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

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

refactor: Clean up AGENTS.md and remove outdated test files

.claude/commands/opsx/apply.md

@@ -0,0 +1,152 @@
+---
+name: "OPSX: Apply"
+description: Implement tasks from an OpenSpec change (Experimental)
+category: Workflow
+tags: [workflow, artifacts, experimental]
+---
+
+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

.claude/commands/opsx/archive.md

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+---
+name: "OPSX: Archive"
+description: Archive a completed change in the experimental workflow
+category: Workflow
+tags: [workflow, archive, experimental]
+---
+
+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

.claude/commands/opsx/explore.md

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+---
+name: "OPSX: Explore"
+description: "Enter explore mode - think through ideas, investigate problems, clarify requirements"
+category: Workflow
+tags: [workflow, explore, experimental, thinking]
+---
+
+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

.claude/commands/opsx/propose.md

@@ -0,0 +1,106 @@
+---
+name: "OPSX: Propose"
+description: Propose a new change - create it and generate all artifacts in one step
+category: Workflow
+tags: [workflow, artifacts, experimental]
+---
+
+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

.claude/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

.claude/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

.claude/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

.claude/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

.gitattributes

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

.github/workflows/release.yml

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

.gitignore

@@ -1,6 +1,51 @@
+# Tempary files
+temp
+sandbox.*
+notes/
+
+# Environments
+.env
+.envrc
+.venv
+.env.*
+!.env.example
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+.secrets
+.secrets.*
+!.secrets.example
+secrets/
+SECRETS/
+secrets.bak/
+
+# Claude
+.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
@@ -123,16 +210,187 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-pythonlib*
+# pytype static type analyzer
+.pytype/
 
-*.blend1
+# Cython debug symbols
+cython_debug/
 
-blendcache_*
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
 
-*.ipynb
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
 
-.secrets
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
 
-.vdb
+# Ruff stuff:
+.ruff_cache/
 
+# 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/
+
+
+# Scipy
 !scipy_ndimage/*/**

.obsidian/app.json

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

.obsidian/snippets/omoolab.css

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

.python-version

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

.vscode/BioxelNodes.code-workspace

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

AGENTS.md

@@ -0,0 +1,19 @@
+## 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

CLAUDE.md

@@ -0,0 +1 @@
+@AGENTS.md

LICENSE

@@ -1,21 +1,674 @@
-MIT License
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
 
-Copyright (c) 2024 OmooLab
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+                            Preamble
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
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+
+  Some devices are designed to deny users access to install or run
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+
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+
+  The precise terms and conditions for copying, distribution and
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+
+                       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
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+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -13,50 +13,33 @@ Bioxel Nodes is a Blender addon for scientific volumetric data visualization. It
 
 ![cover](https://omoolab.github.io/BioxelNodes/latest/assets/cover.png)
 
+## Features
+
 -   Realistic rendering result, also support EEVEE NEXT.
--   Support multiple formats.
+-   Support many formats：.dcm, .jpg, .tif, .nii, .nrrd, .ome, .mrc...
 -   Support 4D volumetric data.
--   All kinds of cutters.
+-   Many kinds of cutters.
 -   Simple and powerful nodes.
 -   Based on blender natively, can work without addon.
 
+| ![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://omoolab.github.io/BioxelNodes/latest/installation) to begin your journey into visualizing volumetric data!**
 
 Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any problems with this add-on.
 
-## Support Multiple Formats
+## Citation
 
-| Format | EXT                                      |
-| ------ | ---------------------------------------- |
-| DICOM  | .dcm, .DCM, .DICOM, .ima, .IMA           |
-| BMP    | .bmp, .BMP                               |
-| JPEG   | .jpg, .JPG, .jpeg, .JPEG                 |
-| PNG    | .png, .PNG                               |
-| TIFF   | .tif, .TIF, .tiff, .TIFF                 |
-| Nifti  | .nia, .nii, .nii.gz, .hdr, .img, .img.gz |
-| Nrrd   | .nrrd, .nhdr                             |
-| HDF5   | .hdf, .h4, .hdf4, .he2, .h5, .hdf5, .he5 |
-| OME    | .ome.tiff, .ome.tif                      |
-| MRC    | .mrc, .mrc.gz, .map, .map.gz             |
+If you want to cite this work, you can cite it from Zenodo:
 
-## Support 4D volumetric data
-
-![4d](https://omoolab.github.io/BioxelNodes/latest/assets/4d-time.gif)
-
-🥰 4D volumetric data can also be imported into Blender.
-
-## Support EEVEE NEXT
-
-![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
-
-👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:
-
-1. Only one cutter supported.
-2. EEVEE result is not that great as Cycles does.
+[![DOI](https://zenodo.org/badge/786623459.svg)](https://zenodo.org/badge/latestdoi/786623459)
 
 ## Known Limitations
 
--   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
+-   Only one cutter supported in EEVEE render
+-   Shader fail to work when convert to mesh.
 -   Section surface cannot be generated when convert to mesh (will be supported soon)
 
 ## Roadmap

bioxelnodes/__init__.py

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

bioxelnodes/bioxelutils/common.py

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

bioxelnodes/bioxelutils/container.py

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

bioxelnodes/bioxelutils/layer.py

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

bioxelnodes/bioxelutils/node.py

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

bioxelnodes/blender_manifest.toml

@@ -1,37 +0,0 @@
-schema_version = "1.0.0"
-
-id = "bioxelnodes"
-version = "1.0.4"
-name = "Bioxel Nodes"
-tagline = "For scientific volumetric data visualization in Blender"
-maintainer = "Ma Nan <icrdr2010@outlook.com>"
-type = "add-on"
-website = "https://omoolab.github.io/BioxelNodes/latest"
-
-tags = ["Geometry Nodes", "Render", "Import-Export"]
-blender_version_min = "4.2.0"
-license = ['SPDX:GPL-3.0-or-later']
-copyright = ["2024 OmooLab"]
-platforms = ["windows-x64", "linux-x64", "macos-arm64", "macos-x64"]
-
-wheels = [
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl",
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-macosx_11_0_arm64.whl",
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-win_amd64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_arm64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/lxml-5.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-macosx_11_0_arm64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-macosx_10_9_x86_64.whl",
-  "./wheels/h5py-3.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-  "./wheels/tifffile-2024.7.24-py3-none-any.whl",
-  "./wheels/pyometiff-1.0.0-py3-none-any.whl",
-  "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
-  "./wheels/transforms3d-0.4.2-py3-none-any.whl"
-]
-
-[permissions]
-files = "Import/export volume data from/to disk"

bioxelnodes/constants.py

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

bioxelnodes/exceptions.py

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

bioxelnodes/menus.py

@@ -1,434 +0,0 @@
-import bpy
-
-from .constants import MENU_ITEMS, VERSIONS
-from .node_menu import NodeMenu
-
-from .bioxelutils.common import (get_container_obj,
-                                 get_container_layer_objs, get_layer_label,
-                                 get_layer_prop_value, get_node_version, is_incompatible)
-from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer,
-                              RemoveSelectedLayers, SaveSelectedLayersCache,
-                              ResampleLayer, SignScalar, CombineLabels,
-                              FillByLabel, FillByThreshold, FillByRange)
-from .operators.container import (AddLocator, AddSlicer, ContainerProps,
-                                  SaveContainerLayersCache, RemoveContainerMissingLayers,
-                                  SaveContainer, LoadContainer,
-                                  AddPieCutter, AddPlaneCutter,
-                                  AddCylinderCutter, AddCubeCutter, AddSphereCutter,
-                                  ExtractBboxWire, ExtractMesh, ExtractShapeWire,
-                                  ExtractNodeMesh, ExtractNodeBboxWire, ExtractNodeShapeWire)
-
-from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor)
-from .operators.misc import (CleanTemp, Help,
-                             ReLinkNodeLib, RemoveAllMissingLayers,
-                             RenderSettingPreset, SaveAllLayersCache,
-                             SaveNodeLib, SliceViewer)
-
-
-class IncompatibleMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_INCOMPATIBLE"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        tip_text = "please downgrade addon version."
-        node_version = get_node_version()
-        if node_version:
-            version_str = "v"+".".join([str(i) for i in list(node_version)])
-            tip_text = f"please downgrade addon version to {version_str}."
-
-        layout = self.layout
-        layout.label(text="Incompatible node version detected.")
-        layout.separator()
-        layout.label(
-            text="If you still want to edit this file with bioxel nodes, ")
-        layout.label(text=tip_text)
-        layout.separator()
-        layout.label(text="If this file is archived, "
-                     "please relink node library, ")
-        layout.label(text="check if it still works, "
-                     "then save node library.")
-        layout.separator()
-        layout.menu(ReLinkNodeLibMenu.bl_idname)
-        layout.operator(SaveNodeLib.bl_idname)
-
-        layout.separator()
-        layout.menu(DangerZoneMenu.bl_idname)
-
-        layout.separator()
-        layout.menu(RenderSettingMenu.bl_idname)
-
-        layout.separator()
-        layout.operator(Help.bl_idname,
-                        icon=Help.bl_icon)
-
-
-class FetchLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_ADD_LAYER"
-    bl_label = "Fetch Layer"
-
-    def draw(self, context):
-        container_obj = get_container_obj(bpy.context.active_object)
-        layer_objs = get_container_layer_objs(container_obj)
-        layout = self.layout
-
-        for layer_obj in layer_objs:
-            op = layout.operator(FetchLayer.bl_idname,
-                                 text=get_layer_label(layer_obj))
-            op.layer_obj_name = layer_obj.name
-
-
-class ExtractFromContainerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_PICK"
-    bl_label = "Extract from Container"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ExtractMesh.bl_idname)
-        layout.operator(ExtractShapeWire.bl_idname)
-        layout.operator(ExtractBboxWire.bl_idname)
-
-
-class AddCutterMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_CUTTERS"
-    bl_label = "Add a Cutter"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(AddPlaneCutter.bl_idname,
-                        icon=AddPlaneCutter.bl_icon, text="Plane Cutter")
-        layout.operator(AddCylinderCutter.bl_idname,
-                        icon=AddCylinderCutter.bl_icon, text="Cylinder Cutter")
-        layout.operator(AddCubeCutter.bl_idname,
-                        icon=AddCubeCutter.bl_icon, text="Cube Cutter")
-        layout.operator(AddSphereCutter.bl_idname,
-                        icon=AddSphereCutter.bl_icon, text="Sphere Cutter")
-        layout.operator(AddPieCutter.bl_idname,
-                        icon=AddPieCutter.bl_icon, text="Pie Cutter")
-
-
-class ImportLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_IMPORTLAYER"
-    bl_label = "Import Volumetric Data (Init)"
-    bl_icon = "FILE_NEW"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ImportAsScalar.bl_idname,
-                        text="as Scalar")
-        layout.operator(ImportAsLabel.bl_idname,
-                        text="as Label")
-        layout.operator(ImportAsColor.bl_idname,
-                        text="as Color")
-
-
-class AddLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_ADDLAYER"
-    bl_label = "Import Volumetric Data (Add)"
-    bl_icon = "FILE_NEW"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ImportAsScalar.bl_idname,
-                        text="as Scalar")
-        layout.operator(ImportAsLabel.bl_idname,
-                        text="as Label")
-        layout.operator(ImportAsColor.bl_idname,
-                        text="as Color")
-
-
-class ModifyLayerMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_MODIFYLAYER"
-    bl_label = "Modify Layer"
-    bl_icon = "FILE_NEW"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(SignScalar.bl_idname,
-                        icon=SignScalar.bl_icon)
-        layout.operator(FillByThreshold.bl_idname,
-                        icon=FillByThreshold.bl_icon)
-        layout.operator(FillByRange.bl_idname,
-                        icon=FillByRange.bl_icon)
-        layout.operator(FillByLabel.bl_idname,
-                        icon=FillByLabel.bl_icon)
-        layout.operator(CombineLabels.bl_idname,
-                        icon=CombineLabels.bl_icon)
-
-
-class ReLinkNodeLibMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_RELINK"
-    bl_label = "Relink Node Library"
-
-    def draw(self, context):
-        layout = self.layout
-
-        for index, version in enumerate(VERSIONS):
-            op = layout.operator(ReLinkNodeLib.bl_idname,
-                                 text=version["label"])
-            op.index = index
-
-
-class RenderSettingMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_RENDER"
-    bl_label = "Render Setting Presets"
-
-    def draw(self, context):
-        layout = self.layout
-        for k, v in RenderSettingPreset.PRESETS.items():
-            op = layout.operator(RenderSettingPreset.bl_idname,
-                                 text=v)
-            op.preset = k
-
-
-class DangerZoneMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_DANGER"
-    bl_label = "Danger Zone"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(CleanTemp.bl_idname)
-
-
-class BioxelNodesTopbarMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_TOPBAR"
-    bl_label = "Bioxel Nodes"
-
-    def draw(self, context):
-        layout = self.layout
-
-        layout.menu(ImportLayerMenu.bl_idname,
-                    icon=ImportLayerMenu.bl_icon)
-        layout.operator(LoadContainer.bl_idname)
-
-        layout.separator()
-        layout.operator(SaveAllLayersCache.bl_idname)
-        layout.operator(RemoveAllMissingLayers.bl_idname)
-
-        layout.separator()
-        layout.menu(ReLinkNodeLibMenu.bl_idname)
-        layout.operator(SaveNodeLib.bl_idname)
-
-        layout.separator()
-        layout.menu(DangerZoneMenu.bl_idname)
-
-        layout.separator()
-        layout.menu(RenderSettingMenu.bl_idname)
-
-        layout.separator()
-        layout.operator(Help.bl_idname,
-                        icon=Help.bl_icon)
-
-
-def TOPBAR(self, context):
-    layout = self.layout
-
-    if is_incompatible():
-        layout.menu(IncompatibleMenu.bl_idname)
-    else:
-        layout.menu(BioxelNodesTopbarMenu.bl_idname)
-
-
-class NodeHeadMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_NODE_HEAD"
-    bl_label = "Bioxel Nodes"
-    bl_icon = "FILE_VOLUME"
-
-    def draw(self, context):
-
-        layout = self.layout
-        layout.menu(AddLayerMenu.bl_idname,
-                    icon=AddLayerMenu.bl_icon)
-        layout.operator(SaveContainer.bl_idname)
-
-        layout.separator()
-        layout.operator(ContainerProps.bl_idname)
-        layout.menu(ExtractFromContainerMenu.bl_idname)
-
-        layout.separator()
-        layout.operator(SaveContainerLayersCache.bl_idname,
-                        icon=SaveContainerLayersCache.bl_icon)
-        layout.operator(RemoveContainerMissingLayers.bl_idname)
-
-        layout.separator()
-        layout.operator(AddLocator.bl_idname,
-                        icon=AddLocator.bl_icon)
-        layout.operator(AddSlicer.bl_idname,
-                        icon=AddSlicer.bl_icon)
-        layout.menu(AddCutterMenu.bl_idname)
-
-        layout.separator()
-        layout.menu(FetchLayerMenu.bl_idname)
-
-
-class NodeContextMenu(bpy.types.Menu):
-    bl_idname = "BIOXELNODES_MT_NODE_CONTEXT"
-    bl_label = "Bioxel Nodes"
-    bl_icon = "FILE_VOLUME"
-
-    def draw(self, context):
-        layout = self.layout
-        layout.operator(ExtractNodeMesh.bl_idname)
-        layout.operator(ExtractNodeShapeWire.bl_idname)
-        layout.operator(ExtractNodeBboxWire.bl_idname)
-
-        layout.separator()
-        layout.operator(SaveSelectedLayersCache.bl_idname,
-                        icon=SaveSelectedLayersCache.bl_icon)
-        layout.operator(RemoveSelectedLayers.bl_idname)
-
-        layout.separator()
-        layout.operator(RenameLayer.bl_idname,
-                        icon=RenameLayer.bl_icon)
-        layout.operator(RetimeLayer.bl_idname)
-        layout.operator(RelocateLayer.bl_idname)
-
-        layout.separator()
-        layout.operator(ResampleLayer.bl_idname,
-                        icon=ResampleLayer.bl_icon)
-        layout.operator(SignScalar.bl_idname)
-        layout.operator(FillByThreshold.bl_idname)
-        layout.operator(FillByRange.bl_idname)
-        layout.operator(FillByLabel.bl_idname)
-        layout.operator(CombineLabels.bl_idname)
-
-
-def NODE_CONTEXT(self, context):
-    if is_incompatible():
-        return
-
-    container_obj = context.object
-    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
-    is_container = get_container_obj(container_obj)
-
-    if not is_geo_nodes or not is_container:
-        return
-
-    layout = self.layout
-    layout.separator()
-    layout.menu(NodeContextMenu.bl_idname)
-
-
-def NODE_HEAD(self, context):
-    if is_incompatible():
-        return
-
-    container_obj = context.object
-    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
-    is_container = get_container_obj(container_obj)
-
-    if not is_geo_nodes or not is_container:
-        return
-
-    layout = self.layout
-    layout.separator()
-    layout.menu(NodeHeadMenu.bl_idname)
-
-
-def NODE_PROP(self, context):
-    if is_incompatible():
-        return
-
-    container_obj = context.object
-    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
-    is_container = get_container_obj(container_obj)
-    self.bl_label = "Group"
-
-    if not is_geo_nodes or not is_container:
-        return
-
-    if container_obj.modifiers[0].node_group != context.space_data.edit_tree:
-        return
-
-    self.bl_label = "Bioxel Nodes"
-
-    layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL
-    layer_list = layer_list_UL.layer_list
-    layer_list.clear()
-
-    for layer_obj in get_container_layer_objs(container_obj):
-        layer_item = layer_list.add()
-        layer_item.label = get_layer_label(layer_obj)
-        layer_item.obj_name = layer_obj.name
-        layer_item.info_text = "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}"
-                                          for prop in ["kind",
-                                                       "bioxel_size",
-                                                       "shape",
-                                                       "frame_count",
-                                                       "channel_count",
-                                                       "min", "max"]])
-
-    layout = self.layout
-    layout.label(text="Layer List")
-    split = layout.row()
-    split.template_list(listtype_name="BIOXELNODES_UL_layer_list",
-                        list_id="layer_list",
-                        dataptr=layer_list_UL,
-                        propname="layer_list",
-                        active_dataptr=layer_list_UL,
-                        active_propname="layer_list_active",
-                        item_dyntip_propname="info_text",
-                        rows=20)
-
-    # sidebar = split.column(align=True)
-    # sidebar.menu(AddLayerMenu.bl_idname,
-    #              icon=AddLayerMenu.bl_icon, text="")
-
-    # sidebar.operator(SaveContainerLayersCache.bl_idname,
-    #                  icon=SaveContainerLayersCache.bl_icon, text="")
-    # sidebar.operator(RemoveContainerMissingLayers.bl_idname,
-    #                  icon=RemoveContainerMissingLayers.bl_icon, text="")
-
-    # sidebar.separator()
-    # sidebar.operator(SaveSelectedLayersCache.bl_idname,
-    #                  icon=SaveSelectedLayersCache.bl_icon, text="")
-    # sidebar.operator(RemoveSelectedLayers.bl_idname,
-    #                  icon=RemoveSelectedLayers.bl_icon, text="")
-
-    # sidebar.separator()
-    # sidebar.operator(RenameLayer.bl_idname,
-    #                  icon=RenameLayer.bl_icon, text="")
-    # sidebar.operator(ResampleLayer.bl_idname,
-    #                  icon=ResampleLayer.bl_icon, text="")
-    # sidebar.operator(RetimeLayer.bl_idname,
-    #                  icon=RetimeLayer.bl_icon, text="")
-
-    # sidebar.separator()
-    # sidebar.operator(SignScalar.bl_idname,
-    #                  icon=SignScalar.bl_icon, text="")
-    # sidebar.operator(FillByThreshold.bl_idname,
-    #                  icon=FillByThreshold.bl_icon, text="")
-    # sidebar.operator(FillByRange.bl_idname,
-    #                  icon=FillByRange.bl_icon, text="")
-    # sidebar.operator(FillByLabel.bl_idname,
-    #                  icon=FillByLabel.bl_icon, text="")
-
-    # sidebar.separator()
-    # layout.separator()
-
-
-def VIEW3D_TOPBAR(self, context):
-    layout = self.layout
-    layout.operator(SliceViewer.bl_idname)
-
-
-node_menu = NodeMenu(
-    menu_items=MENU_ITEMS
-)
-
-
-def add():
-    node_menu.register()
-    bpy.types.VIEW3D_HT_header.append(VIEW3D_TOPBAR)
-    bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR)
-    bpy.types.NODE_PT_node_tree_properties.prepend(NODE_PROP)
-    bpy.types.NODE_MT_editor_menus.append(NODE_HEAD)
-    bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT)
-
-
-def remove():
-    bpy.types.VIEW3D_HT_header.remove(VIEW3D_TOPBAR)
-    bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR)
-    bpy.types.NODE_PT_node_tree_properties.remove(NODE_PROP)
-    bpy.types.NODE_MT_editor_menus.remove(NODE_HEAD)
-    bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT)
-    node_menu.unregister()

bioxelnodes/node_menu.py

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

bioxelnodes/operators/container.py

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

bioxelnodes/operators/layer.py

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

bioxelnodes/operators/misc.py

@@ -1,276 +0,0 @@
-import webbrowser
-import bpy
-from pathlib import Path
-import shutil
-
-from ..bioxelutils.common import get_all_layer_objs, get_node_lib_path, get_node_version, is_missing_layer, set_file_prop
-from .layer import RemoveLayers, SaveLayersCache
-
-from ..constants import LATEST_NODE_LIB_PATH, VERSIONS
-from ..utils import get_cache_dir
-
-
-class ReLinkNodeLib(bpy.types.Operator):
-    bl_idname = "bioxelnodes.relink_node_lib"
-    bl_label = "Relink Node Library"
-    bl_description = "Relink all nodes to addon library source"
-    bl_options = {'UNDO'}
-
-    index: bpy.props.IntProperty()  # type: ignore
-
-    def execute(self, context):
-        node_version = VERSIONS[self.index]['node_version']
-        lib_path = get_node_lib_path(node_version) \
-            if self.index != 0 else LATEST_NODE_LIB_PATH
-
-        node_libs = []
-        for node_group in bpy.data.node_groups:
-            if node_group.name.startswith("BioxelNodes"):
-                node_lib = node_group.library
-                if node_lib:
-                    node_libs.append(node_lib)
-
-        node_libs = list(set(node_libs))
-
-        for node_lib in node_libs:
-            node_lib.filepath = str(lib_path)
-            # FIXME: may cause crash
-            node_lib.reload()
-
-        set_file_prop("node_version", node_version)
-
-        self.report({"INFO"}, f"Successfully relinked.")
-
-        return {'FINISHED'}
-
-
-class SaveNodeLib(bpy.types.Operator):
-    bl_idname = "bioxelnodes.save_node_lib"
-    bl_label = "Save Node Library"
-    bl_description = "Save node library file to local"
-    bl_options = {'UNDO'}
-
-    lib_dir: bpy.props.StringProperty(
-        name="Library Directory",
-        subtype='DIR_PATH',
-        default="//"
-    )  # type: ignore
-
-    def execute(self, context):
-        node_version = get_node_version()
-
-        if node_version is None:
-            node_version = VERSIONS[0]["node_version"]
-        else:
-            if node_version not in [v["node_version"] for v in VERSIONS]:
-                node_version = VERSIONS[0]["node_version"]
-
-        if node_version == VERSIONS[0]["node_version"]:
-            lib_path = LATEST_NODE_LIB_PATH
-        else:
-            lib_path = get_node_lib_path(node_version)
-
-        version_str = "v"+".".join([str(i) for i in list(node_version)])
-
-        lib_dir = bpy.path.abspath(self.lib_dir)
-        local_lib_path: Path = Path(lib_dir,
-                                    f"BioxelNodes_{version_str}.blend").resolve()
-        node_lib_path: Path = lib_path
-        blend_path = Path(bpy.path.abspath("//")).resolve()
-
-        if local_lib_path != node_lib_path:
-            shutil.copy(node_lib_path, local_lib_path)
-
-        libs = []
-        for node_group in bpy.data.node_groups:
-            if node_group.name.startswith("BioxelNodes"):
-                if node_group.library:
-                    libs.append(node_group.library)
-
-        libs = list(set(libs))
-        for lib in libs:
-            lib.filepath = bpy.path.relpath(str(local_lib_path),
-                                            start=str(blend_path))
-
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_props_dialog(self)
-        return {'RUNNING_MODAL'}
-
-    @classmethod
-    def poll(cls, context):
-        return bpy.data.is_saved
-
-
-class CleanTemp(bpy.types.Operator):
-    bl_idname = "bioxelnodes.clear_temp"
-    bl_label = "Clean Temp"
-    bl_description = "Clean all cache in temp (include other project cache)"
-
-    def execute(self, context):
-        cache_dir = get_cache_dir()
-        try:
-            shutil.rmtree(cache_dir)
-            self.report({"INFO"}, f"Successfully cleaned temp.")
-            return {'FINISHED'}
-        except:
-            self.report({"WARNING"},
-                        "Fail to clean temp, you may do it manually.")
-            return {'CANCELLED'}
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message="All temp files will be removed, include other project cache, do you still want to clean?")
-        return {'RUNNING_MODAL'}
-
-
-class RenderSettingPreset(bpy.types.Operator):
-    bl_idname = "bioxelnodes.render_setting_preset"
-    bl_label = "Render Setting Presets"
-    bl_description = "Render setting presets for bioxel"
-    bl_options = {'UNDO'}
-
-    PRESETS = {
-        "performance": "Performance",
-        "balance": "Balance",
-        "quality": "Quality",
-    }
-
-    preset: bpy.props.EnumProperty(name="Preset",
-                                   default="balance",
-                                   items=[(k, v, "")
-                                          for k, v in PRESETS.items()])  # type: ignore
-
-    def execute(self, context):
-        if self.preset == "performance":
-            # EEVEE
-            bpy.context.scene.eevee.use_taa_reprojection = False
-            bpy.context.scene.eevee.volumetric_tile_size = '2'
-            bpy.context.scene.eevee.volumetric_shadow_samples = 32
-            bpy.context.scene.eevee.volumetric_samples = 64
-            bpy.context.scene.eevee.volumetric_ray_depth = 1
-            bpy.context.scene.eevee.use_volumetric_shadows = True
-
-            # Cycles
-            bpy.context.scene.cycles.shading_system = True
-            bpy.context.scene.cycles.volume_bounces = 0
-            bpy.context.scene.cycles.transparent_max_bounces = 4
-            bpy.context.scene.cycles.volume_preview_step_rate = 4
-            bpy.context.scene.cycles.volume_step_rate = 4
-
-        elif self.preset == "balance":
-            # EEVEE
-            bpy.context.scene.eevee.use_taa_reprojection = False
-            bpy.context.scene.eevee.volumetric_tile_size = '2'
-            bpy.context.scene.eevee.volumetric_shadow_samples = 64
-            bpy.context.scene.eevee.volumetric_samples = 128
-            bpy.context.scene.eevee.volumetric_ray_depth = 8
-            bpy.context.scene.eevee.use_volumetric_shadows = True
-
-            # Cycles
-            bpy.context.scene.cycles.shading_system = True
-            bpy.context.scene.cycles.volume_bounces = 4
-            bpy.context.scene.cycles.transparent_max_bounces = 8
-            bpy.context.scene.cycles.volume_preview_step_rate = 1
-            bpy.context.scene.cycles.volume_step_rate = 1
-
-        elif self.preset == "quality":
-            # EEVEE
-            bpy.context.scene.eevee.use_taa_reprojection = False
-            bpy.context.scene.eevee.volumetric_tile_size = '2'
-            bpy.context.scene.eevee.volumetric_shadow_samples = 128
-            bpy.context.scene.eevee.volumetric_samples = 256
-            bpy.context.scene.eevee.volumetric_ray_depth = 16
-            bpy.context.scene.eevee.use_volumetric_shadows = True
-
-            # Cycles
-            bpy.context.scene.cycles.shading_system = True
-            bpy.context.scene.cycles.volume_bounces = 8
-            bpy.context.scene.cycles.transparent_max_bounces = 16
-            bpy.context.scene.cycles.volume_preview_step_rate = 0.5
-            bpy.context.scene.cycles.volume_step_rate = 0.5
-
-        return {'FINISHED'}
-
-
-class SliceViewer(bpy.types.Operator):
-    bl_idname = "bioxelnodes.slice_viewer"
-    bl_label = "Slice Viewer"
-    bl_description = "A preview scene setting for viewing slicers"
-    bl_icon = "FILE_VOLUME"
-
-    def execute(self, context):
-        bpy.context.scene.eevee.use_taa_reprojection = False
-        bpy.context.scene.eevee.volumetric_tile_size = '2'
-        bpy.context.scene.eevee.volumetric_shadow_samples = 128
-        bpy.context.scene.eevee.volumetric_samples = 128
-        bpy.context.scene.eevee.volumetric_ray_depth = 1
-        bpy.context.scene.eevee.use_volumetric_shadows = False
-
-        for area in bpy.context.screen.areas:
-            if area.type == 'VIEW_3D':
-                area.spaces[0].shading.type = 'MATERIAL'
-                area.spaces[0].shading.studio_light = 'studio.exr'
-                area.spaces[0].shading.studiolight_intensity = 2.5
-                area.spaces[0].shading.use_scene_lights = False
-                area.spaces[0].shading.use_scene_world = False
-
-        return {'FINISHED'}
-
-
-def get_all_layers(layer_filter=None):
-    def _layer_filter(layer_obj):
-        return True
-
-    layer_filter = layer_filter or _layer_filter
-    layer_objs = get_all_layer_objs()
-    return [obj for obj in layer_objs if layer_filter(obj)]
-
-
-class SaveAllLayersCache(bpy.types.Operator, SaveLayersCache):
-    bl_idname = "bioxelnodes.save_all_layers_cache"
-    bl_label = "Save All Layers Cache"
-    bl_description = "Save all cache of this file"
-    bl_icon = "FILE_TICK"
-
-    success_msg = "Successfully saved all layers."
-
-    def get_layers(self, context):
-        def is_not_missing(layer_obj):
-            return not is_missing_layer(layer_obj)
-        return get_all_layers(is_not_missing)
-
-
-class RemoveAllMissingLayers(bpy.types.Operator, RemoveLayers):
-    bl_idname = "bioxelnodes.remove_all_missing_layers"
-    bl_label = "Remove All Missing Layers"
-    bl_description = "Remove all current container missing layers"
-    bl_icon = "BRUSH_DATA"
-
-    success_msg = "Successfully removed all missing layers."
-
-    def get_layers(self, context):
-        def is_missing(layer_obj):
-            return is_missing_layer(layer_obj)
-        return get_all_layers(is_missing)
-
-    def invoke(self, context, event):
-        context.window_manager.invoke_confirm(self,
-                                              event,
-                                              message=f"Are you sure to remove all **Missing** layers?")
-        return {'RUNNING_MODAL'}
-
-
-class Help(bpy.types.Operator):
-    bl_idname = "bioxelnodes.help"
-    bl_label = "Need Help?"
-    bl_description = "Online Manual for Beginner"
-    bl_icon = "HELP"
-
-    def execute(self, context):
-        webbrowser.open(
-            'https://omoolab.github.io/BioxelNodes/latest/', new=2)
-
-        return {'FINISHED'}

bioxelnodes/preferences.py

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

bioxelnodes/props.py

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

bioxelnodes/utils.py

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

build.py

@@ -12,12 +12,14 @@ class Platform:
     blender_tag: str
 
 
-required_packages = ["SimpleITK==2.3.1",
+required_packages = ["SimpleITK==2.5.5",
                      "pyometiff==1.0.0",
                      "mrcfile==1.5.1",
-                     "h5py==3.11.0",
+                     "h5py==3.14.0",
                      "transforms3d==0.4.2",
-                     "tifffile==2024.7.24"]
+                     "tifffile==2024.7.24",
+                     "matplotlib==3.10.7",
+                     "pillow==11.2.1"]
 
 
 platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
@@ -40,9 +42,9 @@ def run_python(args: str):
     subprocess.run([python] + args.split(" "))
 
 
-def build_extension(platform: Platform, python_version="3.11") -> None:
-    wheel_dirpath = Path("./bioxelnodes/wheels")
-    toml_filepath = Path("bioxelnodes/blender_manifest.toml")
+def build_extension(platform: Platform, python_version: str) -> None:
+    wheel_dirpath = Path("./src/bioxelnodes/wheels")
+    toml_filepath = Path("./src/bioxelnodes/blender_manifest.toml")
     scipy_ndimage_dirpath = Path("./scipy_ndimage", platform.blender_tag)
 
     # download required_packages
@@ -50,17 +52,19 @@ def build_extension(platform: Platform, python_version="3.11") -> None:
         f"-m pip download {' '.join(required_packages)} --dest {wheel_dirpath.as_posix()} --only-binary=:all: --python-version={python_version} --platform={platform.pypi_suffix}"
     )
 
-    for f in wheel_dirpath.glob('*.whl'):
+    for f in wheel_dirpath.glob("*.whl"):
         if any([package in f.name for package in packages_to_remove]):
             f.unlink(missing_ok=True)
 
-        elif platform.blender_tag == "macos-arm64" and \
-                "lxml" in f.name and "universal2" in f.name:
-            f.rename(Path(f.parent,
-                          f.name.replace("universal2", "arm64")))
+        elif (
+            platform.blender_tag == "macos-arm64"
+            and "lxml" in f.name
+            and "universal2" in f.name
+        ):
+            f.rename(Path(f.parent, f.name.replace("universal2", "arm64")))
 
     for ndimage_filepath in scipy_ndimage_dirpath.iterdir():
-        to_filepath = Path("./bioxelnodes/bioxel/scipy", ndimage_filepath.name)
+        to_filepath = Path("./src/bioxelnodes/bioxel/scipy", ndimage_filepath.name)
         shutil.copy(ndimage_filepath, to_filepath)
         
     # Load the TOML file
@@ -68,14 +72,8 @@ def build_extension(platform: Platform, python_version="3.11") -> None:
         manifest = tomlkit.parse(file.read())
 
     manifest["platforms"] = [platform.blender_tag]
-    manifest["wheels"] = [f"./wheels/{f.name}"
-                          for f in wheel_dirpath.glob('*.whl')]
-
-    # build = tomlkit.table(True)
-    # generated = tomlkit.table()
-    # generated["platforms"] = [platform.blender_tag]
-    # generated["wheels"] = [f"./wheels/{f.name}"
-    #                        for f in wheel_dirpath.glob('*.whl')]
+    manifest["wheels"] = [
+        f"./wheels/{f.name}" for f in wheel_dirpath.glob("*.whl")]
 
     # build.append('generated', generated)
     # manifest.append('build', build)
@@ -88,8 +86,9 @@ def build_extension(platform: Platform, python_version="3.11") -> None:
 
 def main():
     platform_name = sys.argv[1]
+    python_version = sys.argv[2] or "3.11"
     platform = platforms[platform_name]
-    build_extension(platform)
+    build_extension(platform, python_version)
 
 
 if __name__ == "__main__":

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

@@ -1,30 +1,34 @@
-[tool.poetry]
+[project]
 name = "bioxelnodes"
-version = "1.0.4"
+version = "1.0.9"
 description = ""
-authors = ["Ma Nan <icrdr2010@outlook.com>"]
-license = "MIT"
+authors = [{ name = "Ma Nan", 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",
+]
 
-[tool.poetry.dependencies]
-python = ">=3.11.0,<3.12.dev0"
-simpleitk = "2.3.1"
-pyometiff = "1.0.0"
-mrcfile = "1.5.1"
-h5py = "3.11.0"
-transforms3d = "0.4.2"
-
-[tool.poetry.group.dev.dependencies]
-bpy = "^4.2.0"
-pytest = "^8.3.2"
-pytest-dependency = "^0.6.0"
-pytest-cov = "^5.0.0"
-mkdocs = "^1.6.0"
-mkdocs-material = "^9.5.30"
-autopep8 = "^2.3.1"
-mike = "^2.1.2"
-tomlkit = "^0.13.0"
+[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",
+]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"

requirements.txt

@@ -1,5 +0,0 @@
-SimpleITK==2.3.1     # Insight Segmentation and Registration Toolkit.
-pyometiff==1.0.0     # .ome.tiff
-mrcfile==1.5.1       # .map
-h5py==3.11.0         # .h5
-transforms3d==0.4.2  # transforms

src/bioxelnodes/__init__.py

@@ -0,0 +1,92 @@
+import bpy
+import bpy.utils.previews as previews
+
+from .constants import NODE_LIB_DIRPATH, PREVIEW_COLLECTIONS
+from .props import _bioxel_layer_items, _update_layer_gallery, _update_snapshot_z
+
+from . import auto_load
+from . import menus
+
+auto_load.init()
+
+
+def add_asset_library():
+    """Add Bioxel asset library, ensuring only one exists by removing duplicates first."""
+    if not NODE_LIB_DIRPATH.exists():
+        print(f"Node library path does not exist - {NODE_LIB_DIRPATH}")
+        return
+
+    lib_path_str = str(NODE_LIB_DIRPATH)
+    prefs = bpy.context.preferences.filepaths.asset_libraries
+
+    # Add new library
+    new_lib = prefs.new()
+    new_lib.name = "O Bioxel"
+    new_lib.path = lib_path_str
+    new_lib.import_method = "PACK"
+
+    print(f"Add Bioxel Nodes library: {lib_path_str}")
+
+
+def remove_asset_library_if_exists():
+    """Remove the Bioxel asset library entry if it was added (by path or name)."""
+    lib_path_str = str(NODE_LIB_DIRPATH)
+    prefs = bpy.context.preferences.filepaths.asset_libraries
+
+    for lib in list(prefs):
+        try:
+            if "Bioxel" in lib.name or lib.path == lib_path_str:
+                prefs.remove(lib)
+        except Exception:
+            continue
+
+
+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()
+    remove_asset_library_if_exists()
+    add_asset_library()
+
+
+def unregister():
+    remove_asset_library_if_exists()
+    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()

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

@@ -38,24 +38,19 @@ def register():
 
 def unregister():
     for cls in reversed(ordered_classes):
-        try:
         bpy.utils.unregister_class(cls)
-        except Exception as e:
-            print(f"Fail to unregister {cls}, skiped")
 
     for module in modules:
-        try:
         if module.__name__ == __name__:
             continue
         if hasattr(module, "unregister"):
             module.unregister()
-        except Exception as e:
-            print(f"Fail to unregister {module}, skiped")
 
 
 # Import modules
 #################################################
 
+
 def get_all_submodules(directory):
     return list(iter_submodules(directory, __package__))
 
@@ -78,6 +73,7 @@ def iter_submodule_names(path, root=""):
 # Find classes to register
 #################################################
 
+
 def get_ordered_classes_to_register(modules):
     return toposort(get_register_deps_dict(modules))
 
@@ -119,7 +115,7 @@ def get_dependency_from_annotation(value):
 
 
 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)
@@ -130,7 +126,7 @@ def iter_my_deps_from_parent_id(cls, my_classes_by_idname):
 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
 
@@ -150,29 +146,45 @@ def iter_classes_in_module(module):
 
 
 def get_register_base_types():
-    return set(getattr(bpy.types, name) for name in [
-        "Panel", "Operator", "PropertyGroup", "FileHandler",
-        "AddonPreferences", "Header", "Menu",
-        "Node", "NodeSocket", "NodeTree",
-        "UIList", "RenderEngine",
-        "Gizmo", "GizmoGroup",
-    ] if hasattr(bpy.types, name))
+    return set(
+        getattr(bpy.types, name)
+        for name in [
+            "Panel",
+            "Operator",
+            "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}
+        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/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/layer.py

@@ -1,6 +1,12 @@
 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 . import scipy
 from . import scipy as ndi
 
@@ -150,3 +156,32 @@ class Layer():
 
         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/scipy/_filters.py

@@ -39,7 +39,6 @@ from . import _ni_support
 from . import _nd_image
 
 
-
 def _invalid_origin(origin, lenw):
     return (origin < -(lenw // 2)) or (origin > (lenw - 1) // 2)
 
@@ -73,7 +72,6 @@ def _complex_via_real_components(func, input, weights, output, cval, **kwargs):
     return output
 
 
-
 def correlate1d(input, weights, axis=-1, output=None, mode="reflect",
                 cval=0.0, origin=0):
     """Calculate a 1-D correlation along the given axis.
@@ -133,7 +131,6 @@ def correlate1d(input, weights, axis=-1, output=None, mode="reflect",
     return output
 
 
-
 def convolve1d(input, weights, axis=-1, output=None, mode="reflect",
                cval=0.0, origin=0):
     """Calculate a 1-D convolution along the given axis.
@@ -205,7 +202,6 @@ def _gaussian_kernel1d(sigma, order, radius):
         return q * phi_x
 
 
-
 def gaussian_filter1d(input, sigma, axis=-1, order=0, output=None,
                       mode="reflect", cval=0.0, truncate=4.0, *, radius=None):
     """1-D Gaussian filter.
@@ -274,7 +270,6 @@ def gaussian_filter1d(input, sigma, axis=-1, order=0, output=None,
     return correlate1d(input, weights, axis, output, mode, cval, 0)
 
 
-
 def gaussian_filter(input, sigma, order=0, output=None,
                     mode="reflect", cval=0.0, truncate=4.0, *, radius=None,
                     axes=None):
@@ -381,7 +376,6 @@ def gaussian_filter(input, sigma, order=0, output=None,
     return output
 
 
-
 def prewitt(input, axis=-1, output=None, mode="reflect", cval=0.0):
     """Calculate a Prewitt filter.
 
@@ -443,7 +437,6 @@ def prewitt(input, axis=-1, output=None, mode="reflect", cval=0.0):
     return output
 
 
-
 def sobel(input, axis=-1, output=None, mode="reflect", cval=0.0):
     """Calculate a Sobel filter.
 
@@ -501,7 +494,6 @@ def sobel(input, axis=-1, output=None, mode="reflect", cval=0.0):
     return output
 
 
-
 def generic_laplace(input, derivative2, output=None, mode="reflect",
                     cval=0.0,
                     extra_arguments=(),
@@ -549,7 +541,6 @@ def generic_laplace(input, derivative2, output=None, mode="reflect",
     return output
 
 
-
 def laplace(input, output=None, mode="reflect", cval=0.0):
     """N-D Laplace filter based on approximate second derivatives.
 
@@ -584,7 +575,6 @@ def laplace(input, output=None, mode="reflect", cval=0.0):
     return generic_laplace(input, derivative2, output, mode, cval)
 
 
-
 def gaussian_laplace(input, sigma, output=None, mode="reflect",
                      cval=0.0, **kwargs):
     """Multidimensional Laplace filter using Gaussian second derivatives.
@@ -637,7 +627,6 @@ def gaussian_laplace(input, sigma, output=None, mode="reflect",
                            extra_keywords=kwargs)
 
 
-
 def generic_gradient_magnitude(input, derivative, output=None,
                                mode="reflect", cval=0.0,
                                extra_arguments=(), extra_keywords=None):
@@ -690,7 +679,6 @@ def generic_gradient_magnitude(input, derivative, output=None,
     return output
 
 
-
 def gaussian_gradient_magnitude(input, sigma, output=None,
                                 mode="reflect", cval=0.0, **kwargs):
     """Multidimensional gradient magnitude using Gaussian derivatives.
@@ -792,7 +780,6 @@ def _correlate_or_convolve(input, weights, output, mode, cval, origin,
     return output
 
 
-
 def correlate(input, weights, output=None, mode='reflect', cval=0.0,
               origin=0):
     """
@@ -856,7 +843,6 @@ def correlate(input, weights, output=None, mode='reflect', cval=0.0,
                                   origin, False)
 
 
-
 def convolve(input, weights, output=None, mode='reflect', cval=0.0,
              origin=0):
     """
@@ -967,7 +953,6 @@ def convolve(input, weights, output=None, mode='reflect', cval=0.0,
                                   origin, True)
 
 
-
 def uniform_filter1d(input, size, axis=-1, output=None,
                      mode="reflect", cval=0.0, origin=0):
     """Calculate a 1-D uniform filter along the given axis.
@@ -1018,7 +1003,6 @@ def uniform_filter1d(input, size, axis=-1, output=None,
     return output
 
 
-
 def uniform_filter(input, size=3, output=None, mode="reflect",
                    cval=0.0, origin=0, *, axes=None):
     """Multidimensional uniform filter.
@@ -1088,7 +1072,6 @@ def uniform_filter(input, size=3, output=None, mode="reflect",
     return output
 
 
-
 def minimum_filter1d(input, size, axis=-1, output=None,
                      mode="reflect", cval=0.0, origin=0):
     """Calculate a 1-D minimum filter along the given axis.
@@ -1145,7 +1128,6 @@ def minimum_filter1d(input, size, axis=-1, output=None,
     return output
 
 
-
 def maximum_filter1d(input, size, axis=-1, output=None,
                      mode="reflect", cval=0.0, origin=0):
     """Calculate a 1-D maximum filter along the given axis.
@@ -1302,7 +1284,6 @@ def _min_or_max_filter(input, size, footprint, structure, output, mode,
     return output
 
 
-
 def minimum_filter(input, size=None, footprint=None, output=None,
                    mode="reflect", cval=0.0, origin=0, *, axes=None):
     """Calculate a multidimensional minimum filter.
@@ -1350,7 +1331,6 @@ def minimum_filter(input, size=None, footprint=None, output=None,
                               cval, origin, 1, axes)
 
 
-
 def maximum_filter(input, size=None, footprint=None, output=None,
                    mode="reflect", cval=0.0, origin=0, *, axes=None):
     """Calculate a multidimensional maximum filter.
@@ -1398,7 +1378,6 @@ def maximum_filter(input, size=None, footprint=None, output=None,
                               cval, origin, 0, axes)
 
 
-
 def _rank_filter(input, rank, size=None, footprint=None, output=None,
                  mode="reflect", cval=0.0, origin=0, operation='rank',
                  axes=None):
@@ -1491,7 +1470,6 @@ def _rank_filter(input, rank, size=None, footprint=None, output=None,
         return output
 
 
-
 def rank_filter(input, rank, size=None, footprint=None, output=None,
                 mode="reflect", cval=0.0, origin=0, *, axes=None):
     """Calculate a multidimensional rank filter.
@@ -1535,7 +1513,6 @@ def rank_filter(input, rank, size=None, footprint=None, output=None,
                         origin, 'rank', axes=axes)
 
 
-
 def median_filter(input, size=None, footprint=None, output=None,
                   mode="reflect", cval=0.0, origin=0, *, axes=None):
     """
@@ -1586,7 +1563,6 @@ def median_filter(input, size=None, footprint=None, output=None,
                         origin, 'median', axes=axes)
 
 
-
 def percentile_filter(input, percentile, size=None, footprint=None,
                       output=None, mode="reflect", cval=0.0, origin=0, *,
                       axes=None):
@@ -1630,7 +1606,6 @@ def percentile_filter(input, percentile, size=None, footprint=None,
                         cval, origin, 'percentile', axes=axes)
 
 
-
 def generic_filter1d(input, function, filter_size, axis=-1,
                      output=None, mode="reflect", cval=0.0, origin=0,
                      extra_arguments=(), extra_keywords=None):
@@ -1718,7 +1693,6 @@ def generic_filter1d(input, function, filter_size, axis=-1,
     return output
 
 
-
 def generic_filter(input, function, size=None, footprint=None,
                    output=None, mode="reflect", cval=0.0, origin=0,
                    extra_arguments=(), extra_keywords=None):

src/bioxelnodes/bioxel/scipy/_interpolation.py

@@ -21,6 +21,7 @@ def _prepad_for_spline_filter(input, mode, cval):
         padded = input
     return padded, npad
 
+
 def spline_filter1d(input, order=3, axis=-1, output=np.float64,
                     mode='mirror'):
     """

src/bioxelnodes/bioxel/scipy/_ni_support.py

@@ -83,7 +83,8 @@ def _get_output(output, input, shape=None, complex_output=False):
     elif isinstance(output, (type, np.dtype)):
         # Classes (like `np.float32`) and dtypes are interpreted as dtype
         if complex_output and np.dtype(output).kind != 'c':
-            warnings.warn("promoting specified output dtype to complex", stacklevel=3)
+            warnings.warn(
+                "promoting specified output dtype to complex", stacklevel=3)
             output = np.promote_types(output, np.complex64)
         output = np.zeros(shape, dtype=output)
     elif isinstance(output, str):

src/bioxelnodes/bioxel/skimage/_warps.py

@@ -3,6 +3,7 @@ import numpy as np
 from .. import scipy as ndi
 from ._utils import convert_to_float
 
+
 def _clip_warp_output(input_image, output_image, mode, cval, clip):
     """Clip output image to range of values of input image.
 

src/bioxelnodes/bioxel/skimage/dtype.py

@@ -39,7 +39,8 @@ _integer_types = (
     np.uintp,
     np.uintc,
 )
-_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max) for t in _integer_types}
+_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max)
+                   for t in _integer_types}
 dtype_range = {
     bool: (False, True),
     np.bool_: (False, True),
@@ -175,7 +176,8 @@ def _scale(a, n, m, copy=True):
         # downscale with precision loss
         if copy:
             b = np.empty(a.shape, _dtype_bits(kind, m))
-            np.floor_divide(a, 2 ** (n - m), out=b, dtype=a.dtype, casting='unsafe')
+            np.floor_divide(a, 2 ** (n - m), out=b,
+                            dtype=a.dtype, casting='unsafe')
             return b
         else:
             a //= 2 ** (n - m)
@@ -282,7 +284,8 @@ def _convert(image, dtype, force_copy=False, uniform=False):
         return image
 
     if not (dtype_in in _supported_types and dtype_out in _supported_types):
-        raise ValueError(f'Cannot convert from {dtypeobj_in} to ' f'{dtypeobj_out}.')
+        raise ValueError(
+            f'Cannot convert from {dtypeobj_in} to ' f'{dtypeobj_out}.')
 
     if kind_in in 'ui':
         imin_in = np.iinfo(dtype_in).min
@@ -318,7 +321,8 @@ def _convert(image, dtype, force_copy=False, uniform=False):
 
         if not uniform:
             if kind_out == 'u':
-                image_out = np.multiply(image, imax_out, dtype=computation_type)
+                image_out = np.multiply(
+                    image, imax_out, dtype=computation_type)
             else:
                 image_out = np.multiply(
                     image, (imax_out - imin_out) / 2, dtype=computation_type
@@ -327,7 +331,8 @@ def _convert(image, dtype, force_copy=False, uniform=False):
             np.rint(image_out, out=image_out)
             np.clip(image_out, imin_out, imax_out, out=image_out)
         elif kind_out == 'u':
-            image_out = np.multiply(image, imax_out + 1, dtype=computation_type)
+            image_out = np.multiply(
+                image, imax_out + 1, dtype=computation_type)
             np.clip(image_out, 0, imax_out, out=image_out)
         else:
             image_out = np.multiply(

src/bioxelnodes/blender_manifest.toml

@@ -0,0 +1,45 @@
+schema_version = "1.0.0"
+
+id = "bioxelnodes"
+version = "2.0.0"
+name = "Bioxel Nodes"
+tagline = "For scientific volumetric data visualization in Blender"
+maintainer = "Nan <icrdr2010@outlook.com>"
+type = "add-on"
+website = "https://omoolab.github.io/BioxelNodes/latest"
+
+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/packaging-26.2-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/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 +1,278 @@
+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_json(layers: List[Layer], cache_dir: str) -> List[int]:
+    """
+    Save multiple Layer objects into the internal layers text datablock.
+
+    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>/.
+    - Appends an entry describing the layer into the b i o x e l _ l a y e r s text datablock.
+
+    Returns:
+    - List of generated cache ids for the saved layers.
+    """
+    existing_data = get_layer_caches()
+    added_ids = []
+
+    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,
+        }
+
+        existing_data.append(cache_info)
+        added_ids.append(cache_id)
+
+    set_layer_caches(existing_data)
+    print(f"Successfully added {len(added_ids)} layers to the internal text datablock")
+    return added_ids

src/bioxelnodes/menus.py

@@ -0,0 +1,105 @@
+import bpy
+from .operators.structure import ExtractMesh
+
+from .operators.io import ImportAsLabel, ImportAsScalar, ImportAsColor
+from .operators.misc import (
+    CleanTemp,
+    Help,
+    RenderSettingPreset,
+    TogglePhantom,
+)
+
+
+class ImportLayerMenu(bpy.types.Menu):
+    bl_idname = "BIOXEL_MT_IMPORTLAYER"
+    bl_label = "Import Volumetric Data (Init)"
+    bl_icon = "FILE_NEW"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(ImportAsScalar.bl_idname, text="as Scalar")
+        layout.operator(ImportAsLabel.bl_idname, text="as Label")
+        layout.operator(ImportAsColor.bl_idname, text="as Color")
+
+
+class RenderSettingMenu(bpy.types.Menu):
+    bl_idname = "BIOXEL_MT_RENDER"
+    bl_label = "Render Setting Presets"
+
+    def draw(self, context):
+        layout = self.layout
+        for k, v in RenderSettingPreset.PRESETS.items():
+            op = layout.operator(RenderSettingPreset.bl_idname, text=v)
+            op.preset = k
+
+
+class DangerZoneMenu(bpy.types.Menu):
+    bl_idname = "BIOXEL_MT_DANGER"
+    bl_label = "Danger Zone"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(CleanTemp.bl_idname)
+
+
+class BioxelNodesTopbarMenu(bpy.types.Menu):
+    bl_idname = "BIOXEL_MT_TOPBAR"
+    bl_label = "Bioxel Nodes"
+
+    def draw(self, context):
+        layout = self.layout
+
+        layout.separator()
+        layout.menu(DangerZoneMenu.bl_idname)
+
+        layout.separator()
+        layout.operator(Help.bl_idname, icon=Help.bl_icon)
+
+
+class NodeContextMenu(bpy.types.Menu):
+    bl_idname = "BIOXEL_MT_NODE_CONTEXT"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(ExtractMesh.bl_idname)
+
+
+class ObjectContextMenu(bpy.types.Menu):
+    bl_idname = "BIOXEL_MT_OBJECT_CONTEXT"
+    bl_label = "Bioxel Nodes"
+    bl_icon = "FILE_VOLUME"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(TogglePhantom.bl_idname)
+
+
+def NODE_CONTEXT(self, context):
+    container_obj = context.object
+    is_geo_nodes = context.area.ui_type == "GeometryNodeTree"
+
+    if not is_geo_nodes or not container_obj:
+        return
+
+    layout = self.layout
+    layout.separator()
+    layout.menu(NodeContextMenu.bl_idname)
+
+
+# 定义添加到右键菜单的函数，放在首位
+def OBJECT_CONTEXT(self, context):
+    layout = self.layout
+    layout.separator()
+    layout.menu(ObjectContextMenu.bl_idname)
+
+
+def add():
+    bpy.types.VIEW3D_MT_object_context_menu.append(OBJECT_CONTEXT)
+    # bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT)
+
+
+def remove():
+    bpy.types.VIEW3D_MT_object_context_menu.remove(OBJECT_CONTEXT)
+    # bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT)

src/bioxelnodes/node.py

@@ -0,0 +1,149 @@
+from pathlib import Path
+import bpy
+
+# LookupError replaced with built-in LookupError
+from .constants import LATEST_NODE_LIB_PATH, NODE_LIB_FILENAME
+
+
+def move_node_to_node(node, target_node, offset=(0, 0)):
+    node.location.x = target_node.location.x + offset[0]
+    node.location.y = target_node.location.y + offset[1]
+
+
+def move_node_between_nodes(node, target_nodes, offset=(0, 0)):
+    xs = []
+    ys = []
+    for target_node in target_nodes:
+        xs.append(target_node.location.x)
+        ys.append(target_node.location.y)
+
+    node.location.x = sum(xs) / len(xs) + offset[0]
+    node.location.y = sum(ys) / len(ys) + offset[1]
+
+
+def get_node_type(node):
+    node_type = type(node).__name__
+    if node_type == "GeometryNodeGroup":
+        node_type = node.node_tree.name
+
+    return node_type
+
+
+def get_nodes_by_type(node_group, type_name: str):
+    return [node for node in node_group.nodes if get_node_type(node) == type_name]
+
+
+def get_node_tree(node_type: str, use_link=True):
+    try:
+        return bpy.data.node_groups[node_type]
+    except KeyError:
+        lib_path_str = str(LATEST_NODE_LIB_PATH)
+        with bpy.data.libraries.load(lib_path_str, link=use_link, relative=True) as (
+            data_from,
+            data_to,
+        ):
+            data_to.node_groups = [
+                n for n in data_from.node_groups if n == node_type]
+        node_tree = data_to.node_groups[0]
+
+        if node_tree is None:
+            raise LookupError("No custom node found")
+
+        return node_tree
+
+
+def assign_node_tree(node, node_tree):
+    node.node_tree = node_tree
+    node.width = 200.0
+    node.name = node_tree.name
+    return node
+
+
+def add_node_to_graph(node_name: str, node_group, node_label=None, use_link=True):
+    node_type = f"O {node_name}"
+    node_label = node_label or node_name
+
+    # Deselect all nodes first
+    for node in node_group.nodes:
+        if node.select:
+            node.select = False
+
+    node_tree = get_node_tree(node_type, use_link)
+    node = node_group.nodes.new("GeometryNodeGroup")
+    assign_node_tree(node, node_tree)
+
+    node.label = node_label
+    node.show_options = False
+    bpy.ops.node.view_selected()
+    return node
+
+
+def get_output_node(node_group):
+    try:
+        output_node = get_nodes_by_type(node_group, "NodeGroupOutput")[0]
+    except:
+        output_node = node_group.nodes.new("NodeGroupOutput")
+
+    return output_node
+
+
+def add_bioxel_node(name: str):
+    # bpy.ops.node.add_group_asset(
+    #     asset_library_type="CUSTOM",
+    #     asset_library_identifier = "O Bioxel",
+    #     relative_asset_identifier = "NodeTreO Crop Layer"
+    # )
+    # bpy.ops.node.add_group_asset(
+    #     asset_library_type="CUSTOM",
+    #     asset_library_identifier="O Bioxel",
+    #     relative_asset_identifier="Nodes.blend\\NodeTree\\O Render Structure"
+    # )
+
+    try:
+        node_tree = bpy.data.node_groups[name]
+    except KeyError:
+        bpy.ops.object.modifier_add_node_group(
+            asset_library_type="CUSTOM",
+            asset_library_identifier="O Bioxel",
+            relative_asset_identifier=f"{NODE_LIB_FILENAME}\\NodeTree\\{name}",
+        )
+        bpy.ops.object.modifier_remove(modifier=name)
+        try:
+            node_tree = bpy.data.node_groups[name]
+        except Exception as e:
+            raise e
+
+    bpy.ops.node.add_node(
+        "INVOKE_DEFAULT", type="GeometryNodeGroup", use_transform=True
+    )
+
+    node = bpy.context.active_node
+    node.node_tree = node_tree
+    node.show_options = False
+
+    return bpy.context.active_node
+
+
+def get_layer_nodes(node_group):
+    """Return all O Layer nodes in the given node_tree."""
+    return [
+        n
+        for n in node_group.nodes
+        if n.bl_idname == "GeometryNodeGroup"
+        and getattr(n, "node_tree", None)
+        and n.node_tree.name.startswith("O Layer")
+    ]
+
+
+def get_main_node_group(context):
+    space = getattr(context, "space_data", None) or getattr(
+        context, "space", None)
+    if not space:
+        return None
+    node_tree = getattr(space, "node_tree", None)
+    if not node_tree:
+        return None
+    # accept GeometryNodeTree by bl_idname or class name for compatibility
+    if getattr(node_tree, "bl_idname", "") == "GeometryNodeTree" or node_tree.__class__.__name__ == "GeometryNodeTree":
+        return node_tree
+    return None

src/bioxelnodes/operators/layer.py

@@ -0,0 +1,314 @@
+from pathlib import Path
+import shutil
+
+import bpy
+
+from ..node import add_bioxel_node, get_layer_nodes, get_main_node_group
+from ..utils import refresh_bioxel_panels
+from ..layer import get_layer_caches, set_layer_caches
+
+
+class RenameLayer(bpy.types.Operator):
+    """Rename a cached Bioxel layer"""
+
+    bl_idname = "bioxel.rename_layer"
+    bl_label = "Rename Layer"
+    bl_options = {"REGISTER", "UNDO"}
+
+    cache_id: bpy.props.StringProperty(options={"HIDDEN"})  # type: ignore
+    new_name: bpy.props.StringProperty(name="New name", default="")  # type: ignore
+
+    def invoke(self, context, event):
+        caches = get_layer_caches()
+        entry = next((c for c in caches if str(c.get("id", "")) == self.cache_id), None)
+        if entry:
+            self.new_name = str(entry.get("name", ""))
+        return context.window_manager.invoke_props_dialog(self)
+
+    def execute(self, context):
+        if not self.new_name:
+            self.report({"ERROR"}, "Name cannot be empty")
+            return {"CANCELLED"}
+
+        caches = get_layer_caches()
+        for c in caches:
+            if str(c.get("id", "")) == self.cache_id:
+                c["name"] = self.new_name
+                break
+
+        try:
+            set_layer_caches(caches)
+            refresh_bioxel_panels(context)
+            self.report({"INFO"}, "Layer renamed")
+            return {"FINISHED"}
+        except Exception as e:
+            self.report({"ERROR"}, f"Failed to save changes: {e}")
+            return {"CANCELLED"}
+
+
+class DeleteLayer(bpy.types.Operator):
+    """Delete a saved Bioxel layer"""
+
+    bl_idname = "bioxel.delete_layer"
+    bl_label = "Delete Layer"
+    bl_options = {"REGISTER", "UNDO"}
+
+    cache_id: bpy.props.StringProperty()  # type: ignore
+
+    def invoke(self, context, event):
+        return context.window_manager.invoke_confirm(self, event)
+
+    def execute(self, context):
+        if not self.cache_id:
+            self.report({"ERROR"}, "Missing cache id")
+            return {"CANCELLED"}
+
+        caches = get_layer_caches()
+        new_list = [c for c in caches if str(c.get("id", "")) != self.cache_id]
+        removed = next(
+            (c for c in caches if str(c.get("id", "")) == self.cache_id), None
+        )
+
+        try:
+            set_layer_caches(new_list)
+            refresh_bioxel_panels(context)
+        except Exception as e:
+            self.report({"ERROR"}, f"Failed to update layer list: {e}")
+            return {"CANCELLED"}
+
+        self.report({"INFO"}, "Layer removed")
+        return {"FINISHED"}
+
+
+# 添加图层到节点图的操作器
+class AddLayerNode(bpy.types.Operator):
+    """将选中的图层添加到几何节点图"""
+
+    bl_idname = "bioxel.add_layer_node"
+    bl_label = "添加图层节点"
+    bl_options = {"REGISTER", "UNDO"}
+
+    cache_id: bpy.props.StringProperty()  # type: ignore # 图层ID
+
+    def execute(self, context):
+        # 获取图层数据
+        caches = get_layer_caches()
+
+        # 查找目标图层
+        entry = next(
+            (c for c in caches if str(c.get("id", "")) == str(self.cache_id)), None
+        )
+
+        if not entry:
+            self.report({"ERROR"}, "Layer not found")
+            return {"CANCELLED"}
+
+        # 创建并设置节点属性
+        try:
+            layer_node = add_bioxel_node("O Layer")
+        except:
+            self.report({"ERROR"}, "Fail to add layer node")
+            return {"CANCELLED"}
+
+        layer_node.node_tree.make_local()
+        layer_node.inputs["Path"].default_value = entry["path"]
+        layer_node.inputs["Name"].default_value = entry["name"]
+        layer_node.inputs["Shape"].default_value = entry["shape"]
+        layer_node.inputs["Min"].default_value = entry["min"]
+        layer_node.inputs["Max"].default_value = entry["max"]
+        layer_node.inputs["ID"].default_value = entry["id"]
+
+        # 将特定属性隐藏到hidden面板
+        hidden_sockets = ["Path", "Shape", "Min", "Max", "ID", "Animation"]
+
+        if entry["frame_count"] > 1:
+            layer_node.inputs["Frame Count"].default_value = entry["frame_count"]
+            layer_node.inputs["Animation"].default_value = True
+        else:
+            hidden_sockets = hidden_sockets + ["Frame Count", "Frame Offset", "Cycle"]
+
+        # 将特定属性隐藏到hidden面板
+        for socket_name in hidden_sockets:
+            if socket_name in layer_node.inputs:
+                layer_node.inputs[socket_name].hide = True
+
+        for socket_name in layer_node.outputs.keys():
+            if socket_name != entry["kind"].capitalize():
+                layer_node.outputs[socket_name].hide = True
+
+        self.report({"INFO"}, f"Successfully created node: {entry['name']}")
+        return {"FINISHED"}
+
+
+class RelocatePath(bpy.types.Operator):
+    """Locate and update the missing layer folder, and update all related nodes"""
+
+    bl_idname = "bioxel.find_layer_folder"
+    bl_label = "Relocate"
+    bl_options = {"REGISTER", "UNDO"}
+
+    cache_id: bpy.props.StringProperty(options={"HIDDEN"})  # type: ignore
+
+    use_relative: bpy.props.BoolProperty(
+        name="Relative Path",
+        description="Store the path relative to the current Blender file",
+        default=True,
+    )  # type: ignore
+
+    directory: bpy.props.StringProperty(
+        name="Layer Folder",
+        description="Select the correct folder for this layer",
+        subtype="DIR_PATH",
+    )  # type: ignore
+
+    def invoke(self, context, event):
+        context.window_manager.fileselect_add(self)
+        return {"RUNNING_MODAL"}
+
+    def execute(self, context):
+        if not self.cache_id:
+            self.report({"ERROR"}, "Missing cache id")
+            return {"CANCELLED"}
+        if not self.directory:
+            self.report({"ERROR"}, "Please select a folder")
+            return {"CANCELLED"}
+
+        caches = get_layer_caches()
+        entry = next((c for c in caches if str(c.get("id", "")) == self.cache_id), None)
+        if not entry:
+            self.report({"ERROR"}, "Layer not found")
+            return {"CANCELLED"}
+
+        old_path = entry["path"]
+        new_path = (
+            bpy.path.relpath(self.directory)
+            if self.use_relative and bpy.data.filepath
+            else bpy.path.abspath(self.directory)
+        )
+        entry["path"] = new_path
+
+        set_layer_caches(caches)
+        refresh_bioxel_panels(context)
+
+        # 更新所有 node group 中 O Layer 节点的 Path
+        for node_group in bpy.data.node_groups:
+            for node in get_layer_nodes(node_group):
+                node_path = getattr(node.inputs.get("Path"), "default_value")
+                if node_path and node_path == old_path:
+                    node.inputs["Path"].default_value = new_path
+
+        self.report({"INFO"}, f"Cache path updated: {new_path}")
+        return {"FINISHED"}
+
+
+class SaveLayer(bpy.types.Operator):
+    """Copy the entire layer folder (named by id) to a target folder and update its path in the cache"""
+
+    bl_idname = "bioxel.cache_layer_to_folder"
+    bl_label = "Save Layer"
+    bl_options = {"REGISTER", "UNDO"}
+
+    cache_id: bpy.props.StringProperty(options={"HIDDEN"})  # type: ignore
+
+    use_relative: bpy.props.BoolProperty(
+        name="Relative Path",
+        description="Store the path relative to the current Blender file",
+        default=True,
+    )  # type: ignore
+
+    directory: bpy.props.StringProperty(
+        name="Target Folder",
+        description="Select a folder to cache the layer files",
+        subtype="DIR_PATH",
+    )  # type: ignore
+
+    def invoke(self, context, event):
+        # Default to Blender file directory if possible
+        blend_dir = Path(bpy.data.filepath).parent if bpy.data.filepath else Path.cwd()
+        context.window_manager.fileselect_add(self)
+        if not self.directory:
+            self.directory = str(blend_dir)
+        return {"RUNNING_MODAL"}
+
+    def execute(self, context):
+        if not self.cache_id:
+            self.report({"ERROR"}, "Missing cache id")
+            return {"CANCELLED"}
+        if not self.directory:
+            self.report({"ERROR"}, "Please select a target folder")
+            return {"CANCELLED"}
+
+        caches = get_layer_caches()
+        entry = next((c for c in caches if str(c.get("id")) == self.cache_id), None)
+        cache_id = entry.get("id")
+
+        if not entry:
+            self.report({"ERROR"}, "Layer not found")
+            return {"CANCELLED"}
+
+        old_path = entry["path"]
+        src_path = bpy.path.abspath(old_path)
+        if not src_path or not Path(src_path).is_dir():
+            self.report({"ERROR"}, "Source folder not found")
+            return {"CANCELLED"}
+
+        src_dir = Path(src_path).resolve()
+        dst_root = Path(self.directory)
+        # copy as a subfolder named by id
+        dst_dir = (dst_root / src_dir.name).resolve()
+
+        try:
+            if src_dir != dst_dir:
+                if dst_dir.exists():
+                    shutil.rmtree(dst_dir)
+                shutil.copytree(src_dir, dst_dir)
+
+                # Save as relative path if requested and possible
+
+            new_path = (
+                bpy.path.relpath(str(dst_dir))
+                if self.use_relative and bpy.data.filepath
+                else bpy.path.abspath(str(dst_dir))
+            )
+
+            entry["path"] = new_path
+
+            set_layer_caches(caches)
+            refresh_bioxel_panels(context)
+
+            # 遍历所有 node group
+            for node_group in bpy.data.node_groups:
+                for node in get_layer_nodes(node_group):
+                    if cache_id == getattr(node.inputs.get("ID"), "default_value"):
+                        node.inputs["Path"].default_value = new_path
+
+            self.report({"INFO"}, f"Layer cached to {dst_dir}")
+            return {"FINISHED"}
+        except Exception as e:
+            self.report({"ERROR"}, f"Failed to cache layer: {e}")
+            return {"CANCELLED"}
+
+
+class SelectAndFocusNode(bpy.types.Operator):
+    """Select and focus the specified node in the current node tree"""
+
+    bl_idname = "bioxel.select_and_focus_node"
+    bl_label = "Select and Focus Node"
+    node_name: bpy.props.StringProperty()  # type: ignore
+
+    def execute(self, context):
+        node_group = get_main_node_group(context)
+        if not node_group:
+            self.report({"ERROR"}, "No node group found.")
+            return {"CANCELLED"}
+        node = node_group.nodes.get(self.node_name)
+        if not node:
+            self.report({"ERROR"}, f"Node '{self.node_name}' not found.")
+            return {"CANCELLED"}
+        # Deselect all, select and focus this node
+        for n in node_group.nodes:
+            n.select = False
+        node.select = True
+        node_group.nodes.active = node
+        bpy.ops.node.view_selected()
+        return {"FINISHED"}

src/bioxelnodes/operators/misc.py

@@ -0,0 +1,251 @@
+import json
+import uuid
+import webbrowser
+import bpy
+from pathlib import Path
+import shutil
+
+from ..constants import LATEST_NODE_LIB_PATH
+from ..utils import (
+    get_all_layer_objs,
+    get_cache_dir,
+    get_node_version,
+    is_missing_layer,
+)
+
+
+class CleanTemp(bpy.types.Operator):
+    bl_idname = "bioxel.clear_temp"
+    bl_label = "Clean Temp"
+    bl_description = "Clean all cache in temp (include other project cache)"
+
+    def execute(self, context):
+        cache_dir = get_cache_dir()
+        try:
+            shutil.rmtree(cache_dir)
+            self.report({"INFO"}, f"Successfully cleaned temp.")
+            return {"FINISHED"}
+        except:
+            self.report(
+                {"WARNING"}, "Fail to clean temp, you may do it manually.")
+            return {"CANCELLED"}
+
+    def invoke(self, context, event):
+        context.window_manager.invoke_confirm(
+            self,
+            event,
+            message="All temp files will be removed, include other project cache, do you still want to clean?",
+        )
+        return {"RUNNING_MODAL"}
+
+
+class RenderSettingPreset(bpy.types.Operator):
+    bl_idname = "bioxel.render_setting_preset"
+    bl_label = "Render Setting Presets"
+    bl_description = "Render setting presets for bioxel"
+    bl_options = {"UNDO"}
+
+    PRESETS = {
+        "performance": "Performance",
+        "balance": "Balance",
+        "quality": "Quality",
+    }
+
+    preset: bpy.props.EnumProperty(
+        name="Preset", default="balance", items=[(k, v, "") for k, v in PRESETS.items()]
+    )  # type: ignore
+
+    def execute(self, context):
+        if self.preset == "performance":
+            # EEVEE
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            # bpy.context.scene.eevee.use_shadow_jitter_viewport = True
+            bpy.context.scene.eevee.volumetric_tile_size = "4"
+            bpy.context.scene.eevee.volumetric_shadow_samples = 32
+            bpy.context.scene.eevee.volumetric_samples = 64
+            bpy.context.scene.eevee.volumetric_ray_depth = 1
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.volume_bounces = 4
+            bpy.context.scene.cycles.transparent_max_bounces = 4
+            bpy.context.scene.cycles.volume_biased = True
+            bpy.context.scene.cycles.volume_preview_step_rate = 100
+            bpy.context.scene.cycles.volume_step_rate = 100
+
+        elif self.preset == "balance":
+            # EEVEE
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            # bpy.context.scene.eevee.use_shadow_jitter_viewport = True
+            bpy.context.scene.eevee.volumetric_tile_size = "2"
+            bpy.context.scene.eevee.volumetric_shadow_samples = 64
+            bpy.context.scene.eevee.volumetric_samples = 128
+            bpy.context.scene.eevee.volumetric_ray_depth = 8
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.volume_bounces = 8
+            bpy.context.scene.cycles.transparent_max_bounces = 16
+            bpy.context.scene.cycles.volume_biased = True
+            bpy.context.scene.cycles.volume_preview_step_rate = 10
+            bpy.context.scene.cycles.volume_step_rate = 10
+
+        elif self.preset == "quality":
+            # EEVEE
+            bpy.context.scene.eevee.use_taa_reprojection = False
+            # bpy.context.scene.eevee.use_shadow_jitter_viewport = True
+            bpy.context.scene.eevee.volumetric_tile_size = "1"
+            bpy.context.scene.eevee.volumetric_shadow_samples = 128
+            bpy.context.scene.eevee.volumetric_samples = 256
+            bpy.context.scene.eevee.volumetric_ray_depth = 16
+            bpy.context.scene.eevee.use_volumetric_shadows = True
+
+            # Cycles
+            bpy.context.scene.cycles.volume_bounces = 16
+            bpy.context.scene.cycles.transparent_max_bounces = 32
+            bpy.context.scene.cycles.volume_biased = False
+
+        return {"FINISHED"}
+
+
+class Help(bpy.types.Operator):
+    bl_idname = "bioxel.help"
+    bl_label = "Need Help?"
+    bl_description = "Online Manual for Beginner"
+    bl_icon = "HELP"
+
+    def execute(self, context):
+        webbrowser.open("https://docs.omoolab.xyz/bioxelnodes/latest/", new=2)
+
+        return {"FINISHED"}
+
+
+# 定义虚无化切换操作
+class TogglePhantom(bpy.types.Operator):
+    """Toggle object phantom state (ray invisible, no shadows, semi-transparent wireframe)"""
+
+    bl_idname = "bioxel.toggle_phantom"
+    bl_label = "Toggle Phantom"
+    bl_options = {"REGISTER", "UNDO"}
+
+    def execute(self, context):
+
+        obj = context.active_object
+        if not obj:
+            self.report({"WARNING"}, "No object selected")
+            return {"CANCELLED"}
+
+        # 获取3D视图空间
+        view_space = None
+        for area in bpy.context.screen.areas:
+            if area.type == "VIEW_3D":
+                for space in area.spaces:
+                    if space.type == "VIEW_3D":
+                        view_space = space
+                        break
+                if view_space:
+                    break
+
+        # 确保存储状态的文本数据块存在
+        text_name = "phantom_orig_states"
+        if text_name not in bpy.data.texts:
+            bpy.data.texts.new(text_name)
+
+        # 从文本数据块加载状态
+        states_text = bpy.data.texts[text_name]
+        try:
+            states = json.loads(states_text.as_string())
+        except:
+            states = {}
+
+        def get_obj_uuid(obj):
+            if "bioxel_uuid" not in obj:
+                obj["bioxel_uuid"] = uuid.uuid4().hex
+            return obj["bioxel_uuid"]
+
+        # 使用物体的唯一标识符来追踪
+        obj_uuid = get_obj_uuid(obj)
+
+        # 检查物体是否已经处于虚无化状态
+        is_phantom = (
+            obj.display_type == "SOLID"
+            and obj.show_wire
+            and obj.show_in_front
+            and round(obj.color[3], 2) == 0.10
+            and not obj.visible_camera
+            and not obj.visible_diffuse
+            and not obj.visible_glossy
+            and not obj.visible_transmission
+            and not obj.visible_volume_scatter
+            and not obj.visible_shadow
+        )
+
+        if is_phantom:
+            # 恢复原始状态
+            if obj_uuid in states:
+                state = states[obj_uuid]
+                obj.display_type = state["display_type"]
+                obj.show_wire = state["show_wire"]
+                obj.show_in_front = state["show_in_front"]
+                obj.color = state["color"]
+                obj.visible_camera = state["visible_camera"]
+                obj.visible_diffuse = state["visible_diffuse"]
+                obj.visible_glossy = state["visible_glossy"]
+                obj.visible_transmission = state["visible_transmission"]
+                obj.visible_volume_scatter = state["visible_volume_scatter"]
+                obj.visible_shadow = state["visible_shadow"]
+
+                # 恢复视图着色设置（如果之前有保存）
+                if view_space and "viewport_color_type" in state:
+                    view_space.shading.color_type = state["viewport_color_type"]
+
+                del states[obj_uuid]
+                self.report({"INFO"}, f"Object restored")
+        else:
+            # 保存原始状态
+            state_data = {
+                "display_type": obj.display_type,
+                "show_wire": obj.show_wire,
+                "show_in_front": obj.show_in_front,
+                "color": list(obj.color),  # 保存RGBA颜色值
+                "visible_camera": obj.visible_camera,
+                "visible_diffuse": obj.visible_diffuse,
+                "visible_glossy": obj.visible_glossy,
+                "visible_transmission": obj.visible_transmission,
+                "visible_volume_scatter": obj.visible_volume_scatter,
+                "visible_shadow": obj.visible_shadow,
+            }
+
+            # 检查并处理视图着色设置
+            if view_space:
+                # 保存当前视图着色设置
+                state_data["viewport_color_type"] = view_space.shading.color_type
+
+                # 检查当前是否为object, random或attribute
+                valid_types = {"OBJECT", "RANDOM", "ATTRIBUTE"}
+                if view_space.shading.color_type not in valid_types:
+                    # 改为object模式
+                    view_space.shading.color_type = "OBJECT"
+
+            states[obj_uuid] = state_data
+
+            # 设置虚无化状态
+            obj.display_type = "SOLID"  # 以实体方式显示
+            obj.show_wire = True  # 显示线框
+            obj.show_in_front = True  # 显示在其他物体前面
+            # 保持RGB不变，仅修改alpha透明度为0.1
+            obj.color[3] = 0.1
+            # 关闭所有射线可见性和投影
+            obj.visible_camera = False
+            obj.visible_diffuse = False
+            obj.visible_glossy = False
+            obj.visible_transmission = False
+            obj.visible_volume_scatter = False
+            obj.visible_shadow = False
+            self.report({"INFO"}, f"Object phantomed")
+
+        # 保存状态到文本数据块
+        states_text.clear()
+        states_text.write(json.dumps(states, indent=2))
+
+        return {"FINISHED"}

src/bioxelnodes/operators/node.py

@@ -1,12 +1,12 @@
 import bpy
 
-from ..bioxelutils.common import is_incompatible, local_lib_not_updated
-from ..bioxelutils.node import assign_node_tree, get_node_tree
+from ..utils import is_incompatible, local_lib_not_updated
+from ..node import assign_node_tree, get_node_tree
 from ..utils import get_use_link
 
 
 class AddNode(bpy.types.Operator):
-    bl_idname = "bioxelnodes.add_node"
+    bl_idname = "bioxel.add_node"
     bl_label = "Add Node"
     bl_options = {"REGISTER", "UNDO"}
 
@@ -24,7 +24,7 @@ class AddNode(bpy.types.Operator):
 
     @property
     def node_type(self):
-        return f"BioxelNodes_{self.node_name}"
+        return f"O {self.node_name}"
 
     def execute(self, context):
         space = context.space_data

src/bioxelnodes/operators/structure.py

@@ -0,0 +1,107 @@
+import bpy
+from ..utils import get_use_link
+from ..node import add_node_to_graph, get_output_node, get_main_node_group
+
+
+class ExtractMesh(bpy.types.Operator):
+    bl_idname = "bioxel.extract_mesh"
+    bl_label = "Extract Mesh"
+    bl_description = "Extract Mesh"
+    bl_icon = "OUTLINER_OB_MESH"
+    bl_options = {"UNDO"}
+
+    @classmethod
+    def poll(cls, context):
+        # Check if there is a selected node in the node group
+        node_group = get_main_node_group(context)
+        selected_nodes = [n for n in node_group.nodes if n.select]
+
+        if len(selected_nodes) == 0:
+            return False
+        else:
+            source_node = selected_nodes[0]
+            return "Structure" in source_node.outputs
+
+    def execute(self, context):
+        container_obj = context.object
+
+        if container_obj is None:
+            self.report({"WARNING"}, "Cannot find any bioxel container.")
+            return {"FINISHED"}
+
+        node_group = container_obj.modifiers[0].node_group
+        selected_nodes = [n for n in node_group.nodes if n.select]
+
+        source_node = selected_nodes[0]
+
+        # Check if the selected node has a "Structure" output
+        if "Structure" not in source_node.outputs:
+            self.report({"ERROR"}, "Selected node has no 'Structure' output.")
+            return {"CANCELLED"}
+
+        # 记录原始输出连接（用于后续复原）
+        output_node = get_output_node(node_group)
+        original_links = list(output_node.inputs[0].links)
+
+        # 添加Component to Mesh节点
+        to_mesh_node = add_node_to_graph(
+            "Structure to Mesh", node_group, use_link=get_use_link()
+        )
+
+        # 连接节点：源节点 -> Component to Mesh -> 输出节点
+        node_group.links.new(
+            source_node.outputs["Structure"], to_mesh_node.inputs[0])
+        node_group.links.new(to_mesh_node.outputs[0], output_node.inputs[0])
+
+        new_obj = None
+
+        try:
+            deps = context.evaluated_depsgraph_get()
+            eval_obj = container_obj.evaluated_get(deps)
+            # obtain evaluated mesh (from modifiers including Geometry Nodes)
+            mesh_eval = eval_obj.to_mesh()
+            if mesh_eval is None:
+                raise RuntimeError("Failed to produce evaluated mesh")
+
+            mesh_name = f"{container_obj.name}_Mesh"
+            mesh_copy = mesh_eval.copy()
+            mesh_copy.name = mesh_name
+            # clear the temporary evaluated mesh
+            try:
+                eval_obj.to_mesh_clear()
+            except Exception:
+                pass
+
+            # create the new object with same transform as source
+            new_obj = bpy.data.objects.new(mesh_name, mesh_copy)
+            # link to same collection as the container (fallback to current collection)
+            col = (
+                container_obj.users_collection[0]
+                if getattr(container_obj, "users_collection", None)
+                else context.collection
+            )
+            if col is None:
+                col = context.collection
+            col.objects.link(new_obj)
+
+            # copy world transform exactly
+            new_obj.matrix_world = container_obj.matrix_world.copy()
+        except Exception as e:
+            self.report({"ERROR"}, f"Failed to extract mesh: {e}")
+
+        # 恢复原始连接
+        for link in original_links:
+            node_group.links.new(link.from_socket, output_node.inputs[0])
+
+        # 删除临时添加的Component to Mesh节点
+        node_group.nodes.remove(to_mesh_node)
+        if new_obj:
+            # deselect everything, select and activate new_obj
+            for o in list(context.selected_objects):
+                o.select_set(False)
+            new_obj.select_set(True)
+            context.view_layer.objects.active = new_obj
+            self.report({"INFO"}, f"Mesh extracted: {new_obj.name}")
+            return {"FINISHED"}
+        else:
+            return {"CANCELLED"}

src/bioxelnodes/panels.py

@@ -0,0 +1,180 @@
+from pathlib import Path
+import bpy
+
+from .node import get_layer_nodes, get_main_node_group
+from .utils import load_icon
+from .layer import get_layer_caches
+from .operators.io import ImportAsColor, ImportAsLabel, ImportAsScalar, ImportData
+from .operators.misc import Help, RenderSettingPreset
+from .operators.layer import (
+    AddLayerNode,
+    DeleteLayer,
+    RelocatePath,
+    RenameLayer,
+    SaveLayer,
+)
+
+
+class ImportMenu(bpy.types.Menu):
+    bl_label = "Bioxel Import"
+    bl_idname = "BIOXEL_MT_import"
+
+    def draw(self, context):
+        layout = self.layout
+        layout.operator(ImportAsScalar.bl_idname,
+                        text="Import As Scalar").filepath = ""
+        layout.operator(ImportAsLabel.bl_idname,
+                        text="Import As Label").filepath = ""
+        layout.operator(ImportAsColor.bl_idname,
+                        text="Import As Color").filepath = ""
+
+
+class RenderSettingMenu(bpy.types.Menu):
+    bl_label = "Render Setting Presets"
+    bl_idname = "BIOXEL_MT_render_setting"
+
+    def draw(self, context):
+        layout = self.layout
+        for k, v in RenderSettingPreset.PRESETS.items():
+            op = layout.operator(RenderSettingPreset.bl_idname, text=v)
+            op.preset = k
+
+
+class BioxelPanelBase:
+    """
+    Abstract base panel for all Bioxel UI panels.
+
+    - Ensures the panel appears only when the active area is the Node Editor
+      and the Node Editor is editing a Geometry Nodes tree.
+    - Places the panel under the "Bioxel" sidebar tab.
+    - Provides an optional bl_order for panel ordering inside the category.
+    """
+
+    bl_space_type = "NODE_EDITOR"
+    bl_region_type = "UI"
+    bl_context = "geometry_node"
+    bl_category = "Bioxel Nodes"
+    # try to make Bioxel panels order early (may be respected by Blender)
+
+    @classmethod
+    def poll(cls, context):
+        node_group = get_main_node_group(context)
+        return node_group is not None
+
+
+class HeaderPanel(bpy.types.Panel, BioxelPanelBase):
+    bl_label = "Bioxel Nodes"
+    bl_idname = "BIOXEL_PT_header_panel"
+    bl_order = 0
+
+    def draw(self, context):
+        layout = self.layout
+
+        layout.operator(
+            Help.bl_idname, text="Help", icon=Help.bl_icon  # 复用原操作的图标定义
+        )
+
+        layout.menu(
+            RenderSettingMenu.bl_idname, text="Render Preset", icon="RENDER_STILL"
+        )
+
+
+class LayerNodePanel(BioxelPanelBase, bpy.types.Panel):
+    bl_label = "Layer Nodes"
+    bl_idname = "BIOXEL_PT_o_layer_nodes"
+    bl_order = 1
+
+    def draw(self, context):
+        layout = self.layout
+        node_group = get_main_node_group(context)
+
+        layout.template_list(
+            "BIOXEL_UL_layer_nodes",
+            "",
+            node_group,
+            "nodes",
+            context.window_manager,
+            "bioxel_layer_list_index",
+            rows=3,
+        )
+
+
+class LibraryPanel(BioxelPanelBase, bpy.types.Panel):
+    bl_label = "Layer Library"
+    bl_idname = "BIOXEL_PT_library_panel"
+    bl_order = 2
+
+    def draw(self, context):
+        layout = self.layout
+        wm = context.window_manager
+        caches = get_layer_caches()
+
+        row = layout.row()
+        row.scale_y = 2.0
+        row.operator(ImportData.bl_idname, icon="IMPORT")
+        # row.menu(ImportMenu.bl_idname, icon="IMPORT", text="Import")
+        layout.separator()
+        layout.template_icon_view(
+            bpy.context.window_manager,
+            "bioxel_layer_library",
+            show_labels=False,
+            scale=10.0,
+            scale_popup=6.0,
+        )
+
+        selected_id = getattr(wm, "bioxel_layer_library", None)
+        selected_id = None if selected_id == "nothing_found" else selected_id
+        entry = next((c for c in caches if c.get("id") == selected_id), None)
+        if entry:
+            cache_id = entry["id"]
+            path = entry["path"]
+            name = entry.get("name", "?")
+            kind = entry.get("kind", "?")
+            path_exists = Path(bpy.path.abspath(path)).exists()
+
+            layout.prop(wm, "bioxel_snapshot_z", text="Z Slice", slider=True)
+            layout.separator()
+            # operations and meta_box as before
+            ops_row = layout.row(align=True)
+            if path_exists:
+                ops_row.operator(
+                    AddLayerNode.bl_idname, text="Add", icon="PLUS"
+                ).cache_id = selected_id
+                ops_row.operator(
+                    SaveLayer.bl_idname, text="Save", icon="FILE_TICK"
+                ).cache_id = selected_id
+                ops_row.operator(
+                    RenameLayer.bl_idname, text="Name", icon="FONT_DATA"
+                ).cache_id = selected_id
+                ops_row.operator(
+                    DeleteLayer.bl_idname, text="", icon="TRASH"
+                ).cache_id = selected_id
+            else:
+                ops_row.operator(
+                    RelocatePath.bl_idname, text="Relocate", icon="FILE_FOLDER"
+                ).cache_id = selected_id
+                ops_row.operator(
+                    DeleteLayer.bl_idname, text="", icon="TRASH"
+                ).cache_id = selected_id
+
+                meta_box = layout.box()
+                if hasattr(meta_box, "alert"):
+                    meta_box.alert = True
+                meta_box.label(text=f"Cache is missing...")
+                meta_box.label(text=f"Please relocate the cache path!")
+                return
+
+            meta_box = layout.box()
+            meta_box.label(text=f"Name: {name}")
+            meta_box.label(text=f"Path: {path}")
+            meta_box.label(text=f"Kind: {kind}")
+            meta_box.label(
+                text=f"Dims: [{entry.get('frame_count',1)},{tuple(entry.get('shape',''))},{entry.get('channel_count',1)}]"
+            )
+            if kind in ["scalar", "color", "vector"]:
+                path = Path(bpy.path.abspath(entry["path"]))
+                histogram = load_icon(
+                    path / "histogram.png", f"{cache_id}_histogram")
+                meta_box.template_icon(histogram, scale=10.0)
+        else:
+            layout.label(text="No layer selected", icon="QUESTION")

src/bioxelnodes/preferences.py

@@ -0,0 +1,17 @@
+import bpy
+from pathlib import Path
+
+
+class BioxelNodesPreferences(bpy.types.AddonPreferences):
+    bl_idname = __package__
+
+    cache_dir: bpy.props.StringProperty(
+        name="Set Cache Directory",
+        subtype='DIR_PATH',
+        default=str(Path(Path.home(), '.bioxel'))
+    )  # type: ignore
+
+    def draw(self, context):
+        layout = self.layout
+        layout.label(text="Configuration")
+        layout.prop(self, 'cache_dir')

src/bioxelnodes/props.py

@@ -0,0 +1,134 @@
+from pathlib import Path
+import bpy
+
+from .operators.layer import SelectAndFocusNode
+from .utils import load_icon
+from .layer import get_layer_caches, set_layer_caches
+
+
+def get_snapshot_icon(cache, z: float):
+    cache_id = str(cache["id"])
+    shape = (64, 64, 32)
+    zidx = int(z * (shape[2] - 1))
+
+    path = Path(bpy.path.abspath(cache["path"]))
+    return load_icon(path / f"snapshot_{zidx}.png", f"{cache_id}_{zidx}")
+
+
+def _bioxel_layer_items(self, context):
+    """
+    EnumProperty items callback: 从 get_layer_caches 构造枚举项。
+    使用 PREVIEWS 加载每个 layer 的 thumbnail_png（如果存在）并返回 icon_id。
+    """
+    items = []
+    caches = get_layer_caches()
+
+    for idx, cache in enumerate(caches):
+        cache_id = str(cache["id"])
+        name = cache.get("name", f"Layer ?")
+        description = cache.get("kind", "?")
+        z = cache.get("snapshot_z", 0.5)
+        icon = get_snapshot_icon(cache, z)
+        # 在这个context下，只能加载无法生成。
+        items.append((cache_id, name, description, icon, idx))
+
+    if not items:
+        items = [("nothing_found", "No Layers",
+                  "No layers found", "QUESTION", 0)]
+
+    return items
+
+
+def _update_layer_gallery(self, context):
+    wm = context.window_manager
+    selected_id = getattr(wm, "bioxel_layer_library", None)
+    cache = next(
+        (c for c in get_layer_caches() if str(c.get("id", "")) == str(selected_id)),
+        None,
+    )
+    z = cache.get("snapshot_z", 0.5) if cache else 0.5
+    setattr(wm, "bioxel_snapshot_z", z)
+
+
+def _update_snapshot_z(self, context):
+    """
+    update callback for WindowManager.bioxel_thumb_z
+    - write a slice PNG from the saved .npy
+    - update PREVIEWS entry for the selected layer
+    - force template_icon_view to refresh by briefly cycling the EnumProperty value
+    - force UI redraw
+    """
+    wm = context.window_manager
+    selected_id = getattr(wm, "bioxel_layer_library", None)
+
+    if not selected_id or selected_id == "nothing_found":
+        return
+
+    try:
+        selected_id = int(selected_id)
+    except Exception:
+        return
+
+    caches = get_layer_caches()
+    z = getattr(wm, "bioxel_snapshot_z", 0.5)
+
+    for cache in caches:
+        if int(cache.get("id", -1)) == selected_id:
+            cache["snapshot_z"] = z
+            break
+
+    set_layer_caches(caches)
+
+
+class BIOXEL_Series(bpy.types.PropertyGroup):
+    id: bpy.props.StringProperty()  # type: ignore
+    label: bpy.props.StringProperty()  # type: ignore
+
+
+class BIOXEL_UL_layer_nodes(bpy.types.UIList):
+    """UIList for O Layer nodes only"""
+
+    bl_idname = "BIOXEL_UL_layer_nodes"
+
+    def filter_items(self, context, data, propname):
+        nodes = getattr(data, propname)
+        flt_flags = []
+        flt_neworder = []
+
+        for node in nodes:
+            # 只保留 O Layer 节点
+            if (
+                hasattr(node, "bl_idname")
+                and node.bl_idname.startswith("GeometryNodeGroup")
+                and getattr(getattr(node, "node_tree", None), "name", "").startswith(
+                    "O Layer"
+                )
+            ):
+                flt_flags.append(self.bitflag_filter_item)
+            else:
+                flt_flags.append(0)
+        return flt_flags, flt_neworder
+
+    def draw_item(
+        self, context, layout, data, item, icon, active_data, active_propname, index
+    ):
+        node = item
+        # 这里只画 O Layer 节点，其他已被 filter_items 过滤
+        split = layout.split(factor=0.3, align=True)
+        col1 = split.row(align=True)
+        col2 = split.row(align=True)
+        name_socket = node.inputs["Name"]
+        resample_socket = node.inputs["Resample"]
+        scale_socket = node.inputs["Bioxel Scale"]
+        name = str(node.inputs["Name"].default_value)
+
+        # row.prop(name_socket, "default_value", text="")
+        col1.prop(resample_socket, "default_value",
+                  icon="UV_DATA", text="", toggle=1)
+        col1.prop(scale_socket, "default_value", text="")
+        col2.label(text=name)
+
+        op = col2.operator(
+            SelectAndFocusNode.bl_idname, text="", icon="RESTRICT_SELECT_OFF", emboss=True
+        )
+        op.node_name = node.name

src/bioxelnodes/utils.py

@@ -0,0 +1,402 @@
+from pathlib import Path
+from ast import literal_eval
+
+import shutil
+import bpy
+import numpy as np
+
+from .node import get_nodes_by_type
+from .constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, PREVIEW_COLLECTIONS
+
+
+def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True):
+    source = Path(source_path)
+    target = Path(dir_path)
+
+    # Check if the source exists
+    if not source.exists():
+        raise FileNotFoundError
+
+    # Check if the target exists
+    if not target.exists():
+        target.mkdir(parents=True, exist_ok=True)
+
+    target_path = target / new_name if new_name else target / source.name
+    # If source is a file, copy it to the target directory
+    if source.is_file():
+        try:
+            shutil.copy(source, target_path)
+        except shutil.SameFileError:
+            if exist_ok:
+                pass
+            else:
+                raise shutil.SameFileError
+    # If source is a directory, copy its contents to the target directory
+    elif source.is_dir():
+        shutil.copytree(source, target_path, dirs_exist_ok=exist_ok)
+
+    if not target_path.exists():
+        raise Exception
+
+
+def select_object(target_obj):
+    for obj in bpy.data.objects:
+        obj.select_set(False)
+
+    target_obj.select_set(True)
+    bpy.context.view_layer.objects.active = target_obj
+
+
+def progress_bar(self, context):
+    row = self.layout.row()
+    row.progress(
+        factor=context.window_manager.bioxel_progress_factor,
+        type="BAR",
+        text=context.window_manager.bioxel_progress_text
+    )
+    row.scale_x = 2
+
+
+def progress_update(context, factor, text=""):
+    bpy.context.window_manager.bioxel_progress_factor = factor
+    bpy.context.window_manager.bioxel_progress_text = text
+
+
+def get_preferences():
+    return bpy.context.preferences.addons[__package__].preferences
+
+
+def get_cache_dir():
+    preferences = get_preferences()
+    cache_path = Path(preferences.cache_dir)
+    cache_path.mkdir(parents=True, exist_ok=True)
+    return cache_path
+
+
+def get_use_link():
+    preferences = get_preferences()
+    return preferences.node_import_method == "LINK"
+
+
+def get_container_objs_from_selection():
+    container_objs = []
+    for obj in bpy.context.selected_objects:
+        if get_container_obj(obj):
+            container_objs.append(obj)
+
+    return list(set(container_objs))
+
+
+def get_container_obj(current_obj):
+    if current_obj:
+        if current_obj.get('bioxel_container'):
+            return current_obj
+        elif current_obj.get('bioxel_layer'):
+            parent = current_obj.parent
+            return parent if parent.get('bioxel_container') else None
+    return None
+
+
+def get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    prop = layer_node.inputs.get(prop_name)
+    if prop is None:
+        return None
+
+    value = prop.default_value
+
+    if type(value).__name__ == "bpy_prop_array":
+        value = tuple(value)
+        return tuple([int(v) for v in value]) \
+            if prop in ["shape"] else value
+    elif type(value).__name__ == "str":
+        return str(value)
+    elif type(value).__name__ == "float":
+        value = float(value)
+        return round(value, 2) \
+            if prop in ["bioxel_size"] else value
+    elif type(value).__name__ == "int":
+        value = int(value)
+        return value
+    else:
+        return value
+
+
+def get_layer_name(layer_obj):
+    return get_layer_prop_value(layer_obj, "name")
+
+
+def get_layer_kind(layer_obj):
+    return get_layer_prop_value(layer_obj, "kind")
+
+
+def get_layer_label(layer_obj):
+    name = get_layer_name(layer_obj)
+    # kind = get_layer_kind(layer_obj)
+
+    label = f"{name}"
+
+    if is_missing_layer(layer_obj):
+        return "**MISSING**" + label
+    elif is_temp_layer(layer_obj):
+        return "* " + label
+    else:
+        return label
+
+
+def is_missing_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    return not cache_filepath.is_file()
+
+
+def is_temp_layer(layer_obj):
+    cache_filepath = Path(bpy.path.abspath(
+        layer_obj.data.filepath)).resolve()
+    cache_dirpath = Path(get_cache_dir())
+    return cache_dirpath in cache_filepath.parents
+
+
+def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value):
+    node_group = layer_obj.modifiers[0].node_group
+    layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0]
+    layer_node.inputs[prop].default_value = value
+
+
+def get_layer_obj(current_obj: bpy.types.Object):
+    if current_obj:
+        if current_obj.get('bioxel_layer') and current_obj.parent:
+            if current_obj.parent.get('bioxel_container'):
+                return current_obj
+    return None
+
+
+def get_container_layer_objs(container_obj: bpy.types.Object):
+    layer_objs = []
+    for obj in bpy.data.objects:
+        if obj.parent == container_obj and get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def get_all_layer_objs():
+    layer_objs = []
+    for obj in bpy.data.objects:
+        if get_layer_obj(obj):
+            layer_objs.append(obj)
+
+    return layer_objs
+
+
+def add_driver(target, target_prop, var_sources, expression):
+    driver = target.driver_add(target_prop)
+    is_vector = isinstance(driver, list)
+    drivers = driver if is_vector else [driver]
+
+    for i, driver in enumerate(drivers):
+        for j, var_source in enumerate(var_sources):
+
+            source = var_source['source']
+            prop = var_source['prop']
+
+            var = driver.driver.variables.new()
+            var.name = f"var{j}"
+
+            var.targets[0].id_type = source.id_type
+            var.targets[0].id = source
+            var.targets[0].data_path = f'["{prop}"][{i}]'\
+                if is_vector else f'["{prop}"]'
+
+        driver.driver.expression = expression
+
+
+def add_direct_driver(target, target_prop, source, source_prop):
+    drivers = [
+        {
+            "source": source,
+            "prop": source_prop
+        }
+    ]
+    expression = "var0"
+    add_driver(target, target_prop, drivers, expression)
+
+
+def read_file_prop(content: str):
+    props = {}
+    for line in content.split("\n"):
+        line = line.replace(" ", "")
+        p = line.split("=")[0]
+        if p != "":
+            v = line.split("=")[-1]
+            props[p] = v
+    return props
+
+
+def write_file_prop(props: dict):
+    lines = []
+    for p, v in props.items():
+        lines.append(f"{p} = {v}")
+    return "\n".join(lines)
+
+
+def set_file_prop(prop, value):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    props[prop] = value
+    bpy.data.texts["BioxelNodes"].clear()
+    bpy.data.texts["BioxelNodes"].write(write_file_prop(props))
+
+
+def get_file_prop(prop):
+    if bpy.data.texts.get("BioxelNodes") is None:
+        bpy.data.texts.new("BioxelNodes")
+
+    props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string())
+    return props.get(prop)
+
+
+def get_node_version():
+    node_version = get_file_prop("node_version")
+    return literal_eval(node_version) if node_version else None
+
+
+def is_incompatible():
+    return False
+
+
+def get_node_lib_path(node_version):
+    version_str = "v"+".".join([str(i) for i in list(node_version)])
+    lib_filename = f"BioxelNodes_{version_str}.blend"
+    return Path(NODE_LIB_DIRPATH,
+                lib_filename).resolve()
+
+
+def local_lib_not_updated():
+    return False
+
+
+def ndarray_to_png(array: np.ndarray, save_path: str):
+    """
+    Create a PNG from a 2D or 3-channel slice array using Blender API.
+    slice_arr expected shape: (W, H) or (W, H, 1) or (W,H,3). Values assumed numeric.
+
+    The function:
+    - Converts single-channel arrays to RGB by repeating channel.
+    - Flips the image vertically to match Blender's origin.
+    - Writes the image file to save_path using a temporary Blender image datablock.
+
+    Parameters:
+    - array: numpy ndarray representing the slice (W,H,C) or (W,H,1) or (W,H)
+    - save_path: destination PNG filepath
+    """
+    save_path = Path(save_path)
+    h, w = array.shape[0], array.shape[1]
+    if array.shape[2] == 1:
+        img = np.concatenate([array, array, array], axis=2)
+    else:
+        img = array[..., :3]
+
+    # Blender expects pixels as sequence of floats in RGBA, length w*h*4
+    # NOTE: Blender's image origin is bottom-left; we'll flip vertically for visual consistency.
+    img = np.flipud(img)
+    pixels = np.empty((h * w * 4,), dtype=np.float32)
+    # fill
+    pixels[0::4] = img[..., 0].ravel()
+    pixels[1::4] = img[..., 1].ravel()
+    pixels[2::4] = img[..., 2].ravel()
+    pixels[3::4] = 1.0
+
+    # create a temporary image datablock, save then remove
+    name = "tmp"
+    image = bpy.data.images.new(
+        name, width=w, height=h, alpha=True, float_buffer=False)
+    image.pixels = pixels.tolist()
+    # ensure format and filepath then save
+    image.filepath_raw = str(save_path)
+    image.file_format = "PNG"
+    image.save()
+    # remove from data to avoid clutter
+    try:
+        bpy.data.images.remove(image)
+    except Exception:
+        pass
+
+
+def split_text_to_lines(text: str, max_chars: int = 60) -> list:
+    """
+    Split `text` into multiple lines not exceeding `max_chars` where possible.
+    Breaks on whitespace; long words are chunked.
+    Returns list of line strings.
+    """
+    if not text:
+        return []
+    words = text.split()
+    lines = []
+    cur = ""
+    for w in words:
+        if cur:
+            candidate = cur + " " + w
+        else:
+            candidate = w
+        if len(candidate) <= max_chars:
+            cur = candidate
+        else:
+            if cur:
+                lines.append(cur)
+            # if single word longer than max_chars, chunk it
+            if len(w) > max_chars:
+                for i in range(0, len(w), max_chars):
+                    lines.append(w[i: i + max_chars])
+                cur = ""
+            else:
+                cur = w
+    if cur:
+        lines.append(cur)
+    return lines
+
+
+def wrapped_label(layout, text: str, max_chars: int = 42):
+    """
+    Helper to add multiple layout.label calls for a long text.
+    """
+    for line in split_text_to_lines(text, max_chars=max_chars):
+        layout.label(text=line)
+
+
+def refresh_bioxel_panels(context):
+    """
+    Force Bioxel UI to refresh.
+
+    - Tags relevant areas for redraw.
+    - Nudges the bioxel_layer_gallery EnumProperty to force items() re-evaluation
+      when possible (helps template_icon_view pick up updated icons/paths).
+    Use this from operators after they change b i o x e l _ l a y e r s or previews.
+    """
+
+    # tag redraw for all windows/areas
+    for window in context.window_manager.windows:
+        for area in window.screen.areas:
+            # target node editor and other UI areas that may show previews
+            if area.type in {"NODE_EDITOR", "VIEW_3D", "IMAGE_EDITOR", "OUTLINER"}:
+                area.tag_redraw()
+
+
+def load_icon(filepath: Path, key: str):
+    pcoll = PREVIEW_COLLECTIONS["layers"]
+
+    try:
+        icon = pcoll[key].icon_id
+    except KeyError:
+        if filepath.exists():
+            pcoll.load(key, str(filepath), "IMAGE")
+
+        try:
+            icon = pcoll[key].icon_id
+        except KeyError:
+            icon = "TEXTURE"
+
+    return icon