unveil-python 0.6.0__tar.gz → 0.7.1__tar.gz

{unveil_python-0.6.0/src/unveil_python.egg-info → unveil_python-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: unveil-python
-Version: 0.6.0
+Version: 0.7.1
 Summary: Implementation of UNVEIL
 Author-email: Nicolas Delinte <nicolas.delinte@uclouvain.be>
 License-Expression: GPL-3.0-only

{unveil_python-0.6.0 → unveil_python-0.7.1}/pyproject.toml

@@ -18,7 +18,7 @@ classifiers = ['Intended Audience :: Science/Research',
 dependencies = ['dipy',
                 'pyvista',
                 'pyvistaqt',
-                'PyQt6'
+                'PyQt6',
 ]
 dynamic = ["version"]
 

{unveil_python-0.6.0 → unveil_python-0.7.1}/src/unveil/__init__.py

@@ -1,5 +1,5 @@
 """
 This package contains an UNVEIL, a lightweight tractography viewer implemented in python."""
 
-__version__ = "0.6.0"
+__version__ = "0.7.1"
 __author__ = 'Nicolas Delinte'

{unveil_python-0.6.0 → unveil_python-0.7.1}/src/unveil/core.py

@@ -12,7 +12,7 @@ from pyvistaqt import QtInteractor
 from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (QApplication, QWidget, QHBoxLayout, QVBoxLayout,
                              QPushButton, QFileDialog, QCheckBox, QSlider,
-                             QLabel, QComboBox, QMainWindow, QLineEdit,
+                             QLabel, QComboBox, QMainWindow,
                              QDockWidget, QTreeWidget, QTreeWidgetItem,
                              QColorDialog, QTabWidget, QDoubleSpinBox,
                              QGroupBox)
@@ -23,7 +23,7 @@ from matplotlib.colors import LinearSegmentedColormap
 from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg
 from matplotlib.figure import Figure
 # from unravel.utils import get_streamline_density
-from binama.utils import dilate_atlas_labels
+from unveil.utils import dilate_atlas_labels
 
 
 def gifti_to_pyvista(gii_path):
@@ -187,6 +187,27 @@ def plot_trk(trk_file, scalar=None, color_map='plasma', opacity: float = 1,
     p.background_color = background
 
 
+def load_gii_data(gii_path):
+    """
+    Load all data contained in the GifTi file except vertex coordinates and triangles.
+    Returns : dictionnary {"Gii table name" : data}
+    """
+    gii_img = nib.load(gii_path)
+    vertex_coords = gii_img.get_arrays_from_intent(
+        "NIFTI_INTENT_POINTSET")[0].data
+    gii_data = {}
+
+    # Iterate over all tables of the GIfTI
+    for darray in gii_img.darrays:
+        # Vertex coords and triangles are stored with None as 'Name'
+        if darray.meta.get("Name") is not None:
+            # Check that the table contains 1 value per vertex
+            if darray.data.shape == vertex_coords[:, 0].shape:
+                gii_data[darray.meta.get("Name")] = darray.data
+
+    return gii_data
+
+
 class TrkViewer(QWidget):
     def __init__(self):
         super().__init__()
@@ -423,7 +444,7 @@ class TrkViewer(QWidget):
         self.giiColorModeComboBox = QComboBox()
         self.giiColorModeComboBox.addItems(['Solid', 'NIfTI values'])
         self.giiColorModeComboBox.currentIndexChanged.connect(
-            self.update_gii_viewer)
+            lambda index: self.update_gii_viewer(update_color_range=True))
         color_mode_gii_row.addWidget(self.giiColorModeComboBox)
         gii_layout.addLayout(color_mode_gii_row)
 
@@ -500,39 +521,47 @@ class TrkViewer(QWidget):
         options = QFileDialog.Options()
         filePath, _ = QFileDialog.getOpenFileName(
             self, "Open .nii.gz File", "", "Nifti Files (*.nii.gz)", options=options)
-        if filePath:
-            print(f"Loaded NIfTI file: {filePath}")
-            img = nib.load(filePath)
-            self.nii_affine = img.affine
-            self.nii_data = img.get_fdata()
 
-            self.update_volume_color_range_from_nifti()
-            self.update_surface_color_range_from_nifti()
+        if not filePath:
+            return
+
+        print(f"Loaded NIfTI file: {filePath}")
+        img = nib.load(filePath)
+        self.nii_affine = img.affine
+        self.nii_data = img.get_fdata()
+
+        self.update_volume_color_range_from_nifti()
 
-            grid = pv.ImageData()
-            grid.dimensions = np.array(self.nii_data.shape) + 1
-            grid.cell_data['values'] = self.nii_data.flatten(order='F')
-            self.grid = grid
+        grid = pv.ImageData()
+        grid.dimensions = np.array(self.nii_data.shape) + 1
+        grid.cell_data['values'] = self.nii_data.flatten(order='F')
+        self.grid = grid
 
         self.XSlider.setMaximum(self.nii_data.shape[0])
         self.YSlider.setMaximum(self.nii_data.shape[1])
         self.ZSlider.setMaximum(self.nii_data.shape[2])
 
         self.update_nii_viewer(reset_camera=False)
+
+        # Dilation for surface
+        self.nii_data_dilated = dilate_atlas_labels(
+            self.nii_data, dilation_width=4)
+        self.nii_data_dilated = np.where(self.nii_data_dilated == 0, np.nan,
+                                         self.nii_data_dilated)
+
         if hasattr(self, "gii_mesh"):
+            # Sample NIfTI values at each surface vertex
+            self.nii_surface_values = self.sample_nifti_on_surface(
+                self.gii_mesh)
             self.update_gii_viewer(reset_camera=False)
+        else:
+            self.nii_surface_values = None
         self.window().refreshActorList()
 
         # Update 2D view with current colormap
         ortho_data = self.nii_data.copy()
         ortho_data[ortho_data == 0] = None
 
-        # Dilation for surface
-        self.nii_data_dilated = dilate_atlas_labels(
-            self.nii_data, dilation_width=4)
-        self.nii_data_dilated = np.where(self.nii_data_dilated == 0, np.nan,
-                                         self.nii_data_dilated)
-
         self.window().ortho_viewer.set_volume(ortho_data, self.nii_affine)
         self.window().ortho_viewer.set_colormap(self.niiColorMapComboBox.currentText())
 
@@ -577,14 +606,8 @@ class TrkViewer(QWidget):
 
     def loadGiftiFile(self):
         options = QFileDialog.Options()
-
         filePath, _ = QFileDialog.getOpenFileName(
-            self,
-            "Open .gii File",
-            "",
-            "Gifti Files (*.gii)",
-            options=options
-        )
+            self, "Open .gii File", "", "Gifti Files (*.gii)", options=options)
 
         if not filePath:
             return
@@ -593,8 +616,25 @@ class TrkViewer(QWidget):
 
         self.gii_mesh = gifti_to_pyvista(filePath)
 
+        self.gii_data = load_gii_data(filePath)
+
+        self.giiColorModeComboBox.setCurrentIndex(0)
+
+        for _ in range(self.giiColorModeComboBox.count()-2):
+            self.giiColorModeComboBox.removeItem(2)
+
+        self.giiColorModeComboBox.addItems(list(self.gii_data.keys()))
+
         self.actor_types["gii_surface"] = "gii"
 
+        if hasattr(self, "nii_data"):
+            # Sample NIfTI values at each surface vertex
+            self.nii_surface_values = self.sample_nifti_on_surface(
+                self.gii_mesh)
+            self.update_gii_viewer(reset_camera=False)
+        else:
+            self.nii_surface_values = None
+
         self.update_gii_viewer(reset_camera=False)
         self.window().refreshActorList()
 
@@ -740,7 +780,7 @@ class TrkViewer(QWidget):
                                 reset_camera=reset_camera, clim=[vmin, vmax],
                                 user_matrix=self.nii_affine)
 
-    def update_gii_viewer(self, reset_camera=False):
+    def update_gii_viewer(self, reset_camera=False, update_color_range=False):
         """Update the GIFTI surface rendering."""
 
         if not hasattr(self, "gii_mesh"):
@@ -760,9 +800,13 @@ class TrkViewer(QWidget):
                                   reset_camera=reset_camera,
                                   point_size=0, render_lines_as_tubes=True)
 
-        elif color_mode == "NIfTI values":
+        else:
+            if color_mode == "NIfTI values":
+                scalars = self.nii_surface_values
+            else:
+                scalars = self.gii_data[color_mode]
 
-            if self.nii_data is None:
+            if scalars is None:
                 self.plotter.add_mesh(self.gii_mesh, color="ghostwhite",
                                       culling="back", smooth_shading=True,
                                       opacity=opacity, name="gii_surface",
@@ -770,18 +814,15 @@ class TrkViewer(QWidget):
                                       point_size=0, render_lines_as_tubes=True)
                 return
 
-            # Sample NIfTI values at each surface vertex
-            scalars = self.sample_nifti_on_surface(self.gii_mesh)
-
-            if scalars is None:
-                return
-
             # Copy the mesh so that the original GIFTI mesh is not modified
             surface_mesh = self.gii_mesh.copy(deep=True)
-            surface_mesh.point_data["NIfTI values"] = scalars
+            surface_mesh.point_data[color_mode] = scalars
 
             cmap_name = self.giiColorMapComboBox.currentText()
 
+            if update_color_range:
+                self.update_surface_color_range(scalars)
+
             vmin = self.giiMinSpinBox.value()
             vmax = self.giiMaxSpinBox.value()
 
@@ -789,7 +830,7 @@ class TrkViewer(QWidget):
             if vmax <= vmin:
                 vmax = vmin + 1e-6
 
-            self.plotter.add_mesh(surface_mesh, scalars="NIfTI values",
+            self.plotter.add_mesh(surface_mesh, scalars=color_mode,
                                   cmap=cmap_name, clim=[vmin, vmax],
                                   culling="back", smooth_shading=True,
                                   opacity=opacity, name="gii_surface",
@@ -829,12 +870,12 @@ class TrkViewer(QWidget):
         self.niiMinSpinBox.blockSignals(False)
         self.niiMaxSpinBox.blockSignals(False)
 
-    def update_surface_color_range_from_nifti(self):
+    def update_surface_color_range(self, data):
 
-        if self.nii_data is None:
+        if data is None:
             return
 
-        data = np.asarray(self.nii_data, dtype=float)
+        data = np.asarray(data, dtype=float)
         finite = np.isfinite(data)
 
         if not np.any(finite):
@@ -997,7 +1038,7 @@ class TrkViewer(QWidget):
         """Enable surface scalar controls only when using NIfTI values."""
 
         use_nifti = (self.giiColorModeComboBox.currentText()
-                     == "NIfTI values")
+                     != "Solid")
 
         self.giiColorMapLabel.setEnabled(use_nifti)
         self.giiColorMapComboBox.setEnabled(use_nifti)

unveil_python-0.7.1/src/unveil/utils.py

@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Oct 26 10:03:52 2026
+
+@author: N. Delinte
+"""
+
+import numpy as np
+from scipy.ndimage import distance_transform_edt
+
+
+def dilate_atlas_labels(atlas, brain_mask=None, dilation_width: float = 1,
+                        min_label: int = 0):
+    """
+    Dilates cortical atlas labels to include nearby unlabeled voxels (0),
+    constrained by a brain mask.
+    Copied from 'pilab-binama' package.
+
+    Parameters
+    ----------
+    atlas : np.ndarray (3D, int)
+        Cortical atlas with integer labels (0 = unlabeled).
+    brain_mask : np.ndarray (3D, bool or int), optional
+        Binary mask of the brain (same shape as atlas). The default is one
+    dilation_width : float, optional
+        Maximum dilation distance in voxels. The default is None.
+    min_label : int, optional
+        Labels below this values are not dilated
+
+    Returns
+    -------
+    dilated_atlas : np.ndarray (3D, int)
+        Atlas with dilated labels.
+    """
+
+    # Mask unlabeled voxels inside the brain
+    unlabeled = np.where(atlas <= min_label, 1, 0)
+    if brain_mask is not None:
+        unlabeled *= brain_mask.astype('int32')
+
+    # Compute distance transform from labeled voxels
+    # Also retrieve indices of nearest labeled voxel for each position
+    distances, nearest_idx = distance_transform_edt(unlabeled,
+                                                    return_indices=True)
+
+    # Copy atlas to output
+    dilated_atlas = atlas.copy()
+
+    # For unlabeled voxels within dilation_width, assign nearest label
+    within_dilation = unlabeled & (distances <= dilation_width)
+
+    # Map nearest labeled voxel indices back to atlas labels
+    coords = np.argwhere(within_dilation)
+    for x, y, z in coords:
+        nx, ny, nz = nearest_idx[:, x, y, z]
+        dilated_atlas[x, y, z] = atlas[nx, ny, nz]
+
+    return dilated_atlas

{unveil_python-0.6.0 → unveil_python-0.7.1/src/unveil_python.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: unveil-python
-Version: 0.6.0
+Version: 0.7.1
 Summary: Implementation of UNVEIL
 Author-email: Nicolas Delinte <nicolas.delinte@uclouvain.be>
 License-Expression: GPL-3.0-only

{unveil_python-0.6.0 → unveil_python-0.7.1}/src/unveil_python.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 src/unveil/__init__.py
 src/unveil/__main__.py
 src/unveil/core.py
+src/unveil/utils.py
 src/unveil_python.egg-info/PKG-INFO
 src/unveil_python.egg-info/SOURCES.txt
 src/unveil_python.egg-info/dependency_links.txt