                )
-                item['menu_class'] = menu_class
-
-        # create menu class
-        class Menu(bpy.types.Menu):
-            bl_idname = idname
-            bl_label = label
-
-            def draw(self, context):
-                layout = self.layout
-                for item in items:
-                    if item == "separator":
-                        layout.separator()
-                    elif item.get('menu_class'):
-                        layout.menu(
-                            item.get('menu_class').bl_idname,
-                            icon=item.get('icon') or 'NONE'
-                        )
-                    else:
-                        op = layout.operator(
-                            AddNode.bl_idname,
-                            text=item.get('label'),
-                            icon=item.get('icon') or 'NONE'
-                        )
-                        op.node_name = item['name']
-                        op.node_label = item.get('label') or ""
-                        op.node_description = item.get(
-                            'node_description') or ""
-
-        menu_classes.append(Menu)
-        return Menu
-
-    def register(self):
-        for cls in self.menu_classes:
-            bpy.utils.register_class(cls)
-        bpy.types.NODE_MT_add.append(self.drew_menu)
-
-    def unregister(self):
-        bpy.types.NODE_MT_add.remove(self.drew_menu)
-        for cls in reversed(self.menu_classes):
-            bpy.utils.unregister_class(cls)

bioxelnodes/operators/container.py

@@ -1,627 +0,0 @@
-import bpy
-
-
-import bmesh
-
-from ..constants import COMPONENT_OUTPUT_NODES
-from ..utils import get_cache_dir, get_use_link, select_object
-from ..bioxel.io import load_container, save_container
-from ..bioxelutils.container import container_to_obj, obj_to_container
-from ..bioxelutils.node import add_node_to_graph
-from ..bioxelutils.common import (get_container_layer_objs, get_container_obj, get_node_type,
-                                  get_nodes_by_type, get_output_node, is_missing_layer,
-                                  move_node_between_nodes,
-                                  move_node_to_node,
-                                  get_all_layer_objs)
-from .layer import RemoveLayers, SaveLayersCache
-
-
-class SaveContainer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_container"
-    bl_label = "Save Container (.bioxel) (BETA)"
-    bl_description = "Clean all caches saved in temp"
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    filename_ext = ".bioxel"
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = obj_to_container(container_obj)
-        save_path = f"{self.filepath.split('.')[0]}.bioxel"
-        save_container(container, save_path, overwrite=True)
-
-        self.report({"INFO"}, f"Successfully save to {save_path}")
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class LoadContainer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.load_container"
-    bl_label = "Load Container (.bioxel) (BETA)"
-    bl_description = "Clean all caches saved in temp"
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    filename_ext = ".bioxel"
-
-    def execute(self, context):
-        load_path = self.filepath
-        container = load_container(self.filepath)
-        is_first_import = len(get_all_layer_objs()) == 0
-
-        container_obj = container_to_obj(container,
-                                         scene_scale=0.01,
-                                         cache_dir=get_cache_dir())
-        select_object(container_obj)
-
-        if is_first_import:
-            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
-                                                      preset="preview_c")
-
-        self.report({"INFO"}, f"Successfully load {load_path}")
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class ExtractNodeObject():
-    bl_options = {'UNDO'}
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        # nodes = [node for node in context.selected_nodes
-        #          if get_node_type(node).removeprefix("BioxelNodes_") in COMPONENT_OUTPUT_NODES]
-
-        if len(context.selected_nodes) == 0:
-            self.report({"WARNING"}, "No node selected.")
-            return {'FINISHED'}
-
-        selected_node = context.selected_nodes[0]
-        container_node_group = container_obj.modifiers[0].node_group
-
-        container_output_node = get_output_node(container_node_group)
-
-        if len(container_output_node.inputs[0].links) == 0:
-            pre_socket = None
-        else:
-            pre_socket = container_output_node.inputs[0].links[0].from_socket
-
-        container_node_group.links.new(selected_node.outputs[0],
-                                       container_output_node.inputs[0])
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        obj = bpy.context.active_object
-
-        obj.name = f"{container_obj.name}_{self.object_type}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = obj.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}",
-                                            node_group,
-                                            node_label=f"Fetch {self.object_type}",
-                                            use_link=get_use_link())
-
-        fetch_mesh_node.inputs[0].default_value = container_obj
-        node_group.links.new(fetch_mesh_node.outputs[0], output_node.inputs[0])
-
-        for modifier in obj.modifiers:
-            bpy.ops.object.modifier_apply(modifier=modifier.name)
-
-        obj.data.materials.clear()
-
-        if pre_socket:
-            container_node_group.links.new(pre_socket,
-                                           container_output_node.inputs[0])
-
-        select_object(obj)
-
-        self.report({"INFO"}, f"Successfully picked")
-
-        return {'FINISHED'}
-
-
-class ExtractNodeMesh(bpy.types.Operator, ExtractNodeObject):
-    bl_idname = "bioxelnodes.extract_node_mesh"
-    bl_label = "Extract Mesh"
-    bl_description = "Extract Mesh"
-    bl_icon = "OUTLINER_OB_MESH"
-    object_type = "Mesh"
-
-
-class ExtractNodeShapeWire(bpy.types.Operator, ExtractNodeObject):
-    bl_idname = "bioxelnodes.extract_node_shape_wire"
-    bl_label = "Extract Shape Wire"
-    bl_description = "Extract Shape Wire"
-    bl_icon = "FILE_VOLUME"
-    object_type = "ShapeWire"
-
-
-class ExtractNodeBboxWire(bpy.types.Operator, ExtractNodeObject):
-    bl_idname = "bioxelnodes.extract_node_bbox_wire"
-    bl_label = "Extract Bbox Wire"
-    bl_description = "Extract Bbox Wire"
-    bl_icon = "MESH_CUBE"
-    object_type = "BboxWire"
-
-
-class ExtractObject():
-    bl_options = {'UNDO'}
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        obj = bpy.context.active_object
-
-        obj.name = f"{container_obj.name}_{self.object_type}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = obj.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_output_node(node_group)
-
-        fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}",
-                                            node_group,
-                                            node_label=f"Fetch {self.object_type}",
-                                            use_link=get_use_link())
-
-        fetch_mesh_node.inputs[0].default_value = container_obj
-
-        if self.object_type == "Mesh":
-            node_group.links.new(
-                fetch_mesh_node.outputs[0], output_node.inputs[0])
-        else:
-            curve_to_mesh_node = node_group.nodes.new(
-                "GeometryNodeCurveToMesh")
-            node_group.links.new(
-                fetch_mesh_node.outputs[0], curve_to_mesh_node.inputs[0])
-            node_group.links.new(
-                curve_to_mesh_node.outputs[0], output_node.inputs[0])
-
-        for modifier in obj.modifiers:
-            bpy.ops.object.modifier_apply(modifier=modifier.name)
-
-        obj.data.materials.clear()
-
-        select_object(obj)
-
-        self.report({"INFO"}, f"Successfully picked")
-
-        return {'FINISHED'}
-
-
-class ExtractMesh(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.extract_mesh"
-    bl_label = "Extract Mesh"
-    bl_description = "Extract Mesh"
-    bl_icon = "OUTLINER_OB_MESH"
-    object_type = "Mesh"
-
-
-class ExtractShapeWire(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.extract_shape_wire"
-    bl_label = "Extract Shape Wire"
-    bl_description = "Extract Shape Wire"
-    bl_icon = "FILE_VOLUME"
-    object_type = "ShapeWire"
-
-
-class ExtractBboxWire(bpy.types.Operator, ExtractObject):
-    bl_idname = "bioxelnodes.extract_bbox_wire"
-    bl_label = "Extract Bbox Wire"
-    bl_description = "Extract Bbox Wire"
-    bl_icon = "MESH_CUBE"
-    object_type = "BboxWire"
-
-
-class AddCutter():
-    bl_options = {'UNDO'}
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-        # TODO: do not use operator to create obj
-        if self.cutter_type == "plane":
-            bpy.ops.mesh.primitive_plane_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.cutter_type == "cylinder":
-            bpy.ops.mesh.primitive_cylinder_add(
-                radius=1, depth=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-            bpy.context.object.rotation_euler[0] = container_obj.rotation_euler[0]
-        elif self.cutter_type == "cube":
-            bpy.ops.mesh.primitive_cube_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.cutter_type == "sphere":
-            bpy.ops.mesh.primitive_ico_sphere_add(
-                radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.cutter_type == "pie":
-            bpy.ops.mesh.primitive_plane_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-            pie_obj = bpy.context.active_object
-            orig_data = pie_obj.data
-
-            # Create mesh
-            pie_mesh = bpy.data.meshes.new('Pie')
-            pie_obj.data = pie_mesh
-            bpy.data.meshes.remove(orig_data)
-
-            # # Create object
-            # pie = bpy.data.objects.new('Pie', pie_mesh)
-
-            # # Link object to scene
-            # bpy.context.scene.collection.objects.link(pie)
-
-            # Get a BMesh representation
-            bm = bmesh.new()   # create an empty BMesh
-            bm.from_mesh(pie_mesh)   # fill it in from a Mesh
-
-            # Hot to create vertices
-            v_0 = bm.verts.new((0.0, -1.0, 0.0))
-            v_1 = bm.verts.new((-1.0, -1.0, 1.0))
-            v_2 = bm.verts.new((0.0, 1.0, 0.0))
-            v_3 = bm.verts.new((-1.0, 1.0, 1.0))
-            v_4 = bm.verts.new((1.0, -1.0, 1.0))
-            v_5 = bm.verts.new((1.0, 1.0, 1.0))
-
-            # Initialize the index values of this sequence.
-            bm.verts.index_update()
-
-            # How to create a face
-            # it's not necessary to create the edges before, I made it only to show how create
-            # edges too
-            bm.faces.new((v_0, v_1, v_3, v_2))
-            bm.faces.new((v_0, v_2, v_5, v_4))
-
-            # Finish up, write the bmesh back to the mesh
-            bm.to_mesh(pie_mesh)
-            # bpy.context.view_layer.objects.active = pie
-
-        cutter_obj = bpy.context.active_object
-
-        # vcos = [container_obj.matrix_world @
-        #         v.co for v in container_obj.data.vertices]
-
-        # def find_center(l): return (max(l) + min(l)) / 2
-
-        # x, y, z = [[v[i] for v in vcos] for i in range(3)]
-        # center = [find_center(axis) for axis in [x, y, z]]
-
-        # cutter_obj.location = center
-        name = f"{self.cutter_type.capitalize()}_Cutter"
-        cutter_obj.name = name
-        cutter_obj.data.name = name
-        cutter_obj.visible_camera = False
-        cutter_obj.visible_diffuse = False
-        cutter_obj.visible_glossy = False
-        cutter_obj.visible_transmission = False
-        cutter_obj.visible_volume_scatter = False
-        cutter_obj.visible_shadow = False
-        cutter_obj.hide_render = True
-        cutter_obj.display_type = 'WIRE'
-        cutter_obj.lineart.usage = 'EXCLUDE'
-
-        select_object(container_obj)
-
-        modifier = container_obj.modifiers[0]
-        node_group = modifier.node_group
-
-        cut_nodes = get_nodes_by_type(node_group,
-                                      'BioxelNodes_Cut')
-        if len(cut_nodes) == 0:
-            cutter_node = add_node_to_graph("ObjectCutter",
-                                            node_group,
-                                            node_label=f"{self.cutter_type.capitalize()} Cutter",
-                                            use_link=get_use_link())
-            cutter_node.inputs[0].default_value = self.cutter_type.capitalize()
-            cutter_node.inputs[1].default_value = cutter_obj
-
-            cut_node = add_node_to_graph("Cut",
-                                         node_group,
-                                         use_link=get_use_link())
-
-            output_node = get_output_node(node_group)
-
-            if len(output_node.inputs[0].links) == 0:
-                node_group.links.new(cut_node.outputs[0],
-                                     output_node.inputs[0])
-                move_node_to_node(cut_node, output_node, (-300, 0))
-            else:
-                pre_output_node = output_node.inputs[0].links[0].from_node
-                node_group.links.new(pre_output_node.outputs[0],
-                                     cut_node.inputs[0])
-                node_group.links.new(cut_node.outputs[0],
-                                     output_node.inputs[0])
-                move_node_between_nodes(cut_node,
-                                        [pre_output_node, output_node])
-
-            node_group.links.new(cutter_node.outputs[0],
-                                 cut_node.inputs[1])
-
-            move_node_to_node(cutter_node, cut_node, (-300, -300))
-        else:
-            bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
-                                         node_name="ObjectCutter",
-                                         node_label=name)
-            node = bpy.context.active_node
-            node.inputs[0].default_value = self.cutter_type.capitalize()
-            node.inputs[1].default_value = cutter_obj
-
-        return {'FINISHED'}
-
-
-class AddPlaneCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_plane_cutter"
-    bl_label = "Add a Plane Cutter"
-    bl_description = "Add a plane cutter to current container"
-    bl_icon = "MESH_PLANE"
-    cutter_type = "plane"
-
-
-class AddCylinderCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_cylinder_cutter"
-    bl_label = "Add a Cylinder Cutter"
-    bl_description = "Add a cylinder cutter to current container"
-    bl_icon = "MESH_CYLINDER"
-    cutter_type = "cylinder"
-
-
-class AddCubeCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_cube_cutter"
-    bl_label = "Add a Cube Cutter"
-    bl_description = "Add a cube cutter to current container"
-    bl_icon = "MESH_CUBE"
-    cutter_type = "cube"
-
-
-class AddSphereCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_sphere_cutter"
-    bl_label = "Add a Sphere Cutter"
-    bl_description = "Add a sphere cutter to current container"
-    bl_icon = "MESH_UVSPHERE"
-    cutter_type = "sphere"
-
-
-class AddPieCutter(bpy.types.Operator, AddCutter):
-    bl_idname = "bioxelnodes.add_pie_cutter"
-    bl_label = "Add a Pie Cutter"
-    bl_description = "Add a pie cutter to current container"
-    bl_icon = "MESH_CONE"
-    cutter_type = "pie"
-
-
-class AddSlicer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.add_slicer"
-    bl_label = "Add a Slicer"
-    bl_description = "Add a slicer to current container"
-    bl_icon = "TEXTURE"
-    bl_options = {'UNDO'}
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        bpy.ops.mesh.primitive_plane_add(size=2,
-                                         enter_editmode=False,
-                                         align='WORLD',
-                                         location=(0, 0, 0),
-                                         scale=(1, 1, 1))
-
-        slicer_obj = bpy.context.active_object
-        slicer_obj.name = "Slicer"
-        slicer_obj.data.name = "Slicer"
-
-        slicer_obj.visible_camera = False
-        slicer_obj.visible_diffuse = False
-        slicer_obj.visible_glossy = False
-        slicer_obj.visible_transmission = False
-        slicer_obj.visible_volume_scatter = False
-        slicer_obj.visible_shadow = False
-        slicer_obj.hide_render = True
-        slicer_obj.display_type = 'WIRE'
-        slicer_obj.lineart.usage = 'EXCLUDE'
-
-        select_object(container_obj)
-
-        modifier = container_obj.modifiers[0]
-        node_group = modifier.node_group
-
-        slice_node = add_node_to_graph("Slice",
-                                       node_group,
-                                       use_link=get_use_link())
-
-        slice_node.inputs[1].default_value = slicer_obj
-
-        output_node = get_output_node(node_group)
-
-        if len(output_node.inputs[0].links) == 0:
-            node_group.links.new(slice_node.outputs[0],
-                                 output_node.inputs[0])
-            move_node_to_node(slice_node, output_node, (-300, 0))
-        else:
-            pre_output_node = output_node.inputs[0].links[0].from_node
-            node_group.links.new(pre_output_node.outputs[0],
-                                 slice_node.inputs[0])
-            node_group.links.new(slice_node.outputs[0],
-                                 output_node.inputs[0])
-            move_node_between_nodes(slice_node,
-                                    [pre_output_node, output_node])
-
-        return {'FINISHED'}
-
-
-class AddLocator(bpy.types.Operator):
-    bl_idname = "bioxelnodes.add_locator"
-    bl_label = "Add a Locator"
-    bl_description = "Add a locator to current container"
-    bl_icon = "EMPTY_AXIS"
-    bl_options = {'UNDO'}
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        bpy.ops.object.empty_add(type='ARROWS',
-                                 align='WORLD',
-                                 location=(0, 0, 0),
-                                 scale=(1, 1, 1))
-
-        locator_obj = bpy.context.active_object
-        locator_obj.name = "Locator"
-        select_object(container_obj)
-
-        modifier = container_obj.modifiers[0]
-        node_group = modifier.node_group
-
-        parent_node = add_node_to_graph("TransformParent",
-                                        node_group,
-                                        node_label="Transform Parent",
-                                        use_link=get_use_link())
-
-        parent_node.inputs[1].default_value = locator_obj
-
-        output_node = get_output_node(node_group)
-
-        if len(output_node.inputs[0].links) == 0:
-            node_group.links.new(parent_node.outputs[0],
-                                 output_node.inputs[0])
-            move_node_to_node(parent_node, output_node, (-300, 0))
-        else:
-            pre_output_node = output_node.inputs[0].links[0].from_node
-            node_group.links.new(pre_output_node.outputs[0],
-                                 parent_node.inputs[0])
-            node_group.links.new(parent_node.outputs[0],
-                                 output_node.inputs[0])
-            move_node_between_nodes(parent_node,
-                                    [pre_output_node, output_node])
-
-        return {'FINISHED'}
-
-
-class ContainerProps(bpy.types.Operator):
-    bl_idname = "bioxelnodes.container_props"
-    bl_label = "Change Container Properties"
-    bl_description = "Change current ontainer properties"
-    bl_icon = "FILE_TICK"
-
-    scene_scale: bpy.props.FloatProperty(name="Scene Scale",
-                                         soft_min=0.0001, soft_max=10.0,
-                                         min=1e-6, max=1e6,
-                                         default=0.01)  # type: ignore
-
-    step_size: bpy.props.FloatProperty(name="Step Size",
-                                       soft_min=0.1, soft_max=100.0,
-                                       min=0.1, max=1e2,
-                                       default=1)  # type: ignore
-
-    def execute(self, context):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container_obj.scale[0] = self.scene_scale
-        container_obj.scale[1] = self.scene_scale
-        container_obj.scale[2] = self.scene_scale
-        container_obj["scene_scale"] = self.scene_scale
-        container_obj["step_size"] = self.step_size
-
-        for layer_obj in get_container_layer_objs(container_obj):
-            layer_obj.data.render.space = 'WORLD'
-            layer_obj.data.render.step_size = self.scene_scale * self.step_size
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        container_obj = get_container_obj(context.object)
-
-        if container_obj is None:
-            return self.execute(context)
-        else:
-            self.scene_scale = container_obj.get("scene_scale") or 0.01
-            self.step_size = container_obj.get("step_size") or 1
-            context.window_manager.invoke_props_dialog(self)
-            return {'RUNNING_MODAL'}
-
-
-def get_container_layers(context, layer_filter=None):
-    def _layer_filter(layer_obj, context):
-        return True
-
-    layer_filter = layer_filter or _layer_filter
-    container_obj = context.object
-    layer_objs = get_container_layer_objs(container_obj)
-    return [obj for obj in layer_objs if layer_filter(obj, context)]
-
-
-class SaveContainerLayersCache(bpy.types.Operator, SaveLayersCache):
-    bl_idname = "bioxelnodes.save_container_layers_cache"
-    bl_label = "Save Container Layers' Cache"
-    bl_description = "Save all current container layers' cache to directory."
-    bl_icon = "FILE_TICK"
-
-    success_msg = "Successfully saved all container layers."
-
-    def get_layers(self, context):
-        def is_not_missing(layer_obj, context):
-            return not is_missing_layer(layer_obj)
-        return get_container_layers(context, is_not_missing)
-
-
-class RemoveContainerMissingLayers(bpy.types.Operator, RemoveLayers):
-    bl_idname = "bioxelnodes.remove_container_missing_layers"
-    bl_label = "Remove Container Missing Layers"
-    bl_description = "Remove all current container missing layers"
-    bl_icon = "BRUSH_DATA"
-
-    success_msg = "Successfully removed all container missing layers."
-
-    def get_layers(self, context):
-        def is_missing(layer_obj, context):
-            return is_missing_layer(layer_obj)
-        return get_container_layers(context, is_missing)
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message=f"Are you sure to remove all **Missing** layers?")
-        return {'RUNNING_MODAL'}

bioxelnodes/operators/io.py

@@ -1,982 +0,0 @@
-import math
-import bpy
-import shutil
-import threading
-import numpy as np
-from pathlib import Path
-
-from ..exceptions import CancelledByUser
-from ..props import BIOXELNODES_Series
-from ..bioxelutils.common import (get_all_layer_objs, get_container_obj,
-                                  get_layer_obj, is_incompatible)
-from ..bioxelutils.container import (Container,
-                                     add_layers,
-                                     container_to_obj)
-from ..bioxel.layer import Layer
-from ..bioxel.parse import (DICOM_EXTS, SUPPORT_EXTS,
-                            get_ext, parse_volumetric_data)
-
-from ..utils import (get_cache_dir,
-                     progress_update, progress_bar,
-                     select_object)
-
-# 3rd-party
-import SimpleITK as sitk
-import transforms3d
-
-
-def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
-    shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
-             int(orig_shape[1] / bioxel_size * orig_spacing[1]),
-             int(orig_shape[2] / bioxel_size * orig_spacing[2]))
-
-    return (shape[0] if shape[0] > 0 else 1,
-            shape[1] if shape[1] > 0 else 1,
-            shape[2] if shape[2] > 0 else 1)
-
-
-def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0):
-    size = (float(shape[0] * bioxel_size * scale),
-            float(shape[1] * bioxel_size * scale),
-            float(shape[2] * bioxel_size * scale))
-
-    return size
-
-
-"""
-ImportVolumetricData
-                        -> ParseVolumetricData -> ImportVolumetricDataDialog
-FH_ImportVolumetricData
-
- start import                  parse data               execute import
-"""
-
-
-class ImportVolumetricData():
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-
-    read_as = "SCALAR"
-
-    def execute(self, context):
-        data_path = Path(self.filepath).resolve()
-        ext = get_ext(data_path)
-        if ext not in SUPPORT_EXTS:
-            self.report({"WARNING"}, "Not supported format.")
-            return {'CANCELLED'}
-
-        bpy.ops.bioxelnodes.parse_volumetric_data('INVOKE_DEFAULT',
-                                                  filepath=self.filepath,
-                                                  skip_read_as=True,
-                                                  read_as=self.read_as)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class ImportAsScalar(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_scalar"
-    bl_label = "Import as Scalar"
-    bl_description = "Import Volumetric Data to Container as Scalar"
-    bl_icon = "EVENT_S"
-    read_as = "SCALAR"
-
-
-class ImportAsLabel(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_label"
-    bl_label = "Import as Label"
-    bl_description = "Import Volumetric Data to Container as Label"
-    bl_icon = "EVENT_L"
-    read_as = "LABEL"
-
-
-class ImportAsColor(bpy.types.Operator, ImportVolumetricData):
-    bl_idname = "bioxelnodes.import_as_color"
-    bl_label = "Import as Color"
-    bl_description = "Import Volumetric Data to Container as Color"
-    bl_icon = "EVENT_C"
-    read_as = "COLOR"
-
-
-class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
-    bl_idname = "BIOXELNODES_FH_ImportVolumetricData"
-    bl_label = "File handler for dicom import"
-    bl_import_operator = "bioxelnodes.parse_volumetric_data"
-    bl_file_extensions = ";".join(SUPPORT_EXTS)
-
-    @classmethod
-    def poll_drop(cls, context):
-        if not context.area:
-            return False
-
-        if context.area.type == 'VIEW_3D':
-            return True
-        elif context.area.type == 'NODE_EDITOR':
-            container_obj = get_container_obj(context.object)
-            return container_obj is not None
-        else:
-            return False
-
-
-def get_series_ids(self, context):
-    items = []
-    for index, series_id in enumerate(self.series_ids):
-        items.append((
-            series_id.id,
-            series_id.label,
-            "",
-            index
-        ))
-
-    return items
-
-
-class ParseVolumetricData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.parse_volumetric_data"
-    bl_label = "Import Volumetric Data (BioxelNodes)"
-    bl_description = "Import Volumetric Data as Layer"
-    bl_options = {'UNDO'}
-
-    meta = None
-    label_count = 0
-    dtype = None
-    thread = None
-    _timer = None
-
-    progress: bpy.props.FloatProperty(name="Progress",
-                                      options={"SKIP_SAVE"},
-                                      default=1)  # type: ignore
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-
-    skip_read_as: bpy.props.BoolProperty(name="Skip Read As",
-                                         default=False,
-                                         options={"SKIP_SAVE"})  # type: ignore
-
-    skip_series_select: bpy.props.BoolProperty(name="Skip Sries Select",
-                                               default=True,
-                                               options={"SKIP_SAVE"})  # type: ignore
-
-    read_as: bpy.props.EnumProperty(name="Read as",
-                                    default="SCALAR",
-                                    items=[("SCALAR", "Scalar", ""),
-                                           ("LABEL", "Label", ""),
-                                           ("COLOR", "Color", "")])  # type: ignore
-
-    series_id: bpy.props.EnumProperty(name="Select Series",
-                                      items=get_series_ids)  # type: ignore
-
-    series_ids: bpy.props.CollectionProperty(
-        type=BIOXELNODES_Series)  # type: ignore
-
-    def execute(self, context):
-        if is_incompatible():
-            self.report({"ERROR"},
-                        "Current addon verison is not compatible to this file. If you insist on editing this file please keep the same addon version")
-            return {'CANCELLED'}
-
-        if not self.filepath:
-            self.report({"WARNING"}, "No file selected.")
-            return {'CANCELLED'}
-
-        data_path = Path(self.filepath).resolve()
-        ext = get_ext(data_path)
-        if ext not in SUPPORT_EXTS:
-            self.report({"WARNING"}, "Not supported format.")
-            return {'CANCELLED'}
-
-        print("Collecting Meta Data...")
-
-        def parse_volumetric_data_func(self, context, cancel):
-            def progress_callback(factor, text):
-                if cancel():
-                    raise CancelledByUser
-                progress_update(context, factor, text)
-
-            try:
-                series_id = self.series_id if self.series_id != "empty" else ""
-                data, meta = parse_volumetric_data(data_file=self.filepath,
-                                                   series_id=series_id,
-                                                   progress_callback=progress_callback)
-            except CancelledByUser:
-                return
-            except Exception as e:
-                self.has_error = e
-                return
-
-            if cancel():
-                return
-
-            self.meta = meta
-            self.label_count = int(np.max(data))
-            self.dtype = data.dtype
-
-        # Init cancel flag
-        self.is_cancelled = False
-        self.has_error = None
-
-        # Create the thread
-        self.thread = threading.Thread(target=parse_volumetric_data_func,
-                                       args=(self, context, lambda: self.is_cancelled))
-
-        # Start the thread
-        self.thread.start()
-        # Add a timmer for modal
-        self._timer = context.window_manager.event_timer_add(time_step=0.1,
-                                                             window=context.window)
-        # Append progress bar to status bar
-        bpy.types.STATUSBAR_HT_header.append(progress_bar)
-
-        # Start modal handler
-        context.window_manager.modal_handler_add(self)
-        return {'RUNNING_MODAL'}
-
-    def modal(self, context, event):
-        # Check if user press 'ESC'
-        if event.type == 'ESC':
-            self.is_cancelled = True
-            progress_update(context, 0.0, "Canceling...")
-            return {'PASS_THROUGH'}
-
-        # Check if is the timer time
-        if event.type != 'TIMER':
-            return {'PASS_THROUGH'}
-
-        # Force update status bar
-        bpy.context.workspace.status_text_set_internal(None)
-
-        # Check if thread is still running
-        if self.thread.is_alive():
-            return {'PASS_THROUGH'}
-
-        # Release the thread
-        self.thread.join()
-        # Remove the timer
-        context.window_manager.event_timer_remove(self._timer)
-        # Remove the progress bar from status bar
-        bpy.types.STATUSBAR_HT_header.remove(progress_bar)
-        progress_update(context, 1.0)
-
-        # Check if thread is cancelled by user
-        if self.is_cancelled:
-            self.report({"WARNING"}, "Canncelled by user.")
-            return {'CANCELLED'}
-
-        # Check if thread is cancelled by user
-        if self.has_error:
-            raise self.has_error
-
-        # Check if has return
-        if self.meta is None:
-            self.report({"ERROR"}, "Some thing went wrong.")
-            return {'CANCELLED'}
-
-        # If not canncelled...
-        for key, value in self.meta.items():
-            print(f"{key}: {value}")
-
-        if self.read_as == "LABEL":
-            if self.label_count > 100 or self.dtype.kind not in ["i", "u"]:
-                self.report({"ERROR"}, "Invaild label data.")
-                return {'CANCELLED'}
-
-            if self.label_count == 0:
-                self.report({"ERROR"}, "Get no label.")
-                return {'CANCELLED'}
-
-        orig_shape = self.meta['xyz_shape']
-        orig_spacing = self.meta['spacing']
-
-        min_log10 = math.floor(math.log10(min(*orig_spacing)))
-        max_log10 = math.floor(math.log10(max(*orig_spacing)))
-        # min_space = min(*orig_spacing)
-        # max_space = max(*orig_spacing)
-
-        if orig_spacing[2] == 1 and min_log10 < -1:
-            orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-2),
-                            orig_spacing[1] * math.pow(10, -min_log10-2),
-                            1)
-        elif min_log10 > 0:
-            orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-1),
-                            orig_spacing[1] * math.pow(10, -min_log10-1),
-                            orig_spacing[2] * math.pow(10, -min_log10-1))
-        elif max_log10 < 0:
-            orig_spacing = (orig_spacing[0] * math.pow(10, -max_log10-1),
-                            orig_spacing[1] * math.pow(10, -max_log10-1),
-                            orig_spacing[2] * math.pow(10, -max_log10-1))
-
-        bioxel_size = max(min(*orig_spacing), 1.0)
-
-        layer_shape = get_layer_shape(bioxel_size,
-                                      orig_shape,
-                                      orig_spacing)
-        layer_size = get_layer_size(layer_shape,
-                                    bioxel_size,
-                                    0.01)
-        min_log10 = math.floor(math.log10(min(*layer_size)))
-        max_log10 = math.floor(math.log10(max(*layer_size)))
-
-        if min_log10 > 0:
-            scene_scale = math.pow(10, -min_log10-2)
-        elif max_log10 < 0:
-            scene_scale = math.pow(10, -max_log10-2)
-        else:
-            scene_scale = 0.01
-
-        if context.area.type == "NODE_EDITOR":
-            container_obj = context.object
-            container_name = container_obj.name
-            container_obj_name = container_name
-        else:
-            container_name = self.meta['name']
-            container_obj_name = ""
-
-        series_id = self.series_id if self.series_id != "empty" else ""
-        bpy.ops.bioxelnodes.import_volumetric_data_dialog(
-            'INVOKE_DEFAULT',
-            filepath=self.filepath,
-            container_name=container_name,
-            layer_name=self.meta['description'],
-            orig_shape=orig_shape,
-            orig_spacing=orig_spacing,
-            bioxel_size=bioxel_size,
-            series_id=series_id,
-            frame_count=self.meta['frame_count'],
-            channel_count=self.meta['channel_count'],
-            container_obj_name=container_obj_name,
-            read_as=self.read_as,
-            label_count=self.label_count,
-            scene_scale=scene_scale
-        )
-
-        self.report({"INFO"}, "Successfully Readed.")
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        # why not report in execute?
-        # If this operator is executing, a new execute will when pre-one done.
-        if context.window_manager.bioxelnodes_progress_factor < 1:
-            print("A process is executing, please wait for it to finish.")
-            return {'CANCELLED'}
-
-        if not self.filepath:
-            return self.execute(context)
-
-        data_path = Path(self.filepath).resolve()
-        ext = get_ext(data_path)
-
-        if context.area.type == "NODE_EDITOR":
-            title = f"Add to **{context.object.name}**"
-        else:
-            title = "Init a Container"
-
-        # Series Selection
-        if ext in DICOM_EXTS:
-            data_dirpath = data_path.parent
-            reader = sitk.ImageSeriesReader()
-            reader.MetaDataDictionaryArrayUpdateOn()
-            reader.LoadPrivateTagsOn()
-
-            series_ids = reader.GetGDCMSeriesIDs(str(data_dirpath))
-            series_items = {}
-
-            for series_id in series_ids:
-                series_files = reader.GetGDCMSeriesFileNames(
-                    str(data_dirpath), series_id)
-                single = sitk.ImageFileReader()
-                single.SetFileName(series_files[0])
-                single.LoadPrivateTagsOn()
-                single.ReadImageInformation()
-
-                def get_meta(key):
-                    try:
-                        stirng = single.GetMetaData(key).removesuffix(" ")
-                        stirng.encode('utf-8')
-                        if stirng in ["No study description",
-                                      "No series description",
-                                      ""]:
-                            return "Unknown"
-                        else:
-                            return stirng
-                    except:
-                        return "Unknown"
-
-                study_description = get_meta("0008|1030")
-                series_description = get_meta("0008|103e")
-                series_modality = get_meta("0008|0060")
-                size_x = get_meta("0028|0011")
-                size_y = get_meta("0028|0010")
-                count = get_meta("0020|0013")
-                count = count if count != "Unknown" else 1
-
-                # some series image count = 0 ????
-                if int(count) == 0:
-                    continue
-
-                # series_id cannot be "" in blender selection
-                if series_id == "":
-                    series_id = "empty"
-
-                label = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})",
-                                              f"({size_x}x{size_y})x{count}")
-
-                series_items[series_id] = label
-
-            for series_id, label in series_items.items():
-                series_item = self.series_ids.add()
-                series_item.id = series_id
-                series_item.label = label
-
-            if len(series_items.keys()) > 1:
-                self.skip_series_select = False
-                context.window_manager.invoke_props_dialog(self,
-                                                           width=400,
-                                                           title=title)
-                return {'RUNNING_MODAL'}
-            elif len(series_items.keys()) == 1:
-                self.series_id = list(series_items.keys())[0]
-            else:
-                self.report({"ERROR"}, "Get no vaild series.")
-                return {'CANCELLED'}
-
-        if self.skip_read_as:
-            return self.execute(context)
-        else:
-            context.window_manager.invoke_props_dialog(self,
-                                                       width=400,
-                                                       title=title)
-            return {'RUNNING_MODAL'}
-
-    def draw(self, context):
-        layout = self.layout
-        if not self.skip_read_as:
-            layout.label(
-                text='What kind is the data read as?')
-            layout.prop(self, "read_as")
-        if not self.skip_series_select:
-            layout.label(text='Which series to import?')
-            layout.prop(self, "series_id")
-
-
-def get_frame_sources(self, context):
-    items = [("-1", "First Frame (1 frame)", "")]
-    orig_shape = tuple(self.orig_shape)
-    if self.frame_count > 1:
-        items.append(("0", f"Frames ({self.frame_count} frames)", ""))
-    elif self.frame_count == 1 and self.channel_count > 1:
-        items.append(("4", f"Channels ({self.channel_count} frames)", ""))
-    elif self.frame_count == 1 and self.channel_count == 1:
-        items.append(("1", f"X-axis ({orig_shape[0]} frames)", ""))
-        items.append(("2", f"Y-axis ({orig_shape[1]} frames)", ""))
-        items.append(("3", f"Z-axis ({orig_shape[2]} frames)", ""))
-
-    return items
-
-
-class ImportVolumetricDataDialog(bpy.types.Operator):
-    bl_idname = "bioxelnodes.import_volumetric_data_dialog"
-    bl_label = "Import Volumetric Data"
-    bl_description = "Import Volumetric Data as Layer"
-    bl_options = {'UNDO'}
-
-    layers = None
-    thread = None
-    _timer = None
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-
-    container_name: bpy.props.StringProperty(
-        name="Container Name")   # type: ignore
-
-    layer_name: bpy.props.StringProperty(name="Layer Name")   # type: ignore
-
-    series_id: bpy.props.StringProperty()   # type: ignore
-
-    container_obj_name: bpy.props.StringProperty()   # type: ignore
-
-    frame_count: bpy.props.IntProperty()  # type: ignore
-
-    channel_count: bpy.props.IntProperty()  # type: ignore
-
-    label_count: bpy.props.IntProperty()  # type: ignore
-
-    smooth: bpy.props.IntProperty(name="Smooth Size (Larger takes longer time)",
-                                  default=0)  # type: ignore
-
-    read_as: bpy.props.EnumProperty(name="Read as",
-                                    default="SCALAR",
-                                    items=[("SCALAR", "Scalar", ""),
-                                           ("LABEL", "Label", ""),
-                                           ("COLOR", "Color", "")])  # type: ignore
-
-    bioxel_size: bpy.props.FloatProperty(name="Bioxel Size (Larger size means small resolution)",
-                                         soft_min=0.1, soft_max=10.0,
-                                         min=0.1, max=1e2,
-                                         default=1)  # type: ignore
-
-    orig_spacing: bpy.props.FloatVectorProperty(name="Original Spacing",
-                                                default=(1, 1, 1))  # type: ignore
-
-    orig_shape: bpy.props.IntVectorProperty(name="Original Shape",
-                                            default=(100, 100, 100))  # type: ignore
-
-    scene_scale: bpy.props.FloatProperty(name="Scene Scale (Bioxel Unit pre Blender Unit)",
-                                         soft_min=0.0001, soft_max=10.0,
-                                         min=1e-6, max=1e6,
-                                         default=0.01)  # type: ignore
-
-    remap: bpy.props.BoolProperty(name="Remap to 0~1",
-                                  default=False)  # type: ignore
-
-    split_channel: bpy.props.BoolProperty(name="Split Channels",
-                                          default=False)  # type: ignore
-
-    frame_source: bpy.props.EnumProperty(name="Frame From",
-                                         items=get_frame_sources)  # type: ignore
-
-    def execute(self, context):
-        def import_volumetric_data_func(self, context, cancel):
-            progress_update(context, 0.0, "Parsing Volumetirc Data...")
-
-            def progress_callback(factor, text):
-                if cancel():
-                    raise CancelledByUser
-                progress_update(context, factor*0.2, text)
-
-            try:
-                data, meta = parse_volumetric_data(data_file=self.filepath,
-                                                   series_id=self.series_id,
-                                                   progress_callback=progress_callback)
-            except CancelledByUser:
-                return
-            except Exception as e:
-                self.has_error = e
-                return
-
-            if cancel():
-                return
-
-            shape = get_layer_shape(self.bioxel_size,
-                                    self.orig_shape,
-                                    self.orig_spacing)
-
-            mat_scale = transforms3d.zooms.zfdir2aff(self.bioxel_size)
-            affine = np.dot(meta['affine'], mat_scale)
-            kind = self.read_as.lower()
-
-            if cancel():
-                return
-
-            # change shape as sequence or not
-            if self.frame_source == "-1":
-                data = data[0:1, :, :, :, :]
-            elif self.frame_source == "0":
-                # frame as frame
-                pass
-            elif self.frame_source == "1":
-                # X as frame
-                data = data.transpose(1, 0, 2, 3, 4)
-                shape = (1, shape[1], shape[2])
-            elif self.frame_source == "2":
-                # Y as frame
-                data = data.transpose(2, 1, 0, 3, 4)
-                shape = (shape[0], 1, shape[2])
-            elif self.frame_source == "3":
-                # Z as frame
-                data = data.transpose(3, 1, 2, 0, 4)
-                shape = (shape[0], shape[1], 1)
-            else:
-                # channel as frame
-                data = data.transpose(4, 1, 2, 3, 0)
-
-            def progress_callback_factory(layer_name, progress, progress_step):
-                def progress_callback(frame, total):
-                    if cancel():
-                        raise CancelledByUser
-                    sub_progress_step = progress_step/total
-                    sub_progress = progress + frame * sub_progress_step
-                    progress_update(context, sub_progress,
-                                    f"Processing {layer_name} Frame {frame+1}...")
-                    print(f"Processing {layer_name} Frame {frame+1}...")
-                return progress_callback
-
-            layers = []
-            if kind == "label":
-                name = self.layer_name or "Label"
-                data = data.astype(int)
-                label_count = int(np.max(data))
-                progress_step = 0.7/label_count
-
-                for i in range(label_count):
-                    if cancel():
-                        return
-
-                    name_i = f"{name}_{i+1}"
-                    progress = 0.2+i*progress_step
-                    progress_update(context, progress,
-                                    f"Processing {name_i}...")
-
-                    progress_callback = progress_callback_factory(name_i,
-                                                                  progress,
-                                                                  progress_step)
-                    label_data = data == np.full_like(data, i+1)
-                    # label_data = label_data.astype(np.float32)
-                    try:
-                        layer = Layer(data=label_data,
-                                      name=name_i,
-                                      kind=kind)
-
-                        layer.resize(shape=shape,
-                                     smooth=self.smooth,
-                                     progress_callback=progress_callback)
-
-                        layer.affine = affine
-
-                        layers.append(layer)
-                    except CancelledByUser:
-                        return
-                    except Exception as e:
-                        self.has_error = e
-                        return
-
-            if kind == "color":
-                if np.issubdtype(np.uint8, data.dtype):
-                    data = np.multiply(data, 1.0 / 256,
-                                       dtype=np.float32)
-                elif data.dtype.kind in ['u', 'i']:
-                    # Convert the normalized array to float dtype
-                    data = data.astype(np.float32)
-
-                    min_val = data.min()
-                    max_val = data.max()
-                    # Avoid division by zero if all values are the same
-                    if max_val != min_val:
-                        # Normalize the array to the range (0,1)
-                        data = (data - min_val) / (max_val - min_val)
-                    else:
-                        # If all values are the same, the normalized array will be all zeros
-                        data = np.zeros_like(data, dtype=np.float32)
-
-                else:
-                    data = data.astype(np.float32)
-
-                name = self.layer_name or "Color"
-                if data.shape[4] == 1:
-                    data = np.repeat(data, repeats=3, axis=4)
-                elif data.shape[4] == 2:
-                    d_shape = list(data.shape)
-                    d_shape = d_shape[:4] + [1]
-                    zore = np.zeros(tuple(d_shape), dtype=np.float32)
-                    data = np.concatenate((data, zore), axis=-1)
-                elif data.shape[4] > 3:
-                    data = data[:, :, :, :, :3]
-
-                if cancel():
-                    return
-
-                progress_update(context, 0.2,
-                                f"Processing {name}...")
-                progress_callback = progress_callback_factory(name,
-                                                              0.2,
-                                                              0.7)
-
-                try:
-                    layer = Layer(data=data,
-                                  name=name,
-                                  kind=kind)
-
-                    layer.resize(shape=shape,
-                                 progress_callback=progress_callback)
-
-                    layer.affine = affine
-
-                    layers.append(layer)
-                except CancelledByUser:
-                    return
-                except Exception as e:
-                    self.has_error = e
-                    return
-
-            elif kind == "scalar":
-                name = self.layer_name or "Scalar"
-
-                if self.remap:
-                    # Convert the normalized array to float dtype
-                    data = data.astype(np.float32)
-
-                    min_val = data.min()
-                    max_val = data.max()
-                    # Avoid division by zero if all values are the same
-                    if max_val != min_val:
-                        # Normalize the array to the range (0,1)
-                        data = (data - min_val) / (max_val - min_val)
-                    else:
-                        # If all values are the same, the normalized array will be all zeros
-                        data = np.zeros_like(data, dtype=np.float32)
-
-                if self.split_channel:
-                    progress_step = 0.7/self.channel_count
-
-                    for i in range(self.channel_count):
-                        if cancel():
-                            return
-
-                        name_i = f"{name}_{i+1}"
-                        progress = 0.2 + i*progress_step
-                        progress_update(context, progress,
-                                        f"Processing {name_i}...")
-                        progress_callback = progress_callback_factory(name_i,
-                                                                      progress,
-                                                                      progress_step)
-                        try:
-                            layer = Layer(data=data[:, :, :, :, i:i+1],
-                                          name=name_i,
-                                          kind=kind)
-
-                            layer.resize(shape=shape,
-                                         progress_callback=progress_callback)
-
-                            layer.affine = affine
-
-                            layers.append(layer)
-                        except CancelledByUser:
-                            return
-                        except Exception as e:
-                            self.has_error = e
-                            return
-                else:
-                    if cancel():
-                        return
-
-                    progress_update(context, 0.2,
-                                    f"Processing {name}...")
-                    progress_callback = progress_callback_factory(name,
-                                                                  0.2,
-                                                                  0.7)
-
-                    try:
-                        layer = Layer(data=data,
-                                      name=name,
-                                      kind=kind)
-
-                        layer.resize(shape=shape,
-                                     progress_callback=progress_callback)
-
-                        layer.affine = affine
-
-                        layers.append(layer)
-                    except CancelledByUser:
-                        return
-                    except Exception as e:
-                        self.has_error = e
-                        return
-
-            if cancel():
-                return
-
-            self.layers = layers
-            progress_update(context, 0.9, "Creating Layers...")
-
-        self.is_cancelled = False
-        self.has_error = None
-
-        self.thread = threading.Thread(target=import_volumetric_data_func,
-                                       args=(self, context, lambda: self.is_cancelled))
-
-        self.thread.start()
-        self._timer = context.window_manager.event_timer_add(time_step=0.1,
-                                                             window=context.window)
-        bpy.types.STATUSBAR_HT_header.append(progress_bar)
-
-        context.window_manager.modal_handler_add(self)
-        return {'RUNNING_MODAL'}
-
-    def modal(self, context, event):
-        if event.type == 'ESC':
-            self.is_cancelled = True
-            progress_update(context, 0.0, "Canceling...")
-            return {'PASS_THROUGH'}
-
-        if event.type != 'TIMER':
-            return {'PASS_THROUGH'}
-
-        bpy.context.workspace.status_text_set_internal(None)
-        if self.thread.is_alive():
-            return {'PASS_THROUGH'}
-
-        self.thread.join()
-        context.window_manager.event_timer_remove(self._timer)
-        bpy.types.STATUSBAR_HT_header.remove(progress_bar)
-        progress_update(context, 1.0)
-
-        if self.is_cancelled:
-            self.report({"WARNING"}, "Canncelled by user.")
-            return {'CANCELLED'}
-
-        # Check if thread is cancelled by user
-        if self.has_error:
-            raise self.has_error
-
-        # Check if has return
-        if self.layers is None:
-            self.report({"ERROR"}, "Some thing went wrong.")
-            return {'CANCELLED'}
-
-        is_first_import = len(get_all_layer_objs()) == 0
-
-        if self.container_obj_name:
-            container_obj = bpy.data.objects.get(self.container_obj_name)
-            if container_obj is None:
-                raise Exception("Could not find target container")
-
-            container_obj = add_layers(self.layers,
-                                       container_obj=container_obj,
-                                       cache_dir=get_cache_dir())
-        else:
-            name = self.container_name or "Container"
-            container = Container(name=name,
-                                  layers=self.layers)
-
-            step_size = container.layers[0].bioxel_size[0]*10
-            container_obj = container_to_obj(container,
-                                             scene_scale=self.scene_scale,
-                                             step_size=step_size,
-                                             cache_dir=get_cache_dir())
-
-        select_object(container_obj)
-
-        # Change render setting for better result
-        if is_first_import:
-            bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
-                                                      preset="balance")
-            bpy.context.scene.render.engine = 'CYCLES'
-
-        self.report({"INFO"}, "Successfully Imported")
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        layer_kind = self.read_as.capitalize()
-        title = f"Add to **{self.container_obj_name}**, As {layer_kind}" \
-            if self.container_obj_name != "" else f"Init a Container, As {layer_kind}"
-        context.window_manager.invoke_props_dialog(self,
-                                                   width=500,
-                                                   title=title)
-        return {'RUNNING_MODAL'}
-
-    def draw(self, context):
-        layer_shape = get_layer_shape(self.bioxel_size,
-                                      self.orig_shape,
-                                      self.orig_spacing)
-
-        orig_shape = tuple(self.orig_shape)
-
-        # change shape as sequence or not
-        channel_count = self.channel_count
-        frame_count = self.frame_count
-        if self.frame_source == "-1":
-            frame_count = 1
-            pass
-        elif self.frame_source == "0":
-            # frame as frame
-            pass
-        elif self.frame_source == "1":
-            frame_count = orig_shape[0]
-            layer_shape = (1, layer_shape[1], layer_shape[2])
-        elif self.frame_source == "2":
-            frame_count = orig_shape[1]
-            layer_shape = (layer_shape[0], 1, layer_shape[2])
-        elif self.frame_source == "3":
-            frame_count = orig_shape[2]
-            layer_shape = (layer_shape[0], layer_shape[1], 1)
-        else:
-            channel_count = 1
-
-        if self.read_as == "SCALAR":
-            layer_count = channel_count if self.split_channel else 1
-            channel_count = 1
-        elif self.read_as == "LABEL":
-            layer_count = self.label_count
-            channel_count = 1
-        else:
-            layer_count = 1
-            channel_count = 3
-
-        bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
-        orig_shape_text = f"[{self.frame_count}, ({orig_shape[0]},{orig_shape[1]},{orig_shape[2]}), {self.channel_count}]"
-        layer_shape_text = f"{layer_count} x [{frame_count}, ({layer_shape[0]},{layer_shape[1]},{layer_shape[2]}), {channel_count}]"
-
-        if bioxel_count > 100000000:
-            layer_shape_text += "**TOO LARGE!**"
-
-        layer_size = get_layer_size(layer_shape,
-                                    self.bioxel_size,
-                                    self.scene_scale)
-        layer_size_text = f"Size will be: ({layer_size[0]:.2f}, {layer_size[1]:.2f}, {layer_size[2]:.2f}) m"
-
-        layout = self.layout
-        if self.container_obj_name == "":
-            panel = layout.box()
-            panel.prop(self, "container_name")
-            panel.prop(self, "scene_scale")
-            panel.label(text=layer_size_text)
-
-        panel = layout.box()
-        panel.prop(self, "layer_name")
-        panel.prop(self, "bioxel_size")
-        row = panel.row()
-        row.prop(self, "orig_spacing")
-        panel.prop(self, "frame_source")
-
-        if self.read_as == "SCALAR":
-            panel.prop(self, "split_channel",
-                       text=f"Split Channel as Multi Layer")
-        elif self.read_as == "LABEL":
-            panel.prop(self, "smooth")
-
-        panel.label(
-            text="Dimension Order: [Frame, (X-axis,Y-axis,Z-axis), Channel]")
-        panel.label(
-            text=f"Shape from {orig_shape_text} to {layer_shape_text}")
-
-
-class ExportVolumetricData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.export_volumetric_data"
-    bl_label = "Export Layer as VDB"
-    bl_description = "Export Layer as VDB"
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    filename_ext = ".vdb"
-
-    @classmethod
-    def poll(cls, context):
-        layer_obj = get_layer_obj(bpy.context.active_object)
-        return True if layer_obj else False
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-    def execute(self, context):
-        layer_obj = get_layer_obj(bpy.context.active_object)
-
-        filepath = f"{self.filepath.split('.')[0]}.vdb"
-        # "//"
-        source_dir = bpy.path.abspath(layer_obj.data.filepath)
-
-        output_path: Path = Path(filepath).resolve()
-        source_path: Path = Path(source_dir).resolve()
-        # print('output_path', output_path)
-        # print('source_path', source_path)
-        shutil.copy(source_path, output_path)
-
-        self.report({"INFO"}, f"Successfully exported to {output_path}")
-
-        return {'FINISHED'}

bioxelnodes/operators/layer.py

@@ -1,619 +0,0 @@
-from pathlib import Path
-import bpy
-
-import numpy as np
-
-
-from ..exceptions import NoContent
-from ..bioxel.layer import Layer
-from ..bioxelutils.node import add_node_to_graph
-from ..bioxelutils.common import (get_container_obj, get_layer_kind, get_layer_label, get_layer_name,
-                                  get_layer_prop_value,
-                                  get_container_layer_objs,
-                                  get_node_type, is_missing_layer, move_node_to_node, set_layer_prop_value)
-from ..bioxelutils.layer import layer_to_obj, obj_to_layer
-from ..utils import get_cache_dir, copy_to_dir, get_use_link
-
-
-def get_label_layer_selection(self, context):
-    items = [("None", "None", "")]
-    container_obj = get_container_obj(bpy.context.active_object)
-
-    for layer_obj in get_container_layer_objs(container_obj):
-        kind = get_layer_prop_value(layer_obj, "kind")
-        name = get_layer_prop_value(layer_obj, "name")
-        if kind == "label":
-            items.append((layer_obj.name,
-                          name,
-                          ""))
-
-    return items
-
-
-class FetchLayer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fetch_layer"
-    bl_label = "Fetch Layer"
-    bl_description = "Fetch layer from current container"
-    bl_icon = "NODE"
-    bl_options = {'UNDO'}
-
-    layer_obj_name: bpy.props.StringProperty(
-        options={"HIDDEN"})  # type: ignore
-
-    @classmethod
-    def description(cls, context, properties):
-        layer_obj_name = properties.layer_obj_name
-        layer_obj = bpy.data.objects.get(layer_obj_name)
-        return "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
-                          for prop in ["kind",
-                                       "bioxel_size",
-                                       "shape",
-                                       "frame_count",
-                                       "channel_count",
-                                       "min", "max"]])
-
-    @property
-    def layer_obj(self):
-        return bpy.data.objects.get(self.layer_obj_name)
-
-    def execute(self, context):
-        if self.layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        if is_missing_layer(self.layer_obj):
-            self.report({"WARNING"}, "Selected layer is lost.")
-            return {'FINISHED'}
-
-        bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT',
-                                     node_name="FetchLayer",
-                                     node_label="Fetch Layer")
-        node = bpy.context.active_node
-
-        node.inputs[0].default_value = self.layer_obj
-        node.label = get_layer_label(self.layer_obj)
-
-        return {"FINISHED"}
-
-
-def get_selected_layers(context, layer_filter=None):
-    def _layer_filter(layer_obj, context):
-        return True
-
-    layer_filter = layer_filter or _layer_filter
-    select_objs = []
-    # node_group = context.space_data.edit_tree
-    for node in context.selected_nodes:
-        if get_node_type(node) == "BioxelNodes_FetchLayer":
-            layer_obj = node.inputs[0].default_value
-            if layer_obj is not None:
-                if layer_filter(layer_obj, context):
-                    select_objs.append(layer_obj)
-
-    return list(set(select_objs))
-
-
-def get_selected_layer(context, layer_filter=None):
-    layer_objs = get_selected_layers(context, layer_filter)
-    return layer_objs[0] if len(layer_objs) > 0 else None
-
-
-class OutputLayerOperator():
-    new_layer_name: bpy.props.StringProperty(name="New Name",
-                                             options={"SKIP_SAVE"})  # type: ignore
-
-    def operate(self, orig_layer: Layer, context):
-        """do the operation"""
-        return orig_layer
-
-    def add_layer_node(self, context, layer):
-        orig_node = context.selected_nodes[0]
-        layer_obj = layer_to_obj(layer,
-                                 container_obj=context.object,
-                                 cache_dir=get_cache_dir())
-        node_group = context.space_data.edit_tree
-        fetch_node = add_node_to_graph("FetchLayer",
-                                       node_group,
-                                       use_link=get_use_link())
-        fetch_node.label = get_layer_prop_value(layer_obj, "name")
-        fetch_node.inputs[0].default_value = layer_obj
-        move_node_to_node(fetch_node, orig_node, (0, -100))
-
-    def execute(self, context):
-        layer_obj = get_selected_layer(context)
-        if layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        if is_missing_layer(layer_obj):
-            self.report({"WARNING"}, "Selected layer is lost.")
-            return {'FINISHED'}
-
-        orig_layer = obj_to_layer(layer_obj)
-        try:
-            new_layer = self.operate(orig_layer, context)
-        except NoContent as e:
-            self.report({"WARNING"}, e.message)
-            return {'FINISHED'}
-
-        self.add_layer_node(context, new_layer)
-        return {'FINISHED'}
-
-
-class LayerOperator():
-
-    def operate(self, layer_obj: bpy.types.Object, context):
-        """do the operation"""
-        ...
-
-    def execute(self, context):
-        layer_obj = get_selected_layer(context)
-        if layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        if is_missing_layer(layer_obj):
-            self.report({"WARNING"}, "Selected layer is lost.")
-            return {'FINISHED'}
-
-        self.operate(layer_obj, context)
-
-        return {'FINISHED'}
-
-
-class RetimeLayer(bpy.types.Operator, LayerOperator):
-    bl_idname = "bioxelnodes.retime_layer"
-    bl_label = "Retime Sequence"
-    bl_description = "Retime layer time sequence"
-    bl_icon = "TIME"
-
-    frame_duration: bpy.props.IntProperty(name="Frames")  # type: ignore
-    frame_start: bpy.props.IntProperty(name="Start")  # type: ignore
-    frame_offset: bpy.props.IntProperty(name="Offset")  # type: ignore
-    sequence_mode: bpy.props.EnumProperty(name="Mode",
-                                          default="REPEAT",
-                                          items=[("CLIP", "Clip", ""),
-                                                 ("EXTEND", "Extend", ""),
-                                                 ("REPEAT", "Repeat", ""),
-                                                 ("PING_PONG", "Ping-Pong", "")])  # type: ignore
-
-    def operate(self, layer_obj, context):
-        layer_obj.data.frame_duration = self.frame_duration
-        layer_obj.data.frame_start = self.frame_start
-        layer_obj.data.frame_offset = self.frame_offset
-        layer_obj.data.sequence_mode = self.sequence_mode
-
-    def invoke(self, context, event):
-        layer_obj = get_selected_layer(context)
-        if layer_obj:
-            self.frame_duration = layer_obj.data.frame_duration
-            self.frame_start = layer_obj.data.frame_start
-            self.frame_offset = layer_obj.data.frame_offset
-            self.sequence_mode = layer_obj.data.sequence_mode
-            name = get_layer_label(layer_obj)
-            context.window_manager.invoke_props_dialog(self,
-                                                       title=f"Retime {name}")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class RelocateLayer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.relocate_layer"
-    bl_label = "Relocate Layer Cache"
-    bl_description = "Relocate layer cache"
-    bl_icon = "FILE"
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-
-    def execute(self, context):
-        layer_obj = get_selected_layer(context)
-        if layer_obj == None:
-            self.report({"WARNING"}, "Get no layer.")
-            return {'FINISHED'}
-
-        self.operate(layer_obj, context)
-
-        return {'FINISHED'}
-
-    def operate(self, layer_obj, context):
-        layer_obj.data.filepath = self.filepath
-
-    def invoke(self, context, event):
-        layer_obj = get_selected_layer(context)
-        if layer_obj:
-            context.window_manager.fileselect_add(self)
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class RenameLayer(bpy.types.Operator, LayerOperator):
-    bl_idname = "bioxelnodes.rename_layer"
-    bl_label = "Rename Layer"
-    bl_description = "Rename layer"
-    bl_icon = "FILE_FONT"
-
-    new_name: bpy.props.StringProperty(name="New Name",
-                                       options={"SKIP_SAVE"})  # type: ignore
-
-    def operate(self, layer_obj, context):
-        name = f"{layer_obj.parent.name}_{self.new_name}"
-        layer_obj.name = name
-        layer_obj.data.name = name
-
-        set_layer_prop_value(layer_obj, "name", self.new_name)
-
-        node_group = context.space_data.edit_tree
-        for node in node_group.nodes:
-            if get_node_type(node) == "BioxelNodes_FetchLayer":
-                if node.inputs[0].default_value == layer_obj:
-                    node.label = self.new_name
-
-    def invoke(self, context, event):
-        layer_obj = get_selected_layer(context)
-        if layer_obj:
-            self.new_name = get_layer_name(layer_obj)
-            name = get_layer_label(layer_obj)
-            context.window_manager.invoke_props_dialog(self,
-                                                       title=f"Rename {name}")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class ResampleLayer(bpy.types.Operator, OutputLayerOperator):
-    bl_idname = "bioxelnodes.resample_layer"
-    bl_label = "Resample Value"
-    bl_description = "Resample value"
-    bl_icon = "ALIASED"
-
-    smooth: bpy.props.IntProperty(name="Smooth Size",
-                                  default=0,
-                                  soft_min=0, soft_max=5,
-                                  options={"SKIP_SAVE"})  # type: ignore
-
-    bioxel_size: bpy.props.FloatProperty(
-        name="Bioxel Size",
-        soft_min=0.1, soft_max=10.0,
-        default=1,
-    )  # type: ignore
-
-    @staticmethod
-    def get_new_shape(orig_shape, orig_size, new_size):
-        return (int(orig_shape[0]*orig_size/new_size),
-                int(orig_shape[1]*orig_size/new_size),
-                int(orig_shape[2]*orig_size/new_size))
-
-    def operate(self, orig_layer: Layer, context):
-        new_layer = orig_layer.copy()
-        new_shape = self.get_new_shape(new_layer.shape,
-                                       new_layer.bioxel_size[0],
-                                       self.bioxel_size)
-
-        new_layer.resize(new_shape, self.smooth)
-        new_layer.name = self.new_layer_name \
-            or f"{orig_layer.name}_R-{self.bioxel_size:.2f}"
-        return new_layer
-
-    def draw(self, context):
-        layer_obj = get_selected_layer(context)
-        orig_shape = get_layer_prop_value(layer_obj, "shape")
-        orig_size = get_layer_prop_value(layer_obj, "bioxel_size")
-        new_shape = self.get_new_shape(orig_shape,
-                                       orig_size,
-                                       self.bioxel_size)
-
-        orig_shape = tuple(orig_shape)
-        bioxel_count = new_shape[0] * new_shape[1] * new_shape[2]
-
-        layer_shape_text = f"Shape from {str(orig_shape)} to {str(new_shape)}"
-        if bioxel_count > 100000000:
-            layer_shape_text += "**TOO LARGE!**"
-
-        layout = self.layout
-        layout.prop(self, "new_layer_name")
-        layout.prop(self, "bioxel_size")
-        layout.prop(self, "smooth")
-        layout.label(text=layer_shape_text)
-
-    def invoke(self, context, event):
-        layer_obj = get_selected_layer(context)
-        if layer_obj:
-            name = get_layer_label(layer_obj)
-            self.bioxel_size = get_layer_prop_value(layer_obj,
-                                                    "bioxel_size")
-            context.window_manager.invoke_props_dialog(self,
-                                                       title=f"Resample {name}")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class SignScalar(bpy.types.Operator, OutputLayerOperator):
-    bl_idname = "bioxelnodes.sign_scalar"
-    bl_label = "Sign Value"
-    bl_description = "Sign value"
-    bl_icon = "REMOVE"
-
-    def operate(self, orig_layer: Layer, context):
-        new_layer = orig_layer.copy()
-        new_layer.data = -orig_layer.data
-        new_layer.name = self.new_layer_name \
-            or f"{orig_layer.name}_Sign"
-        return new_layer
-
-    def invoke(self, context, event):
-        layer_obj = get_selected_layer(context)
-        if layer_obj:
-            name = get_layer_label(layer_obj)
-            context.window_manager.invoke_props_dialog(self,
-                                                       title=f"Sign {name}")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class FillOperator(OutputLayerOperator):
-
-    fill_value: bpy.props.FloatProperty(
-        name="Fill Value",
-        soft_min=0, soft_max=1024.0,
-        default=0,
-    )  # type: ignore
-
-    invert: bpy.props.BoolProperty(
-        name="Invert Aera",
-        default=True,
-    )  # type: ignore
-
-    def invoke(self, context, event):
-        layer_obj = get_selected_layer(context)
-        if layer_obj:
-            name = get_layer_label(layer_obj)
-            context.window_manager.invoke_props_dialog(self,
-                                                       title=f"Fill {name}")
-            return {'RUNNING_MODAL'}
-        else:
-            return self.execute(context)
-
-
-class FillByThreshold(bpy.types.Operator, FillOperator):
-    bl_idname = "bioxelnodes.fill_by_threshold"
-    bl_label = "Fill Value by Threshold"
-    bl_description = "Fill value by threshold"
-    bl_icon = "EMPTY_SINGLE_ARROW"
-
-    threshold: bpy.props.FloatProperty(
-        name="Threshold",
-        soft_min=0, soft_max=1024,
-        default=128,
-    )  # type: ignore
-
-    def operate(self, orig_layer: Layer, context):
-        data = np.amax(orig_layer.data, -1)
-        mask = data <= self.threshold \
-            if self.invert else data > self.threshold
-
-        new_layer = orig_layer.copy()
-        new_layer.fill(self.fill_value, mask, 0)
-        new_layer.name = self.new_layer_name \
-            or f"{orig_layer.name}_F-{self.threshold:.2f}"
-        return new_layer
-
-
-class FillByRange(bpy.types.Operator, FillOperator):
-    bl_idname = "bioxelnodes.fill_by_range"
-    bl_label = "Fill Value by Range"
-    bl_description = "Fill value by range"
-    bl_icon = "IPO_CONSTANT"
-
-    from_min: bpy.props.FloatProperty(
-        name="From Min",
-        soft_min=0, soft_max=1024,
-        default=128,
-    )  # type: ignore
-
-    from_max: bpy.props.FloatProperty(
-        name="From Max",
-        soft_min=0, soft_max=1024,
-        default=256,
-    )  # type: ignore
-
-    def operate(self, orig_layer: Layer, context):
-        data = np.amax(orig_layer.data, -1)
-        mask = (data <= self.from_min) | (data >= self.from_max) if self.invert else \
-            (data > self.from_min) & (data < self.from_max)
-
-        new_layer = orig_layer.copy()
-        new_layer.fill(self.fill_value, mask, 0)
-        new_layer.name = self.new_layer_name \
-            or f"{orig_layer.name}_F-{self.from_min:.2f}-{self.from_max:.2f}"
-        return new_layer
-
-
-class FillByLabel(bpy.types.Operator, FillOperator):
-    bl_idname = "bioxelnodes.fill_by_label"
-    bl_label = "Fill Value by Label"
-    bl_description = "Fill value by label"
-    bl_icon = "MESH_CAPSULE"
-
-    smooth: bpy.props.IntProperty(name="Smooth Size",
-                                  default=0,
-                                  soft_min=0, soft_max=5,
-                                  options={"SKIP_SAVE"})  # type: ignore
-
-    label_obj_name: bpy.props.EnumProperty(name="Label Layer",
-                                           items=get_label_layer_selection)  # type: ignore
-
-    def operate(self, orig_layer: Layer, context):
-        label_obj = bpy.data.objects.get(self.label_obj_name)
-        if label_obj is None:
-            raise NoContent("Cannot find any label layer.")
-
-        label_layer = obj_to_layer(label_obj)
-        label_layer.resize(orig_layer.shape, self.smooth)
-        mask = np.amax(label_layer.data, -1)
-        if self.invert:
-            mask = 1 - mask
-
-        new_layer = orig_layer.copy()
-        new_layer.fill(self.fill_value, mask, 0)
-        new_layer.name = self.new_layer_name \
-            or f"{orig_layer.name}_F-{label_layer.name}"
-        return new_layer
-
-
-class CombineLabels(bpy.types.Operator, OutputLayerOperator):
-    bl_idname = "bioxelnodes.combine_labels"
-    bl_label = "Combine Labels"
-    bl_description = "Combine all selected labels"
-    bl_icon = "MOD_BUILD"
-
-    def execute(self, context):
-        def layer_filter(layer_obj, context):
-            return get_layer_kind(layer_obj) == "label"
-
-        label_objs = get_selected_layers(context, layer_filter)
-
-        if len(label_objs) < 2:
-            self.report({"WARNING"}, "Not enough layers.")
-            return {'FINISHED'}
-
-        base_obj = label_objs[0]
-        label_objs = label_objs[1:]
-
-        base_layer = obj_to_layer(base_obj)
-        new_layer = base_layer.copy()
-        label_names = [base_layer.name]
-
-        for label_obj in label_objs:
-            label_layer = obj_to_layer(label_obj)
-            label_layer.resize(base_layer.shape)
-            new_layer.data = np.maximum(
-                new_layer.data, label_layer.data)
-            label_names.append(label_layer.name)
-
-        new_layer.name = self.new_layer_name \
-            or f"C-{'-'.join(label_names)}"
-
-        self.add_layer_node(context, new_layer)
-        return {'FINISHED'}
-
-
-class BatchLayerOperator():
-    success_msg = "Successfully done selected layers."
-    fail_msg = "fails."
-
-    def execute(self, context):
-        layer_objs = self.get_layers(context)
-
-        fails = []
-        for layer_obj in layer_objs:
-            try:
-                self.operate(layer_obj, context)
-            except:
-                fails.append(layer_obj)
-
-        if len(fails) == 0:
-            self.report({"INFO"}, self.success_msg)
-        else:
-            self.report(
-                {"WARNING"}, f"{','.join([layer_obj.name for layer_obj in fails])} {self.fail_msg}")
-
-        return {'FINISHED'}
-
-
-class SaveLayersCache(BatchLayerOperator):
-    fail_msg = "fail to save."
-
-    cache_dir: bpy.props.StringProperty(
-        name="Cache Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    def operate(self, layer_obj, context):
-        output_dir = bpy.path.abspath(self.cache_dir)
-        source_dir = bpy.path.abspath(layer_obj.data.filepath)
-
-        source_path: Path = Path(source_dir).resolve()
-        is_sequence = layer_obj.data.is_sequence
-
-        name = layer_obj.name if is_sequence else f"{layer_obj.name}.vdb"
-        output_path: Path = Path(output_dir, name, source_path.name).resolve() \
-            if is_sequence else Path(output_dir, name).resolve()
-
-        if output_path != source_path:
-            copy_to_dir(source_path.parent if is_sequence else source_path,
-                        output_path.parent.parent if is_sequence else output_path.parent,
-                        new_name=name)
-
-        blend_path = Path(bpy.path.abspath("//")).resolve()
-
-        layer_obj.data.filepath = bpy.path.relpath(str(output_path),
-                                                   start=str(blend_path))
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self)
-        return {'RUNNING_MODAL'}
-
-
-class RemoveLayers(BatchLayerOperator):
-    fail_msg = "fail to remove."
-
-    def operate(self, layer_obj, context):
-        for node_group in bpy.data.node_groups:
-            for node in node_group.nodes:
-                if get_node_type(node) == "BioxelNodes_FetchLayer":
-                    if node.inputs[0].default_value == layer_obj:
-                        node_group.nodes.remove(node)
-
-        cache_filepath = Path(bpy.path.abspath(
-            layer_obj.data.filepath)).resolve()
-
-        if cache_filepath.is_file():
-            if layer_obj.data.is_sequence:
-                for f in cache_filepath.parent.iterdir():
-                    f.unlink(missing_ok=True)
-            else:
-                cache_filepath.unlink(missing_ok=True)
-
-        # also remove layer object
-        bpy.data.volumes.remove(layer_obj.data)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message=f"Are you sure to remove them?")
-        return {'RUNNING_MODAL'}
-
-
-class SaveSelectedLayersCache(bpy.types.Operator, SaveLayersCache):
-    bl_idname = "bioxelnodes.save_selected_layers_cache"
-    bl_label = "Save Selected Layers Cache"
-    bl_description = "Save selected layers' Cache"
-    bl_icon = "FILE_TICK"
-
-    success_msg = "Successfully saved all selected layers."
-
-    def get_layers(self, context):
-        def is_not_missing(layer_obj, context):
-            return not is_missing_layer(layer_obj)
-        return get_selected_layers(context, is_not_missing)
-
-
-class RemoveSelectedLayers(bpy.types.Operator, RemoveLayers):
-    bl_idname = "bioxelnodes.remove_selected_layers"
-    bl_label = "Remove Selected Layers"
-    bl_description = "Remove selected layers"
-    bl_icon = "TRASH"
-
-    success_msg = "Successfully removed all selected layers."
-
-    def get_layers(self, context):
-        return get_selected_layers(context)

bioxelnodes/operators/misc.py

@@ -1,262 +0,0 @@
-import bpy
-from pathlib import Path
-import shutil
-
-from ..bioxelutils.common import get_all_layer_objs, get_node_lib_path, get_node_version, is_missing_layer, set_file_prop
-from .layer import RemoveLayers, SaveLayersCache
-
-from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
-from ..utils import get_cache_dir
-
-
-class ReLinkNodeLib(bpy.types.Operator):
-    bl_idname = "bioxelnodes.relink_node_lib"
-    bl_label = "Relink Node Library"
-    bl_description = "Relink all nodes to addon library source"
-    bl_options = {'UNDO'}
-
-    index: bpy.props.IntProperty()  # type: ignore
-
-    def execute(self, context):
-        node_version = VERSIONS[self.index]['node_version']
-        lib_path = get_node_lib_path(node_version) \
-            if self.index != 0 else LATEST_NODE_LIB_PATH
-
-        node_libs = []
-        for node_group in bpy.data.node_groups:
-            if node_group.name.startswith("BioxelNodes"):
-                node_lib = node_group.library
-                if node_lib:
-                    node_libs.append(node_lib)
-
-        node_libs = list(set(node_libs))
-
-        for node_lib in node_libs:
-            node_lib.filepath = str(lib_path)
-            # FIXME: may cause crash
-            node_lib.reload()
-
-        set_file_prop("node_version", node_version)
-
-        self.report({"INFO"}, f"Successfully relinked.")
-
-        return {'FINISHED'}
-
-
-class SaveNodeLib(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_node_lib"
-    bl_label = "Save Node Library"
-    bl_description = "Save node library file to local"
-    bl_options = {'UNDO'}
-
-    lib_dir: bpy.props.StringProperty(
-        name="Library Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    def execute(self, context):
-        node_version = get_node_version()
-
-        if node_version is None:
-            node_version = VERSIONS[0]["node_version"]
-        else:
-            if node_version not in [v["node_version"] for v in VERSIONS]:
-                node_version = VERSIONS[0]["node_version"]
-
-        if node_version == VERSIONS[0]["node_version"]:
-            lib_path = LATEST_NODE_LIB_PATH
-        else:
-            lib_path = get_node_lib_path(node_version)
-
-        version_str = "v"+".".join([str(i) for i in list(node_version)])
-
-        lib_dir = bpy.path.abspath(self.lib_dir)
-        local_lib_path: Path = Path(lib_dir,
-                                    f"BioxelNodes_{version_str}.blend").resolve()
-        node_lib_path: Path = lib_path
-        blend_path = Path(bpy.path.abspath("//")).resolve()
-
-        if local_lib_path != node_lib_path:
-            shutil.copy(node_lib_path, local_lib_path)
-
-        libs = []
-        for node_group in bpy.data.node_groups:
-            if node_group.name.startswith("BioxelNodes"):
-                if node_group.library:
-                    libs.append(node_group.library)
-
-        libs = list(set(libs))
-        for lib in libs:
-            lib.filepath = bpy.path.relpath(str(local_lib_path),
-                                            start=str(blend_path))
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self)
-        return {'RUNNING_MODAL'}
-
-    @classmethod
-    def poll(cls, context):
-        return bpy.data.is_saved
-
-
-class CleanTemp(bpy.types.Operator):
-    bl_idname = "bioxelnodes.clear_temp"
-    bl_label = "Clean Temp"
-    bl_description = "Clean all cache in temp (include other project cache)"
-
-    def execute(self, context):
-        cache_dir = get_cache_dir()
-        try:
-            shutil.rmtree(cache_dir)
-            self.report({"INFO"}, f"Successfully cleaned temp.")
-            return {'FINISHED'}
-        except:
-            self.report({"WARNING"},
-                        "Fail to clean temp, you may do it manually.")
-            return {'CANCELLED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message="All temp files will be removed, include other project cache, do you still want to clean?")
-        return {'RUNNING_MODAL'}
-
-
-class RenderSettingPreset(bpy.types.Operator):
-    bl_idname = "bioxelnodes.render_setting_preset"
-    bl_label = "Render Setting Presets"
-    bl_description = "Render setting presets for bioxel"
-    bl_options = {'UNDO'}
-
-    PRESETS = {
-        "performance": "Performance",
-        "balance": "Balance",
-        "quality": "Quality",
-    }
-
-    preset: bpy.props.EnumProperty(name="Preset",
-                                   default="balance",
-                                   items=[(k, v, "")
-                                          for k, v in PRESETS.items()])  # type: ignore
-
-    def execute(self, context):
-        if self.preset == "performance":
-            # EEVEE
-            bpy.context.scene.eevee.use_taa_reprojection = False
-            bpy.context.scene.eevee.volumetric_tile_size = '2'
-            bpy.context.scene.eevee.volumetric_shadow_samples = 32
-            bpy.context.scene.eevee.volumetric_samples = 64
-            bpy.context.scene.eevee.volumetric_ray_depth = 1
-            bpy.context.scene.eevee.use_volumetric_shadows = True
-
-            # Cycles
-            bpy.context.scene.cycles.shading_system = True
-            bpy.context.scene.cycles.volume_bounces = 0
-            bpy.context.scene.cycles.transparent_max_bounces = 4
-            bpy.context.scene.cycles.volume_preview_step_rate = 4
-            bpy.context.scene.cycles.volume_step_rate = 4
-
-        elif self.preset == "balance":
-            # EEVEE
-            bpy.context.scene.eevee.use_taa_reprojection = False
-            bpy.context.scene.eevee.volumetric_tile_size = '2'
-            bpy.context.scene.eevee.volumetric_shadow_samples = 64
-            bpy.context.scene.eevee.volumetric_samples = 128
-            bpy.context.scene.eevee.volumetric_ray_depth = 8
-            bpy.context.scene.eevee.use_volumetric_shadows = True
-
-            # Cycles
-            bpy.context.scene.cycles.shading_system = True
-            bpy.context.scene.cycles.volume_bounces = 4
-            bpy.context.scene.cycles.transparent_max_bounces = 8
-            bpy.context.scene.cycles.volume_preview_step_rate = 1
-            bpy.context.scene.cycles.volume_step_rate = 1
-
-        elif self.preset == "quality":
-            # EEVEE
-            bpy.context.scene.eevee.use_taa_reprojection = False
-            bpy.context.scene.eevee.volumetric_tile_size = '2'
-            bpy.context.scene.eevee.volumetric_shadow_samples = 128
-            bpy.context.scene.eevee.volumetric_samples = 256
-            bpy.context.scene.eevee.volumetric_ray_depth = 16
-            bpy.context.scene.eevee.use_volumetric_shadows = True
-
-            # Cycles
-            bpy.context.scene.cycles.shading_system = True
-            bpy.context.scene.cycles.volume_bounces = 8
-            bpy.context.scene.cycles.transparent_max_bounces = 16
-            bpy.context.scene.cycles.volume_preview_step_rate = 0.5
-            bpy.context.scene.cycles.volume_step_rate = 0.5
-
-        return {'FINISHED'}
-
-
-class SliceViewer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.slice_viewer"
-    bl_label = "Slice Viewer"
-    bl_description = "A preview scene setting for viewing slicers"
-    bl_icon = "FILE_VOLUME"
-
-    def execute(self, context):
-        bpy.context.scene.eevee.use_taa_reprojection = False
-        bpy.context.scene.eevee.volumetric_tile_size = '2'
-        bpy.context.scene.eevee.volumetric_shadow_samples = 128
-        bpy.context.scene.eevee.volumetric_samples = 128
-        bpy.context.scene.eevee.volumetric_ray_depth = 1
-        bpy.context.scene.eevee.use_volumetric_shadows = False
-
-        for area in bpy.context.screen.areas:
-            if area.type == 'VIEW_3D':
-                area.spaces[0].shading.type = 'MATERIAL'
-                area.spaces[0].shading.studio_light = 'studio.exr'
-                area.spaces[0].shading.studiolight_intensity = 2.5
-                area.spaces[0].shading.use_scene_lights = False
-                area.spaces[0].shading.use_scene_world = False
-
-        return {'FINISHED'}
-
-
-def get_all_layers(layer_filter=None):
-    def _layer_filter(layer_obj):
-        return True
-
-    layer_filter = layer_filter or _layer_filter
-    layer_objs = get_all_layer_objs()
-    return [obj for obj in layer_objs if layer_filter(obj)]
-
-
-class SaveAllLayersCache(bpy.types.Operator, SaveLayersCache):
-    bl_idname = "bioxelnodes.save_all_layers_cache"
-    bl_label = "Save All Layers Cache"
-    bl_description = "Save all cache of this file"
-    bl_icon = "FILE_TICK"
-
-    success_msg = "Successfully saved all layers."
-
-    def get_layers(self, context):
-        def is_not_missing(layer_obj):
-            return not is_missing_layer(layer_obj)
-        return get_all_layers(is_not_missing)
-
-
-class RemoveAllMissingLayers(bpy.types.Operator, RemoveLayers):
-    bl_idname = "bioxelnodes.remove_all_missing_layers"
-    bl_label = "Remove All Missing Layers"
-    bl_description = "Remove all current container missing layers"
-    bl_icon = "BRUSH_DATA"
-
-    success_msg = "Successfully removed all missing layers."
-
-    def get_layers(self, context):
-        def is_missing(layer_obj):
-            return is_missing_layer(layer_obj)
-        return get_all_layers(is_missing)
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message=f"Are you sure to remove all **Missing** layers?")
-        return {'RUNNING_MODAL'}

bioxelnodes/preferences.py

@@ -1,29 +0,0 @@
-import bpy
-from pathlib import Path
-
-
-class BioxelNodesPreferences(bpy.types.AddonPreferences):
-    bl_idname = __package__
-
-    cache_dir: bpy.props.StringProperty(
-        name="Set Cache Directory",
-        subtype='DIR_PATH',
-        default=str(Path(Path.home(), '.bioxelnodes'))
-    )  # type: ignore
-
-    change_render_setting: bpy.props.BoolProperty(
-        name="Change Render Setting on First Import",
-        default=True,
-    )  # type: ignore
-
-    node_import_method: bpy.props.EnumProperty(name="Node Import Method",
-                                               default="LINK",
-                                               items=[("LINK", "Link", ""),
-                                                      ("APPEND", "Append (Reuse Data)", "")])  # type: ignore
-
-    def draw(self, context):
-        layout = self.layout
-        layout.label(text="Configuration")
-        layout.prop(self, 'cache_dir')
-        layout.prop(self, "change_render_setting")
-        layout.prop(self, "node_import_method")

bioxelnodes/props.py

@@ -1,44 +0,0 @@
-import bpy
-
-from .bioxelutils.common import get_node_type
-
-
-class BIOXELNODES_UL_layer_list(bpy.types.UIList):
-    def draw_item(self, context, layout, data, item, icon, active_data, active_propname):
-        layout.label(text=item.label, translate=False, icon_value=icon)
-
-
-class BIOXELNODES_Series(bpy.types.PropertyGroup):
-    id: bpy.props.StringProperty()   # type: ignore
-    label: bpy.props.StringProperty()   # type: ignore
-
-
-def select_layer(self, context):
-    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
-    layer_list = layer_list_UL.layer_list
-    layer_list_active = layer_list_UL.layer_list_active
-
-    if len(layer_list) > 0 and layer_list_active != -1 and layer_list_active < len(layer_list):
-        layer_obj = bpy.data.objects[layer_list[layer_list_active].obj_name]
-        node_group = context.space_data.edit_tree
-        for node in node_group.nodes:
-            node.select = False
-            if get_node_type(node) == "BioxelNodes_FetchLayer":
-                if node.inputs[0].default_value == layer_obj:
-                    node.select = True
-
-    layer_list_UL.layer_list_active = -1
-
-
-class BIOXELNODES_Layer(bpy.types.PropertyGroup):
-    obj_name: bpy.props.StringProperty()   # type: ignore
-    label: bpy.props.StringProperty()   # type: ignore
-    info_text: bpy.props.StringProperty()   # type: ignore
-
-
-class BIOXELNODES_LayerListUL(bpy.types.PropertyGroup):
-    layer_list: bpy.props.CollectionProperty(
-        type=BIOXELNODES_Layer)  # type: ignore
-    layer_list_active: bpy.props.IntProperty(default=-1,
-                                             update=select_layer,
-                                             options=set())  # type: ignore

bioxelnodes/utils.py

@@ -1,72 +0,0 @@
-from pathlib import Path
-import shutil
-import bpy
-
-
-def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
-    source = Path(source_path)
-    target = Path(dir_path)
-
-    # Check if the source exists
-    if not source.exists():
-        raise FileNotFoundError
-
-    # Check if the target exists
-    if not target.exists():
-        target.mkdir(parents=True, exist_ok=True)
-
-    target_path = target / new_name if new_name else target / source.name
-    # If source is a file, copy it to the target directory
-    if source.is_file():
-        try:
-            shutil.copy(source, target_path)
-        except shutil.SameFileError:
-            if exist_ok:
-                pass
-            else:
-                raise shutil.SameFileError
-    # If source is a directory, copy its contents to the target directory
-    elif source.is_dir():
-        shutil.copytree(source, target_path, dirs_exist_ok=exist_ok)
-
-    if not target_path.exists():
-        raise Exception
-
-
-def select_object(target_obj):
-    for obj in bpy.data.objects:
-        obj.select_set(False)
-
-    target_obj.select_set(True)
-    bpy.context.view_layer.objects.active = target_obj
-
-
-def progress_bar(self, context):
-    row = self.layout.row()
-    row.progress(
-        factor=context.window_manager.bioxelnodes_progress_factor,
-        type="BAR",
-        text=context.window_manager.bioxelnodes_progress_text
-    )
-    row.scale_x = 2
-
-
-def progress_update(context, factor, text=""):
-    context.window_manager.bioxelnodes_progress_factor = factor
-    context.window_manager.bioxelnodes_progress_text = text
-
-
-def get_preferences():
-    return bpy.context.preferences.addons[__package__].preferences
-
-
-def get_cache_dir():
-    preferences = get_preferences()
-    cache_path = Path(preferences.cache_dir, 'VDBs')
-    cache_path.mkdir(parents=True, exist_ok=True)
-    return str(cache_path)
-
-
-def get_use_link():
-    preferences = get_preferences()
-    return preferences.node_import_method == "LINK"

build.py

@@ -12,12 +12,15 @@ class Platform:
     blender_tag: str
 
 
-required_packages = ["SimpleITK==2.3.1",
+required_packages = ["SimpleITK==2.5.5",
                      "pyometiff==1.0.0",
                      "mrcfile==1.5.1",
-                     "h5py==3.11.0",
+                     "h5py==3.14.0",
                      "transforms3d==0.4.2",
-                     "tifffile==2024.7.24"]
+                     "tifffile==2024.7.24",
+                     "matplotlib==3.10.7",
+                     "pillow==11.2.1",
+                     "scipy==1.16.3"]
 
 
 platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
@@ -31,7 +34,8 @@ platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
 
 packages_to_remove = {
     "imagecodecs",
-    "numpy"
+    "numpy",
+    "packaging"
 }
 
 
@@ -40,42 +44,33 @@ def run_python(args: str):
     subprocess.run([python] + args.split(" "))
 
 
-def build_extension(platform: Platform, python_version="3.11") -> None:
-    wheel_dirpath = Path("./bioxelnodes/wheels")
-    toml_filepath = Path("bioxelnodes/blender_manifest.toml")
-    scipy_ndimage_dirpath = Path("./scipy_ndimage", platform.blender_tag)
+def build_extension(platform: Platform, python_version: str) -> None:
+    wheel_dirpath = Path("./src/bioxelnodes/wheels")
+    toml_filepath = Path("./src/bioxelnodes/blender_manifest.toml")
 
     # download required_packages
     run_python(
         f"-m pip download {' '.join(required_packages)} --dest {wheel_dirpath.as_posix()} --only-binary=:all: --python-version={python_version} --platform={platform.pypi_suffix}"
     )
 
-    for f in wheel_dirpath.glob('*.whl'):
+    for f in wheel_dirpath.glob("*.whl"):
         if any([package in f.name for package in packages_to_remove]):
             f.unlink(missing_ok=True)
 
-        elif platform.blender_tag == "macos-arm64" and \
-                "lxml" in f.name and "universal2" in f.name:
-            f.rename(Path(f.parent,
-                          f.name.replace("universal2", "arm64")))
-
-    for ndimage_filepath in scipy_ndimage_dirpath.iterdir():
-        to_filepath = Path("./bioxelnodes/bioxel/scipy", ndimage_filepath.name)
-        shutil.copy(ndimage_filepath, to_filepath)
-
+        elif (
+            platform.blender_tag == "macos-arm64"
+            and "lxml" in f.name
+            and "universal2" in f.name
+        ):
+            f.rename(Path(f.parent, f.name.replace("universal2", "arm64")))
+        
     # Load the TOML file
     with toml_filepath.open("r") as file:
         manifest = tomlkit.parse(file.read())
 
     manifest["platforms"] = [platform.blender_tag]
-    manifest["wheels"] = [f"./wheels/{f.name}"
-                          for f in wheel_dirpath.glob('*.whl')]
-
-    # build = tomlkit.table(True)
-    # generated = tomlkit.table()
-    # generated["platforms"] = [platform.blender_tag]
-    # generated["wheels"] = [f"./wheels/{f.name}"
-    #                        for f in wheel_dirpath.glob('*.whl')]
+    manifest["wheels"] = [
+        f"./wheels/{f.name}" for f in wheel_dirpath.glob("*.whl")]
 
     # build.append('generated', generated)
     # manifest.append('build', build)
@@ -88,8 +83,9 @@ def build_extension(platform: Platform, python_version="3.11") -> None:
 
 def main():
     platform_name = sys.argv[1]
+    python_version = sys.argv[2] or "3.11"
     platform = platforms[platform_name]
-    build_extension(platform)
+    build_extension(platform, python_version)
 
 
 if __name__ == "__main__":

docs/SARS-Cov-2.en.md

@@ -0,0 +1,99 @@
+# SARS-Cov-2
+
+![alt text](assets/SARS-Cov-2/image.png)
+
+![alt text](assets/SARS-Cov-2/image-1.png)
+
+In this tutorial, we'll make a structural visualzation of the SARS-Cov-2 Virus. Please see [step by step](step_by_step.md) to make sure you have a basic understanding of how to use the addon, and make sure the addon version is v1.0.2 or higher!
+
+Research data is from paper published in September 2020 in Cell Press ([https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4](<https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4>)) by Li Sai team at Tsinghua University. This research revealed the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Here is an official video of this study
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/JSKl5VY4k5w?si=t4LhrCRebxrX_Saf&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+"It remains enigmatic how coronaviruses pack the ∼30-kb RNA into the ∼80-nm-diameter viral lumen. Are the RNPs ordered relative to each other to avoid RNA entangling, knotting, or even damage or are they involved in virus assembly?" Three assembly classes were proposed in the paper, we will make a visualzation of the "eggs-in-a-nest"-shaped RNPs assembly, based on real cryo-ET data.
+
+## Download and import data
+
+The data of this research is hosted on EMDB ([https://www.ebi.ac.uk/emdb](https://www.ebi.ac.uk/emdb)), and the website of SARS-Cov-2 virus is [here](https://www.ebi.ac.uk/emdb/EMD-30430). Open the page, find "Download" button and select the first selection "3D Volume (.map.gz)".
+
+In case you can't download data, you can download here.
+
+[SARS-Cov-2.map](https://drive.google.com/file/d/1LMybsmTVbwQ38_eqAx6hbZTc5p2fdcjK/view?usp=sharing)
+
+After downloading, put it into any directory and import the data. In the import options, it is recommended to adjust the Bioxel Size to 5, in order to reduce the shape of the data to increase the speed of calculation and rendering. If you are confident in the performance of your hardware, you can leave the original 2.72 unchanged. After adjusting the Bioxel Size, the shape of the converted data will be calculated below based on the current bioxel size. The amount of data will increase exponentially with larger shape, and may result in OOM (out of memory).
+
+## Cutout the Virus
+
+After importing, you can get the virus by creating and connecting nodes and setting parameters as shown below
+
+![alt text](assets/SARS-Cov-2/image-2.png)
+
+Place the light and the camera in the way as below. The backlight is a area light, color white, intensity 500W, spread 90°, and inside the virus, place a point light, color `FFD08D`, intensity 5W. Camera focal length is 200 mm. the background color is pure black. The Look of the color management is High Contrast.
+
+![alt text](assets/SARS-Cov-2/image-3.png)
+
+Continue editing the node, followed by "Set Properies" and "Set Color by Ramp 4" node, the parameters of these two nodes are set as shown in the figure, where the color part, from top to bottom, is set to `E1D0FC` (1.0), `FFE42D` (0.5), `3793FF` (0.5), `FFFF8EC` (0.1) (alpha value in parentheses). Color alpha also affects density.
+
+![alt text](assets/SARS-Cov-2/image-4.png)
+
+If you feel that rendering is too slow, see [here](improve_performance.md) for suggestions
+
+## Color the RNPs alone
+
+The current rendering is pretty good, but considering that my goal is to make it clear how the RNPs are arranged within the virus, the RNPs should be colored differently than the others. So how to color the RNPs alone?
+
+First of all, we have to separate the RNPs. The value of RNPs is between the membrane and S protein, so it is very difficult to separate. The good thing is that the virus is spherical, we can separate the RNPs part of the virus from the rest by using a sphere cutter. To do so, in the Geometry Nodes panel menu of the container, click **Bioxel Nodes > Add a Cutter > Sphere Cutter**, and adjust the scale and position of the newly created sphere object named "Sphere_Cutter" appropriately, so that it can just separate the internal RNPs and membrane of the virus.
+
+![alt text](assets/SARS-Cov-2/image-5.png)
+
+The process of changing the position of the "Sphere_Cutter" object can be very laggy, then you can turn off "With Surface" and do it in Slice Viewer mode. Once you are happy with it, you can restore the settings.
+
+Then we turn on Invert in the "Sphere Cutter" node and you can see the opposite result. This way we've managed to separate the two, next let's color them separately and finally merge them with Join Component. Create and join the nodes as shown below, where the second Cutter node is copied and the color value in Set Color is `FFDDFE` (0.5). If all is well, the rendering should look like below.
+
+![alt text](assets/SARS-Cov-2/image-6.png)
+
+At this point, the rendering of a SARS-Cov-2 virus is complete!
+
+## Render RNPs and Membranes
+
+Realistic rendering is great, but Non-photorealistic rendering (NPR) is better for presenting structural information. So I will render ultrastructure of the RNPs assembly with toon shader.
+
+![alt text](assets/SARS-Cov-2/image-7.png)
+
+The silhouettes of RNPs uses Blender's Line Art feature, but Line Art must be based on a mesh. Select the nodes that are extruding the RNPs (i.e., the "Cut" nodes that are in charge of cutting out the RNPs), and right-click, click **Bioxel Nodes > Extract Mesh**. This gives you a new mesh object of the RNPs.
+
+Extract the membrane mesh in the same way.
+
+The membrane has a much higher value than the rest of the virus, so let's create a new "Cutout" node, also after the ReCenter, but with the threshold adjusted to 0.13. After the Cutout, connect to the "To Surface" node and parameterize it as shown in the figure, noting that the Remove Island Threshold is set to 1000 so that any fragments smaller than 1000 pts be eliminated. Then select the "To Surface" node, and perform the operation of extracting the mesh.
+
+![alt text](assets/SARS-Cov-2/image-8.png)
+
+The mesh of the membrane needs to be cut in half, this can be done with the Box Trim brush in sculpt mode or with the Boolean modifier. the mesh of the RNPs may also need some repair work, I cleaned up some of the broken surfaces of the RNPs. all the meshes are now ready to be used.
+
+![alt text](assets/SARS-Cov-2/image-9.png)
+
+For Line Art, please see the video tutorial from Blender Secrets.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/aIWdBq7-ias?si=CrcStx5VVJBwDpzu&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+Finally, an infographic on the ultrastructure of RNPs is done!
+
+![alt text](assets/SARS-Cov-2/image-1.png)
+
+If you have trouble following the docs, you can download the project files.
+
+[SARS-Cov-2.zip](https://drive.google.com/file/d/15GpIoIjVAE-Jr98zWo7oupuk1KfRVPmk/view?usp=sharing)
+
+## Homework
+
+Other data relevant to the study are provided in the paper, you could try visualizing them.
+
+![alt text](assets/SARS-Cov-2/image-10.png)
+
+Go to the official EMDB website https://www.ebi.ac.uk/emdb/ and enter the EMD number in the search box to get them.
+
+The Electron Microscopy Data Bank (EMDB) is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. If you want to get data on other virus, just enter their name in the search box. For example, hepatitis B virus, enter it into the search box, then select Virus in the Sample Type on the left side, and download the data you need (it is better to find the corresponding paper to clarify the data information).
+
+**Try to visualize hepatitis B virus.**
+
+![alt text](assets/SARS-Cov-2/image-11.png)

docs/SARS-Cov-2.md

@@ -4,96 +4,96 @@
 
 ![alt text](assets/SARS-Cov-2/image-1.png)
 
-In this tutorial, we'll make a structural visualzation of the SARS-Cov-2 Virus. Please see [step by step](step_by_step.md) to make sure you have a basic understanding of how to use the addon, and make sure the addon version is v1.0.2 or higher!
+在本教程中，我们将制作 SARS-Cov-2 病毒的结构可视化。请确保您已阅读[分步指南](step_by_step.md)以了解插件的基本使用方法，并确保插件版本为 v1.0.2 或更高！
 
-Research data is from paper published in September 2020 in Cell Press ([https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4](<https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4>)) by Li Sai team at Tsinghua University. This research revealed the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Here is an official video of this study
+研究数据来自 2020 年 9 月发表在 Cell Press 的论文（[https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4](<https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4>)），作者是清华大学李赛团队。该研究使用冷冻电子断层扫描（cryo-ET）和亚断层图平均（STA）揭示了真实 SARS-CoV-2 病毒的分子组装。以下是该研究的官方视频：
 
 <iframe width="560" height="315" src="https://www.youtube.com/embed/JSKl5VY4k5w?si=t4LhrCRebxrX_Saf&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
 
-"It remains enigmatic how coronaviruses pack the ∼30-kb RNA into the ∼80-nm-diameter viral lumen. Are the RNPs ordered relative to each other to avoid RNA entangling, knotting, or even damage or are they involved in virus assembly?" Three assembly classes were proposed in the paper, we will make a visualzation of the "eggs-in-a-nest"-shaped RNPs assembly, based on real cryo-ET data.
+"冠状病毒如何将约 30kb 的 RNA 包装到约 80nm 直径的病毒腔内仍然是个谜。RNP 彼此之间是否有序以避免 RNA 缠结、打结或损坏，还是它们参与病毒组装？" 论文中提出了三类组装方式，我们将基于真实的冷冻电镜数据，制作"巢中蛋"形 RNP 组装的可视化。
 
-## Download and import data
+## 下载和导入数据
 
-The data of this research is hosted on EMDB ([https://www.ebi.ac.uk/emdb](https://www.ebi.ac.uk/emdb)), and the website of SARS-Cov-2 virus is [here](https://www.ebi.ac.uk/emdb/EMD-30430). Open the page, find "Download" button and select the first selection "3D Volume (.map.gz)".
+该研究的数据托管在 EMDB（[https://www.ebi.ac.uk/emdb](https://www.ebi.ac.uk/emdb)），SARS-Cov-2 病毒网站是[这里](https://www.ebi.ac.uk/emdb/EMD-30430)。打开页面，找到"Download"按钮，选择第一个选项"3D Volume (.map.gz)"。
 
-In case you can't download data, you can download here.
+如果您无法下载数据，可以从这里下载。
 
 [SARS-Cov-2.map](https://drive.google.com/file/d/1LMybsmTVbwQ38_eqAx6hbZTc5p2fdcjK/view?usp=sharing)
 
-After downloading, put it into any directory and import the data. In the import options, it is recommended to adjust the Bioxel Size to 5, in order to reduce the shape of the data to increase the speed of calculation and rendering. If you are confident in the performance of your hardware, you can leave the original 2.72 unchanged. After adjusting the Bioxel Size, the shape of the converted data will be calculated below based on the current bioxel size. The amount of data will increase exponentially with larger shape, and may result in OOM (out of memory).
+下载后，放到任意目录并导入数据。在导入选项中，建议将 Bioxel Size 调整为 5，以减小数据形状，提高计算和渲染速度。如果您对硬件性能有信心，可以保持原始的 2.72 不变。调整 Bioxel Size 后，下方会根据当前的 bioxel size 计算转换后数据的形状。数据量会随着形状增大呈指数增长，可能会导致内存不足（OOM）。
 
-## Cutout the Virus
+## 切割病毒
 
-After importing, you can get the virus by creating and connecting nodes and setting parameters as shown below
+导入后，您可以通过创建和连接节点并设置参数来获取病毒，如下图所示。
 
 ![alt text](assets/SARS-Cov-2/image-2.png)
 
-Place the light and the camera in the way as below. The backlight is a area light, color white, intensity 500W, spread 90°, and inside the virus, place a point light, color `FFD08D`, intensity 5W. Camera focal length is 200 mm. the background color is pure black. The Look of the color management is High Contrast.
+按下图所示放置灯光和相机。背光是区域光，白色，强度 500W，扩散 90°；在病毒内部放置一个点光源，颜色 `FFD08D`，强度 5W。相机焦距为 200mm。背景颜色为纯黑色。颜色管理的 Look 为 High Contrast。
 
 ![alt text](assets/SARS-Cov-2/image-3.png)
 
-Continue editing the node, followed by "Set Properies" and "Set Color by Ramp 4" node, the parameters of these two nodes are set as shown in the figure, where the color part, from top to bottom, is set to `E1D0FC` (1.0), `FFE42D` (0.5), `3793FF` (0.5), `FFFF8EC` (0.1) (alpha value in parentheses). Color alpha also affects density.
+继续编辑节点，接着是"Set Properties"和"Set Color by Ramp 4"节点，这两个节点的参数设置如下图，其中颜色部分，从上到下设置为 `E1D0FC`（1.0）、`FFE42D`（0.5）、`3793FF`（0.5）、`FFFF8EC`（0.1）（括号中为 alpha 值）。颜色的 alpha 值也会影响密度。
 
 ![alt text](assets/SARS-Cov-2/image-4.png)
 
-If you feel that rendering is too slow, see [here](improve_performance.md) for suggestions
+如果您觉得渲染太慢，请参阅[这里](improve_performance.md)获取建议。
 
-## Color the RNPs alone
+## 单独为 RNP 着色
 
-The current rendering is pretty good, but considering that my goal is to make it clear how the RNPs are arranged within the virus, the RNPs should be colored differently than the others. So how to color the RNPs alone?
+当前的渲染效果很好，但考虑到我的目标是让您清楚看到 RNP 在病毒内部的排列方式，RNP 应该与其他部分用不同颜色着色。那么如何单独为 RNP 着色呢？
 
-First of all, we have to separate the RNPs. The value of RNPs is between the membrane and S protein, so it is very difficult to separate. The good thing is that the virus is spherical, we can separate the RNPs part of the virus from the rest by using a sphere cutter. To do so, in the Geometry Nodes panel menu of the container, click **Bioxel Nodes > Add a Cutter > Sphere Cutter**, and adjust the scale and position of the newly created sphere object named "Sphere_Cutter" appropriately, so that it can just separate the internal RNPs and membrane of the virus.
+首先，我们必须分离 RNP。RNP 的值介于膜和 S 蛋白之间，因此很难分离。好在病毒是球形的，我们可以使用球形切割器将病毒的 RNP 部分与其余部分分离。为此，在容器的几何节点面板菜单中，点击 **Bioxel Nodes > Add a Cutter > Sphere Cutter**，并适当调整新创建的名为"Sphere_Cutter"的球体对象的大小和位置，使其恰好能将病毒内部的 RNP 和膜分离。
 
 ![alt text](assets/SARS-Cov-2/image-5.png)
 
-The process of changing the position of the "Sphere_Cutter" object can be very laggy, then you can turn off "With Surface" and do it in Slice Viewer mode. Once you are happy with it, you can restore the settings.
+改变"Sphere_Cutter"对象的位置可能会非常卡顿，此时您可以关闭"With Surface"并在 Slice Viewer 模式下操作。满意后，恢复设置。
 
-Then we turn on Invert in the "Sphere Cutter" node and you can see the opposite result. This way we've managed to separate the two, next let's color them separately and finally merge them with Join Component. Create and join the nodes as shown below, where the second Cutter node is copied and the color value in Set Color is `FFDDFE` (0.5). If all is well, the rendering should look like below.
+然后在"Sphere Cutter"节点中打开 Invert，您可以看到相反的结果。这样我们就成功将两者分离了。接下来让我们分别着色，最后用 Join Component 合并。按如下图所示创建和连接节点，其中第二个 Cutter 节点是复制的，Set Color 中的颜色值设置为 `FFDDFE`（0.5）。如果一切正常，渲染结果应该如下图所示。
 
 ![alt text](assets/SARS-Cov-2/image-6.png)
 
-At this point, the rendering of a SARS-Cov-2 virus is complete!
+此时，SARS-Cov-2 病毒的渲染完成了！
 
-## Render RNPs and Membranes
+## 渲染 RNP 和膜
 
-Realistic rendering is great, but Non-photorealistic rendering (NPR) is better for presenting structural information. So I will render ultrastructure of the RNPs assembly with toon shader.
+写实渲染很棒，但非写实渲染（NPR）在呈现结构信息方面更好。因此，我将使用卡通着色器来渲染 RNP 组装的首尾结构。
 
 ![alt text](assets/SARS-Cov-2/image-7.png)
 
-The silhouettes of RNPs uses Blender's Line Art feature, but Line Art must be based on a mesh. Select the nodes that are extruding the RNPs (i.e., the "Cut" nodes that are in charge of cutting out the RNPs), and right-click, click **Bioxel Nodes > Extract Mesh**. This gives you a new mesh object of the RNPs.
+RNP 的轮廓使用 Blender 的线稿（Line Art）功能，但线稿必须基于网格。选择挤出 RNP 的节点（即负责切割出 RNP 的"Cut"节点），右键点击 **Bioxel Nodes > Extract Mesh**。这将为您创建一个 RNP 的新网格对象。
 
-Extract the membrane mesh in the same way.
+用同样的方式提取膜网格。
 
-The membrane has a much higher value than the rest of the virus, so let's create a new "Cutout" node, also after the ReCenter, but with the threshold adjusted to 0.13. After the Cutout, connect to the "To Surface" node and parameterize it as shown in the figure, noting that the Remove Island Threshold is set to 1000 so that any fragments smaller than 1000 pts be eliminated. Then select the "To Surface" node, and perform the operation of extracting the mesh.
+膜的病毒值远高于其他部分，因此让我们创建一个新的"Cutout"节点，同样在 ReCenter 之后，但阈值调整为 0.13。Cutout 后，连接到"To Surface"节点并按如下图所示设置参数，注意 Remove Island Threshold 设置为 1000，以便消除小于 1000 pts 的任何碎片。然后选择"To Surface"节点，执行提取网格的操作。
 
 ![alt text](assets/SARS-Cov-2/image-8.png)
 
-The mesh of the membrane needs to be cut in half, this can be done with the Box Trim brush in sculpt mode or with the Boolean modifier. the mesh of the RNPs may also need some repair work, I cleaned up some of the broken surfaces of the RNPs. all the meshes are now ready to be used.
+膜的网格需要切成两半，这可以通过雕刻模式中的 Box Trim 笔刷或布尔修改器来完成。RNP 的网格也可能需要一些修复工作，我清理了一些 RNP 的破损表面。所有网格现在都可以使用了。
 
 ![alt text](assets/SARS-Cov-2/image-9.png)
 
-For Line Art, please see the video tutorial from Blender Secrets.
+关于线稿，请参阅 Blender Secrets 的视频教程。
 
 <iframe width="560" height="315" src="https://www.youtube.com/embed/aIWdBq7-ias?si=CrcStx5VVJBwDpzu&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
 
-Finally, an infographic on the ultrastructure of RNPs is done!
+最后，RNP 超微结构的信息图完成了！
 
 ![alt text](assets/SARS-Cov-2/image-1.png)
 
-If you have trouble following the docs, you can download the project files.
+如果您按照文档有困难，可以下载项目文件。
 
 [SARS-Cov-2.zip](https://drive.google.com/file/d/15GpIoIjVAE-Jr98zWo7oupuk1KfRVPmk/view?usp=sharing)
 
-## Homework
+## 作业
 
-Other data relevant to the study are provided in the paper, you could try visualizing them.
+论文中提供了其他相关数据，您可以尝试可视化它们。
 
 ![alt text](assets/SARS-Cov-2/image-10.png)
 
-Go to the official EMDB website https://www.ebi.ac.uk/emdb/ and enter the EMD number in the search box to get them.
+前往官方 EMDB 网站 https://www.ebi.ac.uk/emdb/，在搜索框中输入 EMD 编号即可获取。
 
-The Electron Microscopy Data Bank (EMDB) is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. If you want to get data on other virus, just enter their name in the search box. For example, hepatitis B virus, enter it into the search box, then select Virus in the Sample Type on the left side, and download the data you need (it is better to find the corresponding paper to clarify the data information).
+电子显微镜数据银行（EMDB）是一个公共仓库，用于存放冷冻样品的电子显微镜（cryoEM）体积和代表性断层图。如果您想获取其他病毒的数据，只需在搜索框中输入其名称即可。例如，乙型肝炎病毒，在搜索框中输入，然后选择左侧 Sample Type 中的 Virus，下载您需要的数据（最好找到相应的论文来明确数据信息）。
 
-**Try to visualize hepatitis B virus.**
+**尝试可视化乙型肝炎病毒。**
 
-![alt text](assets/SARS-Cov-2/image-11.png)
+![alt text](assets/SARS-Cov-2/image-11.png)

docs/advanced.en.md

@@ -0,0 +1,46 @@
+# Advanced Usage
+
+## Cut "Structure"
+
+"Structure" can be cut to show partial structure, accomplished through the O Cut series nodes. For example, add the **O Cut to Region** node as shown below and connect it. Add any object from the scene as the "Region", and input it into the node:
+
+![](assets/cut-to-region.png)
+
+By properly adjusting the position and rotation of the "Region" object, you can see that the skull structure is confined within the region.
+
+!!! note
+    The add-on provides a function to quickly make objects phantom. In 3D Viewport mode, right-click the "Region" object and select **Bioxel Nodes > Toggle Phantom** from the menu.
+
+!!! warning
+    Cutting increases computation and affects real-time performance. Check Resample on O Layer to improve performance.
+
+**O Cut Small Parts** node is a cleanup tool that quickly removes scattered fragments and keeps only clean, continuous large structures. However, the computation is particularly time-consuming, so be aware of performance.
+
+![](assets/cut-small-parts.png)
+
+If you are familiar with geometry nodes, you can also directly define the cutting execution range through **O Cut Structure**. For example, in the image below, select the part where the cutting position X is greater than 0.
+
+![](assets/cut-structure.png)
+
+## Structure Property Settings
+
+Expand the Properties of **O Cutout by Threshold**, where you can directly modify various property values, but they can only be set uniformly. We can use field-type data to assign differences. Take the color property as an example: for instance, connecting a Position node directly produces the effect shown below:
+
+![](assets/set-color-by-pos.png)
+
+We can also map layer values to color gradients, which requires the **O Scalar Layer to Color** node (such conversion function nodes are all under Add > O Bioxel > Utilities in the node menu). Adjust as follows:
+
+- **O Cutout by Threshold**: Set Threshold to 20
+- **O Scalar Layer to Color**: Set From Min and From Max to 20 and 90 respectively
+
+![](assets/scalar-to-color.png)
+
+Since soft tissue CT values are lower than bone tissue, when the threshold is lowered, you can see that in addition to the skull, the attached soft tissue is also presented. The From Min and From Max of **O Scalar Layer to Color** define the color mapping range from 0 to 1. Therefore, low-value soft tissue appears black, and high-value bone tissue appears white.
+
+We can also customize the mapping method through the **Closure** node in Blender 5.0+. For example, connect a **Color Ramp** node to change the black area belonging to soft tissue to dark red:
+
+![](assets/scalar-to-color-ramp.png)
+
+Ta-da! The anatomical rendering is done!
+
+Other "Structure" properties can also be adjusted in this way. In addition to **O Scalar Layer to Color**, there is also **O Scalar Layer to Factor** to convert to a single value from 0 to 1.

docs/advanced.md

@@ -0,0 +1,49 @@
+# 高级玩法
+
+## 切割「结构体」
+
+「结构体」可以被切割，呈现部分结构，通过 O Cut 系列节点完成。比如按下图添加 **O Cut to Region** 节点并连接，添加任意来自场景的物体作为「区域」，输入到节点：
+
+![](assets/cut-to-region.png)
+
+适当调整作为「区域」物体的位置旋转，可以看到头骨结构被限制在区域范围内。
+
+!!! note
+    插件提供快速让物体虚化的功能，在 3D 视图模式下，右键「区域」物体，菜单选择 **Bioxel Nodes > Toggle Phantom**
+
+!!! warning
+    切割会增加计算量，影响实时性能，勾选 O Layer 的 Resample 来提高性能
+
+
+
+**O Cut Small Parts** 节点，是清理神器，能快速把零碎的结构删除，只干净连续的大结构。但是计算特别耗时，注意性能。
+
+![](assets/cut-small-parts.png)
+
+如果你对几何节点很了解，你也可以通过 **O Cut Structure** 直接定义切割的执行范围，比如下图中，选择切割位置 X 大于 0 的部分。
+
+![](assets/cut-structure.png)
+
+
+## 「结构体」属性设置
+
+展开 **O Cutout by Threshold** 的 Properties，你可以直接修改各项属性值，但都只能均一设置，我们可以用场类型数据赋予差异。以颜色属性为例，比如直接接入 Position 节点，效果如下：
+
+![](assets/set-color-by-pos.png)
+
+我们还可以把数据层的值映射为颜色渐变，这里需要用到 **O Scalar Layer to Color** 节点（这类转换功能的节点都在节点菜单，Add > O Bioxel > Utilities 下）。调整如下
+
+- **O Cutout by Threshold**：Threshold 设置为 20
+- **O Scalar Layer to Color**：From Min 和 From Max 分别设置为 20 和 90
+
+![](assets/scalar-to-color.png)
+
+由于软组织的 CT 值小于骨质，当阈值降低，可以看到除了头骨外，附着的软组织也被呈现了出来。**O Scalar Layer to Color** 的 From Min 和 From Max，定义了颜色从 0~1 的取值范围。因此低值的软组织呈现黑色，高值的骨质呈现白色
+
+我们还可以通过 Blender 5.0+ 的 **Closure** 节点来自定义映射方式。比如连接 **Color Ramp** 节点，把属于软组织的黑区，改为暗红色
+
+![](assets/scalar-to-color-ramp.png)
+
+哒哒！解剖渲染就做好啦👍
+
+其他「结构体」属性也可以按这样的方式调整，除了 **O Scalar Layer to Color**，还有 **O Scalar Layer to Factor** 来转换为 0~1 的单值

docs/advanced_usage.md

@@ -1,118 +0,0 @@
-# Advanced Usage
-
-## Concepts
-
-In the previous section, I mentioned some key concepts, I'll describe them in detail so that you can better understand the following operations.
-
-### Container
-
-First is the **Container**, it is the easiest to describe, you can think of it as a scene, or a solver container. it is the stage that carries all stuffs.
-
-### Layer
-
-Second is the **Layer**, which represents different fields of data under the same location in container of the same subject. Just as view layers in any map app, one as roads, one as satellite view, while in Bioxel, one as MRI, one as CT, one as electrical signals, etc. Some layers are for material, such as color, density, etc., we call them **Material Layer**. One container contains different layers of one subject each. Any external data imported into the container is converted into the layer.
-
-### Component
-
-Finally, the **Component**, which is a fragment of **Material Layer**. Multiple materials (Matters) may exist within the same area with different meanings of presentation, like objects in blender, each representing a part of the scene. Bioxel Nodes provides a series of nodes and tools that allow the user to create material layers (Components) based on the other layers (serve as source data), In the previous section, we used the CT data (layer) to make the material (matter) of skull, this process known as materialization.
-
-## Attache the Muscles to the Skull
-
-Multiple components can exist in one container, just as multiple objects can exist in one scene. They can be controlled individually or combined with each other to build complex scenes. Next, let's try cutouting muscle from the VHP anatomical images and attaching the muscles to the skull that created in the previous section. The anatomical images are very large, so I've cropped and scaled them down to 1/4 of their original size for ease of use. Download the file and unzip it into a new directory.
-
-[VHP_M_AnatomicalImages_Head.zip](https://drive.google.com/file/d/164AjQX0tmgUpWZlleJ5i1IKHco4ytDu2/view?usp=drive_link)
-
-You can also download the data directly from the official website, [https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/PNG_format/head/index.html](https://data.lhncbc.nlm.nih.gov/public/Visible-Human/Male-Images/PNG_format/head/index.html)
-
-First import the CT data as described in [step by step](step_by_step.md). Then import the anatomical images, but unlike before, this time from the Geometry Nodes menu of the existing container (not the top menu), click **Bioxel Nodes > Import Volumetric Data (Init) > as Color**, locate to the unzipped folder, and select any .png file (do not multi-select, and do not select the folder). This way the imported layer will be in the same container as the previous CT data. You can also import by dragging it into the container geometry node interface instead of the 3D Viewport interface. Also note that **as Color** (not as Scalar) is clicked because the anatomical images are RGB data.
-
-![alt text](assets/advanced_usage/image.png)
-
-Let's take more time in the import options this time 🫡, first let's talk about what the **Original Spacing** is in the options, you can simply think of it as the original "pixel size" of a image, since the volume is 3D, its pixels (i.e., voxels) are cuboids with a length, width, and height rather than 2D rectangles. And their length, width, and height size is the **Spacing**.
-
-Normally, Bioxel Nodes can read the spacing from the data header, and you don't need to fill in the value, but there is no record of that in any PNG image, so you need to input it manually. in the official description of the VHP, it is mentioned that each pixel of the anatomical images corresponds to the size of .33mm, and the thickness of each slice is 1mm, so the Original Spacing of the anatomical images should be set to `(0.33, 0.33, 1)`.
-
-However, the file I provided is scaled by 1/4 for each image, so the X and Y axes need to be multiplied by 4. So the final Original Spacing should be set to `(1.33, 1.33, 1)`, which should be understandable, right? (If you are importing an official file, then it should still be set to `(0.33, 0.33, 1)`)
-Layer Name should be set to "Anatomical Images", other options remain default, click Ok.
-
-![alt text](assets/advanced_usage/image-1.png)
-
-After importing, connect the "Cutout by Hue" node (Add > Bioxel Nodes > Component > Cutout by Hue) after the newly created "Fetch Layer" node, and turn on the Slice Viewer mode preview, as shown below.
-
-![alt text](assets/advanced_usage/image-2.png)
-
-In addition to spacing, the Dicom file also records the subject's position and orientation, but those information is apparently not recorded in PNG format. This results in a mismatch between the CT data and the anatomical images in position. We need to manually align this two layers: First, set the threshold of the "Cutout by Threshold" node to 0.2 so that the full head can be cutouted and displayed. Then add "ReCenter" node before "Cutout by Hue" node and "Cutout by Threshold" node each, then add Locater to the "anatomical images" workflow (see [step by step](step_by_step.md) for details), and finally add "Join Component" node (Add > Bioxel Nodes > Component > Join Component), and connect them as shown below, with the parameters set as shown.
-
-![alt text](assets/advanced_usage/image-3.png)
-
-The "Join Component" node allows you to merge two components together. Move and rotate the Locater object so that the two components are exactly the same in position. If you're having trouble matching them up, here's the exact transform values to fill in the Locater object properties.
-
-![alt text](assets/advanced_usage/image-4.png)
-
-Next let's cutout the muscles individually.
-
-First let's talk about the "Cutout by Hue" node. Literally, it cutout regions by hue of color. If you select this node and press "M" key to temporarily mute it, you'll see that the data becomes a cube with blue parts in Slice Viewer mode. the default value of Hue in the "Cutout by Hue" node is red, meaning that the node retains areas of the body that are close to red, and strip out the blue, which is on the opposite side of the red in the hue ring, leaving the human body parts.
-
-If you turn down the value of Sensitivity, you'll see that the visabile part is decreasing, leaving only the part more closer to red, and the muscle happens to be red, so we can easily cutout the muscle. The color of the specimen tissue is not as vibrant as it is in the live state, and we can fine-tune the color to restore the vibrancy by using the "Set Color by Color" node (Add > Bioxel Nodes > Property > Set Color by Color).
-
-To finally put it all together, connect and set the nodes as shown below, where the two colors in "Set Color by Ramp 2" node are `E7D2C5` and `FFEDEC`. If everything is working correctly, you'll get the rendering below.
-
-![alt text](assets/advanced_usage/image-5.png)
-
-You can also add "Transfrom" and "Cutter" nodes at the end and all components.
-
-![alt text](assets/advanced_usage/image-6.png)
-
-The multimodal data of VHP do not have any deformation or scaling differences, but only positional differences, so all data can be aligned easily. However, in most cases, the differences of different modalities are so great that they need to be registered first, which is not possible with Bioxel Nodes at the moment (but it is in plan). Nevertheless, you can build different components based on the same layer and combine them together. For example, based on the CT data, with the "Cutout by Range" node, you can eliminate the low value regions (fat), eliminate the high value regions (bone), and you can still get the muscle. And then attach it to the skull.
-
-![alt text](assets/advanced_usage/image-7.png)
-
-However, the CT values of brain and muscle are very close to each other, so it is extremely difficult to separate the brain from the muscle by threshold. So how should cutout the brain?
-
-## Cutout the Brain
-
-We can use AI technology to realize the division of brain regions, this process is called Segmentation, and the brain regions are as label. There are many models and methods for medical image segmentation, here we recommend [Total Segmentator](https://github.com/wasserth/TotalSegmentator).
-
-It is an out-of-the-box CT/MRI medical image segmentation Python library. You can deploy Total Segmentator locally or process your data through the official online site [https://totalsegmentator.com](https://totalsegmentator.com).
-
-Let me demonstrate the operation, we are still using the CT data from VHP. Click on "Drop DICOM.zip or ..." and select the VHP_M_CT_Head.zip file. Enter "brain" below "Selected task", press Enter to confirm. Finally click "Process data" button.
-
-![alt text](assets/advanced_usage/image-8.png)
-
-Wait for the uploading and processing, after all, you will be redirected to the following page, click "Download results" button, download and unzip segmentations.zip to any folder directory.
-
-![alt text](assets/advanced_usage/image-9.png)
-
-In case you can't get the brain segment (label), you can download it directly (without unzipping it).
-
-[VHP_M_CT_Head_Brain.nii.gz](https://drive.google.com/file/d/1KGiZ3G11YLXkGszSrvWQ9kTF4TMpxUPd/view?usp=drive_link)
-
-Next we import the brain segment (label) into the container in the same way as we imported the anatomical imagess(under the same container), but this time selecting **as Label**, with the Layer Name set to "Brain", and leaving the other options as default. Once the import is complete, a new "Fetch Layer" node will be added. Create and set the node as shown below, and you should be able to see the surface of brain.
-
-![alt text](assets/advanced_usage/image-10.png)
-
-Do you see the "step" like shape on surface? this is due to the low precision of the AI segmentation results. So How to addressing the issue? Select the Fetch Layer node of the brain label, right-click to pop up menu, click **Bioxel Nodes > Resample Value**, in the dialog box, change the "Smooth Size" to 3 or higher (the higher it is, the slower the calculation will be), click OK and wait for the calculation to finish. When it is done, a new layer will be added, replace the original one, is it smoother? The following figure lists different levels of smoothing.
-
-![alt text](assets/advanced_usage/image-11.png)
-
-The smoother it is, the more comfortable it looks, but it also means that more details are lost and the calculation is slower.
-
-But if you cut the brain, you will find that the cross-section is homogeneous, this is because the label type layer is does not contain any modality data itself. Bioxel Nodes provides a function to fill in any layer values by label, if you set the value below brain tissue in the non-brain region of CT data, then any "Cutout" node will only keep the brain region.
-
-The operation is like this, select the "Fetch Layer" node of the CT data, right-click to pop up the menu, click **Bioxel Nodes > Fill Value by Label**, in the dialog box, Label is set to the newly imported brain label layer, Fill Value is set to -100 (as long as it is less than the Hu value of the brain tissue), click OK. wait for the data processing, a new data layer will be added to the container when it is finished.
-
-As shown in the following figure, connect the nodes and set the node parameters, in which the two colors of "Set Color by Ramp 2" node are `B26267` and `EBC5B7`, and the "Cutout by Range" and "Set Color by Ramp 2" node are changed to "Value" mode (the default is "Factor" mode), because the maximum and minimum values of the brain are too close to each other and difficult to adjust in "Factor" mode. To make the brain tissue look more transparent, I add the "Set Properties" (Add > Bioxel Nodes > Property > Set Properties) node at the end and changed the "Density" to 0.5.
-
-![alt text](assets/advanced_usage/image-12.png)
-
-(Still feel not smooth enough? It's really hard to get rid of "step" surface completely at the moment)
-
-Now the brain is done. Finally we combine all together and you get something like the following.
-
-![alt text](assets/advanced_usage/image-13.png)
-
-🤗 If you've followed the docs up to this point, give yourself a round of applause, you've mastered this addon! If you have trouble following the docs instruction, you can download the project files to understand how the nodes work.
-
-[VHP.zip](https://drive.google.com/file/d/1EHB7sxNSvJNwmoTfFnpyOSsm2M_2Y0hO/view?usp=sharing)
-
-AI segmentation is an essential part of volumetric data visualization. Therefore, the future Bioxel Nodes will integrate some commonly used AI segmentation models, so that users can complete the volumetric data visualization in place!

docs/basics.en.md

@@ -0,0 +1,50 @@
+# Bacsic Usage
+
+## 1. Download Data
+
+Download and unzip [VHP_M_CT_Head.zip](https://drive.google.com/file/d/1bBGpt5pQ0evr-0-f4KDNRnKPoUYj2bJ-/view?usp=drive_link) to a folder.
+The data comes from [Visible Human Project (VHP)](https://www.nlm.nih.gov/research/visible/visible_human.html), which is a CT scan image of a male head.
+
+## 2. Import as "Layer"
+
+Add a geometry node to the cube and open the geometry node interface sidebar. Switch to the Bioxel Nodes tab (1), click the Import Data button (2), and in the file selection dialog, choose any `.dcm` file from the data folder (3), then click the Import Data button (4).
+
+![](assets/import-data.png)
+
+Two dialogs will pop up in sequence, click OK for both. Wait for the data import (you can check the progress bar in the Blender interface status bar at the bottom right). After success, you will see a data preview in the Bioxel Nodes sidebar. Click the Add button at the bottom (1), move the mouse to the node panel, and place the **O Layer** node (2).
+
+![](assets/add-o-layer.png)
+
+The data import is complete!
+
+The data cache is saved as a link in the Blender file in the form of a "Layer", and the "Layer" is loaded into geometry nodes through the **O Layer** node. Their relationship is as follows:
+
+Data Cache -> Layer -> O Layer
+
+## 3. Extract and Render "Structure"
+
+Operations on "Layer" are done through the O Bioxel series geometry nodes.
+
+We need two additional nodes: **O Cutout by Threshold** and **O Realize Structure** nodes (both are in the node menu under Add > O Bioxel > Structure), and connect them as shown below:
+
+![](assets/connect-nodes.png)
+
+If successful, you will see a gray head appear in the viewport. Now let's adjust the node parameters:
+
+- **O Layer**: Check Center, uncheck Resample
+- **O Cutout by Threshold**: Set Threshold to 90
+- **O Realize Structure**: Set Density to 40, check Surface
+
+Rotate the object, adjust the light position, set the renderer to Cycles, and the final effect is shown below:
+
+![](assets/adjust-nodes.png)
+
+Now we have completed the volumetric rendering of the head CT data!
+
+Let's review the execution logic: First, cutout the "Structure" from the "Layer". As the name suggests, "Structure" is responsible for storing biological tissue structure, but its data type is volumetric and cannot be seen directly. It requires **O Realize Structure** to present the "Structure".
+
+## 4. Save Data Cache (Optional)
+
+Since the data cache is only saved as a link in the Blender file, passing only the Blender file to other devices will cause the "Layer" to lose its cache. Click the Save button in the Bioxel Nodes tab, and select a location to save the data cache to manage the cache resource.
+
+Just like images, when sharing, send both the data cache and the Blender file together.

docs/basics.md

@@ -0,0 +1,51 @@
+# 入门
+
+## 1. 下载数据
+
+下载并解压到文件夹中 [VHP_M_CT_Head.zip](https://drive.google.com/file/d/1bBGpt5pQ0evr-0-f4KDNRnKPoUYj2bJ-/view?usp=drive_link)  
+数据来自 [Visible Human Project (VHP)](https://www.nlm.nih.gov/research/visible/visible_human.html)这是一个男性头部的 CT 扫描图像
+
+## 2. 导入为「数据层」
+
+给立方体添加几何节点，并打开几何节点界面侧边栏。切换到 Bioxel Nodes 分页（1），点击 Import Data 按钮（2），在文件选择对话框中，选择数据文件夹中任意一个`.dcm`文件（3），点击 Import Data 按钮（4）
+
+![](assets/import-data.png)
+
+依次会弹出两个对话框，都点击 OK 按钮，等待数据导入（可查看 Blender 界面右下角状态栏的进度条）成功后可以看到 Bioxel Nodes 侧边栏多了数据预览画面。点击下方的 Add 按钮（1），鼠标移动到节点面板，放置 **O Layer** 节点（2）
+
+![](assets/add-o-layer.png)
+
+数据的导入就完成啦👍
+
+数据缓存在主目录里，以「数据层（Layer）」形式添加在 Blender 文件中，「数据层」通过 **O Layer** 节点装载到几何节点。它们的关系如下:
+
+数据缓存 -> 数据层 -> O Layer
+
+
+## 3. 提取并渲染「结构体」
+
+对「数据层」的操作通过 O Bioxel 系列几何节点完成。
+
+我们需要额外两个节点，**O Cutout by Threshold** 和 **O Realize Structure** 节点（它们都在节点菜单，Add > O Bioxel > Structure 下），并按下图连接：
+
+![](assets/connect-nodes.png)
+
+如果成功，可以看到视图中出现了灰色的头部。接下来我们调整节点参数：
+
+- **O Layer**：勾选 Center，取消 Resample
+- **O Cutout by Threshold**：Threshold 设置为 90
+- **O Realize Structure**：Density 设置为 40，勾选 Surface
+
+调整物体转向、灯位置，设置渲染器为 Cycles，最终效果如下图：
+
+![](assets/adjust-nodes.png)
+
+这样我们就完成了头部 CT 数据的体积渲染👍
+
+简单捋一下执行逻辑，「数据层」先被剪出（Cutout）为「结构体」。「结构体」顾名思义就是负责储存生物组织结构的对象，但它本身数据类型是体积，并不能直接被看到。需要 **O Realize Structure** 来呈现「结构体」
+
+## 4. 另存数据缓存（可选）
+
+由于数据缓存只是以链接形式保存在 Blender 文件中，所以只传递 Blender 文件给其他设备，会导致「数据层」遗失缓存。点击 Bioxel Nodes 分页中 Save 按钮，选择数据缓存的另存位置来管理缓存资源。
+
+就像图片一样，传递时把数据缓存和 Blender 文件一起发送。

docs/dataset.md

@@ -0,0 +1,39 @@
+# 支持的格式
+
+迫不及待想使用自己的数据来体验插件了？以下是当前支持的格式列表。
+
+| 格式   | 扩展名                                       |
+| ------ | ---------------------------------------- |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP    | .bmp, .BMP                               |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG    | .png, .PNG                               |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd   | .nrrd, .nhdr                             |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME    | .ome.tiff, .ome.tif                      |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
+
+尽管我尽了最大努力，仍然无法实现对所有体数据格式的完美支持，我将持续努力改进。
+
+## 公开数据库
+
+如果您没有体数据，可以从一些公开数据库下载。
+
+**请注意，虽然它们是公开的且可供下载，但并不意味着您可以将其用于任何目的！请务必查看网站上的可用范围说明。**
+
+| 来源                                                                                 | 对象               |
+| ------------------------------------------------------------------------------------ | ------------------ |
+| [MorphoSource](https://www.morphosource.org/)                                        | 开放研究数据       |
+| [Dryad](https://datadryad.org)                                                       | 开放研究数据       |
+| [Cell Image Library](http://cellimagelibrary.org/home)                               | 细胞               |
+| [OpenOrganelle](https://openorganelle.janelia.org/datasets)                          | 细胞               |
+| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                | 细胞               |
+| [EMDB](https://www.ebi.ac.uk/emdb/)                                                  | 蛋白质、病毒       |
+| [IDC](https://portal.imaging.datacommons.cancer.gov/explore/)                        | 医学图像           |
+| [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/)                | 医学图像           |
+| [Github](https://github.com/sfikas/medical-imaging-datasets)                         | 医学图像           |
+| [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/)                        | 医学图像           |
+| [Medical Segmentation Decathlon](http://medicaldecathlon.com/)                       | 医学图像           |
+| [Visible Human Project](https://www.nih.gov/research/visible/visible_human.html)    | 医学图像           |

docs/faq.en.md

@@ -1,4 +1,4 @@
-# Q & A
+# FAQ
 
 ## Nothing in the scene when rendering?
 

docs/faq.md

@@ -0,0 +1,15 @@
+# 常见问题
+
+## 渲染时场景什么都没有？
+
+如果您使用 GPU 进行 Cycles 渲染，请确保您的 GPU 支持"Optix"，因为 Bioxel Nodes 依赖 OSL（Open Shader Language）进行体渲染，否则您必须使用 CPU 进行渲染。
+
+如果您使用 EEVEE 渲染器，此问题是因为 EEVEE 出于未知原因未加载着色器，保存文件并重启 Blender 即可修复。
+
+## 更新插件后，文件中的节点变红了？
+
+这是因为文件中节点的版本与更新后插件的版本不匹配。
+
+如果您仍想使用 Bioxel Nodes 编辑文件，只能将插件回滚到与节点对应的版本。
+
+如果您只想让文件正常工作，不再依赖 Bioxel Nodes，那么您只需点击顶部菜单 **Bioxel Nodes > Relink Node Library >**，然后选择相应的版本。检查节点是否正常工作并正确渲染，一切正常后，点击 **Bioxel Nodes > Save Node Library**，在对话框中选择保存位置。