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refactor: Clean up AGENTS.md and remove outdated test files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

@@ -0,0 +1,68 @@
+name: Release Version
+
+on:
+  push:
+    tags:
+      # Publish on any tag starting with a `v`, e.g., v0.1.0
+      - 'v*'
+
+jobs:
+  draft_release:
+    name: Draft Release
+    permissions:
+      contents: write
+      pull-requests: write
+    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: Draft Release ${{ steps.set_env.outputs.version }}
+        uses: release-drafter/release-drafter@v5
+        id: draft_release
+        with:
+          name: ${{ steps.set_env.outputs.version }}
+          tag: ${{ steps.set_env.outputs.version }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  build_extension:
+    name: Build Blender Extension
+    needs: draft_release
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        platform: ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          lfs: "true"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Dependencies
+        run: |
+          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:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        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_content_type: application/zip

.github/workflows/upload-assets.yml

@@ -1,106 +0,0 @@
-name: Upload Assets to Release
-
-on:
-  push:
-    branches:
-      - "release/*"
-
-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:
-      contents: write
-      pull-requests: write
-    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: Draft Release ${{ steps.set_env.outputs.version }}
-        uses: release-drafter/release-drafter@v5
-        id: draft_release
-        with:
-          name: ${{ steps.set_env.outputs.version }}
-          tag: ${{ steps.set_env.outputs.version }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-  upload_blender_addon:
-    name: Upload Blender Add-on
-    needs: draft_release
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-        with:
-          lfs: "true"
-      - name: Zip Add-on
-        run: |
-          zip -r package.zip bioxelnodes
-      - name: Upload Release Asset
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: ./package.zip
-          asset_name: BioxelNodes_Addon_${{ needs.draft_release.outputs.version }}.zip
-          asset_content_type: application/zip
-
-  upload_blender_extension:
-    name: Upload Blender Extension
-    needs: draft_release
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-        with:
-          lfs: "true"
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-      - name: Zip Extension
-        run: |
-          pip download SimpleITK==2.3.1 --dest bioxelnodes/wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
-          rm -r bioxelnodes/externalpackage
-          cp extension/__init__.py bioxelnodes/__init__.py
-          cp extension/preferences.py bioxelnodes/preferences.py
-          cp extension/blender_manifest.toml bioxelnodes/blender_manifest.toml
-          zip -r package.zip bioxelnodes
-      - name: Upload Release Asset
-        id: upload-release-asset
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: ./package.zip
-          asset_name: BioxelNodes_Extension_${{ needs.draft_release.outputs.version }}.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
@@ -123,14 +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/
 
-!bioxelnodes/scipy/_nd_image.cp311-win_amd64.pyd
+# Ruff stuff:
+.ruff_cache/
+
+# 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
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+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     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.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+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
+    it under the terms of the GNU General Public License as published by
+    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

@@ -1,67 +1,43 @@
-[中文文档](https://uj6xfhbzp0.feishu.cn/wiki/Qx3VwHuNPimeI8kr6nDcvl1DnHf?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
 
-![Static Badge](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white)
-![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge)
-![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge)
-![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge)
+[![For Blender](https://img.shields.io/badge/Blender-orange?style=for-the-badge&logo=blender&logoColor=white&color=black)](https://blender.org/)
+![GitHub License](https://img.shields.io/github/license/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Release](https://img.shields.io/github/v/release/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+![GitHub Repo stars](https://img.shields.io/github/stars/OmooLab/BioxelNodes?style=for-the-badge&labelColor=black)
+
+[![Discord](https://img.shields.io/discord/1265129134397587457?style=for-the-badge&logo=discord&label=Discord&labelColor=white&color=black)](https://discord.gg/pYkNyq2TjE)
 
 Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It using Blender's powerful **Geometry Nodes** and **Cycles** to process and render volumetric data.
 
 ![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
--   Fantastic rendering result, also support EEVEE NEXT
--   Support multiple formats
--   Support 4D volumetric data
--   All kinds of cutters
--   Simple and powerful nodes
+## Features
+
+-   Realistic rendering result, also support EEVEE NEXT.
+-   Support many formats：.dcm, .jpg, .tif, .nii, .nrrd, .ome, .mrc...
+-   Support 4D volumetric data.
+-   Many kinds of cutters.
+-   Simple and powerful nodes.
 -   Based on blender natively, can work without addon.
 
-**Click [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                       |
 
-## Support Multiple Formats
+**Read the [getting started](https://docs.omoolab.xyz/bioxelnodes/latest/en/installation) to begin your journey into visualizing volumetric data!**
 
-| Format | EXT                                      | Test    |
-| ------ | ---------------------------------------- | ------- |
-| DICOM  | .dcm, .DICOM                             | ✅ pass |
-| BMP    | .bmp, .BMP                               | ✅ pass |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 | ✅ pass |
-| PNG    | .png, .PNG                               | ✅ pass |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 | ✅ pass |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz | ✅ pass |
-| Nrrd   | .nrrd, .nhdr                             | ✅ pass |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 | ✅ pass |
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
-## Support 4D volumetric data
+## Citation
 
-![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif)
+If you want to cite this work, you can cite it from Zenodo:
 
-🥰 4D volumetric data can also be imported into Blender.
+[![DOI](https://zenodo.org/badge/786623459.svg)](https://zenodo.org/badge/latestdoi/786623459)
 
-## 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)
-
-## Compatibile to Newer Version
-
-**Updating this addon may break old files, so read the following carefully before updating**
-
-Before updating this addon, you need to ask yourself whether this project file will be modified again or not, if it's an archived project file, I would recommend that you run **Bioxel Nodes > Save Staged Data** to make the addon nodes permanent. In this way, there will be no potential problem with the nodes not functioning due to the addon update.
-
-After the addon update, your old project files may not work either, this may be because you had executed **Save Staged Data**. If so, you need to execute **Bioxel Nodes > Relink Nodes to Addon** to relink them to make sure that the addon's new functionality and the addon nodes are synchronized.
-
-Also, unlike the newer versions, the older shaders are not based on OSL, so if you find that you can't render volumes, you need to turn on **Open Shading Language (OSL)** in the Render Settings.
 
 ## Roadmap
 

bioxelnodes/__init__.py

@@ -1,28 +0,0 @@
-import bpy
-
-from . import auto_load
-from . import menus
-
-
-bl_info = {
-    "name": "Bioxel Nodes",
-    "author": "Ma Nan",
-    "description": "",
-    "blender": (4, 1, 0),
-    "version": (0, 2, 7),
-    "location": "File -> Import",
-    "warning": "",
-    "category": "Node"
-}
-
-auto_load.init()
-
-
-def register():
-    auto_load.register()
-    menus.add()
-
-
-def unregister():
-    menus.remove()
-    auto_load.unregister()

bioxelnodes/customnodes/__init__.py

@@ -1 +0,0 @@
-from .menus import CustomNodes

bioxelnodes/customnodes/menus.py

@@ -1,148 +0,0 @@
-import shutil
-import bpy
-from pathlib import Path
-from .nodes import AddCustomNode
-
-
-class CustomNodes():
-    def __init__(
-        self,
-        menu_items,
-        nodes_file,
-        class_prefix="CUSTOMNODES_MT_NODES",
-        root_label='CustomNodes',
-        root_icon='NONE'
-    ) -> None:
-        if not Path(nodes_file).is_file():
-            raise FileNotFoundError(str(Path(nodes_file).resolve()))
-
-        self.menu_items = menu_items
-        self.nodes_file = str(Path(nodes_file).resolve())
-        self.class_prefix = class_prefix
-        self.root_label = root_label
-        self.root_icon = root_icon
-        self.class_prefix = class_prefix
-
-        menu_classes = []
-        self._create_menu_class(
-            items=menu_items,
-            label=root_label,
-            menu_classes=menu_classes
-        )
-        self.menu_classes = menu_classes
-
-        idname = f"{class_prefix}_{root_label.replace(' ', '').upper()}"
-
-        def add_node_menu(self, context):
-            if ('GeometryNodeTree' == bpy.context.area.spaces[0].tree_type):
-                layout = self.layout
-                layout.separator()
-                layout.menu(idname, icon=root_icon)
-
-        self.add_node_menu = add_node_menu
-
-    def _create_menu_class(self, menu_classes, items, label='CustomNodes', icon=0, idname_namespace=None):
-        nodes_file = self.nodes_file
-        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
-            nodes_file = self.nodes_file
-
-            def draw(self, context):
-                layout = self.layout
-
-                for item in items:
-                    # print(item)
-                    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(
-                            'customnodes.add_custom_node',
-                            text=item.get('label'),
-                            icon=item.get('icon') or 'NONE'
-                        )
-                        op.nodes_file = nodes_file
-                        op.node_type = item['node_type']
-                        op.node_label = item.get('label') or ""
-                        op.node_description = item.get(
-                            'node_description') or "Add Custom Node."
-                        op.node_link = item.get('link') or True
-                        op.node_callback = item.get('node_callback') or ""
-
-        menu_classes.append(Menu)
-        return Menu
-
-    def _find_item(self, found_items, menu_items, node_type: str):
-
-        for item in menu_items:
-            if item == 'separator':
-                continue
-
-            if item.get("node_type") == node_type:
-                found_items.append(item)
-
-            item_items = item.get('items')
-            if item_items:
-                self._find_item(found_items, item_items, node_type)
-
-    def find_item(self, node_type: str):
-        found_items = []
-        self._find_item(found_items, self.menu_items, node_type)
-        return found_items[0] if len(found_items) > 0 else None
-
-    def add_node(self, node_group, node_type: str):
-        item = self.find_item(node_type)
-        op = AddCustomNode()
-        op.nodes_file = self.nodes_file
-        op.node_type = node_type
-        if item:
-            op.node_label = item.get('label') or ""
-            op.node_link = item.get('link') or True
-            op.node_callback = item.get('node_callback') or ""
-        else:
-            op.node_label = ""
-            op.node_link = True
-            op.node_callback = ""
-        return op.add_node(node_group)
-
-    def register(self):
-        for cls in self.menu_classes:
-            bpy.utils.register_class(cls)
-
-        bpy.types.NODE_MT_add.append(self.add_node_menu)
-        bpy.types.Scene.customnodes_node_dir = bpy.props.StringProperty(
-            name="Node Directory",
-            subtype='DIR_PATH',
-            default="//"
-        )
-
-    def unregister(self):
-        bpy.types.NODE_MT_add.remove(self.add_node_menu)
-        try:
-            for cls in reversed(self.menu_classes):
-                bpy.utils.unregister_class(cls)
-
-        except RuntimeError:
-            pass

bioxelnodes/customnodes/nodes.py

@@ -1,125 +0,0 @@
-import bpy
-
-
-class AddCustomNode():
-
-    nodes_file: bpy.props.StringProperty(
-        name="nodes_file",
-        subtype='FILE_PATH',
-        default=""
-    )  # type: ignore
-
-    node_type: bpy.props.StringProperty(
-        name='node_type',
-        description='',
-        default='',
-        subtype='NONE',
-        maxlen=0
-    )  # type: ignore
-
-    node_label: bpy.props.StringProperty(
-        name='node_label',
-        default=''
-    )  # type: ignore
-
-    node_description: bpy.props.StringProperty(
-        name="node_description",
-        description="",
-        default="Add custom node group.",
-        subtype="NONE"
-    )  # type: ignore
-
-    node_link: bpy.props.BoolProperty(
-        name='node_link',
-        default=True
-    )  # type: ignore
-
-    node_callback: bpy.props.StringProperty(
-        name='node_callback',
-        default=''
-    )  # type: ignore
-
-    @classmethod
-    def description(cls, context, properties):
-        return properties.node_description
-
-    def assign_node_tree(self, node):
-        node.node_tree = bpy.data.node_groups[self.node_type]
-
-        node.width = 200.0
-        node.label = self.node_label or self.node_type
-        node.name = self.node_type
-
-        if self.node_callback:
-            exec(self.node_callback)
-
-        return node
-
-    def get_node_tree(self, node_type, node_link):
-        # try to get node from current file if exists
-        node_tree = bpy.data.node_groups.get(node_type)
-        # if not exists, get it from asset file.
-        if not node_tree:
-            bpy.ops.wm.append(
-                'EXEC_DEFAULT',
-                directory=f"{self.nodes_file}/NodeTree",
-                filename=node_type,
-                link=node_link,
-                use_recursive=True
-            )
-
-        node_tree = bpy.data.node_groups.get(node_type)
-        if node_tree:
-            # self.recursive_append_material(node_tree)
-            return node_tree
-        else:
-            raise RuntimeError('No custom node found')
-
-    def recursive_append_material(self, node_tree):
-        for child in node_tree.nodes:
-            material_socket = child.inputs.get('Material')
-            if material_socket:
-                print(material_socket.default_value)
-            try:
-                self.recursive_append_material(child.node_tree)
-            except:
-                ...
-
-    def add_node(self, node_group):
-        # Deselect all nodes first
-        for node in node_group.nodes:
-            if node.select:
-                node.select = False
-
-        self.get_node_tree(self.node_type, self.node_link)
-        node = node_group.nodes.new("GeometryNodeGroup")
-        self.assign_node_tree(node)
-
-        return node
-
-
-class CUSTOMNODES_OT_Add_Custom_Node(bpy.types.Operator, AddCustomNode):
-    bl_idname = "customnodes.add_custom_node"
-    bl_label = "Add Custom Node"
-    bl_options = {"REGISTER", "UNDO"}
-
-    def execute(self, context):
-        self.get_node_tree(self.node_type, self.node_link)
-
-        # intended to be called upon button press in the node tree
-        prev_context = bpy.context.area.type
-        bpy.context.area.type = 'NODE_EDITOR'
-        # actually invoke the operator to add a node to the current node tree
-        # use_transform=True ensures it appears where the user's mouse is and is currently
-        # being moved so the user can place it where they wish
-        bpy.ops.node.add_node(
-            'INVOKE_DEFAULT',
-            type='GeometryNodeGroup',
-            use_transform=True
-        )
-        bpy.context.area.type = prev_context
-        node = bpy.context.active_node
-
-        self.assign_node_tree(node)
-
-        return {"FINISHED"}

bioxelnodes/externalpackage/__init__.py

@@ -1,2 +0,0 @@
-from .preferences import ExternalPackagePreferences
-from .package import PackageInstaller

bioxelnodes/externalpackage/package.py

@@ -1,393 +0,0 @@
-"""
-Handling installation of external python packages inside of Blender's bundled python.
-"""
-import subprocess
-import sys
-import logging
-from importlib.metadata import version as get_version, PackageNotFoundError
-import bpy
-from pathlib import Path
-
-ADDON_NAME = __package__.split(".")[0]
-
-PYPI_MIRROR = {
-    # the original.
-    'Default': '',
-    # two mirrors in China Mainland to help those poor victims under GFW.
-    'BFSU (Beijing)': 'https://mirrors.bfsu.edu.cn/pypi/web/simple',
-    'TUNA (Beijing)': 'https://pypi.tuna.tsinghua.edu.cn/simple',
-    # append more if necessary.
-}
-
-
-class InstallationError(Exception):
-    """
-    Exception raised when there is an error installing a package.
-
-    Attributes
-    ----------
-    package_name : str
-        The name of the package that failed to install.
-    error_message : str
-        The error message returned by pip.
-
-    """
-
-    def __init__(self, package_name, error_message):
-        self.package_name = package_name
-        self.error_message = error_message
-        super().__init__(f"Failed to install {package_name}: {error_message}")
-
-
-class PackageInstaller():
-    def __init__(
-        self,
-        requirements_dir: str,
-        log_dir: str = None,
-        pypi_mirror_provider='Default',
-    ) -> None:
-        self.pypi_mirror_provider = pypi_mirror_provider
-        self.log_path: Path = Path(log_dir) if log_dir \
-            else Path.home() / '.externalpackage' / 'logs'
-        self.requirements_path: Path = Path(requirements_dir)
-
-    def start_logging(self, logfile_name: str = 'side-packages-install') -> logging.Logger:
-        """
-        Configure and start logging to a file.
-
-        Parameters
-        ----------
-        logfile_name : str, optional
-            The name of the log file. Defaults to 'side-packages-install'.
-
-        Returns
-        -------
-        logging.Logger
-            A Logger object that can be used to write log messages.
-
-        This function sets up a logging configuration with a specified log file name and logging level.
-        The log file will be created in the `ADDON_DIR/logs` directory. If the directory
-        does not exist, it will be created. The function returns a Logger object that can be used to
-        write log messages.
-
-        """
-        # Create the logs directory if it doesn't exist
-        self.log_path.mkdir(parents=True, exist_ok=True)
-
-        # Set up logging configuration
-        logfile_path = Path(self.log_path, f"{logfile_name}.log")
-        logging.basicConfig(filename=logfile_path,
-                            level=logging.INFO, encoding='utf-8')
-
-        # Return logger object
-        return logging.getLogger()
-
-    @property
-    def pypi_mirror_url(self) -> str:
-        """
-        Process a PyPI mirror provider and return the corresponding URL.
-
-        Parameters
-        ----------
-        pypi_mirror_provider : str
-            The PyPI mirror provider to process.
-
-        Returns
-        -------
-        str
-            The URL of the PyPI mirror.
-
-        Raises
-        ------
-        ValueError
-            If the provided PyPI mirror provider is invalid.
-
-        """
-        if self.pypi_mirror_provider.startswith('https:'):
-            return self.pypi_mirror_provider
-        elif self.pypi_mirror_provider in PYPI_MIRROR.keys():
-            return PYPI_MIRROR[self.pypi_mirror_provider]
-        else:
-            raise ValueError(
-                f"Invalid PyPI mirror provider: {self.pypi_mirror_provider}")
-
-    @property
-    def packages(self) -> dict:
-        """
-        Read a requirements file and extract package information into a dictionary.
-
-        Parameters
-        ----------
-        requirements : str, optional
-            The path to the requirements file. If not provided, the function looks for a `requirements.txt`
-            file in the same directory as the script.
-
-        Returns
-        -------
-        dict
-            A dictionary containing package information. Each element of the dictionary is a dictionary containing the package name, version, and description.
-
-        Example
-        -------
-        Given the following requirements file:
-        ```python
-        Flask==1.1.2 # A micro web framework for Python
-        pandas==1.2.3 # A fast, powerful, flexible, and easy-to-use data analysis and manipulation tool
-        numpy==1.20.1 # Fundamental package for scientific computing
-        ```
-        The function would return the following dictionary:
-        ```python
-        [
-            {
-                "package": "Flask",
-                "version": "1.1.2",
-                "description": "A micro web framework for Python"
-            },
-            {
-                "package": "pandas",
-                "version": "1.2.3",
-                "description": "A fast, powerful, flexible, and easy-to-use data analysis and manipulation tool"
-            },
-            {
-                "package": "numpy",
-                "version": "1.20.1",
-                "description": "Fundamental package for scientific computing"
-            }
-        ]
-        ```
-        """
-        requirements_filepath = self.requirements_path / "requirements.txt"
-        if requirements_filepath.is_file():
-            with requirements_filepath.open('r') as f:
-                lines = f.read().splitlines()
-                packages = {}
-                for line in lines:
-                    try:
-                        package, description = line.split('#')
-                        package_meta = package.split('==')
-                        name = package_meta[0].strip()
-                        packages[name] = {
-                            "name": name,
-                            "version": package_meta[1].strip(),
-                            "description": description.strip()
-                        }
-                    except ValueError:
-                        # Skip line if it doesn't have the expected format
-                        pass
-            return packages
-        else:
-            raise FileNotFoundError(requirements_filepath)
-
-    def is_installed(self, package_name: str) -> bool:
-        """
-        Check if the specified package is installed and the version matches that specified
-        in the `requirements.txt` file.
-
-        Parameters
-        ----------
-        package : str
-            The name of the package to check.
-
-        Returns
-        -------
-        bool
-            True if the package is the current version, False otherwise.
-
-        """
-        package = self.packages.get(package_name)
-        try:
-            available_version = get_version(package['name'])
-            return available_version == package['version']
-        except PackageNotFoundError:
-            return False
-
-    def run_python(self, cmd_list: list = None, timeout: int = 600):
-        """
-        Runs pip command using the specified command list and returns the command output.
-
-        Parameters
-        ----------
-        cmd_list : list, optional
-            List of pip commands to be executed. Defaults to None.
-        mirror_url : str, optional
-            URL of a package repository mirror to be used for the command. Defaults to ''.
-        timeout : int, optional
-            Time in seconds to wait for the command to complete. Defaults to 600.
-
-        Returns
-        -------
-        tuple
-            A tuple containing the command list, command return code, command standard output,
-            and command standard error.
-
-        Example
-        -------
-        Install numpy using pip and print the command output
-        ```python
-        cmd_list = ["-m", "pip", "install", "numpy"]
-        mirror_url = 'https://pypi.org/simple/'
-        cmd_output = run_python(cmd_list, timeout=300)
-        print(cmd_output)
-        ```
-
-        """
-
-        # path to python.exe
-        python_exe = str(Path(sys.executable).resolve())
-
-        # build the command list
-        cmd_list = [python_exe] + cmd_list
-
-        # add mirror to the command list if it's valid
-        if self.pypi_mirror_url and self.pypi_mirror_url.startswith('https'):
-            cmd_list += ['-i', self.pypi_mirror_url]
-
-        log = self.start_logging()
-        log.info(f"Running Pip: '{cmd_list}'")
-
-        # run the command and capture the output
-        result = subprocess.run(cmd_list, timeout=timeout,
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-
-        try:
-            if result.returncode != 0:
-                log.error('Command failed: %s', cmd_list)
-                log.error('stdout: %s', result.stdout.decode())
-                log.error('stderr: %s', result.stderr.decode(errors='ignore'))
-            else:
-                log.info('Command succeeded: %s', cmd_list)
-                log.info('stdout: %s', result.stdout.decode())
-        except:
-            ...
-        # return the command list, return code, stdout, and stderr as a tuple
-        return result
-
-    def install_package(self, package: str) -> list:
-        """
-        Install a Python package and its dependencies using pip.
-
-        Parameters
-        ----------
-        package : str
-            The name of the package to install.
-        pypi_mirror_provider : str, optional
-            The name/url of the PyPI mirror provider to use. Default is 'Default'.
-
-        Returns
-        -------
-        list
-            A list of tuples containing the command list, return code, stdout, and stderr
-            for each pip command run.
-
-        Raises
-        ------
-        ValueError
-            If the package name is not provided.
-
-        Example
-        -------
-        To install the package 'requests' from the PyPI mirror 'MyMirror', use:
-        ```
-        install_package('requests', 'MyMirror')
-        ```
-
-        """
-        if not package:
-            raise ValueError("Package name must be provided.")
-
-        print(f"Installing {package}...")
-        print(f"Using PyPI mirror: {self.pypi_mirror_provider}")
-
-        self.run_python(["-m", "ensurepip"]),
-        self.run_python(["-m", "pip", "install", "--upgrade", "pip"])
-        result = self.run_python(["-m", "pip", "install", package, "--user"])
-
-        return result
-
-    def install_all_packages(self, pypi_mirror_provider: str = 'Default') -> list:
-        """
-        Install all packages listed in the 'requirements.txt' file.
-
-        Parameters
-        ----------
-        pypi_mirror_provider : str, optional
-            The PyPI mirror to use for package installation. Defaults to 'Default',
-            which uses the official PyPI repository.
-
-        Returns
-        -------
-        list
-            A list of tuples containing the installation results for each package.
-
-        Raises
-        ------
-        InstallationError
-            If there is an error during package installation.
-
-        Example
-        -------
-        To install all packages listed in the 'requirements.txt' file, run the following command:
-        ```
-        install_all_packages(pypi_mirror_provider='https://pypi.org/simple/')
-        ```
-
-        """
-        results = []
-        for package in self.packages.items():
-
-            try:
-                result = self.install_package(
-                    package=f"{package.get('name')}=={package.get('version')}"
-                )
-                results.append(result)
-            except InstallationError as e:
-                raise InstallationError(
-                    f"Error installing package {package.get('name')}: {str(e)}")
-        return results
-
-
-class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator):
-    bl_idname = 'externalpackage.install_package'
-    bl_label = 'Install Given Python Package'
-    bl_options = {'REGISTER', 'INTERNAL'}
-
-    package: bpy.props.StringProperty(
-        name='Python Package',
-        description='Python Package to Install'
-    )  # type: ignore
-
-    version: bpy.props.StringProperty(
-        name='Python Package',
-        description='Python Package to Install'
-    )  # type: ignore
-
-    description: bpy.props.StringProperty(
-        name='Operator description',
-        default='Install specified python package.'
-    )  # type: ignore
-
-    @classmethod
-    def description(cls, context, properties):
-        return properties.description
-
-    def execute(self, context):
-        preferences = context.preferences.addons[ADDON_NAME].preferences
-        installer = PackageInstaller(
-            pypi_mirror_provider=preferences.pypi_mirror_provider,
-            log_dir=preferences.log_dir,
-            requirements_dir=preferences.requirements_dir
-        )
-
-        result = installer.install_package(f"{self.package}=={self.version}")
-        if result.returncode == 0 or installer.is_installed(self.package):
-            self.report(
-                {'INFO'},
-                f"Successfully installed {self.package} v{self.version}"
-            )
-        else:
-            self.report(
-                {'ERROR'},
-                f"""Error installing package. Please check the log files
-in {preferences.log_dir}."""
-            )
-        return {'FINISHED'}

bioxelnodes/externalpackage/preferences.py

@@ -1,95 +0,0 @@
-import bpy
-import subprocess
-from pathlib import Path
-from .package import PackageInstaller, PYPI_MIRROR
-
-# Defines the preferences panel for the addon, which shows the buttons for
-# installing and reinstalling the required python packages defined in 'requirements.txt'
-
-
-def get_pypi_mirrors(self, context, edit_text):
-    return PYPI_MIRROR.keys()
-
-
-class RebootBlender(bpy.types.Operator):
-    bl_idname = "externalpackage.reboot_blender"
-    bl_label = "Reboot Blender"
-    bl_description = "Reboot Blender"
-    bl_options = {'UNDO'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self, event)
-        return {'RUNNING_MODAL'}
-    
-    def execute(self, context):
-        blender_launcher = Path(
-            bpy.app.binary_path).parent / "blender-launcher.exe"
-        subprocess.run([str(blender_launcher), "-con", "--python-expr",
-                       "import bpy; bpy.ops.wm.recover_last_session()"])
-        bpy.ops.wm.quit_blender()
-        return {'FINISHED'}
-
-
-class ExternalPackagePreferences():
-    requirements_dir: bpy.props.StringProperty(
-        name="requirements.txt Directory",
-        subtype='DIR_PATH',
-        default=str(Path(__file__).parent)
-    )  # type: ignore
-
-    log_dir: bpy.props.StringProperty(
-        name="Python Log Directory",
-        subtype='DIR_PATH',
-        default=str(Path(Path.home(), '.externalpackage', 'logs'))
-    )  # type: ignore
-
-    pypi_mirror_provider: bpy.props.StringProperty(
-        name='pypi_mirror_provider',
-        description='PyPI Mirror Provider',
-        options={'TEXTEDIT_UPDATE', 'LIBRARY_EDITABLE'},
-        default='Default',
-        subtype='NONE',
-        search=get_pypi_mirrors,
-    )  # type: ignore
-
-    def draw(self, context):
-        layout = self.layout
-        layout.label(
-            text='**Install the required packages, then hit "Reboot Blender"**')
-
-        col_main = layout.column(heading='', align=False)
-        row_import = col_main.row()
-        row_import.prop(self, 'pypi_mirror_provider', text='PyPI Mirror')
-
-        installer = PackageInstaller(
-            pypi_mirror_provider=self.pypi_mirror_provider,
-            log_dir=self.log_dir,
-            requirements_dir=self.requirements_dir
-        )
-
-        for package in installer.packages.values():
-
-            name = package.get('name')
-            version = package.get('version')
-            description = package.get('description')
-
-            if installer.is_installed(name):
-                row = layout.row()
-                row.label(text=f"{name} version {version} is installed.")
-                op = row.operator('externalpackage.install_package',
-                                  text=f'Reinstall {name}')
-                op.package = name
-                op.version = version
-                op.description = f'Reinstall {name}'
-            else:
-                row = layout.row(heading=f"Package: {name}")
-                col = row.column()
-                col.label(text=str(description))
-                col = row.column()
-                op = col.operator('externalpackage.install_package',
-                                  text=f'Install {name}')
-                op.package = name
-                op.version = version
-                op.description = f'Install required python package: {name}'
-
-        layout.operator(RebootBlender.bl_idname)

bioxelnodes/io.py

@@ -1,874 +0,0 @@
-import math
-import bpy
-import shutil
-from bpy_extras.io_utils import axis_conversion
-import pyopenvdb as vdb
-import numpy as np
-from pathlib import Path
-from uuid import uuid4
-import mathutils
-import random
-
-from . import skimage as ski
-from .nodes import custom_nodes
-from .props import BIOXELNODES_Series
-from .utils import (calc_bbox_verts, get_all_layers, get_container_from_selection, get_layer, get_text_index_str,
-                    get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, save_vdbs, select_object, show_message)
-
-try:
-    import SimpleITK as sitk
-except:
-    ...
-
-SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM',
-                '.bmp', '.BMP',
-                '.PIC', '.pic',
-                '.gipl', '.gipl.gz',
-                '.jpg', '.JPG', '.jpeg', '.JPEG',
-                '.lsm', '.LSM',
-                '.tif', '.TIF', '.tiff', '.TIFF',
-                '.mnc', '.MNC',
-                '.mrc', '.rec',
-                '.mha', '.mhd',
-                '.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
-                '.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
-                '.nrrd', '.nhdr',
-                '.png', '.PNG',
-                '.vtk']
-
-SEQUENCE_EXTS = ['.dcm', '.DCM', '.DICOM',
-                 '.bmp', '.BMP',
-                 '.jpg', '.JPG', '.jpeg', '.JPEG',
-                 '.tif', '.TIF', '.tiff', '.TIFF',
-                 '.png', '.PNG']
-
-DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM']
-
-FH_EXTS = ['', '.dcm', '.DCM', '.DICOM',
-           '.gipl', '.gipl.gz',
-           '.mnc', '.MNC',
-           '.mrc', '.rec',
-           '.mha', '.mhd',
-           '.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
-           '.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
-           '.nrrd', '.nhdr',
-           '.vtk',
-           '.gz']
-
-
-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
-
-
-def get_ext(filepath: str) -> str:
-    file_path = Path(filepath)
-    if file_path.name.endswith(".nii.gz"):
-        return ".nii.gz"
-    elif file_path.name.endswith(".img.gz"):
-        return ".img.gz"
-    elif file_path.name.endswith(".gipl.gz"):
-        return ".gipl.gz"
-    else:
-        return file_path.suffix
-
-
-def get_sequence_name(filepath: str) -> str:
-    ext = get_ext(filepath)
-    filename = Path(filepath).name.removesuffix(ext)
-    index: str = get_text_index_str(filename)
-    return filename.removesuffix(index)
-
-
-def get_sequence_index(filepath: str) -> int:
-    ext = get_ext(filepath)
-    filename = Path(filepath).name.removesuffix(ext)
-    index: str = get_text_index_str(filename)
-    return int(index) if index else 0
-
-
-def collect_sequence(filepath: str):
-    file_path = Path(filepath).resolve()
-
-    files = list(file_path.parent.iterdir())
-    files = [f for f in files if f.is_file()
-             and get_ext(file_path) == get_ext(f)
-             and get_sequence_name(file_path) == get_sequence_name(f)]
-
-    files.sort(key=get_sequence_index)
-    sequence = [str(f) for f in files]
-    return sequence
-
-
-def parse_volume_data(filepath: str, series_id=""):
-    ext = get_ext(filepath)
-
-    if ext in DICOM_EXTS:
-        dir_path = Path(filepath).resolve().parent
-        reader = sitk.ImageSeriesReader()
-        reader.MetaDataDictionaryArrayUpdateOn()
-        reader.LoadPrivateTagsOn()
-        series_files = reader.GetGDCMSeriesFileNames(
-            str(dir_path), series_id)
-        reader.SetFileNames(series_files)
-
-        itk_volume = reader.Execute()
-        # for k in reader.GetMetaDataKeys(0):
-        #     v = reader.GetMetaData(0, k)
-        #     print(f'({k}) = = "{v}"')
-        name = dir_path.name
-
-    elif ext in SEQUENCE_EXTS:
-        itk_volume = sitk.ReadImage(filepath)
-        if itk_volume.GetDimension() == 2:
-            sequence = collect_sequence(filepath)
-            itk_volume = sitk.ReadImage(sequence)
-            name = get_sequence_name(filepath)
-        else:
-            itk_volume = sitk.ReadImage(filepath)
-            name = Path(filepath).name.removesuffix(ext)
-    else:
-        itk_volume = sitk.ReadImage(filepath)
-        name = Path(filepath).name.removesuffix(ext)
-
-    # for key in itk_volume.GetMetaDataKeys():
-    #     print(f"{key},{itk_volume.GetMetaData(key)}")
-
-    if itk_volume.GetDimension() == 3:
-        itk_volume = sitk.DICOMOrient(itk_volume, 'RAS')
-
-        meta = {
-            "name": name,
-            "shape": tuple(itk_volume.GetSize()),
-            "spacing": tuple(itk_volume.GetSpacing()),
-            "origin": tuple(itk_volume.GetOrigin()),
-            "direction": tuple(itk_volume.GetDirection()),
-            "is_oriented": True
-        }
-
-        volume = sitk.GetArrayFromImage(itk_volume)
-
-        # transpose ijk to kji
-        if volume.ndim == 4:
-            volume = np.transpose(volume, (2, 1, 0, 3))
-        else:
-            volume = np.transpose(volume)
-            volume = np.expand_dims(volume, axis=-1)
-
-    else:
-        # FIXME: not sure...
-        print(itk_volume.GetDirection())
-        direction = np.array(itk_volume.GetDirection())
-        direction = direction.reshape(3, 3) if itk_volume.GetDimension() == 3 \
-            else direction.reshape(4, 4)
-
-        direction = direction[1:, 1:]
-        direction = tuple(direction.flatten())
-
-        meta = {
-            "name": name,
-            "shape": tuple(itk_volume.GetSize()[:3]),
-            "spacing": tuple(itk_volume.GetSpacing()[:3]),
-            "origin": tuple(itk_volume.GetOrigin()[:3]),
-            "direction": direction,
-            "is_oriented": False
-        }
-
-        volume = sitk.GetArrayFromImage(itk_volume)
-
-        if volume.ndim == 5:
-            volume = np.transpose(volume, (0, 3, 2, 1, 4))
-        else:
-            volume = np.transpose(volume, (0, 3, 2, 1))
-            volume = np.expand_dims(volume, axis=-1)
-
-    return volume, meta
-
-
-class ImportVolumeDataDialog(bpy.types.Operator):
-    bl_idname = "bioxelnodes.import_volume_data_dialog"
-    bl_label = "Volumetric Data as Bioxel Layer"
-    bl_description = "Import Volumetric Data as Bioxel Layer"
-    bl_options = {'UNDO'}
-
-    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: bpy.props.StringProperty()   # type: ignore
-
-    read_as: bpy.props.EnumProperty(
-        name="Read as",
-        default="scalar",
-        items=[("scalar", "Scalar", ""),
-               ("label", "Labels", "")]
-    )  # 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
-
-    is_time_sequence: bpy.props.BoolProperty(
-        name="Is Time Sequence",
-        default=False,
-    )  # type: ignore
-
-    split_channels: bpy.props.BoolProperty(
-        name="Split Channels",
-        default=False,
-    )  # type: ignore
-
-    def execute(self, context):
-        is_first_import = len(get_all_layers()) == 0
-        volume, meta = parse_volume_data(self.filepath)
-        container_name = self.container_name or meta['name'] or "Container"
-        bioxel_size = self.bioxel_size
-        orig_spacing = self.orig_spacing
-
-        layer_spacing = (
-            meta['spacing'][0] / orig_spacing[0] * bioxel_size,
-            meta['spacing'][1] / orig_spacing[1] * bioxel_size,
-            meta['spacing'][2] / orig_spacing[2] * bioxel_size
-        )
-
-        dtype_index = volume.dtype.num
-
-        layer_shape = get_layer_shape(
-            bioxel_size, meta['shape'], orig_spacing)
-
-        # After sitk.DICOMOrient(), origin and direction will also orient base on LPS
-        # so we need to convert them into RAS
-        mat_lps2ras = axis_conversion(
-            from_forward='-Z',
-            from_up='-Y',
-            to_forward='-Z',
-            to_up='Y'
-        ).to_4x4()
-
-        mat_location = mathutils.Matrix.Translation(
-            mathutils.Vector(meta['origin'])
-        )
-
-        mat_rotation = mathutils.Matrix(
-            np.array(meta['direction']).reshape((3, 3))
-        ).to_4x4()
-
-        mat_scale = mathutils.Matrix.Scale(
-            bioxel_size, 4
-        )
-
-        transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale \
-            if meta['is_oriented'] else mat_location @ mat_rotation @ mat_scale
-
-        # Wrapper a Container
-        if not self.container:
-            # Make transformation
-            scene_scale = float(self.scene_scale)
-
-            # (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 = mathutils.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 = bpy.context.active_object
-
-            bbox_verts = calc_bbox_verts((0, 0, 0), layer_shape)
-            for index, vert in enumerate(container.data.vertices):
-                vert.co = transfrom @ mathutils.Vector(bbox_verts[index])
-
-            container.matrix_world = mat_ras2blender @ mat_scene_scale
-            container.name = container_name
-            container.data.name = container_name
-
-            container['bioxel_container'] = True
-            container['scene_scale'] = scene_scale
-            bpy.ops.node.new_geometry_nodes_modifier()
-            container_node_group = container.modifiers[0].node_group
-            input_node = get_nodes_by_type(container_node_group,
-                                           'NodeGroupInput')[0]
-            container_node_group.links.remove(input_node.outputs[0].links[0])
-
-        else:
-            container = bpy.data.objects[self.container]
-            container_node_group = container.modifiers[0].node_group
-
-        preferences = context.preferences.addons[__package__].preferences
-
-        # TODO: change to transform when 4.2?
-        loc, rot, sca = transfrom.decompose()
-        layer_origin = tuple(loc)
-        layer_rotation = tuple(rot.to_euler())
-
-        def create_layer(volume, layer_name, layer_shape, layer_type="scalar"):
-            if volume.ndim == 4:
-                grids_sequence = []
-                for f in range(volume.shape[0]):
-                    print(f"Resampling...")
-                    frame = ski.resize(volume[f, :, :, :],
-                                       layer_shape,
-                                       preserve_range=True,
-                                       anti_aliasing=volume.dtype.kind != "b")
-
-                    grid = vdb.FloatGrid()
-                    frame = frame.copy().astype(np.float32)
-                    grid.copyFromArray(frame)
-                    grid.transform = vdb.createLinearTransform(
-                        transfrom.transposed())
-                    grid.name = layer_type
-                    grids_sequence.append([grid])
-
-                vdb_paths = save_vdbs(grids_sequence, context)
-
-                # Read VDB
-                print(f"Loading the cache to Blender scene...")
-                files = [{"name": str(vdb_path.name), "name": str(vdb_path.name)}
-                         for vdb_path in vdb_paths]
-
-                bpy.ops.object.volume_import(filepath=str(vdb_paths[0]), directory=str(vdb_paths[0].parent),
-                                             files=files, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-            else:
-                volume = ski.resize(volume,
-                                    layer_shape,
-                                    preserve_range=True,
-                                    anti_aliasing=volume.dtype.kind != "b")
-
-                grid = vdb.FloatGrid()
-                volume = volume.copy().astype(np.float32)
-                grid.copyFromArray(volume)
-                grid.transform = vdb.createLinearTransform(
-                    transfrom.transposed())
-                grid.name = layer_type
-
-                vdb_path = save_vdb([grid], context)
-
-                # Read VDB
-                print(f"Loading the cache to Blender scene...")
-                bpy.ops.object.volume_import(filepath=str(vdb_path),
-                                             align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-            layer = bpy.context.active_object
-            layer.data.sequence_mode = 'REPEAT'
-
-            # Set props to VDB object
-            layer.name = layer_name
-            layer.data.name = layer_name
-
-            lock_transform(layer)
-            hide_in_ray(layer)
-            layer.hide_select = True
-            layer.hide_render = True
-            layer.hide_viewport = True
-            layer.data.display.use_slice = True
-            layer.data.display.density = 1e-05
-
-            layer['bioxel_layer'] = True
-            layer['bioxel_layer_type'] = layer_type
-            layer.parent = container
-
-            for collection in layer.users_collection:
-                collection.objects.unlink(layer)
-
-            for collection in container.users_collection:
-                collection.objects.link(layer)
-
-            print(f"Creating layer ...")
-
-            bpy.ops.node.new_geometry_nodes_modifier()
-            node_group = layer.modifiers[0].node_group
-
-            input_node = get_nodes_by_type(node_group, 'NodeGroupInput')[0]
-            output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-
-            to_layer_node = custom_nodes.add_node(node_group,
-                                                  "BioxelNodes__ConvertToLayer")
-
-            node_group.links.new(input_node.outputs[0],
-                                 to_layer_node.inputs[0])
-            node_group.links.new(to_layer_node.outputs[0],
-                                 output_node.inputs[0])
-
-            # for compatibility to old vdb
-            # to_layer_node.inputs['Not Transfromed'].default_value = True
-            to_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000,
-                                                                            200000000)
-            to_layer_node.inputs['Data Type'].default_value = dtype_index
-            to_layer_node.inputs['Bioxel Size'].default_value = bioxel_size
-            to_layer_node.inputs['Shape'].default_value = layer_shape
-            to_layer_node.inputs['Origin'].default_value = layer_origin
-            to_layer_node.inputs['Rotation'].default_value = layer_rotation
-
-            move_node_between_nodes(to_layer_node, [input_node, output_node])
-
-            return layer
-
-        def create_mask_node(layer, node_type, node_label, offset):
-            mask_node = custom_nodes.add_node(container_node_group,
-                                              node_type)
-            mask_node.label = node_label
-            mask_node.inputs[0].default_value = layer
-
-            # Connect to output if no output linked
-            output_node = get_nodes_by_type(container_node_group,
-                                            'NodeGroupOutput')[0]
-            if len(output_node.inputs[0].links) == 0:
-                container_node_group.links.new(mask_node.outputs[0],
-                                               output_node.inputs[0])
-                move_node_to_node(mask_node, output_node, (-300, 0))
-            else:
-                move_node_to_node(mask_node, output_node, offset)
-
-        # change shape as sequence or not
-        if self.is_time_sequence:
-            # 4->5 or 5->5
-            if volume.ndim == 4:
-                # channel as frame
-                volume = volume.transpose(3, 0, 1, 2)
-                volume = np.expand_dims(volume, axis=-1)
-
-        else:
-            # 4->4 or 5->4
-            if volume.ndim == 5:
-                # select frame 0
-                volume = volume[0, :, :, :, :]
-
-        if self.read_as == "label":
-            layer_name = self.layer_name or "Label"
-            volume = np.amax(volume, -1)
-            volume = volume.astype(int)
-            orig_max = int(np.max(volume))
-            orig_min = int(np.min(volume))
-
-            for i in range(orig_max):
-                label = volume == np.full_like(volume, i+1)
-                layer_name_i = f"{layer_name}_{i+1}"
-
-                layer = create_layer(volume=label,
-                                     layer_name=f"{container_name}_{layer_name_i}",
-                                     layer_shape=layer_shape,
-                                     layer_type="label")
-
-                mask_node = create_mask_node(layer=layer,
-                                             node_type='BioxelNodes_MaskByLabel',
-                                             node_label=layer_name_i,
-                                             offset=(0, -100 * (i+1)))
-
-        else:
-            layer_name = self.layer_name or "Scalar"
-            # SHOULD NOT change any value!
-            volume = volume.astype(np.float32)
-
-            if self.split_channels:
-                for i in range(volume.shape[-1]):
-                    scalar = volume[:, :, :, :,
-                                    0] if self.is_time_sequence else volume[:, :, :, i]
-                    orig_max = float(np.max(scalar))
-                    orig_min = float(np.min(scalar))
-
-                    scalar_offset = 0
-                    if orig_min < 0:
-                        scalar_offset = -orig_min
-                        scalar = scalar + np.full_like(scalar, scalar_offset)
-
-                    layer_name_i = f"{layer_name}_{i+1}"
-                    layer = create_layer(volume=scalar,
-                                         layer_name=f"{container_name}_{layer_name_i}",
-                                         layer_shape=layer_shape,
-                                         layer_type="scalar")
-
-                    layer_node_group = layer.modifiers[0].node_group
-                    to_layer_node = layer_node_group.nodes['BioxelNodes__ConvertToLayer']
-                    to_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
-                    to_layer_node.inputs['Scalar Max'].default_value = orig_max
-                    to_layer_node.inputs['Scalar Min'].default_value = orig_min
-
-                    mask_node = create_mask_node(layer=layer,
-                                                 node_type='BioxelNodes_MaskByThreshold',
-                                                 node_label=layer_name_i,
-                                                 offset=(0, -100 * (i+1)))
-
-            else:
-                volume = np.amax(volume, -1)
-                orig_max = float(np.max(volume))
-                orig_min = float(np.min(volume))
-
-                scalar_offset = 0
-                if orig_min < 0:
-                    scalar_offset = -orig_min
-                    volume = volume + np.full_like(volume, scalar_offset)
-
-                layer = create_layer(volume=volume,
-                                     layer_name=f"{container_name}_{layer_name}",
-                                     layer_shape=layer_shape,
-                                     layer_type="scalar")
-
-                layer_node_group = layer.modifiers[0].node_group
-                to_layer_node = layer_node_group.nodes['BioxelNodes__ConvertToLayer']
-                to_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
-                to_layer_node.inputs['Scalar Max'].default_value = orig_max
-                to_layer_node.inputs['Scalar Min'].default_value = orig_min
-
-                mask_node = create_mask_node(layer=layer,
-                                             node_type='BioxelNodes_MaskByThreshold',
-                                             node_label=layer_name,
-                                             offset=(0, -100))
-
-        select_object(container)
-
-        # Change render setting for better result
-        if preferences.do_change_render_setting and is_first_import:
-            bpy.context.scene.render.engine = 'CYCLES'
-            try:
-                bpy.context.scene.cycles.shading_system = True
-                bpy.context.scene.cycles.volume_bounces = 12
-                bpy.context.scene.cycles.transparent_max_bounces = 16
-                bpy.context.scene.cycles.volume_preview_step_rate = 10
-                bpy.context.scene.cycles.volume_step_rate = 10
-                bpy.context.scene.eevee.volumetric_tile_size = '2'
-                bpy.context.scene.eevee.volumetric_shadow_samples = 128
-                bpy.context.scene.eevee.volumetric_samples = 256
-            except:
-                pass
-
-        self.report({"INFO"}, "Successfully Imported")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        if self.read_as == "label":
-            volume_dtype = "Label"
-        elif self.read_as == "scalar":
-            volume_dtype = "Scalar"
-        title = f"Import as **{volume_dtype}** (Add to Container: {self.container})" \
-            if self.container != "" else f"Import as **{volume_dtype}** (Init a Container)"
-        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)
-        layer_size = get_layer_size(layer_shape,
-                                    self.bioxel_size,
-                                    self.scene_scale)
-
-        bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2]
-        layer_shape_text = f"Shape will be: {str(layer_shape)} {bioxel_count:,} "
-        if bioxel_count > 100000000:
-            layer_shape_text += "**TOO LARGE!**"
-
-        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 == "":
-            layout.prop(self, "container_name")
-        layout.prop(self, "layer_name")
-
-        panel = layout.box()
-        panel.prop(self, "bioxel_size")
-        row = panel.row()
-        row.prop(self, "orig_spacing")
-        panel.label(text=layer_shape_text)
-
-        panel = layout.box()
-        panel.prop(self, "is_time_sequence")
-        if self.read_as == "scalar":
-            panel.prop(self, "split_channels")
-
-        if self.container == "":
-            panel = layout.box()
-            panel.prop(self, "scene_scale")
-            panel.label(text=layer_size_text)
-
-
-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 ParseVolumeData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.parse_volume_data"
-    bl_label = "Volumetric Data as Bioxel Layer"
-    bl_description = "Import Volumetric Data as Bioxel Layer"
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-    directory: bpy.props.StringProperty(subtype='DIR_PATH')  # type: ignore
-    container: bpy.props.StringProperty()   # type: ignore
-
-    read_as: bpy.props.EnumProperty(
-        name="Read as",
-        default="scalar",
-        items=[("scalar", "Scalar", ""),
-               ("label", "Labels", "")]
-    )  # 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):
-        ext = get_ext(self.filepath)
-        if ext not in SUPPORT_EXTS:
-            self.report({"WARNING"}, "Not supported extension.")
-            return {'CANCELLED'}
-
-        print("Collecting Meta Data...")
-        volume, meta = parse_volume_data(self.filepath)
-
-        for key, value in meta.items():
-            print(f"{key}: {value}")
-
-        if self.read_as == "label":
-            not_int = volume.dtype.kind != "b" and volume.dtype.kind != "i" and volume.dtype.kind != "u"
-            too_large = np.max(volume) > 100
-
-            if not_int or too_large:
-                self.report(
-                    {"WARNING"}, "This volume data does not looks like label, please check again.")
-                return {'CANCELLED'}
-
-        # do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS
-
-        orig_shape = meta['shape']
-        orig_spacing = meta['spacing']
-        min_size = min(orig_spacing[0], orig_spacing[1], orig_spacing[2])
-        bioxel_size = max(min_size, 1.0)
-
-        layer_size = get_layer_size(orig_shape,
-                                    bioxel_size)
-        log10 = math.floor(math.log10(max(*layer_size)))
-        scene_scale = math.pow(10, -log10)
-
-        if self.container:
-            container = bpy.data.objects[self.container]
-            container_name = container.name
-        else:
-            container_name = meta['name']
-
-        bpy.ops.bioxelnodes.import_volume_data_dialog(
-            'INVOKE_DEFAULT',
-            filepath=self.filepath,
-            container_name=container_name,
-            orig_shape=orig_shape,
-            orig_spacing=orig_spacing,
-            bioxel_size=bioxel_size,
-            series_id=self.series_id or "",
-            # do_orient=do_orient,
-            container=self.container,
-            read_as=self.read_as,
-            scene_scale=scene_scale
-        )
-
-        self.report({"INFO"}, "Successfully Readed.")
-
-        return {'FINISHED'}
-
-    def modal(self, context, event):
-        self.execute(context)
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        if not self.filepath and not self.directory:
-            return {'CANCELLED'}
-
-        show_message('Parsing volume data, it may take a while...',
-                     'Please be patient...')
-
-        if get_ext(self.filepath) == '.dcm':
-            dir_path = Path(self.filepath).parent
-            reader = sitk.ImageSeriesReader()
-            reader.MetaDataDictionaryArrayUpdateOn()
-            reader.LoadPrivateTagsOn()
-            series_ids = reader.GetGDCMSeriesIDs(str(dir_path))
-
-            for _id in series_ids:
-                series_id = self.series_ids.add()
-                series_id.id = _id
-                series_id.label = _id
-
-            if len(series_ids) > 1:
-                context.window_manager.invoke_props_dialog(self, width=400)
-                return {'RUNNING_MODAL'}
-            else:
-                self.series_id = series_ids[0]
-
-        context.window_manager.modal_handler_add(self)
-        return {'RUNNING_MODAL'}
-
-    def draw(self, context):
-        layout = self.layout
-        layout.prop(self, "series_id")
-        layout.label(
-            text="Reading image data, it may take a while...")
-        layout.label(
-            text="Please be patient...")
-
-
-class ImportVolumeData():
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(subtype="FILE_PATH")  # type: ignore
-    directory: bpy.props.StringProperty(subtype='DIR_PATH')  # type: ignore
-
-    read_as = "scalar"
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) > 0:
-            bpy.ops.bioxelnodes.parse_volume_data(
-                'INVOKE_DEFAULT',
-                filepath=self.filepath,
-                directory=self.directory,
-                container=containers[0].name,
-                read_as=self.read_as
-            )
-        else:
-            bpy.ops.bioxelnodes.parse_volume_data(
-                'INVOKE_DEFAULT',
-                filepath=self.filepath,
-                directory=self.directory,
-                read_as=self.read_as
-            )
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class ImportAsScalarLayer(bpy.types.Operator, ImportVolumeData):
-    bl_idname = "bioxelnodes.import_as_scalar_layer"
-    bl_label = "Import as Scalar"
-    bl_description = "Import Volumetric Data to Container as Scalar"
-    read_as = "scalar"
-
-
-class ImportAsLabelLayer(bpy.types.Operator, ImportVolumeData):
-    bl_idname = "bioxelnodes.import_as_label_layer"
-    bl_label = "Import as Label"
-    bl_description = "Import Volumetric Data to Container as Label"
-    read_as = "label"
-
-
-try:
-    class BIOXELNODES_FH_ImportVolumeData(bpy.types.FileHandler):
-        bl_idname = "BIOXELNODES_FH_ImportVolumeData"
-        bl_label = "File handler for dicom import"
-        bl_import_operator = "bioxelnodes.parse_volume_data"
-        bl_file_extensions = ";".join(FH_EXTS)
-
-        @classmethod
-        def poll_drop(cls, context):
-            return (context.area and context.area.type == 'VIEW_3D')
-except:
-    ...
-
-
-class ExportVolumeData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.export_volume_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 = get_layer(bpy.context.active_object)
-        return True if layer else False
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-    def execute(self, context):
-        layer = get_layer(bpy.context.active_object)
-
-        filepath = f"{self.filepath.split('.')[0]}.vdb"
-        # "//"
-        source_dir = bpy.path.abspath(layer.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/io_points.py

@@ -1,25 +0,0 @@
-# TODO: WIP
-import bpy
-import bmesh
-
-
-def create_points_obj(points, name="points"):
-    bpy.ops.mesh.primitive_cube_add(
-        enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
-    )
-    obj = bpy.context.active_object
-    mesh = obj.data
-
-    bm = bmesh.new()
-    value_layer = bm.verts.layers.float.new('value')
-
-    for point in points:
-        pos = point['pos']
-        value = point['value']
-        vert = bm.verts.new(pos)  # add a new vert
-        vert[value_layer] = value
-
-    # make the bmesh the object's mesh
-    bm.to_mesh(mesh)
-    bm.free()  # always do this when finished
-    return obj

bioxelnodes/menus.py

@@ -1,189 +0,0 @@
-import bpy
-
-from .utils import get_container_from_selection
-from .operators import (AddPieCutter, AddPlaneCutter, AddCylinderCutter, AddCubeCutter, AddSphereCutter, CombineLabels,
-                        ConvertToMesh, InvertScalar, FillByLabel, FillByThreshold, FillByRange, PickBboxWire, PickMesh, PickVolume)
-from .io import ExportVolumeData, ImportAsLabelLayer, ImportAsScalarLayer
-from .save import CleanAllCaches, ReLinkNodes, SaveLayers, SaveStagedData
-
-
-class PickFromContainerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_PICK"
-    bl_label = "Pick from Container"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-
-
-class ModifyLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_MODIFY_LAYERS"
-    bl_label = "Modify Layer"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(InvertScalar.bl_idname)
-        layout.operator(FillByThreshold.bl_idname)
-        layout.operator(FillByRange.bl_idname)
-        layout.operator(FillByLabel.bl_idname)
-        layout.operator(CombineLabels.bl_idname)
-
-
-class AddCutterMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_CUTTERS"
-    bl_label = "Add a Cutter to Container"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(AddPlaneCutter.bl_idname, text="Plane Cutter")
-        layout.operator(AddCylinderCutter.bl_idname, text="Cylinder Cutter")
-        layout.operator(AddCubeCutter.bl_idname, text="Cube Cutter")
-        layout.operator(AddSphereCutter.bl_idname, text="Sphere Cutter")
-        layout.operator(AddPieCutter.bl_idname, text="Pie Cutter")
-
-
-class ImportLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_LAYERS"
-    bl_label = "Import Volumetric Data"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ImportAsScalarLayer.bl_idname, text="as Scalar")
-        layout.operator(ImportAsLabelLayer.bl_idname, text="as Label")
-
-
-class BioxelNodesView3DMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_VIEW3D"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        layout = self.layout
-        containers = get_container_from_selection()
-        is_selected = len(containers) > 0
-        layout.operator(ImportAsScalarLayer.bl_idname,
-                        text=ImportAsScalarLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
-        layout.operator(ImportAsLabelLayer.bl_idname,
-                        text=ImportAsLabelLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsLabelLayer.bl_label+" (Init)")
-        layout.separator()
-        layout.operator(AddPlaneCutter.bl_idname)
-        layout.operator(AddCylinderCutter.bl_idname)
-        layout.operator(AddCubeCutter.bl_idname)
-        layout.operator(AddSphereCutter.bl_idname)
-        layout.operator(AddPieCutter.bl_idname)
-        layout.separator()
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-        layout.separator()
-        layout.operator(SaveLayers.bl_idname)
-
-
-class BioxelNodesOutlinerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_OUTLINER"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        layout = self.layout
-        containers = get_container_from_selection()
-        is_selected = len(containers) > 0
-        layout.operator(ImportAsScalarLayer.bl_idname,
-                        text=ImportAsScalarLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsScalarLayer.bl_label+" (Init)")
-        layout.operator(ImportAsLabelLayer.bl_idname,
-                        text=ImportAsLabelLayer.bl_label+" (Add to)"
-                        if is_selected else ImportAsLabelLayer.bl_label+" (Init)")
-        layout.separator()
-        layout.operator(AddPlaneCutter.bl_idname)
-        layout.operator(AddCylinderCutter.bl_idname)
-        layout.operator(AddCubeCutter.bl_idname)
-        layout.operator(AddSphereCutter.bl_idname)
-        layout.operator(AddPieCutter.bl_idname)
-        layout.separator()
-        layout.operator(PickMesh.bl_idname)
-        layout.operator(PickVolume.bl_idname)
-        layout.operator(PickBboxWire.bl_idname)
-        layout.separator()
-        layout.operator(SaveLayers.bl_idname)
-        layout.separator()
-        layout.operator(InvertScalar.bl_idname)
-        layout.operator(FillByThreshold.bl_idname)
-        layout.operator(FillByRange.bl_idname)
-        layout.operator(FillByLabel.bl_idname)
-        layout.operator(CombineLabels.bl_idname)
-        layout.separator()
-        layout.operator(ExportVolumeData.bl_idname)
-
-
-def TOPBAR_FILE_IMPORT(self, context):
-    layout = self.layout
-    containers = get_container_from_selection()
-    is_selected = len(containers) > 0
-
-    layout.separator()
-    layout.menu(ImportLayerMenu.bl_idname, text="Volumetric Data as Bioxel (Add to)"
-                if is_selected else "Volumetric Data as Bioxel (Init)")
-
-
-def TOPBAR_FILE_EXPORT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.operator(ExportVolumeData.bl_idname,
-                    text="Bioxel Layer (.vdb)")
-
-
-def VIEW3D_OBJECT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.menu(BioxelNodesView3DMenu.bl_idname, icon="FILE_VOLUME")
-
-
-def OUTLINER_OBJECT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.menu(BioxelNodesOutlinerMenu.bl_idname, icon="FILE_VOLUME")
-
-
-class BioxelNodesTopbarMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_TOPBAR"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        layout = self.layout
-        containers = get_container_from_selection()
-        is_selected = len(containers) > 0
-
-        layout.menu(ImportLayerMenu.bl_idname, text=ImportLayerMenu.bl_label+" (Add to)"
-                    if is_selected else ImportLayerMenu.bl_label+" (Init)")
-        layout.separator()
-        layout.menu(AddCutterMenu.bl_idname)
-        layout.menu(PickFromContainerMenu.bl_idname)
-        layout.separator()
-        layout.operator(SaveStagedData.bl_idname)
-        layout.operator(ReLinkNodes.bl_idname)
-        layout.separator()
-        layout.operator(CleanAllCaches.bl_idname)
-
-
-def TOPBAR(self, context):
-    layout = self.layout
-    layout.menu(BioxelNodesTopbarMenu.bl_idname)
-
-
-def add():
-    bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
-    bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)
-    bpy.types.OUTLINER_MT_object.append(OUTLINER_OBJECT)
-    bpy.types.VIEW3D_MT_object_context_menu.append(VIEW3D_OBJECT)
-    bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR)
-
-
-def remove():
-    bpy.types.TOPBAR_MT_file_import.remove(TOPBAR_FILE_IMPORT)
-    bpy.types.TOPBAR_MT_file_export.remove(TOPBAR_FILE_EXPORT)
-    bpy.types.OUTLINER_MT_object.remove(OUTLINER_OBJECT)
-    bpy.types.VIEW3D_MT_object_context_menu.remove(VIEW3D_OBJECT)
-    bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR)

bioxelnodes/nodes.py

@@ -1,282 +0,0 @@
-
-from pathlib import Path
-from .customnodes import CustomNodes
-import bpy
-
-# def set_object_to_node_factory(object_type:str):
-#     if object_type == "plane":
-#         create_object = """
-#     bpy.ops.mesh.primitive_plane_add(size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-#         """
-#     callback_str = f"""
-# import bpy
-# from ..utils import get_container
-# container = get_container(bpy.context.active_object)
-# if container:
-#     {create_object}
-#     object = bpy.context.active_object
-#     node.inputs[0].default_value = object
-# else:
-#     print('Cannot find any Bioxel Container.')
-#     """
-#     return callback_str
-
-
-# def add_driver_to_node_factory(source_prop, target_prop):
-#     callback_str = f"""
-# import bpy
-# from .utils import add_direct_driver, get_bioxels_obj
-# bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-# if bioxels_obj:
-#     container_obj = bioxels_obj.parent
-#     add_direct_driver(
-#         target=node,
-#         target_prop='{target_prop}',
-#         source=container_obj,
-#         source_prop='{source_prop}'
-#     )
-# else:
-#     print('Cannot find any bioxels.')
-#     """
-#     return callback_str
-
-
-# def set_prop_to_node_factory(source_prop, target_prop):
-#     callback_str = f"""
-# import bpy
-# from .utils import get_bioxels_obj
-# bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-# if bioxels_obj:
-#     container_obj = bioxels_obj.parent
-#     node.inputs.get('{target_prop}').default_value = container_obj.get(
-#         '{source_prop}')
-# else:
-#     print('Cannot find any bioxels.')
-#     """
-#     return callback_str
-
-
-NODE_FILE = "BioxelNodes_4.1"
-
-MENU_ITEMS = [
-    {
-        'label': 'Methods',
-        'icon': 'OUTLINER_DATA_VOLUME',
-        'items': [
-            {
-                'label': 'Mask by Threshold',
-                'icon': 'EMPTY_SINGLE_ARROW',
-                'node_type': 'BioxelNodes_MaskByThreshold',
-                'node_description': ''
-            },
-            {
-                'label': 'Mask by Range',
-                'icon': 'IPO_CONSTANT',
-                'node_type': 'BioxelNodes_MaskByRange',
-                'node_description': ''
-            },
-            {
-                'label': 'Mask by Label',
-                'icon': 'MESH_CAPSULE',
-                'node_type': 'BioxelNodes_MaskByLabel',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Shaders',
-        'icon': 'SHADING_RENDERED',
-        'items': [
-            {
-                'label': 'Membrane Shader',
-                'icon': 'NODE_MATERIAL',
-                'node_type': 'BioxelNodes_AssignMembraneShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Solid Shader',
-                'icon': 'SHADING_SOLID',
-                'node_type': 'BioxelNodes_AssignSolidShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Slime Shader',
-                'icon': 'OUTLINER_DATA_META',
-                'node_type': 'BioxelNodes_AssignSlimeShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Volume Shader',
-                'icon': 'VOLUME_DATA',
-                'node_type': 'BioxelNodes_AssignVolumeShader',
-                'node_description': ''
-            },
-            {
-                'label': 'Universal Shader',
-                'icon': 'MATSHADERBALL',
-                'node_type': 'BioxelNodes_AssignUniversalShader',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Colors',
-        'icon': 'COLOR',
-        'items': [
-            {
-                'label': 'Color Presets',
-                'icon': 'COLOR',
-                'node_type': 'BioxelNodes_ColorPresets',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Presets MRI',
-                'icon': 'COLOR',
-                'node_type': 'BioxelNodes_ColorPresets_MRI',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Color Ramp 2',
-                'icon': 'IPO_QUAD',
-                'node_type': 'BioxelNodes_SetColorRamp2',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Ramp 3',
-                'icon': 'IPO_CUBIC',
-                'node_type': 'BioxelNodes_SetColorRamp3',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Ramp 4',
-                'icon': 'IPO_QUART',
-                'node_type': 'BioxelNodes_SetColorRamp4',
-                'node_description': ''
-            },
-            {
-                'label': 'Color Ramp 5',
-                'icon': 'IPO_QUINT',
-                'node_type': 'BioxelNodes_SetColorRamp5',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Cutters',
-        'icon': 'MOD_BEVEL',
-        'items': [
-            {
-                'label': 'Cut',
-                'icon': 'MOD_BEVEL',
-                'node_type': 'BioxelNodes_Cut',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Primitive Cutter',
-                'icon': 'MOD_LINEART',
-                'node_type': 'BioxelNodes_PrimitiveCutter',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Plane Cutter',
-                'icon': 'MESH_PLANE',
-                'node_type': 'BioxelNodes_PlaneObjectCutter',
-                'node_description': ''
-            },
-            {
-                'label': 'Cylinder Cutter',
-                'icon': 'MESH_CYLINDER',
-                'node_type': 'BioxelNodes_CylinderObjectCutter',
-                'node_description': '',
-            },
-            {
-                'label': 'Cube Cutter',
-                'icon': 'MESH_CUBE',
-                'node_type': 'BioxelNodes_CubeObjectCutter',
-                'node_description': '',
-            },
-            {
-                'label': 'Sphere Cutter',
-                'icon': 'MESH_UVSPHERE',
-                'node_type': 'BioxelNodes_SphereObjectCutter',
-                'node_description': '',
-            },
-            {
-                'label': 'Pie Cutter',
-                'icon': 'MESH_CONE',
-                'node_type': 'BioxelNodes_PieObjectCutter',
-                'node_description': '',
-            }
-        ]
-    },
-    {
-        'label': 'Utils',
-        'icon': 'MODIFIER',
-        'items': [
-            {
-                'label': 'Join Component',
-                'icon': 'CONSTRAINT_BONE',
-                'node_type': 'BioxelNodes_JoinComponent',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Pick Mesh',
-                'icon': 'OUTLINER_OB_MESH',
-                'node_type': 'BioxelNodes_PickMesh',
-                'node_description': ''
-            },
-            {
-                'label': 'Pick Volume',
-                'icon': 'OUTLINER_OB_VOLUME',
-                'node_type': 'BioxelNodes_PickVolume',
-                'node_description': ''
-            },
-            {
-                'label': 'Pick Bbox Wire',
-                'icon': 'MESH_CUBE',
-                'node_type': 'BioxelNodes_PickBboxWire',
-                'node_description': ''
-            },
-            "separator",
-            {
-                'label': 'Inflate',
-                'icon': 'OUTLINER_OB_META',
-                'node_type': 'BioxelNodes_M_Inflate',
-                'node_description': ''
-            },
-            {
-                'label': 'Smooth',
-                'icon': 'MOD_SMOOTH',
-                'node_type': 'BioxelNodes_M_Smooth',
-                'node_description': ''
-            },
-            {
-                'label': 'Remove Small Island',
-                'icon': 'FORCE_LENNARDJONES',
-                'node_type': 'BioxelNodes_M_RemoveSmallIsland',
-                'node_description': ''
-            }
-        ]
-    }
-]
-
-
-custom_nodes = CustomNodes(
-    menu_items=MENU_ITEMS,
-    nodes_file=Path(__file__).parent / f"assets/Nodes/{NODE_FILE}.blend",
-    class_prefix="BIOXELNODES_MT_NODES",
-    root_label='Bioxel Nodes',
-    root_icon="FILE_VOLUME",
-)
-
-
-def register():
-    custom_nodes.register()
-
-
-def unregister():
-    custom_nodes.unregister()

bioxelnodes/operators.py

@@ -1,929 +0,0 @@
-from pathlib import Path
-import random
-import bpy
-import pyopenvdb as vdb
-import numpy as np
-import bmesh
-from . import skimage as ski
-from . import scipy
-from .nodes import custom_nodes
-from .utils import (get_container, get_container_from_selection, get_container_layers,
-                    get_layer, get_nodes_by_type, hide_in_ray, lock_transform, move_node_between_nodes, move_node_to_node, save_vdb, select_object)
-
-
-def get_layer_name(layer):
-    container = layer.parent
-    return layer.name.removeprefix(container.name).replace("_", "")
-
-
-def get_grids(layer):
-    layer_dir = bpy.path.abspath(layer.data.filepath)
-    grids, base_metadata = vdb.readAll(layer_dir)
-    return grids
-
-
-def set_volume(grids, index, volume):
-    grids[index].clear()
-    grids[index].copyFromArray(volume.copy().astype(np.float32))
-
-
-def get_volume(grids, index, shape):
-    volume = np.ndarray(shape, np.float32)
-    volume.fill(index)
-    grids[0].copyToArray(volume)
-    return volume
-
-
-def get_shape(layer):
-    layer_node = layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-    return [int(a)
-            for a in layer_node.inputs['Shape'].default_value]
-
-
-def get_layer_meta(layer, key: str):
-    layer_node = layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-    return layer_node.inputs[key].default_value
-
-
-def set_layer_meta(layer, key: str, value):
-    layer_node = layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-    layer_node.inputs[key].default_value = value
-
-
-def add_mask_node(container, layer, node_type: str, node_label: str):
-    modifier = container.modifiers[0]
-    container_node_group = modifier.node_group
-
-    mask_node = custom_nodes.add_node(container_node_group, node_type)
-    mask_node.label = node_label
-    mask_node.inputs[0].default_value = layer
-
-    # Connect to output if no output linked
-    output_node = get_nodes_by_type(container_node_group,
-                                    'NodeGroupOutput')[0]
-
-    if len(output_node.inputs[0].links) == 0:
-        container_node_group.links.new(mask_node.outputs[0],
-                                       output_node.inputs[0])
-        move_node_to_node(mask_node, output_node, (-300, 0))
-    else:
-        move_node_to_node(mask_node, output_node, (0, -100))
-
-    return mask_node
-
-
-def deep_copy_layer(vdb_path, base_layer, name):
-    # Read VDB
-    print(f"Loading the cache to Blender scene...")
-    bpy.ops.object.volume_import(
-        filepath=str(vdb_path), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-    copyed_layer = bpy.context.active_object
-
-    # Set props to VDB object
-    copyed_layer.name = name
-    copyed_layer.data.name = name
-
-    lock_transform(copyed_layer)
-    hide_in_ray(copyed_layer)
-    copyed_layer.hide_select = True
-    copyed_layer.hide_render = True
-    copyed_layer.hide_viewport = True
-    copyed_layer.data.display.use_slice = True
-    copyed_layer.data.display.density = 1e-05
-
-    copyed_layer['bioxel_layer'] = True
-    copyed_layer['bioxel_layer_type'] = base_layer['bioxel_layer_type']
-    copyed_layer.parent = base_layer.parent
-
-    for collection in copyed_layer.users_collection:
-        collection.objects.unlink(copyed_layer)
-
-    for collection in base_layer.users_collection:
-        collection.objects.link(copyed_layer)
-
-    # add convert to layer node
-    base_layer_node = base_layer.modifiers[0].node_group.nodes['BioxelNodes__ConvertToLayer']
-
-    not_transformed = base_layer_node.inputs['Not Transfromed'].default_value
-    dtype_index = base_layer_node.inputs['Data Type'].default_value
-    bioxel_size = base_layer_node.inputs['Bioxel Size'].default_value
-    layer_shape = base_layer_node.inputs['Shape'].default_value
-    layer_origin = base_layer_node.inputs['Origin'].default_value
-    layer_rotation = base_layer_node.inputs['Rotation'].default_value
-    scalar_offset = base_layer_node.inputs['Scalar Offset'].default_value
-    scalar_min = base_layer_node.inputs['Scalar Min'].default_value
-    scalar_max = base_layer_node.inputs['Scalar Max'].default_value
-
-    bpy.ops.node.new_geometry_nodes_modifier()
-    node_group = copyed_layer.modifiers[0].node_group
-
-    input_node = get_nodes_by_type(node_group, 'NodeGroupInput')[0]
-    output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-
-    copyed_layer_node = custom_nodes.add_node(node_group,
-                                              "BioxelNodes__ConvertToLayer")
-
-    node_group.links.new(input_node.outputs[0], copyed_layer_node.inputs[0])
-    node_group.links.new(copyed_layer_node.outputs[0], output_node.inputs[0])
-
-    # for compatibility to old vdb
-    copyed_layer_node.inputs['Not Transfromed'].default_value = not_transformed
-    copyed_layer_node.inputs['Layer ID'].default_value = random.randint(-200000000,
-                                                                        200000000)
-    copyed_layer_node.inputs['Data Type'].default_value = dtype_index
-    copyed_layer_node.inputs['Bioxel Size'].default_value = bioxel_size
-    copyed_layer_node.inputs['Shape'].default_value = layer_shape
-    copyed_layer_node.inputs['Origin'].default_value = layer_origin
-    copyed_layer_node.inputs['Rotation'].default_value = layer_rotation
-    copyed_layer_node.inputs['Scalar Offset'].default_value = scalar_offset
-    copyed_layer_node.inputs['Scalar Min'].default_value = scalar_min
-    copyed_layer_node.inputs['Scalar Max'].default_value = scalar_max
-
-    return copyed_layer
-
-
-def get_scalar_layer_selection(self, context):
-    items = [("None", "None", "")]
-    container = get_container(bpy.context.active_object)
-    for layer in get_container_layers(container):
-        if layer.get("bioxel_layer_type") == "scalar":
-            items.append((
-                layer.name,
-                layer.name,
-                ""
-            ))
-
-    return items
-
-
-def get_label_layer_selection(self, context):
-    items = [("None", "None", "")]
-    container = get_container(bpy.context.active_object)
-    for layer in get_container_layers(container):
-        if layer.get("bioxel_layer_type") == "label":
-            items.append((
-                layer.name,
-                layer.name,
-                ""
-            ))
-
-    return items
-
-
-# class JoinLayers(bpy.types.Operator):
-#     bl_idname = "bioxelnodes.join_layers"
-#     bl_label = "Join Bioxel Layers"
-#     bl_description = "Join Additional Bioxel Layers"
-#     bl_options = {'UNDO'}
-
-#     base_layer: bpy.props.StringProperty(
-#         options={"HIDDEN"}
-#     )   # type: ignore
-
-#     scalar_layer: bpy.props.EnumProperty(
-#         name="Scalar Layer",
-#         items=get_scalar_layer_selection
-#     )  # type: ignore
-
-#     label_layer: bpy.props.EnumProperty(
-#         name="Label Layer",
-#         items=get_label_layer_selection
-#     )  # type: ignore
-#     # color_layer: bpy.props.StringProperty()   # type: ignore
-
-#     @classmethod
-#     def poll(cls, context):
-#         layer = get_layer(bpy.context.active_object)
-#         return True if layer else False
-
-#     def execute(self, context):
-#         base_layer = bpy.data.objects[self.base_layer]
-
-#         if not base_layer:
-#             self.report({"WARNING"}, "Cannot find any bioxel layer as base.")
-#             return {'FINISHED'}
-
-#         base_layer_dir = bpy.path.abspath(base_layer.data.filepath)
-#         base_grids, base_metadata = vdb.readAll(base_layer_dir)
-
-#         layers = []
-#         if self.scalar_layer != "None":
-#             scalar_layer = bpy.data.objects[self.scalar_layer]
-#             layers.append(scalar_layer)
-
-#         if self.label_layer != "None":
-#             label_layer = bpy.data.objects[self.label_layer]
-#             layers.append(label_layer)
-
-#         # TODO: add color and vector
-
-#         if len(layers) == 0:
-#             self.report({"WARNING"}, "No additinal layers setted.")
-#             return {'FINISHED'}
-
-#         for layer in layers:
-#             layer_dir = bpy.path.abspath(layer.data.filepath)
-#             grids, metadata = vdb.readAll(layer_dir)
-#             base_grids.extend(grids)
-
-#         vdb_path = save_vdb(base_grids, context)
-
-#         joined_layer = deep_copy_layer(vdb_path,
-#                                        base_layer,
-#                                        f"{base_layer.name}_Joined")
-
-#         return {'FINISHED'}
-
-#     def invoke(self, context, event):
-#         base_layer = get_layer(bpy.context.active_object)
-#         self.base_layer = base_layer.name
-#         context.window_manager.invoke_props_dialog(self, width=400)
-#         return {'RUNNING_MODAL'}
-
-
-class InvertScalar(bpy.types.Operator):
-    bl_idname = "bioxelnodes.invert_scalar"
-    bl_label = "Invert Scalar"
-    bl_description = "Invert the scalar value"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-
-        container = base_layer.parent
-        inverted_layer_name = f"{get_layer_name(base_layer)}_Inverted"
-
-        base_shape = get_shape(base_layer)
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-
-        base_volume = -(base_volume - scalar_offset)
-
-        base_min = float(np.min(base_volume))
-        base_max = float(np.max(base_volume))
-
-        scalar_offset = 0
-        if base_min < 0:
-            scalar_offset = -base_min
-            base_volume = base_volume + scalar_offset
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        inverted_layer = deep_copy_layer(vdb_path,
-                                         base_layer,
-                                         f"{container.name}_{inverted_layer_name}")
-        set_layer_meta(inverted_layer, 'Scalar Offset', scalar_offset)
-        set_layer_meta(inverted_layer, 'Scalar Min', base_min)
-        set_layer_meta(inverted_layer, 'Scalar Max', base_max)
-
-        add_mask_node(container,
-                      inverted_layer,
-                      "BioxelNodes_MaskByThreshold",
-                      inverted_layer_name)
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-
-class FillByThreshold(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_threshold"
-    bl_label = "Fill Value by Threshold"
-    bl_description = "Fill Value by Threshold"
-    bl_options = {'UNDO'}
-
-    threshold: bpy.props.FloatProperty(
-        name="Threshold",
-        soft_min=0, soft_max=1024,
-        default=128,
-    )  # type: ignore
-
-    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 Area",
-        default=True,
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-
-        container = base_layer.parent
-        filled_layer_name = f"{get_layer_name(base_layer)}_{self.threshold}-Filled"
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-        base_shape = get_shape(base_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-        mask = base_volume > (self.threshold + scalar_offset)
-        mask = scipy.median_filter(mask.astype(np.float32), size=2)
-        if self.invert:
-            base_volume = mask * base_volume + \
-                (1-mask) * (self.fill_value + scalar_offset)
-        else:
-            base_volume = (1-mask) * base_volume + \
-                mask * (self.fill_value + scalar_offset)
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        filled_layer = deep_copy_layer(vdb_path,
-                                       base_layer,
-                                       f"{container.name}_{filled_layer_name}")
-        mask_node = add_mask_node(container,
-                                  filled_layer,
-                                  "BioxelNodes_MaskByThreshold",
-                                  filled_layer_name)
-
-        mask_node.inputs[1].default_value = self.threshold
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        base_layer = get_layer(bpy.context.active_object)
-        scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
-
-
-class FillByRange(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_range"
-    bl_label = "Fill Value by Range"
-    bl_description = "Fill Value by Range"
-    bl_options = {'UNDO'}
-
-    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
-
-    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 Area",
-        default=True,
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-
-        container = base_layer.parent
-        filled_layer_name = f"{get_layer_name(base_layer)}_{self.from_min}-{self.from_max}-Filled"
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-        base_shape = get_shape(base_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-
-        mask = (base_volume > self.from_min + scalar_offset) \
-            & (base_volume < self.from_max + scalar_offset)
-        mask = scipy.median_filter(mask.astype(np.float32), size=2)
-
-        if self.invert:
-            base_volume = mask * base_volume + \
-                (1-mask) * (self.fill_value + scalar_offset)
-        else:
-            base_volume = (1-mask) * base_volume + \
-                mask * (self.fill_value + scalar_offset)
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        filled_layer = deep_copy_layer(vdb_path,
-                                       base_layer,
-                                       f"{container.name}_{filled_layer_name}")
-        mask_node = add_mask_node(container,
-                                  filled_layer,
-                                  "BioxelNodes_MaskByThreshold",
-                                  filled_layer_name)
-
-        mask_node.inputs[1].default_value = self.from_min
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        base_layer = get_layer(bpy.context.active_object)
-        scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
-
-
-class FillByLabel(bpy.types.Operator):
-    bl_idname = "bioxelnodes.fill_by_label"
-    bl_label = "Fill Value by Label"
-    bl_description = "Fill Value by Label Area"
-    bl_options = {'UNDO'}
-
-    label_layer: bpy.props.EnumProperty(
-        name="Label Layer",
-        items=get_label_layer_selection
-    )  # type: ignore
-
-    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 Label",
-        default=True,
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        layer = get_layer(bpy.context.active_object)
-        if layer:
-            return layer.get("bioxel_layer_type") == "scalar"
-        else:
-            return False
-
-    def execute(self, context):
-        base_layer = get_layer(bpy.context.active_object)
-        label_layer = bpy.data.objects[self.label_layer]
-
-        if not label_layer:
-            self.report({"WARNING"}, "Cannot find any label layer.")
-            return {'FINISHED'}
-
-        container = base_layer.parent
-        filled_layer_name = f"{get_layer_name(base_layer)}_{get_layer_name(label_layer)}-Filled"
-        scalar_offset = get_layer_meta(base_layer, "Scalar Offset")
-        base_shape = get_shape(base_layer)
-        label_shape = get_shape(label_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-
-        label_grids = get_grids(label_layer)
-        mask = get_volume(label_grids, 0, label_shape)
-        mask = ski.resize(mask,
-                          base_shape,
-                          preserve_range=True,
-                          anti_aliasing=True)
-        mask = scipy.median_filter(mask.astype(np.float32), size=2)
-
-        if self.invert:
-            base_volume = mask * base_volume + \
-                (1-mask) * (self.fill_value + scalar_offset)
-        else:
-            base_volume = (1-mask) * base_volume + \
-                mask * (self.fill_value + scalar_offset)
-
-        set_volume(base_grids, 0, base_volume)
-        vdb_path = save_vdb(base_grids, context)
-        filled_layer = deep_copy_layer(vdb_path,
-                                       base_layer,
-                                       f"{container.name}_{filled_layer_name}")
-        add_mask_node(container,
-                      filled_layer,
-                      "BioxelNodes_MaskByThreshold",
-                      filled_layer_name)
-
-        select_object(container)
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        base_layer = get_layer(bpy.context.active_object)
-        scalar_min = get_layer_meta(base_layer, "Scalar Min")
-        self.fill_value = scalar_min
-        context.window_manager.invoke_props_dialog(self, width=400)
-        return {'RUNNING_MODAL'}
-
-
-class CombineLabels(bpy.types.Operator):
-    bl_idname = "bioxelnodes.combine_labels"
-    bl_label = "Combine Labels"
-    bl_description = "Combine all selected labels"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        labels = [obj for obj in context.selected_ids
-                  if obj.get("bioxel_layer_type") == "label"]
-        return True if len(labels) > 1 else False
-
-    def execute(self, context):
-        labels = [obj for obj in context.selected_ids
-                  if obj.get("bioxel_layer_type") == "label"]
-        base_layer = labels[0]
-        labels = labels[1:]
-        container = base_layer.parent
-        label_names = [get_layer_name(base_layer)]
-        base_shape = get_shape(base_layer)
-
-        base_grids = get_grids(base_layer)
-        base_volume = get_volume(base_grids, 0, base_shape)
-        base_volume = base_volume
-
-        for label in labels:
-            label_shape = get_shape(label)
-            label_grids = get_grids(label)
-            label_volume = get_volume(label_grids, 0, label_shape)
-            label_volume = ski.resize(label_volume,
-                                      base_shape,
-                                      preserve_range=True,
-                                      anti_aliasing=True)
-            base_volume = np.maximum(base_volume, label_volume)
-            label_names.append(get_layer_name(label))
-
-        set_volume(base_grids, 0, base_volume)
-
-        combined_layer_name = f"{'-'.join(label_names)}-Combined"
-        vdb_path = save_vdb(base_grids, context)
-        combined_layer = deep_copy_layer(vdb_path,
-                                         base_layer,
-                                         f"{container.name}_{combined_layer_name}")
-        add_mask_node(container,
-                      combined_layer,
-                      "BioxelNodes_MaskByLabel",
-                      combined_layer_name)
-
-        select_object(container)
-        return {'FINISHED'}
-
-
-class ConvertToMesh(bpy.types.Operator):
-    bl_idname = "bioxelnodes.convert_to_mesh"
-    bl_label = "Convert To Mesh"
-    bl_description = "Convert Container To Mesh"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        mesh = bpy.context.active_object
-
-        mesh.name = f"Mesh_{container.name}"
-
-        # bpy.ops.object.constraint_add(type='COPY_TRANSFORMS')
-        # mesh.constraints[0].target = container
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = mesh.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        to_mesh_node = custom_nodes.add_node(node_group,
-                                             "BioxelNodes_PickMesh")
-
-        to_mesh_node.inputs[0].default_value = container
-        node_group.links.new(to_mesh_node.outputs[0], output_node.inputs[0])
-
-        # bpy.ops.constraint.apply(
-        #     constraint=mesh.constraints[0].name, owner='OBJECT')
-        bpy.ops.object.modifier_apply(modifier=mesh.modifiers[0].name)
-
-        select_object(mesh)
-
-        self.report({"INFO"}, f"Successfully convert to mesh")
-
-        return {'FINISHED'}
-
-
-class PickMesh(bpy.types.Operator):
-    bl_idname = "bioxelnodes.pick_mesh"
-    bl_label = "Pick Mesh"
-    bl_description = "Pick Container Mesh"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        mesh = bpy.context.active_object
-
-        mesh.name = f"Mesh_{container.name}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = mesh.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_mesh_node = custom_nodes.add_node(node_group,
-                                               "BioxelNodes_PickMesh")
-
-        pick_mesh_node.inputs[0].default_value = container
-        node_group.links.new(pick_mesh_node.outputs[0], output_node.inputs[0])
-
-        select_object(mesh)
-
-        self.report({"INFO"}, f"Successfully picked mesh")
-
-        return {'FINISHED'}
-
-
-class PickVolume(bpy.types.Operator):
-    bl_idname = "bioxelnodes.pick_volume"
-    bl_label = "Pick Volume"
-    bl_description = "Pick Container Volume"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        volume = bpy.context.active_object
-
-        volume.name = f"Volume_{container.name}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = volume.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_volume_node = custom_nodes.add_node(node_group,
-                                                 "BioxelNodes_PickVolume")
-
-        pick_volume_node.inputs[0].default_value = container
-        node_group.links.new(
-            pick_volume_node.outputs[0], output_node.inputs[0])
-
-        select_object(volume)
-
-        self.report({"INFO"}, f"Successfully picked volume")
-
-        return {'FINISHED'}
-
-
-class PickBboxWire(bpy.types.Operator):
-    bl_idname = "bioxelnodes.pick_bbox_wire"
-    bl_label = "Pick Bbox Wire"
-    bl_description = "Pick Container Bbox Wire"
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        bpy.ops.mesh.primitive_cube_add(
-            size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        bbox_wire = bpy.context.active_object
-
-        bbox_wire.name = f"Wire_{container.name}"
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        modifier = bbox_wire.modifiers[0]
-        node_group = modifier.node_group
-
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        pick_bbox_wire_node = custom_nodes.add_node(node_group,
-                                                    "BioxelNodes_PickBboxWire")
-
-        pick_bbox_wire_node.inputs[0].default_value = container
-        node_group.links.new(
-            pick_bbox_wire_node.outputs[0], output_node.inputs[0])
-
-        select_object(bbox_wire)
-
-        self.report({"INFO"}, f"Successfully picked bbox wire")
-
-        return {'FINISHED'}
-
-
-class AddCutter():
-    bl_options = {'UNDO'}
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        container = containers[0]
-
-        if self.object_type == "plane":
-            node_type = "BioxelNodes_PlaneObjectCutter"
-            bpy.ops.mesh.primitive_plane_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "cylinder":
-            node_type = "BioxelNodes_CylinderObjectCutter"
-            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.rotation_euler[0]
-        elif self.object_type == "cube":
-            node_type = "BioxelNodes_CubeObjectCutter"
-            bpy.ops.mesh.primitive_cube_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "sphere":
-            node_type = "BioxelNodes_SphereObjectCutter"
-            bpy.ops.mesh.primitive_ico_sphere_add(
-                radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-        elif self.object_type == "pie":
-            node_type = "BioxelNodes_PieObjectCutter"
-            # Create mesh
-            pie_mesh = bpy.data.meshes.new('Pie')
-
-            # 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 = bpy.context.active_object
-        cutter.visible_camera = False
-        cutter.visible_diffuse = False
-        cutter.visible_glossy = False
-        cutter.visible_transmission = False
-        cutter.visible_volume_scatter = False
-        cutter.visible_shadow = False
-        cutter.hide_render = True
-        cutter.display_type = 'WIRE'
-
-        modifier = container.modifiers[0]
-        node_group = modifier.node_group
-        cutter_node = custom_nodes.add_node(node_group, node_type)
-        cutter_node.inputs[0].default_value = cutter
-
-        cut_nodes = get_nodes_by_type(node_group,
-                                      'BioxelNodes_Cut')
-        output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0]
-        if len(cut_nodes) == 0:
-            cut_node = custom_nodes.add_node(node_group, 'BioxelNodes_Cut')
-            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))
-            select_object(cutter)
-        else:
-            move_node_to_node(cutter_node, output_node, (0, -100))
-            select_object(container)
-
-        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 Container"
-    bl_options = {'UNDO'}
-    object_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 Container"
-    bl_options = {'UNDO'}
-    object_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 Container"
-    bl_options = {'UNDO'}
-    object_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 Container"
-    bl_options = {'UNDO'}
-    object_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 Container"
-    bl_options = {'UNDO'}
-    object_type = "pie"

bioxelnodes/preferences.py

@@ -1,29 +0,0 @@
-import bpy
-from pathlib import Path
-from .externalpackage import ExternalPackagePreferences
-
-
-class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferences):
-    bl_idname = __package__
-
-    cache_dir: bpy.props.StringProperty(
-        name="Set Cache Directory",
-        subtype='DIR_PATH',
-        default=str(Path(Path.home(), '.bioxelnodes'))
-    )  # type: ignore
-
-    do_change_render_setting: bpy.props.BoolProperty(
-        name="Change Render Setting",
-        default=True,
-    )  # type: ignore
-
-    def draw(self, context):
-        layout = self.layout
-
-        # ExternalPackagePreferences Config
-        self.requirements_dir = str(Path(__file__).parent)
-        super().draw(context)
-
-        layout.label(text="Configuration")
-        layout.prop(self, 'cache_dir')
-        layout.prop(self, "do_change_render_setting")

bioxelnodes/props.py

@@ -1,5 +0,0 @@
-import bpy
-
-class BIOXELNODES_Series(bpy.types.PropertyGroup):
-    id: bpy.props.StringProperty()   # type: ignore
-    label: bpy.props.StringProperty()   # type: ignore

bioxelnodes/requirements.txt

@@ -1 +0,0 @@
-SimpleITK==2.3.1     # Insight Segmentation and Registration Toolkit.

bioxelnodes/save.py

@@ -1,212 +0,0 @@
-import re
-import bpy
-from pathlib import Path
-import shutil
-from .utils import copy_to_dir, get_all_layers, get_container, get_container_from_selection, get_container_layers
-from .nodes import custom_nodes
-
-CLASS_PREFIX = "BIOXELNODES_MT_NODES"
-
-
-class ReLinkNodes(bpy.types.Operator):
-    bl_idname = "bioxelnodes.relink_nodes"
-    bl_label = "Relink Nodes to Addon"
-    bl_description = "Relink all nodes to addon source"
-
-    def execute(self, context):
-        file_name = Path(custom_nodes.nodes_file).name
-        for lib in bpy.data.libraries:
-            lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-            lib_name = lib_path.name
-            if lib_name == file_name:
-                if str(lib_path) != custom_nodes.nodes_file:
-                    lib.filepath = custom_nodes.nodes_file
-
-        self.report({"INFO"}, f"Successfully relinked.")
-
-        return {'FINISHED'}
-
-
-class SaveStagedData(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_staged_data"
-    bl_label = "Save Staged Data"
-    bl_description = "Save all staged data in this file for sharing"
-
-    save_layer: bpy.props.BoolProperty(
-        name="Save Layer VDB Cache",
-        default=True,
-    )  # type: ignore
-
-    cache_dir: bpy.props.StringProperty(
-        name="Cache Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    save_lib: bpy.props.BoolProperty(
-        name="Save Node Library File",
-        default=True,
-    )  # type: ignore
-
-    lib_dir: bpy.props.StringProperty(
-        name="Library Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    def execute(self, context):
-        if self.save_lib:
-            files = []
-            for classname in dir(bpy.types):
-                if CLASS_PREFIX in classname:
-                    cls = getattr(bpy.types, classname)
-                    files.append(cls.nodes_file)
-            files = list(set(files))
-
-            for file in files:
-                file_name = Path(file).name
-                # "//"
-                lib_dir = bpy.path.abspath(self.lib_dir)
-
-                output_path: Path = Path(lib_dir, file_name).resolve()
-                source_path: Path = Path(file).resolve()
-
-                if output_path != source_path:
-                    shutil.copy(source_path, output_path)
-
-                for lib in bpy.data.libraries:
-                    lib_path = Path(bpy.path.abspath(lib.filepath)).resolve()
-                    if lib_path == source_path:
-                        blend_path = Path(bpy.path.abspath("//")).resolve()
-                        lib.filepath = bpy.path.relpath(
-                            str(output_path), start=str(blend_path))
-
-                self.report({"INFO"}, f"Successfully saved to {output_path}")
-
-        if self.save_layer:
-            fails = []
-            for layer in get_all_layers():
-                try:
-                    save_layer(layer, self.cache_dir)
-                except:
-                    fails.append(layer)
-
-            if len(fails) == 0:
-                self.report({"INFO"}, f"Successfully saved bioxel layers.")
-            else:
-                self.report(
-                    {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self,
-                                                   width=500)
-        return {'RUNNING_MODAL'}
-
-    @classmethod
-    def poll(cls, context):
-        return bpy.data.is_saved
-
-    def draw(self, context):
-        layout = self.layout
-        panel = layout.box()
-        panel.prop(self, "save_layer")
-        panel.prop(self, "cache_dir")
-        panel = layout.box()
-        panel.prop(self, "save_lib")
-        panel.prop(self, "lib_dir")
-
-
-def save_layer(layer, output_dir):
-
-    pattern = r'\.\d{4}\.'
-
-    # "//"
-    output_dir = bpy.path.abspath(output_dir)
-    source_dir = bpy.path.abspath(layer.data.filepath)
-
-    source_path: Path = Path(source_dir).resolve()
-    is_sequence = re.search(pattern, source_path.name) is not None
-    name = layer.name if is_sequence else f"{layer.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.data.filepath = bpy.path.relpath(
-        str(output_path), start=str(blend_path))
-
-
-class SaveLayers(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_layers"
-    bl_label = "Save Layers"
-    bl_description = "Save Container Layers to Directory."
-
-    cache_dir: bpy.props.StringProperty(
-        name="Layer Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    @classmethod
-    def poll(cls, context):
-        containers = get_container_from_selection()
-        return len(containers) > 0
-
-    def execute(self, context):
-        containers = get_container_from_selection()
-
-        if len(containers) == 0:
-            self.report({"WARNING"}, "Cannot find any bioxel container.")
-            return {'FINISHED'}
-
-        fails = []
-        for container in containers:
-            for layer in get_container_layers(container):
-                try:
-                    save_layer(layer, self.cache_dir)
-                except:
-                    fails.append(layer)
-
-        if len(fails) == 0:
-            self.report({"INFO"}, f"Successfully saved bioxel layers.")
-        else:
-            self.report(
-                {"WARNING"}, f"{','.join([layer.name for layer in fails])} fail to save.")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self,
-                                                   width=500)
-        return {'RUNNING_MODAL'}
-
-
-class CleanAllCaches(bpy.types.Operator):
-    bl_idname = "bioxelnodes.clear_all_caches"
-    bl_label = "Clean All Caches in Temp"
-    bl_description = "Clean all caches saved in temp"
-
-    def execute(self, context):
-        preferences = context.preferences.addons[__package__].preferences
-        cache_dir = Path(preferences.cache_dir, 'VDBs')
-        try:
-            shutil.rmtree(cache_dir)
-            self.report({"INFO"}, f"Successfully cleaned caches.")
-            return {'FINISHED'}
-        except:
-            self.report({"WARNING"},
-                        "Fail to clean caches, you may do it manually.")
-            return {'CANCELLED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message="All caches will be cleaned, include other project files, do you still want to clean?")
-        return {'RUNNING_MODAL'}

bioxelnodes/scipy/__init__.py

@@ -1,2 +0,0 @@
-from ._interpolation import zoom
-from ._filters import gaussian_filter, median_filter

bioxelnodes/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/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/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/skimage/__init__.py

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

bioxelnodes/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/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/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/utils.py

@@ -1,287 +0,0 @@
-import bpy
-import mathutils
-from pathlib import Path
-import pyopenvdb as vdb
-from uuid import uuid4
-import shutil
-
-
-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 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 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 show_message(message="", title="Message Box", icon='INFO'):
-
-    def draw(self, context):
-        self.layout.label(text=message)
-
-    bpy.context.window_manager.popup_menu(draw, title=title, icon=icon)
-
-
-def calc_bbox_verts(origin, size):
-    bbox_origin = mathutils.Vector(
-        (origin[0], origin[1], origin[2]))
-    bbox_size = mathutils.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 lock_transform(obj):
-    obj.lock_location[0] = True
-    obj.lock_location[1] = True
-    obj.lock_location[2] = True
-    obj.lock_rotation[0] = True
-    obj.lock_rotation[1] = True
-    obj.lock_rotation[2] = True
-    obj.lock_scale[0] = True
-    obj.lock_scale[1] = True
-    obj.lock_scale[2] = True
-
-
-def hide_in_ray(obj):
-    obj.visible_camera = False
-    obj.visible_diffuse = False
-    obj.visible_glossy = False
-    obj.visible_transmission = False
-    obj.visible_volume_scatter = False
-    obj.visible_shadow = False
-
-
-def save_vdb(grids, context):
-    preferences = context.preferences.addons[__package__].preferences
-    cache_dir = Path(preferences.cache_dir, 'VDBs')
-    cache_dir.mkdir(parents=True, exist_ok=True)
-
-    vdb_path = Path(cache_dir, f"{uuid4()}.vdb")
-    print(f"Storing the VDB file ({str(vdb_path)})...")
-    vdb.write(str(vdb_path), grids=grids)
-
-    return vdb_path
-
-
-def save_vdbs(grids_sequence, context):
-    preferences = context.preferences.addons[__package__].preferences
-    cache_dir = Path(preferences.cache_dir, 'VDBs')
-    cache_dir.mkdir(parents=True, exist_ok=True)
-    vdb_name = str(uuid4())
-    vdb_dir_path = Path(cache_dir, vdb_name)
-    vdb_dir_path.mkdir(parents=True, exist_ok=True)
-
-    vdb_paths = []
-    for f, grids in enumerate(grids_sequence):
-        vdb_path = Path(vdb_dir_path, f"{vdb_name}.{str(f+1).zfill(4)}.vdb")
-        print(f"Storing the VDB file ({str(vdb_path)})...")
-        vdb.write(str(vdb_path), grids=grids)
-        vdb_paths.append(vdb_path)
-
-    return vdb_paths
-
-
-def get_container_from_selection():
-    containers = []
-    for obj in bpy.context.selected_objects:
-        if get_container(obj):
-            containers.append(obj)
-    # if bpy.context.active_object:
-    #     if bpy.context.active_object.get('bioxel_layer'):
-    #         if bpy.context.active_object.parent.get('bioxel_container'):
-    #             containers.append(bpy.context.active_object.parent)
-
-    return list(set(containers))
-
-
-def get_container(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(current_obj):
-    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_layers(container):
-    layers = []
-    for obj in bpy.data.objects:
-        if obj.parent == container and get_layer(obj):
-            layers.append(obj)
-
-    return layers
-
-
-def get_all_layers():
-    layers = []
-    for obj in bpy.data.objects:
-        if get_layer(obj):
-            layers.append(obj)
-
-    return layers
-
-
-def get_text_index_str(text):
-    # Initialize an empty string to store the digits
-    digits = ""
-
-    # Iterate through the characters in reverse order
-    started = False
-    for char in text[::-1]:
-        if char.isdigit():
-            started = True
-            # If the character is a digit, add it to the digits string
-            digits += char
-        else:
-            if started:
-                # If a non-digit character is encountered, stop the loop
-                break
-
-    # Reverse the digits string to get the correct order
-    last_number = digits[::-1]
-
-    return last_number
-
-
-def add_driver(target_prop, var_sources, expression):
-
-    driver = target_prop.driver_add("default_value")
-    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):
-    target_prop = target.inputs.get(target_prop)
-    drivers = [
-        {
-            "source": source,
-            "prop": source_prop
-        }
-    ]
-    expression = "var0"
-    add_driver(target_prop, drivers, expression)

build.py

@@ -0,0 +1,92 @@
+from pathlib import Path
+import shutil
+import subprocess
+import sys
+from dataclasses import dataclass
+import tomlkit
+
+
+@dataclass
+class Platform:
+    pypi_suffix: str
+    blender_tag: str
+
+
+required_packages = ["SimpleITK==2.5.5",
+                     "pyometiff==1.0.0",
+                     "mrcfile==1.5.1",
+                     "h5py==3.14.0",
+                     "transforms3d==0.4.2",
+                     "tifffile==2024.7.24",
+                     "matplotlib==3.10.7",
+                     "pillow==11.2.1",
+                     "scipy==1.16.3"]
+
+
+platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
+                                     blender_tag="windows-x64"),
+             "linux-x64": Platform(pypi_suffix="manylinux2014_x86_64",
+                                   blender_tag="linux-x64"),
+             "macos-arm64": Platform(pypi_suffix="macosx_12_0_arm64",
+                                     blender_tag="macos-arm64"),
+             "macos-x64": Platform(pypi_suffix="macosx_10_16_x86_64",
+                                   blender_tag="macos-x64")}
+
+packages_to_remove = {
+    "imagecodecs",
+    "numpy",
+    "packaging"
+}
+
+
+def run_python(args: str):
+    python = Path(sys.executable).resolve()
+    subprocess.run([python] + args.split(" "))
+
+
+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"):
+        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")))
+        
+    # 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.append('generated', generated)
+    # manifest.append('build', build)
+
+    # Write the updated TOML file
+    with toml_filepath.open("w") as file:
+        text = tomlkit.dumps(manifest)
+        file.write(text)
+
+
+def main():
+    platform_name = sys.argv[1]
+    python_version = sys.argv[2] or "3.11"
+    platform = platforms[platform_name]
+    build_extension(platform, python_version)
+
+
+if __name__ == "__main__":
+    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

@@ -0,0 +1,99 @@
+# SARS-Cov-2
+
+![alt text](assets/SARS-Cov-2/image.png)
+
+![alt text](assets/SARS-Cov-2/image-1.png)
+
+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！
+
+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>
+
+"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。
+
+## 下载和导入数据
+
+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)"。
+
+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)
+
+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）。
+
+## 切割病毒
+
+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)
+
+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)
+
+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)
+
+如果您觉得渲染太慢，请参阅[这里](improve_performance.md)获取建议。
+
+## 单独为 RNP 着色
+
+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？
+
+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)
+
+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。
+
+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)
+
+此时，SARS-Cov-2 病毒的渲染完成了！
+
+## 渲染 RNP 和膜
+
+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)
+
+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。
+
+用同样的方式提取膜网格。
+
+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)
+
+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)
+
+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>
+
+最后，RNP 超微结构的信息图完成了！
+
+![alt text](assets/SARS-Cov-2/image-1.png)
+
+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)
+
+## 作业
+
+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)
+
+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。
+
+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）。
+
+**尝试可视化乙型肝炎病毒。**
+
+![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