Second check

docs/processing.md

@@ -41,7 +41,10 @@ Here, we provide functionalities designed specifically for 3D image analysis and
             - maximum
             - minimum
             - tophat
-            - Pipeline
+::: qim3d.filters.Pipeline
+    options:
+        members:
+            - append
 
 ::: qim3d.features
     options:

qim3d/features/_common_features_methods.py

@@ -27,8 +27,8 @@ def volume(obj: np.ndarray|trimesh.Trimesh,
         mesh = qim3d.io.load_mesh('path/to/mesh.obj')
 
         # Compute the volume of the mesh
-        vol = qim3d.features.volume(mesh)
-        print('Volume:', vol)
+        volume = qim3d.features.volume(mesh)
+        print('Volume:', volume)
         ```
 
         Compute volume from a np.ndarray:

qim3d/generate/_aggregators.py

@@ -189,10 +189,10 @@ def noise_object_collection(
 
         # Generate synthetic collection of objects
         num_objects = 15
-        synthetic_collection, labels = qim3d.generate.noise_object_collection(num_objects = num_objects)
+        vol, labels = qim3d.generate.noise_object_collection(num_objects = num_objects)
 
         # Visualize synthetic collection
-        qim3d.viz.volumetric(synthetic_collection)
+        qim3d.viz.volumetric(vol)
         ```
         <iframe src="https://platform.qim.dk/k3d/synthetic_collection_default.html" width="100%" height="500" frameborder="0"></iframe>
 
@@ -213,7 +213,7 @@ def noise_object_collection(
         import qim3d
 
         # Generate synthetic collection of dense objects
-        synthetic_collection, labels = qim3d.generate.collection(
+        vol, labels = qim3d.generate.collection(
                                     min_high_value = 255,
                                     max_high_value = 255,
                                     min_object_noise = 0.05,
@@ -224,7 +224,7 @@ def noise_object_collection(
                                     max_gamma = 0.02)
 
         # Visualize synthetic collection
-        qim3d.viz.vol(synthetic_collection)
+        qim3d.viz.vol(vol)
         ```
         <iframe src="https://platform.qim.dk/k3d/synthetic_collection_dense.html" width="100%" height="500" frameborder="0"></iframe>
 

qim3d/generate/_generators.py

@@ -43,16 +43,16 @@ def noise_object(
         import qim3d
 
         # Generate synthetic blob
-        synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
+        vol = qim3d.generate.noise_object(noise_scale = 0.015)
 
         # Visualize 3D volume
-        qim3d.viz.volumetric(synthetic_blob)
+        qim3d.viz.volumetric(vol)
         ```
         <iframe src="https://platform.qim.dk/k3d/synthetic_blob.html" width="100%" height="500" frameborder="0"></iframe>
 
         ```python
         # Visualize slices
-        qim3d.viz.slices_grid(synthetic_blob, value_min = 0, value_max = 255, num_slices = 15)
+        qim3d.viz.slices_grid(vol, value_min = 0, value_max = 255, num_slices = 15)
         ```
         ![synthetic_blob](assets/screenshots/synthetic_blob_slices.png)
 

qim3d/operations/_common_operations_methods.py

@@ -81,7 +81,7 @@ def fade_mask(
     Example:
         ```python
         import qim3d
-        vol = qim3d.io.load('yourVolume.tif')
+        vol = qim3d.io.load('heartScan.tif')
         qim3d.viz.volumetric(vol)
         ```
         Image before edge fading has visible artifacts from the support. Which obscures the object of interest.

qim3d/processing/_local_thickness.py

@@ -40,8 +40,8 @@ def local_thickness(
         ```python
         import qim3d
 
-        fly = qim3d.examples.fly_150x256x256 # 3D volume
-        lt_fly = qim3d.processing.local_thickness(fly, visualize=True, axis=0)
+        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)
 
@@ -49,11 +49,10 @@ def local_thickness(
         import qim3d
 
         # Generate synthetic collection of blobs
-        num_objects = 15
-        synthetic_collection, labels = qim3d.generate.noise_object_collection(num_objects = num_objects)
+        vol, labels = qim3d.generate.noise_object_collection(num_objects=15)
 
         # Extract one slice to show that localthickness works on 2D slices too
-        slice = synthetic_collection[:,:,50]
+        slice = vol[:,:,50]
         lt_blobs = qim3d.processing.local_thickness(slice, visualize=True)
 
         ```