v2.4.0

.zenodo.json

@@ -52,6 +52,33 @@
     {
       "id": "021nxhr62::2118240"
     }
+  ],
+  "references": [
+    "Blender Development Team (2026). Blender (Version 5.1) [Computer software]. https://www.blender.org",
+    "Contreras-Figueroa, G. & Aragón, J. L. (2023). A mathematical model for mollusc shells based on parametric surfaces and the construction of theoretical morphospaces. Diversity 15, 431. https://doi.org/10.3390/d15030431",
+    "Okabe, T. & Yoshimura, J. (2017). Optimal designs of mollusk shells from bivalves to snails. Scientific Reports 7, 42445. https://doi.org/10.1038/srep42445",
+    "Porto, A. MorphoWeave: Atlas-based 3D landmark transfer and statistical shape modeling. GitHub repository. https://github.com/agporto/SlicerMorphoWeave"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "https://www.blender.org",
+      "relation": "requires",
+      "resource_type": "software"
+    },
+    {
+      "identifier": "10.3390/d15030431",
+      "relation": "cites",
+      "resource_type": "publication-article"
+    },
+    {
+      "identifier": "10.1038/srep42445",
+      "relation": "cites",
+      "resource_type": "publication-article"
+    },
+    {
+      "identifier": "https://github.com/agporto/SlicerMorphoWeave",
+      "relation": "cites",
+      "resource_type": "software"
+    }
   ]
 }
-

README.md

@@ -14,7 +14,7 @@ TraitBlender is a Blender add-on for generating museum-style images and 3D meshe
 
 - **Shell (Default)** — A 3D shell morphospace that combines the parametric coiling model of [Contreras-Figueroa & Aragón (2023)](https://doi.org/10.3390/d15030431) with thickness allometry from [Okabe & Yoshimura (2017)](https://doi.org/10.1038/srep42445). Traits control whorl expansion, aperture shape, ribbing, and scaling; hyperparameters tune mesh resolution and options.
 - **Circle Grid** — A simple morphospace (e.g. for testing): a gridded plane of circles with configurable traits.
-- **ATLAS** — Deforms a template mesh from an [ATLAS DATABASE](https://github.com/agporto/ATLAS) export using PCA on dense correspondences and local RBF interpolation (same workflow as the ATLAS DATABASE explorer).
+- **MorphoWeave** — Deforms a template mesh from a [MorphoWeave](https://github.com/agporto/SlicerMorphoWeave) export using PCA on dense correspondences and local RBF interpolation (same workflow as the MorphoWeave Model Library / SSM Explorer).
 
 **Dataset import, editing, and saving** — Specimen trait values are read from CSV, TSV, or Excel. The built-in dataset editor supports filtering, sorting, pagination, and saving changes back to file, so you can curate and tweak trait tables without leaving Blender.
 

traitblender/assets/morphospace_modules/ATLAS/__init__.py → traitblender/assets/morphospace_modules/MorphoWeave/__init__.py

@@ -1,20 +1,21 @@
 """
-ATLAS morphospace: template-centered PCA on dense correspondences + Local RBF warp.
+MorphoWeave morphospace: template-centered PCA on dense correspondences + Local RBF warp.
 
-Traits ``pc1`` … ``pcK`` are σ-multiples (ATLAS DATABASE sliders). Reconstruction:
-``target = template_dense + Σ z_i √(λ_i) mode_i``, then Local RBF mesh warp (LPS/RAS aware).
+Traits ``pc1`` … ``pcK`` are σ-multiples (MorphoWeave Model Library / SSM Explorer sliders).
+Reconstruction: ``target = template_dense + Σ z_i √(λ_i) mode_i``, then Local RBF mesh warp
+(LPS/RAS aware).
 """
 
 from __future__ import annotations
 
 from .morphospace import (
-    generate_atlas_sample,
+    generate_morphoweave_sample,
     pc_values_from_trait_kwargs,
     resolve_n_modes_for_hyperparams,
 )
 from .orientations import ORIENTATIONS
 
-NAME = "ATLAS"
+NAME = "MorphoWeave"
 
 HYPERPARAMETERS = {
     "database_dir": "",
@@ -33,9 +34,9 @@ def get_trait_parameters_with_defaults(merged_hyperparameters):
     return {f"pc{i}": 0.0 for i in range(1, n + 1)}
 
 
-def sample(name="ATLAS", hyperparameters=None, **traits):
+def sample(name="MorphoWeave", hyperparameters=None, **traits):
     """Generate a specimen; PC coefficients are passed as pc1, pc2, … keyword traits."""
-    return generate_atlas_sample(
+    return generate_morphoweave_sample(
         name,
         hyperparameters or {},
         pc_values_from_trait_kwargs(traits),
@@ -48,6 +49,6 @@ def sample(name="ATLAS", hyperparameters=None, **traits):
     "HYPERPARAMETERS",
     "ORIENTATIONS",
     "get_trait_parameters_with_defaults",
-    "generate_atlas_sample",
+    "generate_morphoweave_sample",
     "resolve_n_modes_for_hyperparams",
 ]

traitblender/assets/morphospace_modules/MorphoWeave/morphospace/__init__.py

@@ -0,0 +1,13 @@
+from .morphoweave_morphospace import (
+    generate_morphoweave_sample,
+    pc_values_from_trait_kwargs,
+    resolve_n_modes_for_hyperparams,
+)
+from .morphoweave_morphospace_sample import MorphoWeaveMorphospaceSample
+
+__all__ = [
+    "generate_morphoweave_sample",
+    "MorphoWeaveMorphospaceSample",
+    "pc_values_from_trait_kwargs",
+    "resolve_n_modes_for_hyperparams",
+]

traitblender/assets/morphospace_modules/ATLAS/morphospace/atlas_core.py → traitblender/assets/morphospace_modules/MorphoWeave/morphospace/morphoweave_core.py

@@ -1,7 +1,7 @@
 """
-ATLAS DATABASE core (PCA + Local RBF), matching agporto/ATLAS DATABASE explorer.
+MorphoWeave Model Library core (PCA + Local RBF), matching agporto/SlicerMorphoWeave.
 
-Ported from the working ATLASViewer reference implementation:
+Ported from the MorphoWeave / former ATLASViewer reference implementation:
   - Template-centered PCA: target = template_dense + sum_i (z_i * sqrt(lambda_i) * mode_i)
   - Local RBF: k=min(32, n_landmarks), Gaussian weights, h = 75th percentile k-th NN distance
   - LPS/RAS: dense landmarks and SSM in RAS; template PLY typically LPS on disk
@@ -21,7 +21,7 @@
 
 
 def resolve_database_paths(database_dir: str | Path) -> dict[str, Path]:
-    """Resolve model, dense, sparse (optional), and ssm paths in an ATLAS DATABASE folder."""
+    """Resolve model, dense, sparse (optional), and ssm paths in a MorphoWeave Model Library / DATABASE folder."""
     root = Path(database_dir).expanduser().resolve()
     if not root.is_dir():
         raise FileNotFoundError(f"Database folder not found: {root}")
@@ -254,7 +254,7 @@ def ssm_std_devs(eigenvalues: np.ndarray) -> np.ndarray:
     return np.sqrt(np.maximum(np.asarray(eigenvalues, dtype=np.float64).ravel(), 0.0))
 
 
-def atlas_pc_coefficients(
+def morphoweave_pc_coefficients(
     sigma_weights: np.ndarray | Sequence[float],
     eigenvalues: np.ndarray,
 ) -> np.ndarray:
@@ -287,7 +287,7 @@ def reconstruct_dense_target(
     if k == 0 or np.allclose(z[:k], 0.0):
         return template.copy()
 
-    coeff = atlas_pc_coefficients(z[:k], ev[:k])
+    coeff = morphoweave_pc_coefficients(z[:k], ev[:k])
     agg = np.tensordot(modes_arr[..., :k], coeff, axes=(2, 0))
     return template + agg
 

traitblender/assets/morphospace_modules/ATLAS/morphospace/atlas_morphospace.py → traitblender/assets/morphospace_modules/MorphoWeave/morphospace/morphoweave_morphospace.py

@@ -1,5 +1,5 @@
 """
-ATLAS morphospace sample generation (TraitBlender wrapper around atlas_core).
+MorphoWeave morphospace sample generation (TraitBlender wrapper around morphoweave_core).
 """
 
 from __future__ import annotations
@@ -9,8 +9,8 @@
 import bpy
 import numpy as np
 
-from .atlas_core import build_deformed_mesh_arrays, load_ssm, resolve_database_paths
-from .atlas_morphospace_sample import AtlasMorphospaceSample
+from .morphoweave_core import build_deformed_mesh_arrays, load_ssm, resolve_database_paths
+from .morphoweave_morphospace_sample import MorphoWeaveMorphospaceSample
 
 
 def resolve_n_modes_for_hyperparams(hyperparameters: dict | None) -> int | None:
@@ -49,30 +49,31 @@ def pc_values_from_trait_kwargs(traits: dict) -> list[float]:
 
 
 def _log(msg: str) -> None:
-    print(f"[ATLAS] {msg}")
+    print(f"[MorphoWeave] {msg}")
 
 
-def generate_atlas_sample(
+def generate_morphoweave_sample(
     name: str,
     hyperparameters: dict | None,
     pc_values: list[float],
-) -> AtlasMorphospaceSample:
+) -> MorphoWeaveMorphospaceSample:
     hp = dict(hyperparameters or {})
     db_raw = (hp.get("database_dir") or hp.get("database_path") or "").strip()
     if not db_raw:
         raise ValueError(
-            "ATLAS morphospace: set hyperparameter 'database_dir' to your DATABASE folder "
+            "MorphoWeave morphospace: set hyperparameter 'database_dir' to your "
+            "MorphoWeave Model Library / DATABASE folder "
             "(manifest + template model + dense correspondences + ssm_model.npz)."
         )
     db_root = Path(bpy.path.abspath(db_raw))
     if not db_root.is_dir():
-        raise ValueError(f"ATLAS database_dir is not a directory: {db_root}")
+        raise ValueError(f"MorphoWeave database_dir is not a directory: {db_root}")
 
     n_comp_cfg = max(0, int(hp.get("n_components", 10)))
     scale = float(hp.get("scale", 1.0))
 
     if scale <= 0.0:
-        raise ValueError("ATLAS hyperparameter 'scale' must be positive")
+        raise ValueError("MorphoWeave hyperparameter 'scale' must be positive")
 
     paths = resolve_database_paths(db_root)
     ssm = load_ssm(paths)
@@ -117,4 +118,4 @@ def generate_atlas_sample(
 
     _log(f"  mesh: {vertices.shape[0]} verts, {len(faces)} faces")
     verts = [tuple(map(float, row)) for row in vertices]
-    return AtlasMorphospaceSample(name, verts, faces)
+    return MorphoWeaveMorphospaceSample(name, verts, faces)

traitblender/assets/morphospace_modules/ATLAS/morphospace/atlas_morphospace_sample.py → traitblender/assets/morphospace_modules/MorphoWeave/morphospace/morphoweave_morphospace_sample.py

@@ -1,9 +1,9 @@
-"""Blender mesh creation for an ATLAS warped template."""
+"""Blender mesh creation for a MorphoWeave warped template."""
 
 import bpy
 
 
-class AtlasMorphospaceSample:
+class MorphoWeaveMorphospaceSample:
     def __init__(self, name: str, vertices: list, faces: list):
         self.name = name
         self.vertices = vertices

traitblender/assets/morphospace_modules/ATLAS/orientations/__init__.py → traitblender/assets/morphospace_modules/MorphoWeave/orientations/__init__.py

@@ -1,5 +1,5 @@
 """
-ATLAS specimen orientations.
+MorphoWeave specimen orientations.
 
 Default: table placement only (tb_location). Other views: rotate one axis by n·π/4
 (n = 1..7), origin to bounds, tb_location reset — then apply_orientation bakes rotation.
@@ -13,7 +13,7 @@
 import bpy
 
 
-def _orient_atlas_default(sample_obj):
+def _orient_morphoweave_default(sample_obj):
     sample_obj.tb_location = (0.0, 0.0, 0.0)
 
 
@@ -28,13 +28,13 @@ def _pi_multiplier_label(n_quarters: int) -> str:
     return f"{num}/{den}"
 
 
-def _make_atlas_axis_rotation(axis: str, n_quarters: int):
+def _make_morphoweave_axis_rotation(axis: str, n_quarters: int):
     angle = (math.pi / 4.0) * n_quarters
     label = _pi_multiplier_label(n_quarters)
     name = f"{axis} {label} π Rotation"
 
     def orient(sample_obj):
-        _orient_atlas_default(sample_obj)
+        _orient_morphoweave_default(sample_obj)
         if axis == "X":
             sample_obj.tb_rotation = (angle, 0.0, 0.0)
         elif axis == "Y":
@@ -48,15 +48,15 @@ def orient(sample_obj):
         sample_obj.tb_location = (0.0, 0.0, 0.0)
         bpy.context.view_layer.update()
 
-    orient.__name__ = f"_orient_atlas_{axis}_{n_quarters}q"
+    orient.__name__ = f"_orient_morphoweave_{axis}_{n_quarters}q"
     return name, orient
 
 
 def _build_orientations() -> dict:
-    out: dict = {"Default": _orient_atlas_default}
+    out: dict = {"Default": _orient_morphoweave_default}
     for axis in ("X", "Y", "Z"):
         for n in range(1, 8):
-            key, fn = _make_atlas_axis_rotation(axis, n)
+            key, fn = _make_morphoweave_axis_rotation(axis, n)
             out[key] = fn
     return out
 

traitblender/core/config/templates/meshes.py

@@ -36,7 +36,7 @@ class MeshesConfig(TraitBlenderConfig):
         description=(
             "If enabled (default), apply the morphospace Default orientation before exporting "
             "meshes (table placement). Disable to export the generated mesh as-is—useful for "
-            "ATLAS, where the SSM already provides a consistent PCA-aligned frame"
+            "MorphoWeave, where the SSM already provides a consistent PCA-aligned frame"
         ),
         default=True,
     )

traitblender/core/datasets/traitblender_dataset.py

@@ -323,7 +323,7 @@ def _get_default_dataframe(self):
     def _ensure_virtual_dataset_traits_synced(self) -> None:
         """
         No filepath: in-memory CSV. Morphospaces with ``get_trait_parameters_with_defaults``
-        (e.g. ATLAS ``n_components``) may change expected trait columns — rewrite CSV to match
+        (e.g. MorphoWeave ``n_components``) may change expected trait columns — rewrite CSV to match
         so the editor and ``loc()`` stay consistent.
         """
         if self.filepath:

traitblender/core/helpers/orientation_helpers.py

@@ -113,7 +113,7 @@ def make_euler_orientation(rx, ry, rz, default_fn=None):
     before bake), then origin at geometry bounds and table center.
 
     Local composition uses ``R_obj @ R_local`` so axes follow the specimen after Default
-    (works for Shell aperture alignment, ATLAS table Default, etc.).
+    (works for Shell aperture alignment, MorphoWeave table Default, etc.).
 
     Args:
         rx, ry, rz: Local Euler rotation in radians (object rotation_euler order).

traitblender/core/morphospaces/list_morphospaces.py

@@ -6,7 +6,7 @@
 from .get_orientations import get_orientations_for_morphospace
 
 # GUI dropdown order (folder names under morphospace_modules/)
-_MORPHOSPACE_ORDER = ("Shell", "CircleGrid", "ATLAS")
+_MORPHOSPACE_ORDER = ("Shell", "CircleGrid", "MorphoWeave")
 
 
 def list_morphospaces():

traitblender/core/morphospaces/trait_params.py

@@ -39,7 +39,7 @@ def get_trait_parameters_with_defaults_for_morphospace(morphospace_name, context
     Get trait parameters and their default values for a morphospace.
 
     If the module defines ``get_trait_parameters_with_defaults(merged_hyperparameters)``, that
-    return value is used (e.g. ATLAS: PC1..PCn from ``n_components``, capped by SSM mode count).
+    return value is used (e.g. MorphoWeave: PC1..PCn from ``n_components``, capped by SSM mode count).
     Otherwise
     parameters are inferred from ``sample()``'s signature.
 

traitblender/docs/api/scene-assets.md

@@ -151,7 +151,7 @@ This reference focuses on the user-facing operators and properties you will use
 <hr>
 
 <p><code>bpy.context.scene.traitblender_config.meshes.orient_before_export</code></p>
-<p>If <code>True</code> (default), apply Default orientation before pipeline mesh export (backward compatible). If <code>False</code>, export the generated mesh as-is—recommended for ATLAS PCA-aligned meshes. Does not affect imaging orientations used for renders. See <a href="../configuration/config-files.md#mesh-export-in-the-imaging-pipeline">Configuration Files</a>.</p>
+<p>If <code>True</code> (default), apply Default orientation before pipeline mesh export (backward compatible). If <code>False</code>, export the generated mesh as-is—recommended for MorphoWeave PCA-aligned meshes. Does not affect imaging orientations used for renders. See <a href="../configuration/config-files.md#mesh-export-in-the-imaging-pipeline">Configuration Files</a>.</p>
 
 <hr>
 

traitblender/docs/configuration/config-files.md

@@ -117,7 +117,7 @@ TraitBlender config files are **YAML** files that store the settings you see in
 <p><strong>meshes</strong></p>
 <ul>
   <li><code>save_meshes</code>: boolean</li>
-  <li><code>orient_before_export</code>: boolean (default <code>true</code>). When saving meshes in the imaging pipeline, apply the morphospace <strong>Default</strong> orientation before export. Set to <code>false</code> to export the generated mesh as-is (recommended for ATLAS, where the SSM already provides a consistent PCA-aligned frame). Imaging orientations are still applied afterward for renders.</li>
+  <li><code>orient_before_export</code>: boolean (default <code>true</code>). When saving meshes in the imaging pipeline, apply the morphospace <strong>Default</strong> orientation before export. Set to <code>false</code> to export the generated mesh as-is (recommended for MorphoWeave, where the SSM already provides a consistent PCA-aligned frame). Imaging orientations are still applied afterward for renders.</li>
   <li><code>file_export_type</code>: <code>obj</code> or <code>ply</code></li>
 </ul>
 
@@ -275,7 +275,7 @@ imaging:
 meshes:
   file_export_type: obj
   save_meshes: true
-  # ATLAS: keep SSM/PCA frame (skip Default table placement before export)
+  # MorphoWeave: keep SSM/PCA frame (skip Default table placement before export)
   # orient_before_export: false
 ```
 
@@ -450,7 +450,7 @@ When `meshes.save_meshes` is `true`, the simulation pipeline writes one mesh per
 | Value | Mesh file contents |
 |-------|--------------------|
 | `true` (default) | Morphospace **Default** applied first (table placement). Same behavior as earlier TraitBlender releases. |
-| `false` | Export the mesh as generated, with no Default/table orientation. Prefer this for **ATLAS**, where the SSM already lives in a shared PCA-aligned frame. Imaging orientations still apply afterward for rendered images only. |
+| `false` | Export the mesh as generated, with no Default/table orientation. Prefer this for **MorphoWeave**, where the SSM already lives in a shared PCA-aligned frame. Imaging orientations still apply afterward for rendered images only. |
 
 ```yaml
 meshes:

traitblender/docs/getting-started/quick-start.md

@@ -78,11 +78,11 @@ Before starting, ensure you have:
 
     - **Shell (Default)** — parametric mollusc shells ([Contreras-Figueroa & Aragón](https://www.mdpi.com/1424-2818/15/3/431); thickness from [Okabe & Yoshimura](https://doi.org/10.1038/srep42445))
     - **Circle Grid** — simple test morphospace (cube with a 4×4 grid of circles)
-    - **ATLAS** — deform a template mesh from an [ATLAS DATABASE](https://github.com/agporto/ATLAS) export using PCA + local RBF ([details](../morphospaces/atlas.md))
+    - **MorphoWeave** — deform a template mesh from a [MorphoWeave](https://github.com/agporto/SlicerMorphoWeave) export using PCA + local RBF ([details](../morphospaces/morphoweave.md))
 
     Select the morphospace that matches your dataset.
 
-    For **ATLAS**, set **`database_dir`** under Configuration → morphospace hyperparameters before generating samples.
+    For **MorphoWeave**, set **`database_dir`** under Configuration → morphospace hyperparameters before generating samples.
 
 ??? note "Step 4: Import and Manage Datasets"
     Expand the **"4 Datasets"** panel.
@@ -155,7 +155,7 @@ Before starting, ensure you have:
 
     1. Choose the mesh export type.
     2. Enable **Save Meshes** if you want the simulation pipeline to export meshes.
-    3. Optionally disable **Orient before export** to save meshes in the morphospace/SSM frame (recommended for ATLAS); leave it on (default) to apply Default table placement first.
+    3. Optionally disable **Orient before export** to save meshes in the morphospace/SSM frame (recommended for MorphoWeave); leave it on (default) to apply Default table placement first.
     4. You can also use **Export Mesh** to save the current sample manually.
 
 ??? note "Step 8: Imaging"