5.0 (#63)

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refactor: Clean up AGENTS.md and remove outdated test files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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

.gitattributes

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

.github/workflows/release.yml

@@ -1,31 +1,12 @@
-name: Upload Assets to Release
+name: Release Version
 
 on:
   push:
-    branches:
+    tags:
-      - "release/*"
+      # Publish on any tag starting with a `v`, e.g., v0.1.0
+      - 'v*'
 
 jobs:
-  # draft_release:
-  #   name: Draft Release
-  #   runs-on: ubuntu-latest
-  #   outputs:
-  #     upload_url: ${{ steps.draft_release.outputs.upload_url }}
-  #     version: ${{ steps.set_env.outputs.version }}
-  #   steps:
-  #     - name: Set Version Env
-  #       id: set_env
-  #       run: |
-  #         ref_name=${{ github.ref_name }}
-  #         echo "version=${ref_name#release/}" >> "$GITHUB_OUTPUT"
-  #     - name: Get release
-  #       id: draft_release
-  #       uses: cardinalby/git-get-release-action@1.2.4
-  #       with:
-  #         releaseName: Draft
-  #       env:
-  #         GITHUB_TOKEN: ${{ github.token }}
-
   draft_release:
     name: Draft Release
     permissions:
@@ -50,19 +31,32 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  upload_blender_addon:
+  build_extension:
-    name: Upload Blender Add-on
+    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'
+          lfs: "true"
-      - name: Zip Add-on
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Dependencies
         run: |
-          zip -r package.zip bioxelnodes
+          uv python install 3.11
-      - name: Upload Release Asset
+          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:
@@ -70,5 +64,5 @@ jobs:
         with:
           upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
           asset_path: ./package.zip
-          asset_name: BioxelNodes_${{ needs.draft_release.outputs.version }}.zip
+          asset_name: BioxelNodes.${{ needs.draft_release.outputs.version }}.${{ matrix.platform }}.zip
           asset_content_type: application/zip

.gitignore

@@ -1,6 +1,51 @@
+# Tempary files
+temp
+sandbox.*
+/notes/
+
+# Environments
+.env
+.envrc
+.venv
+.env.*
+!.env.example
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+.secrets
+.secrets.*
+!.secrets.example
+secrets/
+SECRETS/
+secrets.bak/
+
+# Claude Code
+.claude/settings.local.json
+.claudian
+
+# Obsidian
+.obsidian/*
+!.obsidian/snippets
+!.obsidian/app.json
+
+*.canvas
+
+# Keep odox for extract to openwiki
+!.obsidian/plugins
+.obsidian/plugins/*
+!.obsidian/plugins/odox
+
+# Blender
+*.blend1
+blender_assets.cats.txt~
+blendcache_*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -20,7 +65,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -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
@@ -81,7 +128,9 @@ 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.
@@ -90,21 +139,59 @@ ipython_config.py
 #   install all needed dependencies.
 # 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
@@ -123,12 +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/
+
+# 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;
+}

.prettierrc

@@ -0,0 +1,11 @@
+{
+  "tabWidth": 2,
+  "overrides": [
+    {
+      "files": "*.md",
+      "options": {
+        "tabWidth": 4
+      }
+    }
+  ]
+}

.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 +1,19 @@
+## 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

LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ 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.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
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+
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+  6. Conveying Non-Source Forms.
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+  You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
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+
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+    copy of the Corresponding Source for all the software in the
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+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -1,3 +1,46 @@
-# BioxelNodes
+**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/**
-BioxelNodes is a blender add-on for better volume data visualization with cycles.
 
+[中文文档](https://docs.omoolab.xyz/bioxelnodes/latest/)
+
+# Bioxel Nodes
+
+[![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)
+
+## 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.
+
+| ![4D](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif) | ![EEVEE](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif) |
+| :--------------------------------------------------------------------: | :---------------------------------------------------------------------: |
+|                       Support 4D volumetric data                       |                       Real-time render with eevee                       |
+
+**Read the [getting started](https://docs.omoolab.xyz/bioxelnodes/latest/en/installation) to begin your journey into visualizing volumetric data!**
+
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
+
+## Citation
+
+If you want to cite this work, you can cite it from Zenodo:
+
+[![DOI](https://zenodo.org/badge/786623459.svg)](https://zenodo.org/badge/latestdoi/786623459)
+
+
+## Roadmap
+
+-   Better multi-format import experience
+-   One-click bake model with texture
+-   AI Segmentation to Generate Labels

bioxelnodes/__init__.py

@@ -1,34 +0,0 @@
-from .nodes import custom_nodes
-from . import auto_load
-from . import menu
-
-import bpy
-
-
-bl_info = {
-    "name": "BiovelNodes",
-    "author": "Ma Nan",
-    "description": "",
-    "blender": (4, 0, 0),
-    "version": (0, 1, 0),
-    "location": "File -> Import",
-    "warning": "",
-    "category": "Import-Export"
-}
-
-auto_load.init()
-
-
-def register():
-    auto_load.register()
-    custom_nodes.register()
-    menu.create_menu()
-
-
-def unregister():
-    try:
-        menu.remove_menu()
-        custom_nodes.unregister()
-        auto_load.unregister()
-    except RuntimeError:
-        pass

bioxelnodes/convert.py

@@ -1,46 +0,0 @@
-import bpy
-from .utils import get_bioxels_obj
-
-
-class ConvertToMesh(bpy.types.Operator):
-    bl_idname = "bioxelnodes.convert_to_mesh"
-    bl_label = "Bioxels To Mesh"
-    bl_description = "Convert Bioxels To Mesh."
-    bl_options = {'UNDO'}
-
-    def execute(self, context):
-        bioxels_objs = []
-
-        for obj in bpy.context.selected_objects:
-            bioxels_obj = get_bioxels_obj(obj)
-            if bioxels_obj:
-                bioxels_objs.append(bioxels_obj)
-
-        if len(bioxels_objs)==0:
-            self.report({"WARNING"}, "Cannot find any bioxels.")
-            return {'FINISHED'}
-
-        for bioxels_obj in bioxels_objs:
-            bpy.ops.mesh.primitive_cube_add(
-                size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-            mesh_obj = bpy.context.active_object
-
-            mesh_obj.name = f"{bioxels_obj.parent.name}_Mesh"
-            bpy.ops.node.new_geometry_nodes_modifier()
-            modifier = mesh_obj.modifiers[0]
-            nodes = modifier.node_group.nodes
-            links = modifier.node_group.links
-
-            output_node = nodes.get("Group Output")
-            object_node = nodes.new("GeometryNodeObjectInfo")
-            realize_nodes = nodes.new("GeometryNodeRealizeInstances")
-            object_node.inputs[0].default_value = bioxels_obj
-            object_node.transform_space = 'RELATIVE'
-
-            links.new(object_node.outputs['Geometry'], realize_nodes.inputs[0])
-            links.new(realize_nodes.outputs[0], output_node.inputs[0])
-            bpy.ops.object.convert(target='MESH')
-            bpy.context.object.active_material_index = 1
-            bpy.ops.object.material_slot_remove()
-
-        return {'FINISHED'}

bioxelnodes/custom_nodes/__init__.py

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

bioxelnodes/custom_nodes/node_menu.py

@@ -1,134 +0,0 @@
-import bpy
-from pathlib import Path
-from .nodes import AddCustomNode
-
-
-class CustomNodes():
-    def __init__(
-        self,
-        menu_items,
-        nodes_file,
-        root_label='CustomNodes',
-        root_icon='NONE'
-    ) -> None:
-        if not Path(nodes_file).is_file():
-            raise FileNotFoundError(Path(nodes_file).resolve().as_posix())
-
-        self.menu_items = menu_items
-        self.nodes_file = Path(nodes_file).resolve().as_posix()
-
-        self.root_label = root_label
-        self.root_icon = root_icon
-
-        menu_classes = []
-        self._create_menu_class(
-            items=menu_items,
-            label=root_label,
-            menu_classes=menu_classes
-        )
-        self.menu_classes = menu_classes
-
-        idname = f"CUSTOMNODES_MT_NODES__{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 "CUSTOMNODES_MT_NODES_"
-        idname = f"{idname_namespace}_{label.replace(' ', '').upper()}"
-
-        # create submenu class if item is menu.
-        for item in items:
-            item_items = item.get('items') if item != 'separator' else None
-            if item_items:
-                menu_class = self._create_menu_class(
-                    menu_classes=menu_classes,
-                    items=item_items,
-                    label=item.get('label') or 'CustomNodes',
-                    icon=item.get('icon') or 0,
-                    idname_namespace=idname
-                )
-                item['menu_class'] = menu_class
-
-        # create menu class
-        class Menu(bpy.types.Menu):
-            bl_idname = idname
-            bl_label = label
-
-            def draw(self, context):
-                layout = self.layout
-
-                for item in items:
-                    # 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.get("node_type") == node_type:
-                found_items.append(item)
-
-            item_items = item.get('items') if item != 'separator' else None
-            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_tree, node_type: str):
-        item = self.find_item(node_type)
-        if item:
-            op = AddCustomNode()
-            op.nodes_file = self.nodes_file
-            op.node_type = item['node_type']
-            op.node_label = item.get('label') or ""
-            op.node_link = item.get('link') or True
-            op.node_callback = item.get('node_callback') or ""
-            return op.add_node(node_tree)
-        else:
-            raise RuntimeError("No custom node type found.")
-
-    def register(self):
-        for cls in self.menu_classes:
-            bpy.utils.register_class(cls)
-
-        bpy.types.NODE_MT_add.append(self.add_node_menu)
-
-    def unregister(self):
-        try:
-            for cls in reversed(self.menu_classes):
-                bpy.utils.unregister_class(cls)
-
-            bpy.types.NODE_MT_add.remove(self.add_node_menu)
-        except RuntimeError:
-            pass

bioxelnodes/custom_nodes/nodes.py

@@ -1,120 +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_tree):
-        self.get_node_tree(self.node_type, self.node_link)
-        node = node_tree.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/external_package/__init__.py

@@ -1 +0,0 @@
-from .preferences import ExternalPackagePreferences

bioxelnodes/external_package/package.py

@@ -1,389 +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,
-        log_dir: str,
-        requirements_dir: str,
-        pypi_mirror_provider='Default',
-    ) -> None:
-        self.pypi_mirror_provider = pypi_mirror_provider
-        self.log_path: Path = Path(log_dir)
-        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)
-
-        # 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 = Path(sys.executable).resolve().as_posix()
-
-        # 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)
-
-        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())
-        else:
-            log.info('Command succeeded: %s', cmd_list)
-            log.info('stdout: %s', result.stdout.decode())
-        # 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 and 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/external_package/preferences.py

@@ -1,73 +0,0 @@
-import bpy
-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 ExternalPackagePreferences():
-    requirements_dir: bpy.props.StringProperty(
-        name="requirements.txt Directory",
-        subtype='DIR_PATH',
-        default=Path(__file__).parent.as_posix()
-    )  # type: ignore
-
-    log_dir: bpy.props.StringProperty(
-        name="Python Log Directory",
-        subtype='DIR_PATH',
-        default=Path(Path.home(), '.externalpackage', 'logs').as_posix()
-    )  # 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.")
-
-        col_main = layout.column(heading='', align=False)
-        row_import = col_main.row()
-        row_import.prop(self, 'pypi_mirror_provider', text='Set 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}'

bioxelnodes/io.py

@@ -1,486 +0,0 @@
-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
-from .utils import calc_bbox_verts, extract_last_number, get_bioxels_obj, show_message
-from .nodes import custom_nodes
-
-SUPPORT_EXTS = ['.dcm', '.tif', '.tiff', '.png', '.bmp', '', '.jpg']
-
-
-def get_data_files(filepath: str):
-    file_path = Path(filepath).resolve()
-    suffix = file_path.suffix
-
-    files = list(file_path.parent.iterdir())
-    files = [f for f in files if f.is_file() and f.suffix == suffix]
-
-    def last_number(file: Path):
-        return extract_last_number(file.stem)
-
-    files.sort(key=last_number)
-    files = [f.as_posix() for f in files]
-    return files
-
-
-def on_orig_spacing_changed(self, context):
-    if self.auto:
-        self.auto = False
-        new_orig_spacing = tuple(self.orig_spacing)
-
-        orig_shape = tuple(self.orig_shape)
-        bioxel_size = float(self.bioxel_size)
-
-        self.bioxels_shape = (
-            int(orig_shape[0] / bioxel_size * new_orig_spacing[0]),
-            int(orig_shape[1] / bioxel_size * new_orig_spacing[1]),
-            int(orig_shape[2] / bioxel_size * new_orig_spacing[2]),
-        )
-    else:
-        self.auto = True
-
-
-def on_bioxel_size_changed(self, context):
-    if self.auto:
-        self.auto = False
-        new_bioxel_size = float(self.bioxel_size)
-
-        orig_shape = tuple(self.orig_shape)
-        orig_spacing = tuple(self.orig_spacing)
-
-        self.bioxels_shape = (
-            int(orig_shape[0] / new_bioxel_size * orig_spacing[0]),
-            int(orig_shape[1] / new_bioxel_size * orig_spacing[1]),
-            int(orig_shape[2] / new_bioxel_size * orig_spacing[2]),
-        )
-    else:
-        self.auto = True
-
-
-def on_info_changed(self, context):
-    for region in context.area.regions:
-        if region.type == "UI":
-            region.tag_redraw()
-
-
-class ImportDICOMDialog(bpy.types.Operator):
-    bl_idname = "bioxelnodes.import_dicom_dialog"
-    bl_label = "Volume Data as Biovels"
-    bl_description = "Import Volume Data as Biovels (VDB)."
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH",
-        options={'HIDDEN'}
-    )  # type: ignore
-
-    bioxels_shape: bpy.props.IntVectorProperty(
-        name="Bioxels Shape",
-        min=0,
-        default=(100, 100, 100)
-    )  # type: ignore
-
-    bioxel_size: bpy.props.FloatProperty(
-        name="Bioxel Size",
-        soft_min=0.1, soft_max=10.0,
-        min=1e-2, max=1e2,
-        default=1,
-        update=on_bioxel_size_changed
-    )  # type: ignore
-
-    orig_spacing: bpy.props.FloatVectorProperty(
-        name="Original Spacing",
-        default=(1, 1, 1),
-        update=on_orig_spacing_changed
-    )  # type: ignore
-
-    orig_shape: bpy.props.IntVectorProperty(
-        name="Original Shape",
-        default=(100, 100, 100),
-        options={'HIDDEN'}
-    )  # type: ignore
-
-    auto: bpy.props.BoolProperty(
-        name="Auto Setting",
-        default=False,
-        options={'HIDDEN'}
-    )  # type: ignore
-
-    scene_scale: bpy.props.FloatProperty(
-        name="Scene Scale",
-        soft_min=0.001, soft_max=100.0,
-        min=1e-6, max=1e6,
-        default=0.01,
-    )  # type: ignore
-
-    do_add_segmentnode: bpy.props.BoolProperty(
-        name="Add Segment Node",
-        default=True,
-    )  # type: ignore
-
-    do_change_render_setting: bpy.props.BoolProperty(
-        name="Change Render Setting",
-        default=True,
-    )  # type: ignore
-
-    def execute(self, context):
-        if not self.filepath:
-            self.report({"WARNING"}, "Get no file path.")
-            return {'CANCELLED'}
-
-        if Path(self.filepath).suffix not in SUPPORT_EXTS:
-            self.report({"WARNING"}, "Not Supported extension.")
-            return {'CANCELLED'}
-
-        file_path = Path(self.filepath).resolve()
-        name = file_path.parent.name
-        files = get_data_files(self.filepath)
-
-        import SimpleITK as sitk
-        image = sitk.ReadImage(files)
-
-        bioxel_size = float(self.bioxel_size)
-
-        orig_spacing = tuple(self.orig_spacing)
-        image_spacing = image.GetSpacing()
-        image_shape = image.GetSize()
-
-        bioxels_spacing = (
-            image_spacing[0] / orig_spacing[0] * bioxel_size,
-            image_spacing[1] / orig_spacing[1] * bioxel_size,
-            image_spacing[2] / orig_spacing[2] * bioxel_size
-        )
-
-        bioxels_shape = (
-            int(image_shape[0] / bioxel_size * orig_spacing[0]),
-            int(image_shape[1] / bioxel_size * orig_spacing[1]),
-            int(image_shape[2] / bioxel_size * orig_spacing[2]),
-        )
-
-        print("Bioxel Size:", bioxel_size)
-        print("Bioxels Shape:", bioxels_shape)
-
-        print("Resampling...")
-        image = sitk.Resample(
-            image1=image,
-            size=bioxels_shape,
-            transform=sitk.Transform(),
-            interpolator=sitk.sitkLinear,
-            outputOrigin=image.GetOrigin(),
-            outputSpacing=bioxels_spacing,
-            outputDirection=image.GetDirection(),
-            defaultPixelValue=0,
-            outputPixelType=image.GetPixelID(),
-        )
-
-        try:
-            image = sitk.DICOMOrient(image, 'RAS')
-        except:
-            ...
-
-        array = sitk.GetArrayFromImage(image)
-        orig_dtype = str(array.dtype)
-        print(f"Coverting Dtype {orig_dtype} -> float")
-        array = array.astype(float)
-
-        # ITK indices, by convention, are [i,j,k] while NumPy indices are [k,j,i]
-        # https://www.slicer.org/wiki/Coordinate_systems
-
-        # ITK                  Numpy      3D
-        # R (ight)     i   ->    k   ->   x
-        # A (nterior)  j   ->    j   ->   y
-        # S (uperior)  k   ->    i   ->   z
-
-        array = np.transpose(array)
-        bioxels_max = float(np.max(array))
-        bioxels_min = float(np.min(array))
-
-        bioxels_offset = 0.0
-        if bioxels_min < 0 and orig_dtype[0] != "u":
-            bioxels_offset = -bioxels_min
-            array = array + np.full_like(array, bioxels_offset)
-            bioxels_max = float(np.max(array))
-            bioxels_min = float(np.min(array))
-            print("Offseted Max:", bioxels_max)
-            print("Offseted Min:", bioxels_min)
-
-        # Build VDB
-        grid = vdb.FloatGrid()
-        grid.copyFromArray(array.copy())
-
-        # 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(image.GetOrigin())
-        )
-
-        mat_rotation = mathutils.Matrix(
-            np.array(image.GetDirection()).reshape((3, 3))
-        ).to_4x4()
-
-        mat_scale = mathutils.Matrix.Scale(
-            bioxel_size, 4
-        )
-
-        transfrom = mat_lps2ras @ mat_location @ mat_rotation @ mat_scale
-
-        grid.transform = vdb.createLinearTransform(transfrom.transposed())
-        grid.name = "value"
-
-        preferences = context.preferences.addons[__package__].preferences
-        vdb_dirpath = Path(preferences.cache_dir, 'VDBs')
-        vdb_dirpath.mkdir(parents=True, exist_ok=True)
-        vdb_path = Path(vdb_dirpath, f"{uuid4()}.vdb")
-
-        print(f"Storing the VDB file ({vdb_path.as_posix()})...")
-        vdb.write(vdb_path.as_posix(), grids=[grid])
-
-        # Read VDB
-        print(f"Importing the VDB file to Blender scene...")
-        bpy.ops.object.volume_import(
-            filepath=vdb_path.as_posix(), align='WORLD', location=(0, 0, 0), scale=(1, 1, 1))
-
-        bioxels_obj = bpy.context.active_object
-
-        # Set props to VDB object
-        bioxels_obj.name = f"{name}_Bioxels"
-        bioxels_obj.data.name = f"{name}_Bioxels"
-
-        # 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
-        )
-
-        bioxels_obj.matrix_world = mat_ras2blender @ mat_scene_scale
-
-        bioxels_obj.lock_location[0] = True
-        bioxels_obj.lock_location[1] = True
-        bioxels_obj.lock_location[2] = True
-        bioxels_obj.lock_rotation[0] = True
-        bioxels_obj.lock_rotation[1] = True
-        bioxels_obj.lock_rotation[2] = True
-        bioxels_obj.lock_scale[0] = True
-        bioxels_obj.lock_scale[1] = True
-        bioxels_obj.lock_scale[2] = True
-        bioxels_obj.hide_select = True
-        bioxels_obj['bioxels'] = True
-
-        bpy.ops.node.new_geometry_nodes_modifier()
-        node_tree = bioxels_obj.modifiers[0].node_group
-
-        # Wrapper a Container
-        bpy.ops.mesh.primitive_cube_add(
-            enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)
-        )
-        container_obj = bpy.context.active_object
-        bbox_verts = calc_bbox_verts((0, 0, 0), bioxels_shape)
-        for index, vert in enumerate(container_obj.data.vertices):
-            co = transfrom @ mathutils.Vector(bbox_verts[index])
-            co = mat_ras2blender @ co
-            co = mat_scene_scale @ co
-            vert.co = co
-
-        bioxels_obj.parent = container_obj
-        container_obj.name = name
-        container_obj.data.name = name
-        container_obj.visible_camera = False
-        container_obj.visible_diffuse = False
-        container_obj.visible_glossy = False
-        container_obj.visible_transmission = False
-        container_obj.visible_volume_scatter = False
-        container_obj.visible_shadow = False
-        container_obj.display_type = 'WIRE'
-        container_obj['bioxels_container'] = True
-        container_obj['scene_scale'] = scene_scale
-        container_obj['bioxel_size'] = bioxel_size
-        container_obj['bioxels_max'] = bioxels_max
-        container_obj['bioxels_min'] = bioxels_min
-        container_obj['bioxels_offset'] = bioxels_offset
-        container_obj['bioxels_shape'] = bioxels_shape
-
-        bpy.ops.object.modifier_add(type='NODES')
-        container_obj.modifiers[0].node_group = node_tree
-        container_obj.modifiers[0].show_in_editmode = False
-        container_obj.modifiers[0].show_viewport = False
-        container_obj.modifiers[0].show_render = False
-
-        # Create BioxelNodes to VDB object
-        print(f"Creating BioxelNodes to the VDB...")
-
-        if self.do_add_segmentnode:
-            nodes = node_tree.nodes
-            links = node_tree.links
-
-            input_node = nodes.get("Group Input")
-            output_node = nodes.get("Group Output")
-            segment_node = custom_nodes.add_node(nodes, 'BioxelNodes_Segment')
-
-            links.new(input_node.outputs[0], segment_node.inputs[0])
-            links.new(segment_node.outputs[0], output_node.inputs[0])
-
-        # Change render setting for better result
-        if self.do_change_render_setting:
-            bpy.context.scene.render.engine = 'CYCLES'
-            bpy.context.scene.cycles.volume_bounces = 12
-            bpy.context.scene.cycles.transparent_max_bounces = 64
-
-        self.report({"INFO"}, "Successfully Imported")
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        # print(tuple(self.orig_shape))
-        self.auto = True
-        self.bioxel_size = 1
-        context.window_manager.invoke_props_dialog(self)
-        return {'RUNNING_MODAL'}
-
-
-class ReadDICOM(bpy.types.Operator):
-    bl_idname = "bioxelnodes.read_dicom"
-    bl_label = "Volume Data as Biovels"
-    bl_description = "Import Volume Data as Biovels (VDB)."
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    ok: bpy.props.BoolProperty(
-        default=True
-    )  # type: ignore
-
-    def execute(self, context):
-        files = get_data_files(self.filepath)
-
-        import SimpleITK as sitk
-        image = sitk.ReadImage(files)
-
-        print("Collecting Meta Data...")
-        print("Original Shape:", image.GetSize())
-        print("Original Spacing:", image.GetSpacing())
-        print("Original Origin:", image.GetOrigin())
-        print("Original Direction:", image.GetDirection())
-
-        bpy.ops.bioxelnodes.import_dicom_dialog(
-            'INVOKE_DEFAULT',
-            filepath=self.filepath,
-            orig_shape=image.GetSize(),
-            orig_spacing=image.GetSpacing()
-        )
-
-        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:
-            return {'CANCELLED'}
-
-        if Path(self.filepath).suffix not in SUPPORT_EXTS:
-            return {'CANCELLED'}
-
-        show_message('Reading image data, it may take a while',
-                     'Please be patient...')
-        context.window_manager.modal_handler_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class ImportDICOM(bpy.types.Operator):
-    bl_idname = "bioxelnodes.import_dicom"
-    bl_label = "Volume Data as Biovels"
-    bl_description = "Import Volume Data as Biovels (VDB)."
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    def execute(self, context):
-        bpy.ops.bioxelnodes.read_dicom(
-            'INVOKE_DEFAULT',
-            filepath=self.filepath
-        )
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.fileselect_add(self)
-        return {'RUNNING_MODAL'}
-
-
-class BIOXELNODES_FH_ImportDicom(bpy.types.FileHandler):
-    bl_idname = "BIOXELNODES_FH_ImportDicom"
-    bl_label = "File handler for dicom import"
-    bl_import_operator = "bioxelnodes.read_dicom"
-    bl_file_extensions = ".dcm"
-
-    @classmethod
-    def poll_drop(cls, context):
-        return (context.area and context.area.type == 'VIEW_3D')
-
-
-class ExportVDB(bpy.types.Operator):
-    bl_idname = "bioxelnodes.export_vdb"
-    bl_label = "Bioxels as VDB"
-    bl_description = "Export Bioxels original VDB data."
-    bl_options = {'UNDO'}
-
-    filepath: bpy.props.StringProperty(
-        subtype="FILE_PATH"
-    )  # type: ignore
-
-    filename_ext = ".vdb"
-
-    def invoke(self, context, event):
-        bioxels_obj = None
-        for obj in bpy.context.selected_objects:
-            bioxels_obj = get_bioxels_obj(obj)
-            break
-
-        if bioxels_obj:
-            context.window_manager.fileselect_add(self)
-            return {'RUNNING_MODAL'}
-        else:
-            self.report({"WARNING"}, "Cannot find any bioxels.")
-            return {'CANCELLED'}
-
-    def execute(self, context):
-        bioxels_obj = None
-        for obj in bpy.context.selected_objects:
-            bioxels_obj = get_bioxels_obj(obj)
-            break
-
-        filepath = f"{self.filepath.split('.')[0]}.vdb"
-        output_path: Path = Path(filepath).resolve()
-        source_path: Path = Path(bioxels_obj.data.filepath).resolve()
-        # print('output_path', output_path)
-        # print('source_path', source_path)
-        shutil.copy(source_path, output_path)
-
-        return {'FINISHED'}

bioxelnodes/menu.py

@@ -1,33 +0,0 @@
-import bpy
-from .convert import ConvertToMesh
-from .io import ExportVDB, ImportDICOM
-
-
-def TOPBAR_FILE_IMPORT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.operator(ImportDICOM.bl_idname)
-
-
-def TOPBAR_FILE_EXPORT(self, context):
-    layout = self.layout
-    layout.separator()
-    layout.operator(ExportVDB.bl_idname)
-
-
-def VIEW3D_OBJECT(self, context):
-    layout = self.layout
-    layout.operator(ConvertToMesh.bl_idname)
-    layout.separator()
-
-
-def create_menu():
-    bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
-    bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)
-    bpy.types.VIEW3D_MT_object_context_menu.prepend(VIEW3D_OBJECT)
-
-
-def remove_menu():
-    bpy.types.TOPBAR_MT_file_import.remove(TOPBAR_FILE_IMPORT)
-    bpy.types.TOPBAR_MT_file_export.remove(TOPBAR_FILE_EXPORT)
-    bpy.types.VIEW3D_MT_object_context_menu.remove(VIEW3D_OBJECT)

bioxelnodes/nodes.py

@@ -1,146 +0,0 @@
-
-from pathlib import Path
-from .custom_nodes import CustomNodes
-import bpy
-
-
-def add_driver_to_node_factory(source_prop, target_prop):
-    callback_str = f"""
-import bpy
-from bioxelnodes.utils import add_direct_driver, get_bioxels_obj
-bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-container_obj = bioxels_obj.parent
-if bioxels_obj:
-    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 bioxelnodes.utils import get_bioxels_obj
-bioxels_obj = get_bioxels_obj(bpy.context.active_object)
-container_obj = bioxels_obj.parent
-if bioxels_obj:
-    node.inputs.get('{target_prop}').default_value = container_obj.get('{source_prop}')
-else:
-    print('Cannot find any bioxels.')
-    """
-    return callback_str
-
-
-MENU_ITEMS = [
-    {
-        'label': 'Present',
-        'icon': 'MESH_MONKEY',
-        'items': [
-            {
-                'label': 'Segment',
-                'icon': 'OUTLINER_OB_META',
-                'node_type': 'BioxelNodes_Segment',
-                'node_description': '',
-                'node_callback': "\n".join([
-                    set_prop_to_node_factory("bioxel_size", "Detail Size"),
-                    set_prop_to_node_factory("bioxels_offset", "Offset"),
-                ])
-            },
-            {
-                'label': 'Anatomy',
-                'icon': 'OUTLINER_OB_META',
-                'node_type': 'BioxelNodes_Anatomy',
-                'node_description': '',
-                'node_callback': "\n".join([
-                    set_prop_to_node_factory("bioxel_size", "Detail Size"),
-                    set_prop_to_node_factory("bioxels_offset", "Offset"),
-                ])
-            }
-        ]
-    },
-    {
-        'label': 'Segment',
-        'icon': 'OUTLINER_DATA_VOLUME',
-        'items': [
-            {
-                'label': 'Segment by Level',
-                'icon': 'AREA_JOIN',
-                'node_type': 'BioxelNodes_SegmentByLevel',
-                'node_description': '',
-                'node_callback': "\n".join([
-                    set_prop_to_node_factory("bioxel_size", "Detail Size"),
-                    set_prop_to_node_factory("bioxels_offset", "Offset"),
-                ])
-            },
-            {
-                'label': 'Segment by Range',
-                'icon': 'AREA_SWAP',
-                'node_type': 'BioxelNodes_SegmentByRange',
-                'node_description': '',
-                'node_callback': "\n".join([
-                    set_prop_to_node_factory("bioxel_size", "Detail Size"),
-                    set_prop_to_node_factory("bioxels_offset", "Offset"),
-                ])
-            },
-            {
-                'label': 'Segment by Layers',
-                'icon': 'OUTLINER_OB_FORCE_FIELD',
-                'node_type': 'BioxelNodes_SegmentsByLayers',
-                'node_description': '',
-                'node_callback': "\n".join([
-                    set_prop_to_node_factory("bioxel_size", "Detail Size"),
-                    set_prop_to_node_factory("bioxels_offset", "Offset"),
-                ])
-            }
-        ]
-    },
-    {
-        'label': 'Shader',
-        'icon': 'SHADING_RENDERED',
-        'items': [
-            {
-                'label': 'Segment Shader',
-                'icon': 'OUTLINER_OB_VOLUME',
-                'node_type': 'BioxelNodes_SegmentShader',
-                'node_description': ''
-            }
-        ]
-    },
-    {
-        'label': 'Slicer',
-        'icon': 'CLIPUV_DEHLT',
-        'items': [
-            {
-                'label': 'RAS Slicer',
-                'icon': 'EMPTY_DATA',
-                'node_type': 'BioxelNodes_RAS-Slicer',
-                'node_description': ''
-            },
-            {
-                'label': 'Axis Slicer',
-                'icon': 'OUTLINER_OB_EMPTY',
-                'node_type': 'BioxelNodes_AxisSlicer',
-                'node_description': '',
-            },
-            {
-                'label': 'Box Slicer',
-                'icon': 'MOD_WIREFRAME',
-                'node_type': 'BioxelNodes_BoxSlicer',
-                'node_description': '',
-            }
-        ]
-    },
-]
-
-custom_nodes = CustomNodes(
-    menu_items=MENU_ITEMS,
-    nodes_file=Path(__file__).parent/"assets/Nodes.blend",
-    root_label='BioxelNodes',
-    root_icon="FILE_VOLUME",
-)

bioxelnodes/preferences.py

@@ -1,23 +0,0 @@
-import bpy
-from pathlib import Path
-from .external_package import ExternalPackagePreferences
-
-
-class BioxelNodesPreferences(bpy.types.AddonPreferences, ExternalPackagePreferences):
-    bl_idname = __package__
-    
-    cache_dir: bpy.props.StringProperty(
-        name="Python Log Directory",
-        subtype='DIR_PATH',
-        default=Path(Path.home(), '.bioxelnodes').as_posix()
-    )  # type: ignore
-    
-
-    def draw(self, context):
-        layout = self.layout
-        layout.label(text="Configuration")
-        layout.prop(self, 'cache_dir', text='Set Cache Directory')
-        
-        # ExternalPackagePreferences Config
-        self.requirements_dir = Path(__file__).parent.as_posix()
-        super().draw(context)

bioxelnodes/requirements.txt

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

bioxelnodes/utils.py

@@ -1,135 +0,0 @@
-import bpy
-import mathutils
-
-
-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 get_bioxels_obj(current_obj):
-    bioxels_obj = None
-    if current_obj.get('bioxels_container'):
-        bioxels_values = []
-        for obj in bpy.data.objects:
-            if obj.parent == current_obj and obj.get('bioxels'):
-                bioxels_values.append(obj)
-
-        if len(bioxels_values) > 0:
-            bioxels_obj = bioxels_values[0]
-
-    elif current_obj.get('bioxels') and current_obj.parent:
-        if current_obj.parent.get('bioxels_container'):
-            bioxels_obj = current_obj
-
-    return bioxels_obj
-
-
-def extract_last_number(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 int(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

docs/basics.en.md

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

docs/basics.md

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

docs/dataset.en.md

@@ -0,0 +1,39 @@
+# Support Format
+
+Can't wait to play with the addon using your own data? Here's a list of the formats currently supported.
+
+| Format | EXT                                      |
+| ------ | ---------------------------------------- |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP    | .bmp, .BMP                               |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG    | .png, .PNG                               |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd   | .nrrd, .nhdr                             |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME    | .ome.tiff, .ome.tif                      |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
+
+Despite my best efforts, I still can't achieve perfect support for all volumetric data formats, and I will continue to work on this.
+
+## Open Databases
+
+If you don't have volumetric data, then you can download from some open databases.
+
+**Note that just because they are open and available for download does not mean you can use them for anything! Be sure to look at the description of the available scopes from website.**
+
+| Source                                                                               | Object             |
+| ------------------------------------------------------------------------------------ | ------------------ |
+| [MorphoSource](https://www.morphosource.org/)                                        | Open Research Data |
+| [Dryad](https://datadryad.org)                                                       | Open Research Data |
+| [Cell Image Library](http://cellimagelibrary.org/home)                               | Cells              |
+| [OpenOrganelle](https://openorganelle.janelia.org/datasets)                          | Cells              |
+| [Allen Cell Explorer](https://www.allencell.org/3d-cell-viewer.html)                 | Cells              |
+| [EMDB](https://www.ebi.ac.uk/emdb/)                                                  | Protein, Viruses   |
+| [IDC](https://portal.imaging.datacommons.cancer.gov/explore/)                        | Medical Images     |
+| [Embodi3D](https://www.embodi3d.com/files/category/37-medical-scans/)                | Medical Images     |
+| [Github](https://github.com/sfikas/medical-imaging-datasets)                         | Medical Images     |
+| [NIHR](https://nhsx.github.io/open-source-imaging-data-sets/)                        | Medical Images     |
+| [Medical Segmentation Decathlon](http://medicaldecathlon.com/)                       | Medical Images     |
+| [Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html) | Medical Images     |

docs/dataset.md

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

docs/faq.en.md

@@ -0,0 +1,15 @@
+# FAQ
+
+## Nothing in the scene when rendering?
+
+If you're using the Cycles renderer with GPU, make sure your GPU supports "Optix", as Bioxel Nodes relies on OSL (Open shader language) for volumetric rendering, otherwise you'll have to use the CPU for rendering.
+
+If you're using the EEVEE renderer, this issue is due to EEVEE not loading shaders for some unknown reason, save the file and restart Blender to fix it.
+
+## After updating the addon, the nodes in the file have turned red?
+
+This is because the version of the nodes in the file does not match the current version of the addon after updating.
+
+If you still want to edit the file with Bioxel Nodes, you can only roll back the addon version to the version that corresponds to the nodes.
+
+If you just want the file to work and you won't rely on Bioxel Nodes any more, then you can just click **Bioxel Nodes > Relink Node Library >** in the top menu and select the corresponding version. Check to see if the nodes are working and rendering properly, and when everything is OK, click **Bioxel Nodes > Save Node Library** and select the save location in the dialog box.

docs/faq.md

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

docs/index.en.md

@@ -0,0 +1,59 @@
+**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/**
+
+# Bioxel Nodes
+
+[![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)
+
+-   Realistic rendering result, also support EEVEE NEXT.
+-   Support multiple formats.
+-   Support 4D volumetric data.
+-   All kinds of cutters.
+-   Simple and powerful nodes.
+-   Based on blender natively, can work without addon.
+
+**Read the [getting started](https://docs.omoolab.xyz/bioxelnodes/latest/en/installation) to begin your journey into visualizing volumetric data!**
+
+Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
+
+## Support Multiple Formats
+
+| Format | EXT                                      |
+| ------ | ---------------------------------------- |
+| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP    | .bmp, .BMP                               |
+| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG    | .png, .PNG                               |
+| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd   | .nrrd, .nhdr                             |
+| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME    | .ome.tiff, .ome.tif                      |
+| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
+
+## Support 4D volumetric data
+
+![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif)
+
+🥰 4D volumetric data can also be imported into Blender.
+
+## Support EEVEE NEXT
+
+![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
+
+👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! 
+
+
+## Roadmap
+
+-   Better multi-format import experience
+-   One-click bake model with texture
+-   AI Segmentation to Generate Labels

docs/index.md

@@ -0,0 +1,58 @@
+**v2.0.X 已发布，仅支持 Blender 5.0+，使用方式和之前截然不同，也无法兼容旧版本文件。使用方式查看 http://docs.omoolab.xyz/bioxelnodes/2.0.x/basics/**
+
+# Bioxel Nodes
+
+[![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 是一款用于科学体数据可视化的 Blender 插件。它利用 Blender 强大的 **几何节点 (Geometry Nodes)** 和 **Cycles** 渲染器来处理和渲染体数据。
+
+![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
+
+- 逼真的渲染效果，同时也支持 EEVEE NEXT
+- 支持多种数据格式
+- 支持 4D 体数据
+- 多种切割工具
+- 简洁而强大的节点系统
+- 基于 Blender 原生开发，插件卸载后仍可正常工作
+
+**阅读[安装指南](installation.md)开始您的体数据可视化之旅！**
+
+如果您在使用过程中遇到任何问题，欢迎加入我们的 [Discord 服务器](https://discord.gg/pYkNyq2TjE)。
+
+## 支持多种格式
+
+| 格式  | 扩展名                                   |
+| ----- | ---------------------------------------- |
+| DICOM | .dcm, .DCM, .DICOM, .ima, .IMA           |
+| BMP   | .bmp, .BMP                               |
+| JPEG  | .jpg, .JPG, .jpeg, .JPEG                 |
+| PNG   | .png, .PNG                               |
+| TIFF  | .tif, .TIF, .tiff, .TIFF                 |
+| Nifti | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
+| Nrrd  | .nrrd, .nhdr                             |
+| HDF5  | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
+| OME   | .ome.tiff, .ome.tif                      |
+| MRC   | .mrc, .mrc.gz, .map, .map.gz             |
+
+## 支持 4D 体数据
+
+![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif)
+
+4D 体数据也可以导入到 Blender 中。
+
+## 支持 EEVEE NEXT
+
+![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
+
+EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！
+
+## 路线图
+
+- 更完善的多格式导入体验
+- 一键烘焙带纹理模型
+- AI 分割生成标签

docs/installation.en.md

@@ -0,0 +1,22 @@
+# Installation
+
+!!! warning
+    **v2.0.x only supports Blender 5.0 and above**
+
+The add-on supports multiple installation methods, choose one.
+
+## Blender Preferences (Recommended)
+
+Click the top menu **Edit > Preferences**, search for "biox" in the "Get Extensions" area. Then click Install. Due to the large add-on size (60~100MB), you may need to wait for a while.
+
+![](assets/installation.png)
+
+## Blender Official Extensions Website
+
+Visit [https://extensions.blender.org/add-ons/bioxelnodes/](https://extensions.blender.org/add-ons/bioxelnodes/)
+Click Get Add-on, open Blender, drag the add-on into Blender and follow the prompts to install.
+
+## Manual Installation
+
+You can also download `BioxelNodes.{version}.zip` from [here](https://github.com/OmooLab/BioxelNodes/releases/latest) for manual installation.
+Click the top menu **Edit > Preferences**, select **Add-ons > Install from Disk**, then choose the Zip file you downloaded.

docs/installation.md

@@ -0,0 +1,22 @@
+# 安装
+
+!!! warning
+    **v2.0.x 仅支持 Blender 5.0 及以上版本**
+
+插件支持多种安装方式，选其中之一即可
+
+## Blender 偏好设置（推荐）
+
+点击顶部菜单 **Edit > Preferences**，在 "Get Extensions" 区域搜索 "biox"。然后点击 Install。由于插件体积较大（60~100MB），可能需要等待一段时间。
+
+![](assets/installation.png)
+
+## Blender 官方扩展网站
+
+访问 [https://extensions.blender.org/add-ons/bioxelnodes/](https://extensions.blender.org/add-ons/bioxelnodes/)  
+点击 Get Add-on，打开 Blender，将插件拖入并按照提示安装。
+
+## 手动安装
+
+您也可以从 [这里](https://github.com/OmooLab/BioxelNodes/releases/latest) 下载 `BioxelNodes.{version}.zip` 进行手动安装。
+点击顶部菜单 **Edit > Preferences**，选择 **Add-ons > Install from Disk**，然后选择您下载的 Zip 文件。

docs/performance.en.md

@@ -0,0 +1,25 @@
+# Improve Performance
+
+Voxel reconstruction and voxel rendering are very computation-intensive. Here are some tips to improve the add-on's performance.
+
+## Use Low-Resolution Data as Preview
+
+The resolution of voxels geometrically affects computational efficiency. Enabling Resample on O Layer can greatly improve calculation speed. You can uncheck it when you need to render for real. The Layer Nodes panel in the Bioxel Nodes tab lists all O Layers added in the current geometry nodes. You can uniformly manage whether Resample is enabled and the degree of resampling.
+
+## Balanced Rendering Settings
+
+I list some settings that have the greatest impact on volume rendering, so you can find the most suitable balance for your needs.
+
+- **Light Paths > Max Bounces > Volume** affects the number of bounces for volume data. The higher the value, the more transparent the volume data appears.
+
+- **Light Paths > Max Bounces > Transparent** affects the number of times transparent surfaces are transmitted. The higher the value, the more transparent the transparent surfaces appear.
+
+- **Volumes > Step Rate Render | Viewport** affects the step size of volume rendering. The smaller the value, the more detailed the volume data appears.
+
+Bioxel Nodes provides some render setting presets for quick configuration. Click the top menu **Bioxel Nodes > Render Setting Presets**, including Performance (left), Balance (center), and Quality (right). Here is a comparison:
+
+![alt text](assets/render-performance.png)
+
+## Rendering with EEVEE
+
+EEVEE doesn't render volume as well as Cycles, but it does have the advantage of rendering volumetric data. If you want to get a clear slice view, it is even a better choice. EEVEE's real-time rendering makes it possible to create interactive content in Blender.

docs/performance.md

@@ -0,0 +1,25 @@
+# 提升性能
+
+体素重建和体素渲染是非常消耗计算资源的，以下是一些提升插件性能的建议。
+
+## 使用低分辨率数据作为预览
+
+体素的分辨率几何倍地影响计算效率，O Layer 的 Resample 开启可以大大提高计算速度。当你需要正式渲染的时候再关闭即可。在 Bioxel Nodes 分页的 Layer Nodes 面板罗列了当前几何节点中添加的所有 O Layer，你可以统一管理是否开启 Resample，以及程度。
+
+## 平衡的渲染设置
+
+我列出了一些对体渲染影响最大的设置，以便您找到最适合自己的平衡点。
+
+- **Light Paths > Max Bounces > Volume** 影响体数据的反弹次数，值越高，体数据看起来越透明。
+
+- **Light Paths > Max Bounces > Transparent** 影响透明表面透射的次数，值越高，透明表面看起来越透明。
+
+- **Volumes > Step Rate Render | Viewport** 影响体渲染的步长，值越小，体数据看起来越精细。
+
+Bioxel Nodes 提供了一些渲染设置预设以便快速配置。点击顶部菜单 **Bioxel Nodes > Render Setting Presets**，包括 Performance（左侧）、Balance（中间）和 Quality（右侧）。以下是它们的比较。
+
+![alt text](assets/render-performance.png)
+
+## 使用 EEVEE 渲染
+
+EEVEE 渲染体数据不如 Cycles，但它确实有渲染体数据的优势，如果您想获得清晰的切片视图，它甚至是更好的选择。EEVEE 的实时渲染使得在 Blender 中创建交互式内容成为可能。

docs/stylesheets/extra.css

@@ -0,0 +1,28 @@
+@import url("https://fontsapi.zeoseven.com/292/main/result.css");
+@import url("https://fontsapi.zeoseven.com/293/main/result.css");
+
+/* [data-md-color-scheme="slate"] {
+  --md-code-hl-string-color: #8b8b8b;
+  --md-code-hl-keyword-color: #ffe8a3;
+  --md-code-hl-number-color: #ffe8a3;
+  --md-typeset-a-color: #ffe8a3;
+}
+
+[data-md-color-scheme="default"] {
+  --md-code-hl-string-color: #444444;
+  --md-code-hl-keyword-color: #bd9100;
+  --md-code-hl-number-color: #bd9100;
+}
+
+[data-md-color-scheme=slate][data-md-color-primary=black] {
+  --md-typeset-a-color: #ffe8a3;
+}
+
+[data-md-color-scheme=default][data-md-color-primary=black] {
+  --md-typeset-a-color: #bd9100;
+} */
+
+:root {
+  --md-text-font: "LXGW WenKai";
+  --md-code-font: "LXGW WenKai Mono";
+}

mkdocs.yml

@@ -0,0 +1,100 @@
+site_name: Bioxel Nodes Docs
+site_url: https://docs.omoolab.xyz/bioxelnodes/
+site_author: OmooLab
+site_description: Bioxel Nodes is a Blender add-on for scientific volumetric data visualization.
+
+repo_name: OmooLab/BioxelNodes
+repo_url: https://github.com/OmooLab/BioxelNodes
+
+nav:
+  - 胞素节点:
+      - index.md
+      - gallery.md
+  - 快速开始:
+      - installation.md
+      - basics.md
+      - advanced.md
+      - dataset.md
+      - performance.md
+
+theme:
+  name: material
+  favicon: assets/logo.png
+  logo: assets/logo.png
+  language: zh
+  font:
+    text: Open Sans
+    code: Cascadia Code
+  palette:
+    # Palette toggle for automatic mode
+    - media: "(prefers-color-scheme)"
+      primary: black
+      toggle:
+        icon: fontawesome/solid/circle-half-stroke
+        name: Switch to light mode
+
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: black
+      toggle:
+        icon: fontawesome/regular/moon
+        name: Switch to dark mode
+
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: black
+      toggle:
+        icon: fontawesome/solid/moon
+        name: Switch to system preference
+  features:
+    - header.autohide
+    - navigation.footer
+    - navigation.indexes
+    - navigation.sections
+    - navigation.tabs
+    - navigation.tabs.sticky
+    - content.code.copy
+    - content.code.select
+
+extra:
+  version:
+    provider: mike
+
+extra_css:
+  - stylesheets/extra.css
+
+copyright: Copyright © 2020 - 2024 Omoolab
+
+plugins:
+  - search
+  - mkdocstrings
+  - i18n:
+      docs_structure: suffix
+      languages:
+        - locale: zh
+          name: 中文
+          default: true
+        - locale: en
+          name: English
+          nav_translations:
+            胞素节点: Bioxel Nodes
+            快速开始: Getting Started
+            案例教程: Tutorials
+
+markdown_extensions:
+  - attr_list
+  - md_in_html
+  - mkdocs-click
+  - admonition
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      alternate_style: true

openspec/config.yaml

@@ -0,0 +1,20 @@
+schema: spec-driven
+
+# Project context (optional)
+# This is shown to AI when creating artifacts.
+# Add your tech stack, conventions, style guides, domain knowledge, etc.
+# Example:
+#   context: |
+#     Tech stack: TypeScript, React, Node.js
+#     We use conventional commits
+#     Domain: e-commerce platform
+
+# Per-artifact rules (optional)
+# Add custom rules for specific artifacts.
+# Example:
+#   rules:
+#     proposal:
+#       - Keep proposals under 500 words
+#       - Always include a "Non-goals" section
+#     tasks:
+#       - Break tasks into chunks of max 2 hours

pack.py

@@ -0,0 +1,92 @@
+"""
+Create a zip archive of the src/bioxelnodes package with a top-level folder
+named `bioxelnodes/`. Excludes specified temporary/cache files and folders.
+Does not modify any files in the project.
+
+Usage:
+    python build_package.py <platform_name> [output_zip_path]
+
+Example:
+    python build_package.py windows-x64
+"""
+from pathlib import Path
+import sys
+import zipfile
+import fnmatch
+from datetime import datetime
+
+platforms = {
+    "windows-x64": "windows-x64",
+    "linux-x64": "linux-x64",
+    "macos-arm64": "macos-arm64",
+    "macos-x64": "macos-x64",
+}
+
+# patterns to exclude (filename matching)
+EXCLUDE_FILENAME_PATTERNS = [
+    "*.blend1",
+    "blendcache_*",
+    "*.cats.txt~",
+    "*.pyc",
+    "*.pyo",
+    "*$py.class",
+]
+
+# directory names to exclude entirely
+EXCLUDE_DIR_NAMES = {
+    "__pycache__",
+}
+
+def should_exclude(path: Path) -> bool:
+    name = path.name
+    # exclude directories by name anywhere in the path
+    if any(part in EXCLUDE_DIR_NAMES for part in path.parts):
+        return True
+    # only apply filename patterns to files
+    if path.is_file():
+        for pat in EXCLUDE_FILENAME_PATTERNS:
+            if fnmatch.fnmatch(name, pat):
+                return True
+    return False
+
+def build_package(platform_name: str, out_zip: Path):
+    src_root = Path("src") / "bioxelnodes"
+    if not src_root.exists():
+        raise SystemExit(f"Source folder not found: {src_root.resolve()}")
+
+    out_zip.parent.mkdir(parents=True, exist_ok=True)
+    total = 0
+    with zipfile.ZipFile(out_zip, "w", compression=zipfile.ZIP_DEFLATED) as zf:
+        for p in src_root.rglob("*"):
+            if p.is_dir():
+                continue
+            if should_exclude(p):
+                continue
+            # arcname should place files under top-level 'bioxelnodes/...'
+            rel = p.relative_to(src_root)
+            arcname = Path("bioxelnodes") / rel
+            zf.write(p, arcname.as_posix())
+            total += 1
+    print(f"Packaged {total} files into {out_zip}")
+
+def main():
+    if len(sys.argv) < 2:
+        print("Usage: python build_package.py <platform_name> [output_zip_path]")
+        print("Available platforms:", ", ".join(platforms.keys()))
+        sys.exit(1)
+
+    platform_key = sys.argv[1]
+    if platform_key not in platforms:
+        print("Unknown platform:", platform_key)
+        print("Available platforms:", ", ".join(platforms.keys()))
+        sys.exit(1)
+
+    tag = platforms[platform_key]
+    timestamp = datetime.now().strftime("%Y%m%dT%H%M%S")
+    default_name = f"bioxelnodes-{tag}-{timestamp}.zip"
+    out_path = Path(sys.argv[2]) if len(sys.argv) >= 3 else Path(default_name)
+
+    build_package(platform_key, out_path)
+
+if __name__ == "__main__":
+    main()

pyproject.toml

@@ -0,0 +1,38 @@
+[project]
+name = "bioxelnodes"
+version = "2.0.2"
+description = ""
+authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }]
+requires-python = ">=3.11.0,<3.12.dev0"
+readme = "README.md"
+license = "MIT"
+dependencies = [
+    "simpleitk==2.3.1",
+    "pyometiff==1.0.0",
+    "mrcfile==1.5.1",
+    "h5py==3.11.0",
+    "transforms3d==0.4.2",
+    "matplotlib==3.10.7",
+    "scipy==1.16.3",
+]
+
+[dependency-groups]
+dev = [
+    "bpy>=4.2.0,<5",
+    "pytest>=8.3.2,<9",
+    "pytest-dependency>=0.6.0,<0.7",
+    "pytest-cov>=5.0.0,<6",
+    "mkdocs>=1.6.0,<2",
+    "mkdocs-material>=9.5.30,<10",
+    "autopep8>=2.3.1,<3",
+    "mike>=2.1.2,<3",
+    "tomlkit>=0.13.0,<0.14",
+    "pip>=25.3",
+    "mkdocstrings[python]>=1.0.4",
+    "mkdocs-static-i18n[material]>=1.3.1",
+    "mkdocs-click>=0.9.0",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

src/bioxelnodes/__init__.py

@@ -0,0 +1,80 @@
+import bpy
+import bpy.utils.previews as previews
+
+from .constants import PREVIEW_COLLECTIONS
+from .props import _bioxel_layer_items, _update_layer_gallery, _update_snapshot_z
+
+from . import auto_load
+from . import menus
+
+auto_load.init()
+
+CLI_COMMAND_NAME = "bioxelnodes_import_worker"
+
+
+def register():
+    pcoll = previews.new()
+    pcoll.layer_previews = ()
+    PREVIEW_COLLECTIONS["layers"] = pcoll
+
+    bpy.types.WindowManager.bioxel_progress_factor = bpy.props.FloatProperty(
+        default=1.0
+    )
+
+    bpy.types.WindowManager.bioxel_progress_text = bpy.props.StringProperty()
+
+    bpy.types.WindowManager.bioxel_layer_library = bpy.props.EnumProperty(
+        name="Bioxel Layer Gallery",
+        items=_bioxel_layer_items,
+        update=_update_layer_gallery,
+    )
+
+    bpy.types.WindowManager.bioxel_snapshot_z = bpy.props.FloatProperty(
+        name="Snapshot Z",
+        default=0.5,
+        min=0.0,
+        max=1.0,
+        subtype="FACTOR",
+        update=_update_snapshot_z,
+    )
+
+    bpy.types.WindowManager.bioxel_layer_list_index = bpy.props.IntProperty(
+        default=0)
+
+    auto_load.register()
+    menus.add()
+    register_cli_commands()
+
+
+def unregister():
+    unregister_cli_commands()
+    menus.remove()
+    auto_load.unregister()
+
+    del bpy.types.WindowManager.bioxel_progress_factor
+    del bpy.types.WindowManager.bioxel_progress_text
+    del bpy.types.WindowManager.bioxel_layer_library
+    del bpy.types.WindowManager.bioxel_snapshot_z
+    del bpy.types.WindowManager.bioxel_layer_list_index
+
+    for pcoll in PREVIEW_COLLECTIONS.values():
+        previews.remove(pcoll)
+    PREVIEW_COLLECTIONS.clear()
+
+
+def import_worker_cli(args):
+    from .operators import io_worker
+
+    return io_worker.main(args)
+
+
+def register_cli_commands():
+    unregister_cli_commands()
+    bpy.utils.register_cli_command(CLI_COMMAND_NAME, import_worker_cli)
+
+
+def unregister_cli_commands():
+    try:
+        bpy.utils.unregister_cli_command(CLI_COMMAND_NAME)
+    except Exception:
+        pass

src/bioxelnodes/asset_library.py

@@ -0,0 +1,73 @@
+import bpy
+from pathlib import Path
+
+from .constants import NODE_LIB_DIRPATH
+
+
+ASSET_LIBRARY_NAME = "O Bioxel"
+
+
+def _asset_library_path():
+    return str(NODE_LIB_DIRPATH)
+
+
+def _normalized_path(path):
+    return Path(bpy.path.abspath(path)).resolve()
+
+
+def _asset_libraries():
+    return bpy.context.preferences.filepaths.asset_libraries
+
+
+def get_bioxel_asset_library():
+    lib_path = _normalized_path(_asset_library_path())
+
+    for lib in _asset_libraries():
+        try:
+            if _normalized_path(lib.path) == lib_path:
+                return lib
+        except Exception:
+            continue
+
+    return None
+
+
+def has_bioxel_asset_library():
+    return get_bioxel_asset_library() is not None
+
+
+def add_bioxel_asset_library():
+    if not NODE_LIB_DIRPATH.exists():
+        raise FileNotFoundError(f"Node library path does not exist: {NODE_LIB_DIRPATH}")
+
+    prefs = _asset_libraries()
+    lib = get_bioxel_asset_library()
+
+    if lib is None:
+        for item in prefs:
+            try:
+                if item.name == ASSET_LIBRARY_NAME:
+                    lib = item
+                    break
+            except Exception:
+                continue
+
+    if lib is None:
+        lib = prefs.new()
+
+    lib.name = ASSET_LIBRARY_NAME
+    lib.path = _asset_library_path()
+    lib.import_method = "PACK"
+    return lib
+
+
+def remove_bioxel_asset_library_if_exists():
+    lib_path = _normalized_path(_asset_library_path())
+    prefs = _asset_libraries()
+
+    for lib in list(prefs):
+        try:
+            if "Bioxel" in lib.name or _normalized_path(lib.path) == lib_path:
+                prefs.remove(lib)
+        except Exception:
+            continue

src/bioxelnodes/assets/O_Bioxel/blender_assets.cats.txt

@@ -0,0 +1,12 @@
+# This is an Asset Catalog Definition file for Blender.
+#
+# Empty lines and lines starting with `#` will be ignored.
+# The first non-ignored line should be the version indicator.
+# Other lines are of the format "UUID:catalog/path/for/assets:simple catalog name"
+
+VERSION 1
+
+c0699a8b-6fd6-4d10-bdde-5ea0fa36724d:O Bioxel:O Bioxel
+5ea24e10-5a2b-44d1-b67b-19014c412793:O Bioxel/Layer:O Bioxel-Layer
+17383d65-f1a0-4122-b73a-0baaad4b8ecf:O Bioxel/Structure:O Bioxel-Structure
+d03fc5b0-465c-45ba-ba8e-524a1c52ae3d:O Bioxel/Utilities:O Bioxel-Utilities

src/bioxelnodes/auto_load.py

@@ -15,6 +15,10 @@ blender_version = bpy.app.version
 
 modules = None
 ordered_classes = None
+SKIP_MODULE_NAMES = {
+    "operators.io_worker",
+}
+
 
 def init():
     global modules
@@ -23,6 +27,7 @@ def init():
     modules = get_all_submodules(Path(__file__).parent)
     ordered_classes = get_ordered_classes_to_register(modules)
 
+
 def register():
     for cls in ordered_classes:
         bpy.utils.register_class(cls)
@@ -33,6 +38,7 @@ def register():
         if hasattr(module, "register"):
             module.register()
 
+
 def unregister():
     for cls in reversed(ordered_classes):
         bpy.utils.unregister_class(cls)
@@ -47,13 +53,18 @@ def unregister():
 # Import modules
 #################################################
 
+
 def get_all_submodules(directory):
-    return list(iter_submodules(directory, directory.name))
+    return list(iter_submodules(directory, __package__))
+
 
 def iter_submodules(path, package_name):
     for name in sorted(iter_submodule_names(path)):
+        if name in SKIP_MODULE_NAMES:
+            continue
         yield importlib.import_module("." + name, package_name)
 
+
 def iter_submodule_names(path, root=""):
     for _, module_name, is_package in pkgutil.iter_modules([str(path)]):
         if is_package:
@@ -67,22 +78,28 @@ def iter_submodule_names(path, root=""):
 # Find classes to register
 #################################################
 
+
 def get_ordered_classes_to_register(modules):
     return toposort(get_register_deps_dict(modules))
 
+
 def get_register_deps_dict(modules):
     my_classes = set(iter_my_classes(modules))
-    my_classes_by_idname = {cls.bl_idname : cls for cls in my_classes if hasattr(cls, "bl_idname")}
+    my_classes_by_idname = {
+        cls.bl_idname: cls for cls in my_classes if hasattr(cls, "bl_idname")}
 
     deps_dict = {}
     for cls in my_classes:
-        deps_dict[cls] = set(iter_my_register_deps(cls, my_classes, my_classes_by_idname))
+        deps_dict[cls] = set(iter_my_register_deps(
+            cls, my_classes, my_classes_by_idname))
     return deps_dict
 
+
 def iter_my_register_deps(cls, my_classes, my_classes_by_idname):
     yield from iter_my_deps_from_annotations(cls, my_classes)
     yield from iter_my_deps_from_parent_id(cls, my_classes_by_idname)
 
+
 def iter_my_deps_from_annotations(cls, my_classes):
     for value in typing.get_type_hints(cls, {}, {}).values():
         dependency = get_dependency_from_annotation(value)
@@ -90,6 +107,7 @@ def iter_my_deps_from_annotations(cls, my_classes):
             if dependency in my_classes:
                 yield dependency
 
+
 def get_dependency_from_annotation(value):
     if blender_version >= (2, 93):
         if isinstance(value, bpy.props._PropertyDeferred):
@@ -100,21 +118,24 @@ def get_dependency_from_annotation(value):
                 return value[1]["type"]
     return None
 
+
 def iter_my_deps_from_parent_id(cls, my_classes_by_idname):
-    if bpy.types.Panel in cls.__bases__:
+    if issubclass(cls, bpy.types.Panel):
         parent_idname = getattr(cls, "bl_parent_id", None)
         if parent_idname is not None:
             parent_cls = my_classes_by_idname.get(parent_idname)
             if parent_cls is not None:
                 yield parent_cls
 
+
 def iter_my_classes(modules):
     base_types = get_register_base_types()
     for cls in get_classes_in_modules(modules):
-        if any(base in base_types for base in cls.__bases__):
+        if any(issubclass(cls, base) for base in base_types):
             if not getattr(cls, "is_registered", False):
                 yield cls
 
+
 def get_classes_in_modules(modules):
     classes = set()
     for module in modules:
@@ -122,34 +143,53 @@ def get_classes_in_modules(modules):
             classes.add(cls)
     return classes
 
+
 def iter_classes_in_module(module):
     for value in module.__dict__.values():
         if inspect.isclass(value):
             yield value
 
+
 def get_register_base_types():
-    return set(getattr(bpy.types, name) for name in [
+    return set(
-        "Panel", "Operator", "PropertyGroup", "FileHandler",
+        getattr(bpy.types, name)
-        "AddonPreferences", "Header", "Menu",
+        for name in [
-        "Node", "NodeSocket", "NodeTree",
+            "Panel",
-        "UIList", "RenderEngine",
+            "Operator",
-        "Gizmo", "GizmoGroup",
+            "PropertyGroup",
-    ])
+            "AddonPreferences",
+            "Header",
+            "Menu",
+            "Node",
+            "NodeSocket",
+            "NodeTree",
+            "UIList",
+            "RenderEngine",
+            "Gizmo",
+            "GizmoGroup",
+            "FileHandler"
+        ]
+    )
 
 
 # Find order to register to solve dependencies
 #################################################
 
+
 def toposort(deps_dict):
     sorted_list = []
     sorted_values = set()
     while len(deps_dict) > 0:
         unsorted = []
+        sorted_list_sub = []  # helper for additional sorting by bl_order - in panels
         for value, deps in deps_dict.items():
             if len(deps) == 0:
-                sorted_list.append(value)
+                sorted_list_sub.append(value)
                 sorted_values.add(value)
             else:
                 unsorted.append(value)
-        deps_dict = {value : deps_dict[value] - sorted_values for value in unsorted}
+        deps_dict = {value: deps_dict[value] -
+                     sorted_values for value in unsorted}
+        sorted_list_sub.sort(key=lambda cls: getattr(cls, "bl_order", 0))
+        sorted_list.extend(sorted_list_sub)
     return sorted_list

src/bioxelnodes/bioxel/__init__.py

@@ -0,0 +1,34 @@
+from .layer import Layer
+from .container import Container
+from .io import load_container, save_container
+from .data import (
+    Data,
+    read,
+    read_meta,
+    calc_layer_shape,
+    calc_layer_size,
+    get_ext,
+    SUPPORT_EXTS,
+    DICOM_EXTS,
+    OME_EXTS,
+    MRC_EXTS,
+    SEQUENCE_EXTS
+)
+
+__all__ = [
+    'Layer',
+    'Container',
+    'load_container',
+    'save_container',
+    'Data',
+    'read',
+    'read_meta',
+    'calc_layer_shape',
+    'calc_layer_size',
+    'get_ext',
+    'SUPPORT_EXTS',
+    'DICOM_EXTS',
+    'OME_EXTS',
+    'MRC_EXTS',
+    'SEQUENCE_EXTS'
+]

src/bioxelnodes/bioxel/container.py

@@ -0,0 +1,9 @@
+from .layer import Layer
+
+
+class Container():
+    def __init__(self,
+                 name,
+                 layers: list[Layer] = []) -> None:
+        self.name = name
+        self.layers = layers

src/bioxelnodes/bioxel/data.py

@@ -0,0 +1,831 @@
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Optional, Callable, List
+import numpy as np
+import SimpleITK as sitk
+from pyometiff import OMETIFFReader
+import mrcfile
+import transforms3d
+
+from .layer import Layer
+
+# 类型定义
+ProgressCallback = Optional[Callable[[float, str], None]]
+
+
+SUPPORT_EXTS = [
+    "",
+    ".dcm",
+    ".DCM",
+    ".DICOM",
+    ".ima",
+    ".IMA",
+    ".ome.tiff",
+    ".ome.tif",
+    ".tif",
+    ".TIF",
+    ".tiff",
+    ".TIFF",
+    ".mrc",
+    ".mrc.gz",
+    ".map",
+    ".map.gz",
+    ".bmp",
+    ".BMP",
+    ".png",
+    ".PNG",
+    ".jpg",
+    ".JPG",
+    ".jpeg",
+    ".JPEG",
+    ".PIC",
+    ".pic",
+    ".gipl",
+    ".gipl.gz",
+    ".lsm",
+    ".LSM",
+    ".mnc",
+    ".MNC",
+    ".mrc",
+    ".rec",
+    ".mha",
+    ".mhd",
+    ".hdf",
+    ".h4",
+    ".hdf4",
+    ".he2",
+    ".h5",
+    ".hdf5",
+    ".he5",
+    ".nia",
+    ".nii",
+    ".nii.gz",
+    ".hdr",
+    ".img",
+    ".img.gz",
+    ".nrrd",
+    ".nhdr",
+    ".vtk",
+    ".gz",
+]
+
+OME_EXTS = [".ome.tiff", ".ome.tif", ".tif", ".TIF", ".tiff", ".TIFF"]
+
+MRC_EXTS = [".mrc", ".mrc.gz", ".map", ".map.gz"]
+
+DICOM_EXTS = ["", ".dcm", ".DCM", ".DICOM", ".ima", ".IMA"]
+
+SEQUENCE_EXTS = [
+    ".bmp",
+    ".BMP",
+    ".jpg",
+    ".JPG",
+    ".jpeg",
+    ".JPEG",
+    ".tif",
+    ".TIF",
+    ".tiff",
+    ".TIFF",
+    ".png",
+    ".PNG",
+    ".mrc",
+]
+
+
+@dataclass
+class Data:
+    filepath: str
+    series_id: str
+    _data: Optional[np.ndarray] = field(default=None, repr=False)
+    _meta: Optional[dict] = field(default=None, repr=False)
+
+    @property
+    def data(self) -> np.ndarray:
+        if self._data is None:
+            self.load_data()
+        return self._data
+
+    @property
+    def meta(self) -> dict:
+        if self._meta is None:
+            self.load_meta()
+        return self._meta
+
+    @property
+    def name(self) -> str:
+        return self.meta["name"]
+
+    @property
+    def description(self) -> str:
+        return self.meta["description"]
+
+    @property
+    def shape(self) -> tuple:
+        return (
+            self.meta["frame_count"],
+            *self.meta["xyz_shape"],
+            self.meta["channel_count"],
+        )
+
+    @property
+    def xyz_shape(self) -> tuple:
+        return self.meta["xyz_shape"]
+
+    @property
+    def spacing(self) -> tuple:
+        return self.meta["spacing"]
+
+    @property
+    def affine(self) -> np.ndarray:
+        return self.meta["affine"]
+
+    @property
+    def frame_count(self) -> int:
+        return self.meta["frame_count"]
+
+    @property
+    def channel_count(self) -> int:
+        return self.meta["channel_count"]
+
+    @property
+    def dtype(self) -> np.dtype:
+        return self.meta.get("dtype", np.float32)
+
+    def load_meta(self, progress_callback: ProgressCallback = None):
+        data, meta = self._parse_file(progress_callback)
+        self._meta = meta
+        del data
+
+    def load_data(self, progress_callback: ProgressCallback = None):
+        if not self.is_loaded():
+            data, meta = self._parse_file(progress_callback)
+            self._data = data
+            self._meta = meta
+
+    def is_loaded(self) -> bool:
+        return self._data is not None
+
+    def to_layers(
+        self,
+        kind: str = "scalar",
+        layer_name: str = "",
+        bioxel_size: float = 1.0,
+        smooth: int = 0,
+        remap: bool = False,
+        split_channel: bool = False,
+        frame_source: str = "-1",
+        progress_callback: ProgressCallback = None,
+    ) -> List[Layer]:
+        from .layer import Layer
+
+        data = self.data.copy()
+
+        data, layer_shape = self._transform_shape(data, frame_source)
+
+        data = self._preprocess(data, kind, remap)
+
+        mat_scale = transforms3d.zooms.zfdir2aff(bioxel_size)
+        affine = np.dot(self.meta["affine"], mat_scale)
+
+        base_name = layer_name or kind.capitalize()
+
+        if kind == "label":
+            return self._create_label_layers(
+                data, base_name, layer_shape, affine, smooth, progress_callback
+            )
+        elif kind == "color":
+            return self._create_color_layers(
+                data, base_name, layer_shape, affine, progress_callback
+            )
+        elif kind == "scalar":
+            return self._create_scalar_layers(
+                data,
+                base_name,
+                layer_shape,
+                affine,
+                smooth,
+                split_channel,
+                progress_callback,
+            )
+
+        return []
+
+    def _parse_file(self, progress_callback: ProgressCallback = None):
+        data_path = Path(self.filepath).resolve()
+        ext = self._get_ext(data_path)
+
+        if progress_callback:
+            progress_callback(0.0, "Reading Data...")
+
+        is_sequence = False
+        sequence = None
+        if ext in SEQUENCE_EXTS:
+            sequence = self._collect_sequence(data_path)
+            if sequence and len(sequence) > 1:
+                is_sequence = True
+
+        data = None
+        name = ""
+        description = ""
+        affine = np.identity(4)
+        spacing = (1, 1, 1)
+        origin = (0, 0, 0)
+        direction = (1, 0, 0, 0, 1, 0, 0, 0, 1)
+
+        if data is None and ext in MRC_EXTS and not is_sequence:
+            data, name, spacing = self._parse_mrc(data_path)
+
+        if data is None and ext in OME_EXTS and not is_sequence:
+            data, name, spacing = self._parse_ome_tiff(data_path, progress_callback)
+
+        if data is None:
+            data, name, description, spacing, origin, direction = self._parse_sitk(
+                data_path, ext, is_sequence, sequence, progress_callback
+            )
+
+        t = origin
+        r = np.array(direction).reshape((3, 3))
+        affine = np.dot(affine, transforms3d.affines.compose(t, r, [1, 1, 1]))
+
+        meta = {
+            "name": name,
+            "description": description,
+            "spacing": spacing,
+            "affine": affine,
+            "xyz_shape": data.shape[1:4],
+            "frame_count": data.shape[0],
+            "channel_count": data.shape[-1],
+            "dtype": data.dtype,
+        }
+
+        return data, meta
+
+    def _parse_mrc(self, data_path: Path):
+        print("Parsing with mrcfile...")
+        with mrcfile.open(data_path, "r") as mrc:
+            mrc_data = mrc.data
+
+            if mrc.is_single_image():
+                data = np.expand_dims(np.asarray(mrc_data), axis=0)
+                data = np.expand_dims(data, axis=-1)
+                data = np.expand_dims(data, axis=-1)
+            elif mrc.is_image_stack():
+                data = np.expand_dims(np.asarray(mrc_data), axis=-1)
+                data = np.expand_dims(data, axis=-1)
+            elif mrc.is_volume():
+                data = np.expand_dims(np.asarray(mrc_data), axis=0)
+                data = np.expand_dims(data, axis=-1)
+            elif mrc.is_volume_stack():
+                data = np.expand_dims(np.asarray(mrc_data), axis=-1)
+
+            name = self._get_file_no_digits_name(data_path)
+            spacing = (mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z)
+
+        return data, name, spacing
+
+    def _parse_ome_tiff(self, data_path: Path, progress_callback=None):
+        print("Parsing with OMETIFFReader...")
+        reader = OMETIFFReader(fpath=data_path)
+        ome_image, metadata, xml_metadata = reader.read()
+
+        if progress_callback:
+            progress_callback(0.5, "Transpose to 'TXYZC'...")
+
+        try:
+            ome_order = metadata["DimOrder BF Array"]
+            data = self._transpose_ome_image(ome_image, ome_order)
+
+            try:
+                spacing = (
+                    metadata["PhysicalSizeX"],
+                    metadata["PhysicalSizeY"],
+                    metadata["PhysicalSizeZ"],
+                )
+            except:
+                spacing = (1, 1, 1)
+
+            name = self._get_file_no_digits_name(data_path)
+        except Exception as e:
+            print(f"Error parsing OME-TIFF: {e}")
+            data = np.zeros((1, 1, 1, 1, 1), dtype=np.float32)
+            name = ""
+            spacing = (1, 1, 1)
+
+        return data, name, spacing
+
+    def _parse_sitk(
+        self,
+        data_path: Path,
+        ext: str,
+        is_sequence: bool,
+        sequence: Optional[list],
+        progress_callback=None,
+    ):
+        print("Parsing with SimpleITK...")
+
+        if ext in DICOM_EXTS:
+            data_dirpath = data_path.parent
+            reader = sitk.ImageSeriesReader()
+            reader.MetaDataDictionaryArrayUpdateOn()
+            reader.LoadPrivateTagsOn()
+            series_files = reader.GetGDCMSeriesFileNames(
+                str(data_dirpath), self.series_id
+            )
+            reader.SetFileNames(series_files)
+
+            itk_image = reader.Execute()
+            name, description = self._extract_dicom_meta(reader, data_dirpath)
+
+        elif ext in SEQUENCE_EXTS and is_sequence and sequence:
+            sequence_list = sequence if sequence else []
+            itk_image = sitk.ReadImage(sequence_list)
+            name = self._get_file_no_digits_name(data_path)
+            description = ""
+
+        else:
+            itk_image = sitk.ReadImage(data_path)
+            name = self._get_filename(data_path)
+            description = ""
+
+        if progress_callback:
+            progress_callback(0.5, "Transpose to 'TXYZC'...")
+
+        data = self._convert_sitk_to_numpy(itk_image, ext, is_sequence)
+
+        if itk_image.GetDimension() >= 3 and ext not in SEQUENCE_EXTS:
+            spacing = tuple(itk_image.GetSpacing())
+            origin = tuple(itk_image.GetOrigin())
+            direction = tuple(itk_image.GetDirection())
+        else:
+            spacing = (1, 1, 1)
+            origin = (0, 0, 0)
+            direction = (1, 0, 0, 0, 1, 0, 0, 0, 1)
+
+        return data, name, description, spacing, origin, direction
+
+    def _transpose_ome_image(self, ome_image, ome_order: str):
+        if ome_image.ndim == 2:
+            ome_order = ome_order.replace("T", "").replace("C", "").replace("Z", "")
+            bioxel_order = (ome_order.index("X"), ome_order.index("Y"))
+            data = np.transpose(ome_image, bioxel_order)
+            data = np.expand_dims(data, axis=0)
+            data = np.expand_dims(data, axis=-1)
+            data = np.expand_dims(data, axis=-1)
+
+        elif ome_image.ndim == 3:
+            ome_order = ome_order.replace("T", "").replace("C", "")
+            bioxel_order = (
+                ome_order.index("X"),
+                ome_order.index("Y"),
+                ome_order.index("Z"),
+            )
+            data = np.transpose(ome_image, bioxel_order)
+            data = np.expand_dims(data, axis=0)
+            data = np.expand_dims(data, axis=-1)
+
+        elif ome_image.ndim == 4:
+            ome_order = ome_order.replace("T", "")
+            bioxel_order = (
+                ome_order.index("X"),
+                ome_order.index("Y"),
+                ome_order.index("Z"),
+                ome_order.index("C"),
+            )
+            data = np.transpose(ome_image, bioxel_order)
+            data = np.expand_dims(data, axis=0)
+
+        elif ome_image.ndim == 5:
+            bioxel_order = (
+                ome_order.index("T"),
+                ome_order.index("X"),
+                ome_order.index("Y"),
+                ome_order.index("Z"),
+                ome_order.index("C"),
+            )
+            data = np.transpose(ome_image, bioxel_order)
+
+        return data
+
+    def _convert_sitk_to_numpy(self, itk_image, ext: str, is_sequence: bool):
+        if itk_image.GetDimension() == 2:
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 3:
+                data = np.transpose(data, (1, 0, 2))
+                data = np.expand_dims(data, axis=-2)
+            else:
+                data = np.transpose(data)
+                data = np.expand_dims(data, axis=-1)
+                data = np.expand_dims(data, axis=-1)
+
+            data = np.expand_dims(data, axis=0)
+
+        elif itk_image.GetDimension() == 3:
+            if ext not in SEQUENCE_EXTS:
+                itk_image = sitk.DICOMOrient(itk_image, "RAS")
+
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 4:
+                data = np.transpose(data, (2, 1, 0, 3))
+            else:
+                data = np.transpose(data)
+                data = np.expand_dims(data, axis=-1)
+
+            data = np.expand_dims(data, axis=0)
+
+        elif itk_image.GetDimension() == 4:
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 5:
+                data = np.transpose(data, (0, 3, 2, 1, 4))
+            else:
+                data = np.transpose(data, (0, 3, 2, 1))
+                data = np.expand_dims(data, axis=-1)
+
+        return data
+
+    def _extract_dicom_meta(self, reader, data_dirpath: Path):
+        def get_meta(key):
+            try:
+                string = reader.GetMetaData(0, key).removesuffix(" ")
+                string.encode("utf-8")
+                if string in ["No study description", "No series description", ""]:
+                    return None
+                else:
+                    return string
+            except:
+                return None
+
+        study_description = get_meta("0008|1030") or data_dirpath.name
+        series_description = get_meta("0008|103e")
+        series_modality = get_meta("0008|0060")
+
+        if series_description and series_modality:
+            description = f"{series_description}-{series_modality}"
+        elif series_description:
+            description = series_description
+        elif series_modality:
+            description = series_modality
+        else:
+            description = ""
+
+        name = study_description.replace(" ", "-")
+        description = description.replace(" ", "-")
+
+        return name, description
+
+    @staticmethod
+    def _get_ext(filepath: Path) -> str:
+        if filepath.name.endswith(".nii.gz"):
+            return ".nii.gz"
+        elif filepath.name.endswith(".img.gz"):
+            return ".img.gz"
+        elif filepath.name.endswith(".gipl.gz"):
+            return ".gipl.gz"
+        elif filepath.name.endswith(".ome.tiff"):
+            return ".ome.tiff"
+        elif filepath.name.endswith(".ome.tif"):
+            return ".ome.tif"
+        elif filepath.name.endswith(".mrc.gz"):
+            return ".mrc.gz"
+        elif filepath.name.endswith(".map.gz"):
+            return ".map.gz"
+        else:
+            suffix = filepath.suffix
+            return "" if len(suffix) > 5 else suffix
+
+    @staticmethod
+    def _get_filename(filepath: Path) -> str:
+        ext = Data._get_ext(filepath)
+        return filepath.name.removesuffix(ext)
+
+    @staticmethod
+    def _get_file_no_digits_name(filepath: Path) -> str:
+        prefix, digits, suffix = Data._get_filename_parts(filepath)
+        prefix = Data._remove_end_str(prefix, "_")
+        prefix = Data._remove_end_str(prefix, ".")
+        prefix = Data._remove_end_str(prefix, "-")
+        prefix = Data._remove_end_str(prefix, " ")
+        return prefix + suffix
+
+    @staticmethod
+    def _get_filename_parts(filepath: Path) -> tuple:
+        def has_digits(s):
+            return any(char.isdigit() for char in s)
+
+        name = Data._get_filename(filepath)
+        parts = name.replace(".", " ").replace("_", " ").split(" ")
+        skip_prefixs = ["CH", "ch", "channel"]
+        number_part = None
+        number_part_i = None
+
+        for i, part in enumerate(parts[::-1]):
+            if has_digits(part):
+                if not any([part.startswith(prefix) for prefix in skip_prefixs]):
+                    number_part = part
+                    number_part_i = len(parts) - i
+                    break
+
+        if number_part is None:
+            return name, "", ""
+
+        prefix_parts = parts[: number_part_i - 1]
+        prefix_parts_count = sum([len(part) + 1 for part in prefix_parts])
+
+        digits = ""
+        suffix = ""
+
+        started = False
+        for char in number_part[::-1]:
+            if char.isdigit():
+                started = True
+                digits += char
+            else:
+                if started:
+                    break
+                else:
+                    suffix += char
+
+        digits = digits[::-1]
+
+        prefix_parts_count += len(number_part) - len(digits) - len(suffix)
+
+        prefix = name[:prefix_parts_count]
+        suffix = name[prefix_parts_count + len(digits) :]
+
+        return prefix, digits, suffix
+
+    @staticmethod
+    def _get_file_index(filepath: Path) -> int:
+        prefix, digits, suffix = Data._get_filename_parts(filepath)
+        return int(digits) if digits != "" else 0
+
+    @staticmethod
+    def _collect_sequence(filepath: Path):
+        file_dict = {}
+        for f in filepath.parent.iterdir():
+            if (
+                f.is_file()
+                and Data._get_ext(filepath) == Data._get_ext(f)
+                and Data._get_file_no_digits_name(filepath)
+                == Data._get_file_no_digits_name(f)
+            ):
+                index = Data._get_file_index(f)
+                file_dict[index] = f
+
+        for key in list(file_dict.keys()):
+            if not file_dict.get(key + 1) and not file_dict.get(key - 1):
+                del file_dict[key]
+
+        file_dict = dict(sorted(file_dict.items()))
+        sequence = [str(f) for f in file_dict.values()]
+
+        if len(sequence) == 0:
+            sequence = [str(filepath)]
+
+        return sequence
+
+    @staticmethod
+    def _remove_end_str(string: str, end: str) -> str:
+        while string.endswith(end) and len(string) > 0:
+            string = string.removesuffix(end)
+        return string
+
+    def _transform_shape(self, data, frame_source: str) -> tuple:
+        orig_shape = self.xyz_shape
+
+        if frame_source == "-1":
+            data = data[0:1, :, :, :, :]
+            new_shape = orig_shape
+        elif frame_source == "0":
+            new_shape = orig_shape
+        elif frame_source == "1":
+            data = data.transpose(1, 0, 2, 3, 4)
+            new_shape = (1, orig_shape[1], orig_shape[2])
+        elif frame_source == "2":
+            data = data.transpose(2, 1, 0, 3, 4)
+            new_shape = (orig_shape[0], 1, orig_shape[2])
+        elif frame_source == "3":
+            data = data.transpose(3, 1, 2, 0, 4)
+            new_shape = (orig_shape[0], orig_shape[1], 1)
+        else:
+            data = data.transpose(4, 1, 2, 3, 0)
+            new_shape = orig_shape
+
+        return data, new_shape
+
+    def _preprocess(self, data, kind: str, remap: bool) -> np.ndarray:
+        if kind == "color":
+            if np.issubdtype(data.dtype, np.uint8):
+                data = np.multiply(data, 1.0 / 256, dtype=np.float32)
+            elif data.dtype.kind in ["u", "i"]:
+                data = data.astype(np.float32)
+                min_val, max_val = data.min(), data.max()
+                if max_val != min_val:
+                    data = (data - min_val) / (max_val - min_val)
+                else:
+                    data = np.zeros_like(data, dtype=np.float32)
+            else:
+                data = data.astype(np.float32)
+
+            if data.shape[4] == 1:
+                data = np.repeat(data, repeats=3, axis=4)
+            elif data.shape[4] == 2:
+                zeros_shape = list(data.shape[:4]) + [1]
+                zeros = np.zeros(zeros_shape, dtype=np.float32)
+                data = np.concatenate((data, zeros), axis=-1)
+            elif data.shape[4] > 3:
+                data = data[:, :, :, :, :3]
+
+        elif kind == "scalar":
+            if remap:
+                data = data.astype(np.float32)
+                min_val, max_val = data.min(), data.max()
+                if max_val != min_val:
+                    data = (data - min_val) / (max_val - min_val)
+                else:
+                    data = np.zeros_like(data, dtype=np.float32)
+
+        elif kind == "label":
+            data = data.astype(int)
+
+        return data
+
+    def _create_progress_cb_factory(self, progress_callback):
+        def factory(name, progress, progress_step):
+            def callback(frame, total):
+                if progress_callback:
+                    sub_progress = progress + frame * (progress_step / total)
+                    progress_callback(
+                        sub_progress, f"Processing {name} Frame {frame+1}..."
+                    )
+
+            return callback
+
+        return factory
+
+    def _create_label_layers(
+        self,
+        data,
+        base_name,
+        layer_shape,
+        affine,
+        smooth,
+        progress_callback: ProgressCallback,
+    ):
+        from .layer import Layer
+
+        layers = []
+        label_count = int(np.max(data))
+        if label_count == 0:
+            return layers
+
+        progress_step = 0.7 / label_count
+        cb_factory = self._create_progress_cb_factory(progress_callback)
+
+        for i in range(label_count):
+            name_i = f"{base_name}_{i+1}"
+            progress = 0.2 + i * progress_step
+            if progress_callback:
+                progress_callback(progress, f"Processing {name_i}...")
+
+            label_data = data == np.full_like(data, i + 1)
+            progress_cb = cb_factory(name_i, progress, progress_step)
+
+            layer = Layer(data=label_data, name=name_i, kind="label")
+            layer.resize(
+                shape=layer_shape, smooth=smooth, progress_callback=progress_cb
+            )
+            layer.affine = affine
+            layers.append(layer)
+
+        return layers
+
+    def _create_color_layers(
+        self, data, base_name, layer_shape, affine, progress_callback: ProgressCallback
+    ):
+        from .layer import Layer
+
+        if progress_callback:
+            progress_callback(0.2, f"Processing {base_name}...")
+
+        cb_factory = self._create_progress_cb_factory(progress_callback)
+        progress_cb = cb_factory(base_name, 0.2, 0.7)
+
+        layer = Layer(data=data, name=base_name, kind="color")
+        layer.resize(shape=layer_shape, progress_callback=progress_cb)
+        layer.affine = affine
+
+        return [layer]
+
+    def _create_scalar_layers(
+        self,
+        data,
+        base_name,
+        layer_shape,
+        affine,
+        smooth,
+        split_channel,
+        progress_callback: ProgressCallback,
+    ):
+        from .layer import Layer
+
+        layers = []
+        cb_factory = self._create_progress_cb_factory(progress_callback)
+
+        if split_channel:
+            channel_count = data.shape[-1]
+            progress_step = 0.7 / channel_count
+
+            for i in range(channel_count):
+                name_i = f"{base_name}_{i+1}"
+                progress = 0.2 + i * progress_step
+                if progress_callback:
+                    progress_callback(progress, f"Processing {name_i}...")
+
+                progress_cb = cb_factory(name_i, progress, progress_step)
+                layer = Layer(
+                    data=data[:, :, :, :, i : i + 1], name=name_i, kind="scalar"
+                )
+                layer.resize(
+                    shape=layer_shape, smooth=smooth, progress_callback=progress_cb
+                )
+                layer.affine = affine
+                layers.append(layer)
+        else:
+            if progress_callback:
+                progress_callback(0.2, f"Processing {base_name}...")
+
+            progress_cb = cb_factory(base_name, 0.2, 0.7)
+            layer = Layer(data=data, name=base_name, kind="scalar")
+            layer.resize(
+                shape=layer_shape, smooth=smooth, progress_callback=progress_cb
+            )
+            layer.affine = affine
+            layers.append(layer)
+
+        return layers
+
+
+# 模块级函数签名
+def read(
+    filepath: str, series_id: str = "", progress_callback: ProgressCallback = None
+) -> Data:
+    filepath = Path(filepath).resolve()
+    if not filepath.exists():
+        raise FileNotFoundError(f"File not found: {filepath}")
+
+    data_obj = Data(filepath=filepath, series_id=series_id)
+    data_obj.load_data(progress_callback)
+    return data_obj
+
+
+def read_meta(filepath: str, series_id: str = "") -> Data:
+    data_obj = Data(filepath=filepath, series_id=series_id)
+    data_obj.load_meta()
+    return data_obj
+
+
+def calc_layer_shape(
+    bioxel_size: float, orig_shape: tuple, orig_spacing: tuple
+) -> 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 calc_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0) -> tuple:
+    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: Path) -> str:
+    if filepath.name.endswith(".nii.gz"):
+        return ".nii.gz"
+    elif filepath.name.endswith(".img.gz"):
+        return ".img.gz"
+    elif filepath.name.endswith(".gipl.gz"):
+        return ".gipl.gz"
+    elif filepath.name.endswith(".ome.tiff"):
+        return ".ome.tiff"
+    elif filepath.name.endswith(".ome.tif"):
+        return ".ome.tif"
+    elif filepath.name.endswith(".mrc.gz"):
+        return ".mrc.gz"
+    elif filepath.name.endswith(".map.gz"):
+        return ".map.gz"
+    else:
+        suffix = filepath.suffix
+        return "" if len(suffix) > 5 else suffix

src/bioxelnodes/bioxel/io.py

@@ -0,0 +1,43 @@
+from pathlib import Path
+import uuid
+
+
+# 3rd-party
+import h5py
+
+from .container import Container
+from .layer import Layer
+
+
+def load_container(load_file: str):
+    load_path = Path(load_file).resolve()
+    with h5py.File(load_path, 'r') as file:
+        layers = []
+        for key, layer_dset in file['layers'].items():
+            layers.append(Layer(data=layer_dset[:],
+                                name=layer_dset.attrs['name'],
+                                kind=layer_dset.attrs['kind'],
+                                affine=layer_dset.attrs['affine']))
+
+        container = Container(name=file.attrs['name'],
+                              layers=layers)
+
+        return container
+
+
+def save_container(container: Container, save_file: str, overwrite=False):
+    save_path = Path(save_file).resolve()
+    if overwrite:
+        if save_path.is_file():
+            save_path.unlink()
+
+    with h5py.File(save_path, "w") as file:
+        file.attrs['name'] = container.name
+        layer_group = file.create_group("layers")
+        for layer in container.layers:
+            layer_key = uuid.uuid4().hex[:8]
+            layer_dset = layer_group.create_dataset(name=layer_key,
+                                                    data=layer.data)
+            layer_dset.attrs['name'] = layer.name
+            layer_dset.attrs['kind'] = layer.kind
+            layer_dset.attrs['affine'] = layer.affine

src/bioxelnodes/bioxel/layer.py

@@ -0,0 +1,182 @@
+import copy
+import numpy as np
+
+# 条件导入 openvdb（只在 Blender 环境中存在）
+try:
+    import openvdb as vdb
+except ImportError:
+    vdb = None
+
+from scipy import ndimage as ndi
+
+# 3rd-party
+import transforms3d
+# TODO: turn to dataclasses
+
+
+class Layer():
+    def __init__(self,
+                 data: np.ndarray,
+                 name: str,
+                 kind="scalar",
+                 affine=np.identity(4)) -> None:
+        if data.ndim != 5:
+            raise Exception("Data shape order should be TXYZC")
+
+        affine = np.array(affine)
+        if affine.shape != (4, 4):
+            raise Exception("affine shape should be (4,4)")
+
+        self.data = data
+        self.name = name
+        self.kind = kind
+        self.affine = affine
+
+    @property
+    def bioxel_size(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return z.tolist()
+
+    @property
+    def shape(self):
+        return self.data.shape[1:4]
+
+    @property
+    def dtype(self):
+        return self.data.dtype
+
+    @property
+    def origin(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return t.tolist()
+
+    @property
+    def euler(self):
+        t, r, z, s = transforms3d.affines.decompose44(self.affine)
+        return list(transforms3d.euler.mat2euler(r))
+
+    @property
+    def min(self):
+        return float(np.min(self.data))
+
+    @property
+    def frame_count(self):
+        return self.data.shape[0]
+
+    @property
+    def channel_count(self):
+        return self.data.shape[-1]
+
+    @property
+    def max(self):
+        return float(np.max(self.data))
+
+    def copy(self):
+        return copy.deepcopy(self)
+
+    def fill(self, value: float, mask: np.ndarray, smooth: int = 0):
+        mask_frames = ()
+        if mask.ndim == 4:
+            if mask.shape[0] != self.frame_count:
+                raise Exception("Mask frame count is not same as ")
+            for f in range(self.frame_count):
+                mask_frame = mask[f, :, :, :]
+                if smooth > 0:
+                    mask_frame = ndi.median_filter(mask_frame.astype(np.float32),
+                                                   mode="nearest",
+                                                   size=smooth)
+                mask_frames += (mask_frame,)
+        elif mask.ndim == 3:
+            for f in range(self.frame_count):
+                mask_frame = mask[:, :, :]
+                if smooth > 0:
+                    mask_frame = ndi.median_filter(mask_frame.astype(np.float32),
+                                                   mode="nearest",
+                                                   size=smooth)
+                mask_frames += (mask_frame,)
+        else:
+            raise Exception("Mask shape order should be TXYZ or XYZ")
+
+        _mask = np.stack(mask_frames)
+        _mask = np.expand_dims(_mask, axis=-1)
+        self.data = _mask * value + (1-_mask) * self.data
+
+    def resize(self, shape: tuple, smooth: int = 0, progress_callback=None):
+        if len(shape) != 3:
+            raise Exception("Shape must be 3 dim")
+
+        data = self.data
+
+        # # TXYZC > TXYZ
+        # if self.kind in ['label', 'scalar']:
+        #     data = np.amax(data, -1)
+
+        # if self.kind in ['scalar']:
+        #     dtype = data.dtype
+        # data = data.astype(np.float32)
+
+        data_frames = ()
+        for f in range(self.frame_count):
+            if progress_callback:
+                progress_callback(f, self.frame_count)
+
+            frame = data[f, :, :, :, :]
+            if smooth > 0:
+                frame = ndi.median_filter(frame.astype(np.float32),
+                                          mode="nearest",
+                                          size=smooth)
+
+            factors = np.divide(self.shape, shape)
+            zoom_factors = [1 / f for f in factors]
+            order = 0 if frame.dtype == bool else 1
+            frame = ndi.zoom(frame,
+                             zoom_factors+[1.0],
+                             mode="nearest",
+                             grid_mode=False,
+                             order=order)
+            if smooth > 0:
+                frame = frame.astype(self.dtype)
+            data_frames += (frame,)
+
+        data = np.stack(data_frames)
+
+        # if self.kind in ['scalar']:
+        #     data = data.astype(dtype)
+
+        # TXYZ > TXYZC
+        # if self.kind in ['label', 'scalar']:
+        #     data = np.expand_dims(data, axis=-1)  # expend channel
+
+        self.data = data
+
+        mat_scale = transforms3d.zooms.zfdir2aff(factors[0])
+        self.affine = np.dot(self.affine, mat_scale)
+
+    def snapshot(self, shape: tuple, smooth: int = 0):
+        if len(shape) != 3:
+            raise Exception("Shape must be 3 dim")
+
+        data = self.data
+
+        snapshot = data[0, :, :, :, :]
+
+        factors = np.divide(self.shape, shape)
+        zoom_factors = [1 / f for f in factors]
+        order = 0 if snapshot.dtype == bool else 1
+        snapshot = ndi.zoom(snapshot,
+                            zoom_factors+[1.0],
+                            mode="nearest",
+                            grid_mode=False,
+                            order=order)
+
+        snapshot = snapshot.astype(np.float32)
+
+        if self.kind in ['scalar', 'vector', 'color']:
+            mn = float(np.nanmin(snapshot))
+            mx = float(np.nanmax(snapshot))
+            if mx - mn > 1e-8:
+                snapshot = (snapshot - mn) / (mx - mn)
+            else:
+                snapshot = np.clip(snapshot, 0.0, 1.0)
+
+        return snapshot

src/bioxelnodes/bioxel/parse.py

@@ -0,0 +1,436 @@
+from pathlib import Path
+import numpy as np
+
+# 3rd-party
+import SimpleITK as sitk
+from pyometiff import OMETIFFReader
+import mrcfile
+import transforms3d
+
+
+"""
+Convert any volumetric data to 3D numpy array with order TXYZC
+"""
+
+SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
+                '.ome.tiff', '.ome.tif',
+                '.tif', '.TIF', '.tiff', '.TIFF',
+                '.mrc', '.mrc.gz', '.map', '.map.gz',
+                '.bmp', '.BMP',
+                '.png', '.PNG',
+                '.jpg', '.JPG', '.jpeg', '.JPEG',
+                '.PIC', '.pic',
+                '.gipl', '.gipl.gz',
+                '.lsm', '.LSM',
+                '.mnc', '.MNC',
+                '.mrc', '.rec',
+                '.mha', '.mhd',
+                '.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
+                '.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
+                '.nrrd', '.nhdr',
+                '.vtk',
+                '.gz']
+
+OME_EXTS = ['.ome.tiff', '.ome.tif',
+            '.tif', '.TIF', '.tiff', '.TIFF']
+
+MRC_EXTS = ['.mrc', '.mrc.gz', '.map', '.map.gz']
+
+DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA']
+
+SEQUENCE_EXTS = ['.bmp', '.BMP',
+                 '.jpg', '.JPG', '.jpeg', '.JPEG',
+                 '.tif', '.TIF', '.tiff', '.TIFF',
+                 '.png', '.PNG',
+                 '.mrc']
+
+
+def get_ext(filepath: Path) -> str:
+    if filepath.name.endswith(".nii.gz"):
+        return ".nii.gz"
+    elif filepath.name.endswith(".img.gz"):
+        return ".img.gz"
+    elif filepath.name.endswith(".gipl.gz"):
+        return ".gipl.gz"
+    elif filepath.name.endswith(".ome.tiff"):
+        return ".ome.tiff"
+    elif filepath.name.endswith(".ome.tif"):
+        return ".ome.tif"
+    elif filepath.name.endswith(".mrc.gz"):
+        return ".mrc.gz"
+    elif filepath.name.endswith(".map.gz"):
+        return ".map.gz"
+    else:
+        suffix = filepath.suffix
+        return "" if len(suffix) > 5 else suffix
+
+
+def get_filename(filepath: Path):
+    ext = get_ext(filepath)
+    return filepath.name.removesuffix(ext)
+
+
+def get_filename_parts(filepath: Path) -> str:
+    def has_digits(s):
+        return any(char.isdigit() for char in s)
+
+    name = get_filename(filepath)
+    parts = name.replace(".", " ").replace("_", " ").split(" ")
+    skip_prefixs = ["CH", "ch", "channel"]
+    number_part = None
+    number_part_i = None
+
+    for i, part in enumerate(parts[::-1]):
+        if has_digits(part):
+            if not any([part.startswith(prefix) for prefix in skip_prefixs]):
+                number_part = part
+                number_part_i = len(parts)-i
+                break
+
+    if number_part is None:
+        return name, "", ""
+
+    prefix_parts = parts[:number_part_i-1]
+    prefix_parts_count = sum([len(part)+1 for part in prefix_parts])
+
+    digits = ""
+    suffix = ""
+
+    # Iterate through the characters in reverse order
+    started = False
+    for char in number_part[::-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
+            else:
+                suffix += char
+
+    digits = digits[::-1]
+
+    prefix_parts_count += len(number_part) - \
+        len(digits) - len(suffix)
+
+    # Reverse the digits string to get the correct order
+    prefix = name[:prefix_parts_count]
+    suffix = name[prefix_parts_count+len(digits):]
+
+    return prefix, digits, suffix
+
+
+def get_file_no_digits_name(filepath: Path) -> str:
+    prefix, digits, suffix = get_filename_parts(filepath)
+    prefix = remove_end_str(prefix, "_")
+    prefix = remove_end_str(prefix, ".")
+    prefix = remove_end_str(prefix, "-")
+    prefix = remove_end_str(prefix, " ")
+    return prefix + suffix
+
+
+def get_file_index(filepath: Path) -> int:
+    prefix, digits, suffix = get_filename_parts(filepath)
+    return int(digits) if digits != "" else 0
+
+
+def collect_sequence(filepath: Path):
+    file_dict = {}
+    for f in filepath.parent.iterdir():
+        if f.is_file() \
+                and get_ext(filepath) == get_ext(f) \
+                and get_file_no_digits_name(filepath) == get_file_no_digits_name(f):
+            index = get_file_index(f)
+            file_dict[index] = f
+
+    # reomve isolated seq file
+    for key in file_dict.copy().keys():
+        if not file_dict.get(key+1) \
+                and not file_dict.get(key-1):
+            del file_dict[key]
+
+    file_dict = dict(sorted(file_dict.items()))
+    sequence = [str(f) for f in file_dict.values()]
+
+    if len(sequence) == 0:
+        sequence = [str(filepath)]
+
+    return sequence
+
+
+def remove_end_str(string: str, end: str):
+    while string.endswith(end) and len(string) > 0:
+        string = string.removesuffix(end)
+    return string
+
+
+def parse_volumetric_data(data_file: str, series_id="", progress_callback=None):
+    """Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
+
+    Args:
+        data_file (str): file path
+        series_id (str, optional): DICOM series id. Defaults to "".
+
+    Returns:
+        _type_: _description_
+    """
+
+    data_path = Path(data_file).resolve()
+    ext = get_ext(data_path)
+
+    if progress_callback:
+        progress_callback(0.0, "Reading the Data...")
+
+    is_sequence = False
+    if ext in SEQUENCE_EXTS:
+        sequence = collect_sequence(data_path)
+        if len(sequence) > 1:
+            is_sequence = True
+
+    data = None
+    name = "",
+    description = ""
+    affine = np.identity(4)
+    spacing = (1, 1, 1)
+    origin = (0, 0, 0)
+    direction = (1, 0, 0, 0, 1, 0, 0, 0, 1)
+
+    # Parsing with mrcfile
+    if data is None and ext in MRC_EXTS and not is_sequence:
+        print("Parsing with mrcfile...")
+        # TODO: much to do with mrc
+        with mrcfile.open(data_path, 'r') as mrc:
+            data = mrc.data
+            # mrc.print_header()
+            # print(data.shape)
+            # print(mrc.voxel_size)
+
+            if mrc.is_single_image():
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif mrc.is_image_stack():
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif mrc.is_volume():
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif mrc.is_volume_stack():
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            name = get_file_no_digits_name(data_path)
+            spacing = (mrc.voxel_size.x,
+                       mrc.voxel_size.y,
+                       mrc.voxel_size.z)
+
+    # Parsing with OMETIFFReader
+    if data is None and ext in OME_EXTS and not is_sequence:
+        print("Parsing with OMETIFFReader...")
+        reader = OMETIFFReader(fpath=data_path)
+        ome_image, metadata, xml_metadata = reader.read()
+
+        # TODO: some old bio-format tiff the header is not the same.
+        if progress_callback:
+            progress_callback(0.5, "Transpose to 'TXYZC'...")
+
+        try:
+            # print(ome_image.shape)
+            # for key in metadata:
+            #     print(f"{key},{metadata[key]}")
+            ome_order = metadata['DimOrder BF Array']
+            if ome_image.ndim == 2:
+                ome_order = ome_order.replace("T", "")\
+                    .replace("C", "").replace("Z", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'))
+                data = np.transpose(ome_image, bioxel_order)
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            elif ome_image.ndim == 3:
+                # -> XYZC
+                ome_order = ome_order.replace("T", "").replace("C", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'))
+                data = np.transpose(ome_image, bioxel_order)
+                data = np.expand_dims(data, axis=0)  # expend frame
+                data = np.expand_dims(data, axis=-1)  # expend channel
+            elif ome_image.ndim == 4:
+                # -> XYZC
+                ome_order = ome_order.replace("T", "")
+                bioxel_order = (ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'),
+                                ome_order.index('C'))
+                data = np.transpose(ome_image, bioxel_order)
+                data = np.expand_dims(data, axis=0)  # expend frame
+            elif ome_image.ndim == 5:
+                # -> TXYZC
+                bioxel_order = (ome_order.index('T'),
+                                ome_order.index('X'),
+                                ome_order.index('Y'),
+                                ome_order.index('Z'),
+                                ome_order.index('C'))
+                data = np.transpose(ome_image, bioxel_order)
+
+            try:
+                spacing = (metadata['PhysicalSizeX'],
+                           metadata['PhysicalSizeY'],
+                           metadata['PhysicalSizeZ'])
+            except:
+                ...
+
+            name = get_file_no_digits_name(data_path)
+        except:
+            ...
+
+    # Parsing with SimpleITK
+    if data is None:
+        print("Parsing with SimpleITK...")
+        if ext in DICOM_EXTS:
+            data_dirpath = data_path.parent
+            reader = sitk.ImageSeriesReader()
+            reader.MetaDataDictionaryArrayUpdateOn()
+            reader.LoadPrivateTagsOn()
+            series_files = reader.GetGDCMSeriesFileNames(
+                str(data_dirpath), series_id)
+            reader.SetFileNames(series_files)
+
+            itk_image = reader.Execute()
+            # for k in reader.GetMetaDataKeys(0):
+            #     v = reader.GetMetaData(0, k)
+            #     print(f'({k}) = = "{v}"')
+
+            def get_meta(key):
+                try:
+                    stirng = reader.GetMetaData(0, key).removesuffix(" ")
+                    stirng.encode('utf-8')
+                    if stirng in ["No study description",
+                                  "No series description",
+                                  ""]:
+                        return None
+                    else:
+                        return stirng
+                except:
+                    return None
+
+            study_description = get_meta("0008|1030")
+            series_description = get_meta("0008|103e")
+            series_modality = get_meta("0008|0060")
+
+            name = study_description or data_dirpath.name
+            if series_description and series_modality:
+                description = f"{series_description}-{series_modality}"
+            elif series_description:
+                description = series_description
+            elif series_modality:
+                description = series_modality
+            else:
+                description = ""
+
+            name = name.replace(" ", "-")
+            description = description.replace(" ", "-")
+
+        elif ext in SEQUENCE_EXTS and is_sequence:
+            itk_image = sitk.ReadImage(sequence)
+            name = get_file_no_digits_name(data_path)
+        else:
+            itk_image = sitk.ReadImage(data_path)
+            name = get_filename(data_path)
+
+        # for key in itk_image.GetMetaDataKeys():
+        #     print(f"{key},{itk_image.GetMetaData(key)}")
+
+        if progress_callback:
+            progress_callback(0.5, "Transpose to 'TXYZC'...")
+
+        if itk_image.GetDimension() == 2:
+
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 3:
+                data = np.transpose(data, (1, 0, 2))
+
+                data = np.expand_dims(data, axis=-2)  # expend Z
+            else:
+                data = np.transpose(data)
+                data = np.expand_dims(data, axis=-1)  # expend Z
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            data = np.expand_dims(data, axis=0)  # expend frame
+
+        elif itk_image.GetDimension() == 3:
+            if ext not in SEQUENCE_EXTS:
+                itk_image = sitk.DICOMOrient(itk_image, 'RAS')
+                # After sitk.DICOMOrient(), origin and direction will also orient base on LPS
+                # so we need to convert them into RAS
+                # affine = axis_conversion(from_forward='-Z',
+                #                          from_up='-Y',
+                #                          to_forward='-Z',
+                #                          to_up='Y').to_4x4()
+
+                affine = np.array([[-1.0000,  0.0000, 0.0000, 0.0000],
+                                   [0.0000, -1.0000, 0.0000, 0.0000],
+                                   [0.0000,  0.0000, 1.0000, 0.0000],
+                                   [0.0000,  0.0000, 0.0000, 1.0000]])
+
+            spacing = tuple(itk_image.GetSpacing())
+            origin = tuple(itk_image.GetOrigin())
+            direction = tuple(itk_image.GetDirection())
+
+            data = sitk.GetArrayFromImage(itk_image)
+            # transpose ijk to kji
+            if data.ndim == 4:
+                data = np.transpose(data, (2, 1, 0, 3))
+            else:
+                data = np.transpose(data)
+                data = np.expand_dims(data, axis=-1)  # expend channel
+
+            data = np.expand_dims(data, axis=0)  # expend frame
+
+        elif itk_image.GetDimension() == 4:
+
+            spacing = tuple(itk_image.GetSpacing()[:3])
+            origin = tuple(itk_image.GetOrigin()[:3])
+            # FIXME: not sure...
+            direction = np.array(itk_image.GetDirection())
+            direction = direction.reshape(3, 3) if itk_image.GetDimension() == 3 \
+                else direction.reshape(4, 4)
+
+            direction = direction[1:, 1:]
+            direction = tuple(direction.flatten())
+
+            data = sitk.GetArrayFromImage(itk_image)
+
+            if data.ndim == 5:
+                data = np.transpose(data, (0, 3, 2, 1, 4))
+            else:
+                data = np.transpose(data, (0, 3, 2, 1))
+                data = np.expand_dims(data, axis=-1)
+
+        if itk_image.GetDimension() > 5:
+            raise Exception
+
+    t = origin
+    r = np.array(direction).reshape((3, 3))
+    affine = np.dot(affine,
+                    transforms3d.affines.compose(t, r, [1, 1, 1]))
+
+    meta = {
+        "name": name,
+        "description": description,
+        "spacing": spacing,
+        "affine": affine,
+        "xyz_shape": data.shape[1:4],
+        "frame_count": data.shape[0],
+        "channel_count": data.shape[-1],
+    }
+
+    return data, meta

src/bioxelnodes/blender_manifest.toml

@@ -0,0 +1,46 @@
+schema_version = "1.0.0"
+
+id = "bioxelnodes"
+version = "2.0.2"
+name = "Bioxel Nodes"
+tagline = "For scientific volumetric data visualization in Blender"
+maintainer = "Nan <icrdr2010@outlook.com>"
+type = "add-on"
+website = "https://docs.omoolab.xyz/bioxelnodes/"
+
+tags = ["Geometry Nodes", "Render", "Import-Export"]
+blender_version_min = "5.0.0"
+license = ['SPDX:GPL-3.0-or-later']
+copyright = ["2024 OmooLab"]
+platforms = ["windows-x64"]
+
+wheels = [
+    "./wheels/contourpy-1.3.3-cp311-cp311-win_amd64.whl",
+    "./wheels/contourpy-1.3.3-cp313-cp313-win_amd64.whl",
+    "./wheels/cycler-0.12.1-py3-none-any.whl",
+    "./wheels/fonttools-4.63.0-cp311-cp311-win_amd64.whl",
+    "./wheels/fonttools-4.63.0-cp313-cp313-win_amd64.whl",
+    "./wheels/h5py-3.14.0-cp311-cp311-win_amd64.whl",
+    "./wheels/h5py-3.14.0-cp313-cp313-win_amd64.whl",
+    "./wheels/kiwisolver-1.5.0-cp311-cp311-win_amd64.whl",
+    "./wheels/kiwisolver-1.5.0-cp313-cp313-win_amd64.whl",
+    "./wheels/lxml-6.1.1-cp311-cp311-win_amd64.whl",
+    "./wheels/lxml-6.1.1-cp313-cp313-win_amd64.whl",
+    "./wheels/matplotlib-3.10.7-cp311-cp311-win_amd64.whl",
+    "./wheels/matplotlib-3.10.7-cp313-cp313-win_amd64.whl",
+    "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
+    "./wheels/pillow-11.2.1-cp311-cp311-win_amd64.whl",
+    "./wheels/pillow-11.2.1-cp313-cp313-win_amd64.whl",
+    "./wheels/pyometiff-1.0.0-py3-none-any.whl",
+    "./wheels/pyparsing-3.3.2-py3-none-any.whl",
+    "./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl",
+    "./wheels/scipy-1.17.1-cp311-cp311-win_amd64.whl",
+    "./wheels/scipy-1.17.1-cp313-cp313-win_amd64.whl",
+    "./wheels/simpleitk-2.5.5-cp311-abi3-win_amd64.whl",
+    "./wheels/six-1.17.0-py2.py3-none-any.whl",
+    "./wheels/tifffile-2024.7.24-py3-none-any.whl",
+    "./wheels/transforms3d-0.4.2-py3-none-any.whl",
+]
+
+[permissions]
+files = "Import/export volume data from/to disk"

src/bioxelnodes/constants.py

@@ -0,0 +1,11 @@
+from pathlib import Path
+
+NODE_LIB_FILENAME = "O_Bioxel_Nodes.blend"
+
+NODE_LIB_DIRPATH = Path(Path(__file__).parent,
+                        "assets/O_Bioxel").resolve()
+
+LATEST_NODE_LIB_PATH = Path(NODE_LIB_DIRPATH,
+                            NODE_LIB_FILENAME).resolve()
+
+PREVIEW_COLLECTIONS = {}

src/bioxelnodes/exceptions.py

@@ -0,0 +1,6 @@
+# This file is kept for backward compatibility
+# Custom exceptions have been replaced with built-in exceptions:
+# CancelledByUser -> CancelledError
+# NoContent -> ValueError
+# NoFound -> LookupError
+# Incompatible -> ValueError

src/bioxelnodes/layer.py

@@ -0,0 +1,290 @@
+import json
+import time
+from typing import Any, List, Dict
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+import bpy
+import numpy as np
+
+try:
+    import openvdb as vdb
+except ImportError:
+    vdb = None
+
+from .bioxel.layer import Layer
+from .utils import ndarray_to_png
+
+LAYERS_JSON = "bioxel_layers"
+
+
+def cache_layer_data(layer: Layer, cache_path: str):
+    """
+    Cache the given Layer's data as one or more VDB files.
+
+    - For multi-frame layers, writes per-frame VDB files named data.0001.vdb, data.0002.vdb, ...
+    - For single-frame layers, writes a single data.vdb file.
+    - Applies basic type handling:
+      - label/scalar layers collapse channel dimension via max.
+      - scalar layers are offset to avoid negative values.
+    - The VDB grids will have their transform set from layer.affine but no additional metadata is written.
+
+    Parameters:
+    - layer: Layer object containing ndarray data and metadata.
+    - cache_path: directory path where VDB files will be written (created if missing).
+    """
+    data = layer.data
+
+    # 处理标量/标签类型（去除通道维度）
+    if layer.kind in ["label", "scalar"]:
+        data = np.amax(data, -1)
+
+    # 标量类型偏移处理（避免负值）
+    offset = 0
+    if layer.kind in ["scalar"]:
+        data = data.astype(np.float32)
+        orig_min = float(np.min(data))
+        if orig_min < 0:
+            offset = -orig_min
+        data = data + np.full_like(data, offset)
+
+    # 创建缓存目录
+    cache_path = Path(cache_path)
+    cache_path.mkdir(parents=True, exist_ok=True)
+
+    # 多帧序列处理
+    if layer.frame_count > 1:
+        for f in range(layer.frame_count):
+            # 根据图层类型创建VDB网格
+            if layer.kind in ["label", "scalar"]:
+                grid = vdb.FloatGrid()
+                grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32))
+            else:  # 颜色类型
+                grid = vdb.Vec3SGrid()
+                grid.copyFromArray(data[f, :, :, :, :].copy().astype(np.float32))
+
+            # 仅设置transform，不存储metadata
+            grid.transform = vdb.createLinearTransform(layer.affine.transpose())
+            grid.name = layer.kind
+
+            # 保存序列帧VDB
+            data_filepath = cache_path / f"data.{str(f+1).zfill(4)}.vdb"
+            vdb.write(str(data_filepath), grids=[grid])
+
+    else:
+        # 单帧处理
+        if layer.kind in ["label", "scalar"]:
+            grid = vdb.FloatGrid()
+            grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32))
+        else:  # 颜色类型
+            grid = vdb.Vec3SGrid()
+            grid.copyFromArray(data[0, :, :, :, :].copy().astype(np.float32))
+
+        # 仅设置transform，不存储metadata
+        grid.transform = vdb.createLinearTransform(layer.affine.transpose())
+        grid.name = layer.kind
+
+        # 保存单帧VDB
+        data_filepath = cache_path / "data.vdb"
+        vdb.write(str(data_filepath), grids=[grid])
+
+
+def cache_layer_snapshot(layer: Layer, cache_path: str):
+    """
+    Create and save a low-resolution snapshot (numpy .npy) of the layer and generate PNG slices.
+
+    - Saves a 3D numpy ndarray snapshot to <cache_path>/snapshot.npy.
+    - Then creates per-Z PNGs in the same directory via snapshot_to_pngs.
+
+    Parameters:
+    - layer: Layer to snapshot (expects Layer.snapshot method).
+    - cache_path: destination directory where snapshot.npy and PNGs will be created.
+    """
+    cache_path = Path(cache_path)
+    cache_path.mkdir(parents=True, exist_ok=True)
+
+    snapshot_filepath = cache_path / "snapshot.npy"
+    snapshot = layer.snapshot((64, 64, 32))
+    np.save(str(snapshot_filepath), snapshot)
+    snapshot_to_pngs(
+        snapshot, str(cache_path), normalize=layer.kind in ["scalar", "vector"]
+    )
+
+    if layer.kind in ["scalar", "vector", "color"]:
+        plt.figure(figsize=(8, 8))
+
+        def plot_histogram(plt, data, color="black"):
+            flattened = data.flatten()
+            x_min = np.percentile(flattened, 1)
+            x_max = np.percentile(flattened, 99)
+
+            n, bins, _ = plt.hist(
+                flattened,
+                bins=50,  # 自动根据数据密度调整bins数量（避免空柱）
+                range=(x_min, x_max),  # 只显示核心区域，省略稀疏部分
+                alpha=0,
+                edgecolor="none",  # 去除边框，使柱形更紧凑
+            )
+            bin_centers = 0.5 * (bins[1:] + bins[:-1])  # 计算每个bin的中点
+            plt.plot(bin_centers, n, color=color, linewidth=4)  # 折线
+            plt.fill_between(bin_centers, n, color=color, alpha=0.1)
+
+        if layer.kind == "scalar":
+            plot_histogram(plt, layer.data[:, :, :, 0], color="black")
+        elif layer.kind in ["vector", "color"]:
+            plot_histogram(plt, layer.data[:, :, :, 0], color="tomato")
+            plot_histogram(plt, layer.data[:, :, :, 1], color="yellowgreen")
+            plot_histogram(plt, layer.data[:, :, :, 2], color="xkcd:azure")
+
+        plt.yscale("log")
+        plt.gca().get_yaxis().set_visible(False)
+        plt.xticks(fontsize=32, rotation=45)  # 调整字体大小（数值越大字体越大）
+
+        ax = plt.gca()
+        ax.spines["top"].set_visible(False)
+        ax.spines["right"].set_visible(False)
+        ax.spines["left"].set_visible(False)  # 隐藏左边框
+
+        # 调整布局避免标签被截断
+        plt.tight_layout()
+
+        # 保存图片到指定路径
+        save_path = cache_path / "histogram.png"
+        plt.savefig(save_path, bbox_inches="tight", pad_inches=0.1)  # 减少边缘留白)
+
+        # 关闭图像释放资源
+        plt.close()
+
+
+def snapshot_to_pngs(snapshot, cache_path: str, normalize=False):
+    """
+    Convert a 3D/4D snapshot ndarray into per-slice PNG files.
+
+    - snapshot is expected with axes order X, Y, Z, (C optional).
+    - Writes files snapshot_0.png ... snapshot_{Z-1}.png into cache_path.
+    - Uses ndarray_to_png to perform the per-slice conversion.
+
+    Parameters:
+    - snapshot: numpy ndarray (X, Y, Z[, C])
+    - cache_path: directory where generated PNGs are stored.
+    """
+    cache_path = Path(cache_path)
+    cache_path.mkdir(parents=True, exist_ok=True)
+
+    if normalize:
+        mn = float(np.percentile(snapshot, 50))
+        mx = float(np.percentile(snapshot, 99))
+        if mx - mn > 1e-8:
+            snapshot = (snapshot - mn) / (mx - mn)
+        else:
+            snapshot = np.clip(snapshot, 0.0, 1.0)
+
+    shape = snapshot.shape
+    for zidx in range(shape[2]):
+        array = snapshot[:, :, zidx, :]
+        ndarray_to_png(array, str(cache_path / f"snapshot_{zidx}.png"))
+
+
+def get_layer_caches() -> List[Dict[str, Any]]:
+    """
+    Read the saved layer metadata list from Blender's internal text datablock.
+
+    - Looks for a text datablock named by LAYERS_JSON ("bioxel_layers").
+    - Returns the parsed list of layer dictionaries if present; otherwise returns an empty list.
+
+    Returns:
+    - list of layer metadata dictionaries (possibly empty)
+    """
+    # 检查文本数据块是否存在
+    if LAYERS_JSON not in bpy.data.texts:
+        return []
+
+    # 加载并解析数据
+    layers_text = bpy.data.texts[LAYERS_JSON]
+    try:
+        layers_data = json.loads(layers_text.as_string())
+        # 确保返回格式为列表
+        return layers_data if isinstance(layers_data, list) else []
+    except:
+        return []
+
+
+def set_layer_caches(layers_data: List[Dict[str, Any]]):
+    """
+    Write the provided list of layer metadata dictionaries into the Blender text datablock.
+
+    - Ensures the LAYERS_JSON text datablock exists, then overwrites it with pretty JSON.
+
+    Parameters:
+    - layers_data: list of serializable dictionaries describing the layers
+    """
+    # 获取或创建文本数据块
+    if LAYERS_JSON not in bpy.data.texts:
+        bpy.data.texts.new(LAYERS_JSON)
+    layers_text = bpy.data.texts[LAYERS_JSON]
+    # 写入数据
+    layers_text.clear()
+    layers_text.write(json.dumps(layers_data, indent=4))
+
+
+def save_layers_to_cache(layers: List[Layer], cache_dir: str) -> List[Dict[str, Any]]:
+    """
+    Save multiple Layer objects into cache folders.
+
+    For each layer:
+    - Generates a unique cache id.
+    - Writes VDB files and a low-resolution snapshot (.npy) plus PNG slices under cache_dir/<cache_id>/.
+
+    Returns:
+    - List of layer cache metadata dictionaries.
+    """
+    cache_infos = []
+
+    cache_dir_path = Path(cache_dir)
+    cache_dir_path.mkdir(parents=True, exist_ok=True)
+
+    for idx, layer in enumerate(layers):
+        cache_id = str(int(time.time())) + str(idx)
+        cache_path = cache_dir_path / str(cache_id)
+        cache_layer_data(layer, cache_path)
+        cache_layer_snapshot(layer, cache_path)
+
+        # build layer_info
+        cache_info = {
+            "id": cache_id,
+            "name": layer.name,
+            "kind": layer.kind,
+            "shape": layer.shape,
+            "affine": layer.affine.tolist(),
+            "bioxel_size": layer.bioxel_size[0],
+            "dtype": layer.dtype.str,
+            "dtype_num": layer.dtype.num,
+            "frame_count": layer.frame_count,
+            "channel_count": layer.channel_count,
+            "offset": max(0, -layer.min),
+            "min": layer.min,
+            "max": layer.max,
+            "path": bpy.path.abspath(str(cache_path)),
+            "snapshot_z": 0.5,
+        }
+
+        cache_infos.append(cache_info)
+
+    return cache_infos
+
+
+def save_layers_to_json(layers: List[Layer], cache_dir: str) -> List[int]:
+    """
+    Save multiple Layer objects into cache folders and the internal layers text datablock.
+    """
+    existing_data = get_layer_caches()
+    cache_infos = save_layers_to_cache(layers, cache_dir)
+
+    added_ids = []
+    for cache_info in cache_infos:
+        existing_data.append(cache_info)
+        added_ids.append(cache_info["id"])
+
+    set_layer_caches(existing_data)
+    print(f"Successfully added {len(added_ids)} layers to the internal text datablock")
+    return added_ids