morph-spines-visualizer 0.2.6__tar.gz → 0.2.7__tar.gz

{morph_spines_visualizer-0.2.6 → morph_spines_visualizer-0.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: morph_spines_visualizer
-Version: 0.2.6
+Version: 0.2.7
 Summary: Package to load and visualize morphologies with spines
 Author-email: Marwan Abdellah <marwan.abdellah@openbraininstitute.org>
 Maintainer-email: Marwan Abdellah <marwan.abdellah@openbraininstitute.org>

morph_spines_visualizer-0.2.6/examples/visualize_spiny_morphology.ipynb → morph_spines_visualizer-0.2.7/examples/visualize_morphology_synapses.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "90969a09",
+   "id": "b5f2224f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,8 @@
     "mesh_path = \"../data/864691134900032266.obj\"\n",
     "morphology_path = \"../data/864691134900032266.h5\"\n",
     "\n",
-    "morph_spines_visualizer.visualize_morphology_with_point_cloud(\n",
+    "# Visualize the data \n",
+    "morph_spines_visualizer.visualization_morphology_with_synapses(\n",
     "    morphology_path=morphology_path, \n",
     "    mesh_path=mesh_path\n",
     ")"
@@ -37,7 +38,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

morph_spines_visualizer-0.2.7/examples/visualize_spines_heads_necks.ipynb

@@ -0,0 +1,45 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3d883861",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import morph_spines_visualizer\n",
+    "print(f\"Version: {morph_spines_visualizer.__version__}\")\n",
+    "\n",
+    "# Data paths \n",
+    "mesh_path = \"/ssd1/data/microns_v1718/testing/864691134886335738.obj\"\n",
+    "morphology_path = \"/ssd1/data/microns_v1718/testing/864691134886335738_skeletonization_9/864691134886335738.h5\"\n",
+    "\n",
+    "morph_spines_visualizer.visualize_spines_heads_and_necks(\n",
+    "    morphology_path=morphology_path, \n",
+    "    mesh_path=mesh_path\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

morph_spines_visualizer-0.2.7/examples/visualize_spiny_morphology.ipynb

@@ -0,0 +1,49 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "90969a09",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import morph_spines_visualizer\n",
+    "print(f\"Version: {morph_spines_visualizer.__version__}\")\n",
+    "\n",
+    "# Data paths \n",
+    "mesh_path = \"../data/864691134900032266.obj\"\n",
+    "morphology_path = \"../data/864691134900032266.h5\"\n",
+    "\n",
+    "\n",
+    "mesh_path = \"/ssd1/data/microns_v1718/testing/864691134886335738.obj\"\n",
+    "morphology_path = \"/ssd1/data/microns_v1718/testing/864691134886335738_skeletonization_9/864691134886335738.h5\"\n",
+    "\n",
+    "morph_spines_visualizer.visualize_morphology_with_point_cloud(\n",
+    "    morphology_path=morphology_path, \n",
+    "    mesh_path=mesh_path\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{morph_spines_visualizer-0.2.6 → morph_spines_visualizer-0.2.7}/src/morph_spines_visualizer/__init__.py

@@ -1,5 +1,3 @@
-"""morph_spines."""
-
 from importlib.metadata import version
 
 __version__ = version(__package__)
@@ -24,10 +22,15 @@ from morph_spines_visualizer.core.spines import (
 
 from morph_spines_visualizer.core.k3d_visualization import (
     visualize_morphology_with_point_cloud,
-    visualization_morphology_with_synapses
+    visualization_morphology_with_synapses,
+    visualize_spines_heads_and_necks
 )
 
 from morph_spines_visualizer.utils.mesh_loading import (
     load_mesh_vertices_and_faces,
     load_mesh_vertices
+)
+
+from morph_spines_visualizer.utils.colors import (
+    rgb_to_hex
 )

{morph_spines_visualizer-0.2.6 → morph_spines_visualizer-0.2.7}/src/morph_spines_visualizer/core/k3d_visualization.py

@@ -2,6 +2,7 @@ import k3d
 import numpy as np 
 from morph_spines_visualizer.core import k3d_core, data_loading, geometry
 from morph_spines_visualizer.core import spines as spines_lib
+from morph_spines_visualizer.utils.colors import rgb_to_hex
 import ipywidgets as widgets
 from IPython.display import display
 
@@ -390,3 +391,141 @@ def visualization_morphology_with_synapses(
     # Display everything
     display(container)
 
+def visualize_spines_heads_and_necks(
+        mesh_path: str,
+        morphology_path: str,
+        grid_visible: bool = False,
+        axes_helper: bool = False,
+        head_color: tuple = (1.0, 0.4, 0.4),
+        neck_color: tuple = (0.4, 0.8, 0.4),
+        neuron_color: tuple = (0.5, 0.5, 1.0),
+        neuron_point_size: float = 0.025,
+        background_color: int = 0xffffff):
+    """
+    Visualize a spiny neuron morphology with spine heads and necks shown in distinct colors.
+
+    Spine heads are rendered in one color and necks in another, allowing visual
+    distinction of spine sub-compartments per section.
+
+    Args:
+        mesh_path (str): Path to the mesh file.
+        morphology_path (str): Path to the morphology file.
+        grid_visible (bool, optional): Show grid. Defaults to False.
+        axes_helper (bool, optional): Show axes helper. Defaults to False.
+        head_color (tuple, optional): RGB color for spine heads. Defaults to (1.0, 0.4, 0.4).
+        neck_color (tuple, optional): RGB color for spine necks. Defaults to (0.4, 0.8, 0.4).
+        neuron_color (tuple, optional): RGB color for neuron mesh. Defaults to (0.5, 0.5, 1.0).
+        neuron_point_size (float, optional): Point size for neuron mesh. Defaults to 0.025.
+        background_color (int, optional): Background color (hex). Defaults to 0xffffff.
+    """
+
+    # Convert RGB tuples to hex
+    head_color_hex = rgb_to_hex(*head_color)
+    neck_color_hex = rgb_to_hex(*neck_color)
+    neuron_color_hex = rgb_to_hex(*neuron_color)
+
+    # Load data
+    morphology = data_loading.load_spiny_morphology(morphology_path)
+    mesh_vertices = data_loading.load_mesh_vertices_pyvista(mesh_path, scale_factor=1e-3)
+
+    # Create K3D plot
+    plot = k3d.plot(
+        grid_visible=grid_visible, axes_helper=axes_helper, background_color=background_color)
+
+    # Draw the neuron mesh as point cloud
+    plot += k3d.points(
+        mesh_vertices,
+        point_size=neuron_point_size,
+        color=neuron_color_hex,
+        opacity=0.5,
+        shader='flat',
+    )
+
+    # State: track spine mesh objects for clean removal
+    spine_objs = []
+
+    def display_spine(spine_id):
+        """Display a spine (head/neck) and focus the camera on it."""
+        nonlocal spine_objs, plot
+
+        # Remove previous spine meshes
+        for obj in spine_objs:
+            try:
+                plot -= obj
+            except Exception:
+                pass
+        spine_objs.clear()
+
+        neck = morphology.spines.spine_mesh(spine_id, include_head=False)
+        head = morphology.spines.spine_mesh(spine_id, include_neck=False)
+
+        if len(neck.faces) > 0:
+            obj = k3d.mesh(
+                neck.vertices.astype(np.float32),
+                neck.faces.astype(np.uint32),
+                color=neck_color_hex,
+                flat_shading=True,
+            )
+            plot += obj
+            spine_objs.append(obj)
+
+        if len(head.faces) > 0:
+            obj = k3d.mesh(
+                head.vertices.astype(np.float32),
+                head.faces.astype(np.uint32),
+                color=head_color_hex,
+                flat_shading=True,
+            )
+            plot += obj
+            spine_objs.append(obj)
+
+        # Focus camera on the spine
+        full = morphology.spines.spine_mesh(spine_id)
+        center = full.centroid.astype(np.float32)
+        radius = float(np.linalg.norm(full.vertices - center, axis=1).max())
+        camera_pos = center + np.array([0, 0, 4.0 * radius], dtype=np.float32)
+        plot.camera_auto_fit = False
+        plot.camera = camera_pos.tolist() + center.tolist() + [0, 1, 0]
+
+    # Build list of valid spine indices (those with non-empty meshes)
+    valid_spines = []
+    for i in range(morphology.spines.spine_count):
+        try:
+            mesh = morphology.spines.spine_mesh(i)
+            if mesh is not None and len(mesh.faces) > 0:
+                valid_spines.append(i)
+        except Exception:
+            pass
+    print(f'Valid spines: {len(valid_spines)} / {morphology.spines.spine_count}')
+
+    if not valid_spines:
+        print("No valid spines found.")
+        display(plot)
+        return
+
+    # Dropdown for spine selection
+    dropdown = widgets.Dropdown(
+        options=valid_spines,
+        value=valid_spines[0],
+        description='Spine #:',
+        style={'description_width': 'initial'},
+        layout=widgets.Layout(width='200px'),
+    )
+
+    def on_change(change):
+        if change.get('name') == 'value':
+            display_spine(change['new'])
+
+    dropdown.observe(on_change, names='value')
+
+    # Camera reset button
+    reset_btn = widgets.Button(description='Reset Camera', button_style='primary')
+    reset_btn.on_click(lambda _: (plot.camera_reset(), setattr(plot, 'camera_auto_fit', True)))
+
+    # Layout and display
+    controls = widgets.HBox([dropdown, reset_btn])
+    display(widgets.VBox([plot, controls]))
+
+    # Trigger initial spine display
+    display_spine(valid_spines[0])
+    

morph_spines_visualizer-0.2.7/src/morph_spines_visualizer/utils/colors.py

@@ -0,0 +1,23 @@
+def rgb_to_hex(r, g, b) -> int:
+    """Convert RGB color values to a hex color integer.
+
+    Automatically detects whether inputs are in 0.0-1.0 or 0-255 range.
+    Float values > 1.0 are treated as 0-255 range.
+
+    Args:
+        r: Red channel.
+        g: Green channel.
+        b: Blue channel.
+
+    Returns:
+        Hex color as an integer (e.g., 0xFF8000).
+    """
+    channels = [r, g, b]
+    if all(isinstance(c, float) and c <= 1.0 for c in channels):
+        r, g, b = (int(round(c * 255)) for c in channels)
+    else:
+        r, g, b = (int(round(c)) for c in channels)
+    r = max(0, min(255, r))
+    g = max(0, min(255, g))
+    b = max(0, min(255, b))
+    return (r << 16) | (g << 8) | b

{morph_spines_visualizer-0.2.6 → morph_spines_visualizer-0.2.7}/src/morph_spines_visualizer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: morph_spines_visualizer
-Version: 0.2.6
+Version: 0.2.7
 Summary: Package to load and visualize morphologies with spines
 Author-email: Marwan Abdellah <marwan.abdellah@openbraininstitute.org>
 Maintainer-email: Marwan Abdellah <marwan.abdellah@openbraininstitute.org>

{morph_spines_visualizer-0.2.6 → morph_spines_visualizer-0.2.7}/src/morph_spines_visualizer.egg-info/SOURCES.txt

@@ -10,6 +10,7 @@ data/864691134900032266.obj
 data/neuron.glb
 data/neuron.obj
 examples/visualize_morphology_synapses.ipynb
+examples/visualize_spines_heads_necks.ipynb
 examples/visualize_spiny_morphology.ipynb
 src/morph_spines_visualizer/__init__.py
 src/morph_spines_visualizer.egg-info/PKG-INFO
@@ -23,5 +24,6 @@ src/morph_spines_visualizer/core/geometry.py
 src/morph_spines_visualizer/core/k3d_core.py
 src/morph_spines_visualizer/core/k3d_visualization.py
 src/morph_spines_visualizer/core/spines.py
+src/morph_spines_visualizer/utils/colors.py
 src/morph_spines_visualizer/utils/mesh_loading.py
 src/morph_spines_visualizer/utils/supress.py

morph_spines_visualizer-0.2.6/examples/visualize_morphology_synapses.ipynb

@@ -1,77 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "b5f2224f",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Version: 0.1.dev6\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "\u001b[1;33mHDF5 GROUP:0:warning\u001b[0m\n",
-      "Warning: no soma found in file\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e1552001ff094862b02905926070676c",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(Plot(antialias=3, axes=['x', 'y', 'z'], axes_helper_colors=[16711680, 65280, 255], background_c…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "import morph_spines_visualizer\n",
-    "print(f\"Version: {morph_spines_visualizer.__version__}\")\n",
-    "\n",
-    "# Data paths \n",
-    "mesh_path = \"../data/864691134900032266.obj\"\n",
-    "morphology_path = \"../data/864691134900032266.h5\"\n",
-    "\n",
-    "# Visualize the data \n",
-    "morph_spines_visualizer.visualization_morphology_with_synapses(\n",
-    "    morphology_path=morphology_path, \n",
-    "    mesh_path=mesh_path\n",
-    ")"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.12"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}