data_exploration refactored

qim3d/viz/__init__.py

 from . import colormaps
 from .cc import plot_cc
 from .detection import circles
-from .explore import (
-    interactive_fade_mask,
-    orthogonal,
+from .data_exploration import (
+    fade_mask,
     slicer,
-    slices,
+    slicer_orthogonal,
+    slices_grid,
     chunks,
     histogram,
 )
 from .itk_vtk_viewer import itk_vtk, Installer, NotInstalledError
-from .k3d import vol, mesh
+from .k3d import volumetric, mesh
 from .local_thickness_ import local_thickness
 from .structure_tensor import vectors
 from .metrics import plot_metrics, grid_overview, grid_pred, vol_masked

qim3d/viz/k3d.py

@@ -14,13 +14,13 @@ from qim3d.utils.logger import log
 from qim3d.utils.misc import downscale_img, scale_to_float16
 
 
-def vol(
+def volumetric(
     img,
     aspectmode="data",
     show=True,
     save=False,
     grid_visible=False,
-    cmap=None,
+    color_map='magma',
     constant_opacity=False,
     vmin=None,
     vmax=None,
@@ -43,8 +43,8 @@ def vol(
             If a string is provided, it's interpreted as the file path where the HTML
             file will be saved. Defaults to False.
         grid_visible (bool, optional): If True, the grid is visible in the plot. Defaults to False.
-        cmap (str or matplotlib.colors.Colormap or list, optional): The color map to be used for the volume rendering. If a string is passed, it should be a matplotlib colormap name. Defaults to None.
-        constant_opacity (bool, float): Set to True if doing an object label visualization with a corresponding cmap; otherwise, the plot may appear poorly. Defaults to False.
+        color_map (str or matplotlib.colors.Colormap or list, optional): The color map to be used for the volume rendering. If a string is passed, it should be a matplotlib colormap name. Defaults to None.
+        constant_opacity (bool, float): Set to True if doing an object label visualization with a corresponding color_map; otherwise, the plot may appear poorly. Defaults to False.
         vmin (float, optional): Together with vmax defines the data range the colormap covers. By default colormap covers the full range. Defaults to None.
         vmax (float, optional): Together with vmin defines the data range the colormap covers. By default colormap covers the full range. Defaults to None
         samples (int, optional): The number of samples to be used for the volume rendering in k3d. Defaults to 512.
@@ -60,7 +60,7 @@ def vol(
         ValueError: If `aspectmode` is not `'data'` or `'cube'`.
 
     Tip:
-        The function can be used for object label visualization using a `cmap` created with `qim3d.viz.colormaps.objects` along with setting `objects=True`. The latter ensures appropriate rendering.
+        The function can be used for object label visualization using a `color_map` created with `qim3d.viz.colormaps.objects` along with setting `objects=True`. The latter ensures appropriate rendering.
 
     Example:
         Display a volume inline:
@@ -69,7 +69,7 @@ def vol(
         import qim3d
 
         vol = qim3d.examples.bone_128x128x128
-        qim3d.viz.vol(vol)
+        qim3d.viz.volumetric(vol)
         ```
         <iframe src="https://platform.qim.dk/k3d/fima-bone_128x128x128-20240221113459.html" width="100%" height="500" frameborder="0"></iframe>
 
@@ -78,7 +78,7 @@ def vol(
         ```python
         import qim3d
         vol = qim3d.examples.bone_128x128x128
-        plot = qim3d.viz.vol(vol, show=False, save="plot.html")
+        plot = qim3d.viz.volumetric(vol, show=False, save="plot.html")
         ```
 
     """
@@ -129,21 +129,21 @@ def vol(
     if vmax:
         color_range[1] = vmax
 
-    # Handle the different formats that cmap can take
-    if cmap:
-        if isinstance(cmap, str):
-            cmap = plt.get_cmap(cmap)  # Convert to Colormap object
-        if isinstance(cmap, Colormap):
-            # Convert to the format of cmap required by k3d.volume
-            attr_vals = np.linspace(0.0, 1.0, num=cmap.N)
-            RGB_vals = cmap(np.arange(0, cmap.N))[:, :3]
-            cmap = np.column_stack((attr_vals, RGB_vals)).tolist()
+    # Handle the different formats that color_map can take
+    if color_map:
+        if isinstance(color_map, str):
+            color_map = plt.get_cmap(color_map)  # Convert to Colormap object
+        if isinstance(color_map, Colormap):
+            # Convert to the format of color_map required by k3d.volume
+            attr_vals = np.linspace(0.0, 1.0, num=color_map.N)
+            RGB_vals = color_map(np.arange(0, color_map.N))[:, :3]
+            color_map = np.column_stack((attr_vals, RGB_vals)).tolist()
 
     # Default k3d.volume settings
     opacity_function = []
     interpolation = True
     if constant_opacity:
-        # without these settings, the plot will look bad when cmap is created with qim3d.viz.colormaps.objects
+        # without these settings, the plot will look bad when color_map is created with qim3d.viz.colormaps.objects
         opacity_function = [0.0, float(constant_opacity), 1.0, float(constant_opacity)]
         interpolation = False
 
@@ -155,7 +155,7 @@ def vol(
             if aspectmode.lower() == "data"
             else None
         ),
-        color_map=cmap,
+        color_map=color_map,
         samples=samples,
         color_range=color_range,
         opacity_function=opacity_function,