Merge branch 'doc_update_for_v1.0' into 'main'

Doc update for v1.0

See merge request !149

qim3d/generate/_aggregators.py

@@ -199,14 +199,14 @@ def noise_object_collection(
         ```python
         qim3d.viz.slicer(synthetic_collection)
         ```
-        ![synthetic_collection](assets/screenshots/synthetic_collection_default.gif)
+        ![synthetic_collection](../../assets/screenshots/synthetic_collection_default.gif)
 
         ```python
         # Visualize labels
         cmap = qim3d.viz.colormaps.segmentation(num_labels=num_objects)
         qim3d.viz.slicer(labels, color_map=cmap, value_max=num_objects)
         ```
-        ![synthetic_collection](assets/screenshots/synthetic_collection_default_labels.gif)
+        ![synthetic_collection](../../assets/screenshots/synthetic_collection_default_labels.gif)
 
     Example:
         ```python
@@ -257,7 +257,7 @@ def noise_object_collection(
         # Visualize slices
         qim3d.viz.slices_grid(vol, num_slices=15)
         ```
-        ![synthetic_collection_cylinder](assets/screenshots/synthetic_collection_cylinder_slices.png)    
+        ![synthetic_collection_cylinder](../../assets/screenshots/synthetic_collection_cylinder_slices.png)    
         
     Example:
         ```python
@@ -287,7 +287,7 @@ def noise_object_collection(
         # Visualize slices
         qim3d.viz.slices_grid(vol, num_slices=15, slice_axis=1)
         ```
-        ![synthetic_collection_tube](assets/screenshots/synthetic_collection_tube_slices.png)
+        ![synthetic_collection_tube](../../assets/screenshots/synthetic_collection_tube_slices.png)
     """
     if verbose:
         original_log_level = log.getEffectiveLevel()

qim3d/generate/_generators.py

@@ -54,7 +54,7 @@ def noise_object(
         # Visualize slices
         qim3d.viz.slices_grid(vol, value_min = 0, value_max = 255, num_slices = 15)
         ```
-        ![synthetic_blob](assets/screenshots/synthetic_blob_slices.png)
+        ![synthetic_blob](../../assets/screenshots/synthetic_blob_slices.png)
 
     Example:
         ```python
@@ -78,7 +78,7 @@ def noise_object(
         # Visualize slices
         qim3d.viz.slices_grid(vol, num_slices=15, slice_axis=1)
         ```
-        ![synthetic_blob_cylinder_slice](assets/screenshots/synthetic_blob_cylinder_slice.png)
+        ![synthetic_blob_cylinder_slice](../../assets/screenshots/synthetic_blob_cylinder_slice.png)
 
     Example:
         ```python
@@ -102,7 +102,7 @@ def noise_object(
         # Visualize
         qim3d.viz.slices_grid(vol, num_slices=15)
         ```
-        ![synthetic_blob_tube_slice](assets/screenshots/synthetic_blob_tube_slice.png)    
+        ![synthetic_blob_tube_slice](../../assets/screenshots/synthetic_blob_tube_slice.png)    
     """
 
     if not isinstance(final_shape, tuple) or len(final_shape) != 3:

qim3d/gui/annotation_tool.py

@@ -16,7 +16,7 @@ annotation_tool = qim3d.gui.annotation_tool.Interface()
 # We can directly pass the image we loaded to the interface
 app = annotation_tool.launch(vol[0])
 ```
-![gui-annotation_tool](assets/screenshots/gui-annotation_tool.gif)
+![gui-annotation_tool](../../assets/screenshots/gui-annotation_tool.gif)
 
 """
 

qim3d/gui/layers2d.py

@@ -13,7 +13,7 @@ import qim3d
 layers = qim3d.gui.layers2d.Interface()
 app = layers.launch()
 ```
-![gui-layers](assets/screenshots/GUI-layers.png)
+![gui-layers](../../assets/screenshots/GUI-layers.png)
 
 """
 

qim3d/io/_downloader.py

@@ -54,7 +54,7 @@ class Downloader:
 
         qim3d.viz.slicer_orthogonal(data, color_map="magma")
         ```
-        ![cowry shell](assets/screenshots/cowry_shell_slicer.gif)
+        ![cowry shell](../../assets/screenshots/cowry_shell_slicer.gif)
     """
 
     def __init__(self):

qim3d/operations/_common_operations_methods.py

@@ -32,7 +32,7 @@ def remove_background(
         vol = qim3d.examples.cement_128x128x128
         fig1 = qim3d.viz.slices_grid(vol, value_min=0, value_max=255, num_slices=5, display_figure=True)
         ```
-        ![operations-remove_background_before](assets/screenshots/operations-remove_background_before.png)
+        ![operations-remove_background_before](../../assets/screenshots/operations-remove_background_before.png)
 
         ```python
         vol_filtered  = qim3d.operations.remove_background(vol,
@@ -40,7 +40,7 @@ def remove_background(
                                                               background="bright")
         fig2 = qim3d.viz.slices_grid(vol_filtered, value_min=0, value_max=255, num_slices=5, display_figure=True)
         ```
-        ![operations-remove_background_after](assets/screenshots/operations-remove_background_after.png)
+        ![operations-remove_background_after](../../assets/screenshots/operations-remove_background_after.png)
     """
 
     # Create a pipeline with a median filter and a tophat filter
@@ -85,7 +85,7 @@ def fade_mask(
         qim3d.viz.volumetric(vol)
         ```
         Image before edge fading has visible artifacts from the support. Which obscures the object of interest.
-        ![operations-edge_fade_before](assets/screenshots/operations-edge_fade_before.png)
+        ![operations-edge_fade_before](../../assets/screenshots/operations-edge_fade_before.png)
 
         ```python
         import qim3d
@@ -93,7 +93,7 @@ def fade_mask(
         qim3d.viz.volumetrics(vol_faded)
         ```
         Afterwards the artifacts are faded out, making the object of interest more visible for visualization purposes.
-        ![operations-edge_fade_after](assets/screenshots/operations-edge_fade_after.png)
+        ![operations-edge_fade_after](../../assets/screenshots/operations-edge_fade_after.png)
 
     """
     if 0 > axis or axis >= vol.ndim:

qim3d/processing/_layers.py

@@ -47,8 +47,8 @@ def segment_layers(data: np.ndarray,
         for layer_line in layer_lines:
             plt.plot(layer_line, linewidth = 3)
         ```
-        ![layer_segmentation](assets/screenshots/layers.png)
-        ![layer_segmentation](assets/screenshots/segmented_layers.png)
+        ![layer_segmentation](../../assets/screenshots/layers.png)
+        ![layer_segmentation](../../assets/screenshots/segmented_layers.png)
 
     """
     if isinstance(data, np.ndarray):

qim3d/processing/_local_thickness.py

@@ -43,7 +43,7 @@ def local_thickness(
         vol = qim3d.examples.fly_150x256x256
         lt_vol = qim3d.processing.local_thickness(vol, visualize=True, axis=0)
         ```
-        ![local thickness 3d](assets/screenshots/local_thickness_3d.gif)
+        ![local thickness 3d](../../assets/screenshots/local_thickness_3d.gif)
 
         ```python
         import qim3d
@@ -56,10 +56,10 @@ def local_thickness(
         lt_blobs = qim3d.processing.local_thickness(slice, visualize=True)
 
         ```
-        ![local thickness 2d](assets/screenshots/local_thickness_2d.png)
+        ![local thickness 2d](../../assets/screenshots/local_thickness_2d.png)
 
     !!! info "Runtime and memory usage of the local thickness method for different volume sizes"
-        ![local thickness estimate time and mem](assets/screenshots/Local_thickness_time_mem_estimation.png)
+        ![local thickness estimate time and mem](../../assets/screenshots/Local_thickness_time_mem_estimation.png)
 
         Performance computed on Intel(R) Xeon(R) Gold 6226 CPU @ 2.70GHz.
 

qim3d/processing/_structure_tensor.py

@@ -47,11 +47,11 @@ def structure_tensor(
         vol = qim3d.examples.NT_128x128x128
         val, vec = qim3d.processing.structure_tensor(vol, visualize = True, axis = 2)
         ```
-        ![structure tensor](assets/screenshots/structure_tensor_visualization.gif)
+        ![structure tensor](../../assets/screenshots/structure_tensor_visualization.gif)
 
 
     !!! info "Runtime and memory usage of the structure tensor method for different volume sizes"
-        ![structure tensor estimate time and mem](assets/screenshots/Structure_tensor_time_mem_estimation.png)
+        ![structure tensor estimate time and mem](../../assets/screenshots/Structure_tensor_time_mem_estimation.png)
 
         Performance computed on Intel(R) Xeon(R) Gold 6226 CPU @ 2.70GHz.
 

qim3d/segmentation/_common_segmentation_methods.py

@@ -26,7 +26,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
 
         fig1 = qim3d.viz.slices_grid(bin_vol, slice_axis=1, display_figure=True)
         ```
-        ![operations-watershed_before](assets/screenshots/operations-watershed_before.png)
+        ![operations-watershed_before](../../assets/screenshots/operations-watershed_before.png)
 
         ```python
         labeled_volume, num_labels = qim3d.segmentation.watershed(bin_vol)
@@ -34,7 +34,7 @@ def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, i
         cmap = qim3d.viz.colormaps.segmentation(num_labels)
         fig2 = qim3d.viz.slices_grid(labeled_volume, slice_axis=1, color_map=cmap, display_figure=True)
         ```
-        ![operations-watershed_after](assets/screenshots/operations-watershed_after.png)
+        ![operations-watershed_after](../../assets/screenshots/operations-watershed_after.png)
 
     """
     import skimage

qim3d/viz/_cc.py

@@ -43,8 +43,8 @@ def plot_cc(
         qim3d.viz.plot_cc(cc, crop=True, display_figure=True, overlay=None, num_slices=5, component_indexs=[4,6,7])
         qim3d.viz.plot_cc(cc, crop=True, display_figure=True, overlay=vol, num_slices=5, component_indexs=[4,6,7])
         ```
-        ![plot_cc_no_overlay](assets/screenshots/plot_cc_no_overlay.png)
-        ![plot_cc_overlay](assets/screenshots/plot_cc_overlay.png)
+        ![plot_cc_no_overlay](../../assets/screenshots/plot_cc_no_overlay.png)
+        ![plot_cc_overlay](../../assets/screenshots/plot_cc_overlay.png)
     """
     # if no components are given, plot the first max_cc_to_plot=32 components
     if component_indexs is None:

qim3d/viz/_data_exploration.py

@@ -81,7 +81,7 @@ def slices_grid(
         vol = qim3d.examples.shell_225x128x128
         qim3d.viz.slices_grid(vol, num_slices=15)
         ```
-        ![Grid of slices](assets/screenshots/viz-slices.png)
+        ![Grid of slices](../../assets/screenshots/viz-slices.png)
     """
     if image_size:
         image_height = image_size
@@ -354,7 +354,7 @@ def slicer(
         vol = qim3d.examples.bone_128x128x128
         qim3d.viz.slicer(vol)
         ```
-        ![viz slicer](assets/screenshots/viz-slicer.gif)
+        ![viz slicer](../../assets/screenshots/viz-slicer.gif)
     """
 
     if image_size:
@@ -427,7 +427,7 @@ def slicer_orthogonal(
         vol = qim3d.examples.fly_150x256x256
         qim3d.viz.slicer_orthogonal(vol, color_map="magma")
         ```
-        ![viz slicer_orthogonal](assets/screenshots/viz-orthogonal.gif)
+        ![viz slicer_orthogonal](../../assets/screenshots/viz-orthogonal.gif)
     """
 
     if image_size:
@@ -484,7 +484,7 @@ def fade_mask(
         vol = qim3d.examples.cement_128x128x128
         qim3d.viz.fade_mask(vol)
         ```
-        ![operations-edge_fade_before](assets/screenshots/viz-fade_mask.gif)
+        ![operations-edge_fade_before](../../assets/screenshots/viz-fade_mask.gif)
 
     """
 
@@ -623,7 +623,7 @@ def chunks(zarr_path: str, **kwargs)-> widgets.interactive:
         # Explore chunks
         qim3d.viz.chunks("Escargot.zarr")
         ```
-        ![chunks-visualization](assets/screenshots/chunks_visualization.gif)
+        ![chunks-visualization](../../assets/screenshots/chunks_visualization.gif)
     """
 
     # Load the Zarr dataset
@@ -904,7 +904,7 @@ def histogram(
         vol = qim3d.examples.bone_128x128x128
         qim3d.viz.histogram(vol)
         ```
-        ![viz histogram](assets/screenshots/viz-histogram-vol.png)
+        ![viz histogram](../../assets/screenshots/viz-histogram-vol.png)
 
         ```python
         import qim3d
@@ -912,7 +912,7 @@ def histogram(
         vol = qim3d.examples.bone_128x128x128
         qim3d.viz.histogram(vol, bins=32, slice_idx="middle", axis=1, kde=False, log_scale=True)
         ```
-        ![viz histogram](assets/screenshots/viz-histogram-slice.png)
+        ![viz histogram](../../assets/screenshots/viz-histogram-slice.png)
     """
 
     if not (0 <= axis < volume.ndim):

qim3d/viz/_detection.py

@@ -46,7 +46,7 @@ def circles(blobs: tuple[float,float,float,float], vol: np.ndarray, alpha: float
         # Visualize detected blobs with circles method
         qim3d.viz.circles(blobs, vol, alpha=0.8, color='blue')
         ```
-        ![blob detection](assets/screenshots/blob_detection.gif)
+        ![blob detection](../../assets/screenshots/blob_detection.gif)
     """
 
     def _slicer(z_slice):

qim3d/viz/_local_thickness.py

@@ -46,7 +46,7 @@ def local_thickness(
         lt_fly = qim3d.processing.local_thickness(fly)
         qim3d.viz.local_thickness(fly, lt_fly, axis=0)
         ```
-        ![local thickness 3d](assets/screenshots/local_thickness_3d.gif)
+        ![local thickness 3d](../../assets/screenshots/local_thickness_3d.gif)
 
         
     """

qim3d/viz/_structure_tensor.py

@@ -69,7 +69,7 @@ def vectors(
         # Visualize the structure tensor
         qim3d.viz.vectors(vol, vec, axis = 2, interactive = True)
         ```
-        ![structure tensor](assets/screenshots/structure_tensor_visualization.gif)
+        ![structure tensor](../../assets/screenshots/structure_tensor_visualization.gif)
 
     """
 

qim3d/viz/colormaps/_qim_colors.py

@@ -19,6 +19,6 @@ Example:
 
     display(qim3d.viz.colormaps.qim)
     ```
-    ![colormap objects](assets/screenshots/viz-colormaps-qim.png)
+    ![colormap objects](../../assets/screenshots/viz-colormaps-qim.png)
 """
 colormaps.register(qim)

qim3d/viz/colormaps/_segmentation.py

@@ -71,7 +71,7 @@ def segmentation(
         display(cmap_earth)
         display(cmap_ocean)
         ```
-        ![colormap objects](assets/screenshots/viz-colormaps-objects-all.png)
+        ![colormap objects](../../assets/screenshots/viz-colormaps-objects-all.png)
 
         ```python
         import qim3d
@@ -83,7 +83,7 @@ def segmentation(
         color_map = qim3d.viz.colormaps.segmentation(num_labels, style = 'bright')
         qim3d.viz.slicer(labeled_volume, slice_axis = 1, color_map=color_map)
         ```
-        ![colormap objects](assets/screenshots/viz-colormaps-objects.gif)
+        ![colormap objects](../../assets/screenshots/viz-colormaps-objects.gif)
 
     Tip:
         It can be easily used when calling visualization functions as
@@ -95,7 +95,7 @@ def segmentation(
 
     Tip:
         The `min_dist` parameter can be used to control the distance between neighboring colors.
-        ![colormap objects mind_dist](assets/screenshots/viz-colormaps-min_dist.gif)
+        ![colormap objects mind_dist](../../assets/screenshots/viz-colormaps-min_dist.gif)
     """
     from skimage import color