diff --git a/docs/datahandling.md b/docs/datahandling.md
deleted file mode 100644
index 894f8feda03baf30304efbf1d52dcbd01bf2e8f6..0000000000000000000000000000000000000000
--- a/docs/datahandling.md
+++ /dev/null
@@ -1,28 +0,0 @@
-# Data handling
-Dealing with volumetric data can be done by `qim3d` for the most common image formats available. This includes loading, saving and file conversions.
-
-Currently, it is possible to directly load `tiff`, `h5`, `nii`,`txm`, `vol` and common `PIL` formats using one single function.
-
-Additionally, synthtetic volumetric data can be generated using the `generate` module.
-
-::: qim3d.io
- options:
- members:
- - load
- - save
- - Downloader
- - export_ome_zarr
- - import_ome_zarr
- - save_mesh
- - load_mesh
-
-::: qim3d.mesh
- options:
- members:
- - from_volume
-
-::: qim3d.generate
- options:
- members:
- - noise_object
- - noise_object_collection
diff --git a/docs/cli.md b/docs/doc/cli/cli.md
similarity index 91%
rename from docs/cli.md
rename to docs/doc/cli/cli.md
index c2f878cc1cb4058458f636be21f63d9ebe4510ab..58fae7e2253830a9ab3156712fe7fac14d2c3f24 100644
--- a/docs/cli.md
+++ b/docs/doc/cli/cli.md
@@ -1,3 +1,8 @@
+---
+hide:
+ - navigation
+---
+
# Command line interface
The library also includes a command line interface for easy access to some functionalities, and the convenience of using qim3d directly from your terminal.
@@ -7,7 +12,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
``` title="Command"
qim3d gui --data-explorer
```
- 
+ 
## Graphical User Interfaces
@@ -50,7 +55,7 @@ The command line interface allows you to run graphical user interfaces directly
In this case, the GUI will be available at `http://127.0.0.1:7860`
- 
+ 
!!! Example
@@ -82,7 +87,7 @@ The command line interface allows you to run graphical user interfaces directly
In this case, the GUI will be available at `http://127.0.0.1:47326/gui/fima/47326/`
- 
+ 
@@ -127,7 +132,7 @@ You can launch volumetric visualizations directly from the command line. By defa
A new tab in the default browser will be open with the visualization:
- 
+ 
!!! Example "Example using k3d"
``` title="Command"
@@ -152,7 +157,7 @@ You can launch volumetric visualizations directly from the command line. By defa
```
And a new tab will be opened in the default browser with the interactive k3d plot:
- { width="512" }
+ { width="512" }
Or an specific path for destination can be used. We can also choose to not open the browser:
@@ -196,32 +201,32 @@ File previewing can also be done directly from the command line interface to pre
qim3d preview blobs_256x256x256.tif
```
- { width="512" }
+ { width="512" }
!!! Example
``` title="Command"
qim3d preview blobs_256x256x256.tif --resolution 30
```
- { width="512" }
+ { width="512" }
!!! Example
``` title="Command"
qim3d preview blobs_256x256x256.tif --resolution 50 --axis 1
```
- { width="512" }
+ { width="512" }
!!! Example
``` title="Command"
qim3d preview blobs_256x256x256.tif --resolution 50 --axis 2 --slice 0
```
- { width="512" }
+ { width="512" }
!!! Example
``` title="Command"
qim3d preview qim_logo.png --resolution 40
```
- { width="512" }
+ { width="512" }
diff --git a/docs/doc/data_handling/generate.md b/docs/doc/data_handling/generate.md
new file mode 100644
index 0000000000000000000000000000000000000000..6a414d1681c59031b643e84f36ab82baf5df567a
--- /dev/null
+++ b/docs/doc/data_handling/generate.md
@@ -0,0 +1,7 @@
+# Synthetic data generation
+
+::: qim3d.generate
+ options:
+ members:
+ - noise_object
+ - noise_object_collection
diff --git a/docs/doc/data_handling/io.md b/docs/doc/data_handling/io.md
new file mode 100644
index 0000000000000000000000000000000000000000..82c984bbced233b2a35836bdd072e3c73aa8bf8b
--- /dev/null
+++ b/docs/doc/data_handling/io.md
@@ -0,0 +1,12 @@
+# Input and output
+
+::: qim3d.io
+ options:
+ members:
+ - load
+ - save
+ - Downloader
+ - export_ome_zarr
+ - import_ome_zarr
+ - save_mesh
+ - load_mesh
\ No newline at end of file
diff --git a/docs/gui.md b/docs/doc/gui/gui.md
similarity index 81%
rename from docs/gui.md
rename to docs/doc/gui/gui.md
index ef996896db91d26a02037f28f288ece44d0892d3..681041fc4f2515ce6c89112b07c12d1d407f44f3 100644
--- a/docs/gui.md
+++ b/docs/doc/gui/gui.md
@@ -1,3 +1,8 @@
+---
+hide:
+ - navigation
+---
+
# Graphical User Interfaces
The `qim3d` library provides a set of custom made GUIs that ease the interaction with the available tools.
@@ -21,17 +26,17 @@ For details see [here](cli.md#qim3d-gui).
::: qim3d.gui.data_explorer
options:
members: False
-
+
::: qim3d.gui.local_thickness
options:
members: False
-
+
::: qim3d.gui.iso3d
options:
members: False
-
+
::: qim3d.gui.annotation_tool
options:
diff --git a/docs/detection.md b/docs/doc/image_analysis/detection.md
similarity index 100%
rename from docs/detection.md
rename to docs/doc/image_analysis/detection.md
diff --git a/docs/features.md b/docs/doc/image_analysis/features.md
similarity index 100%
rename from docs/features.md
rename to docs/doc/image_analysis/features.md
diff --git a/docs/filters.md b/docs/doc/image_analysis/filters.md
similarity index 100%
rename from docs/filters.md
rename to docs/doc/image_analysis/filters.md
diff --git a/docs/doc/image_analysis/mesh.md b/docs/doc/image_analysis/mesh.md
new file mode 100644
index 0000000000000000000000000000000000000000..bcedeb5573d6eb28ecb8e1c98d83b6ca4f09c1b7
--- /dev/null
+++ b/docs/doc/image_analysis/mesh.md
@@ -0,0 +1,4 @@
+::: qim3d.mesh
+ options:
+ members:
+ - from_volume
diff --git a/docs/operations.md b/docs/doc/image_analysis/operations.md
similarity index 100%
rename from docs/operations.md
rename to docs/doc/image_analysis/operations.md
diff --git a/docs/processing.md b/docs/doc/image_analysis/processing.md
similarity index 100%
rename from docs/processing.md
rename to docs/doc/image_analysis/processing.md
diff --git a/docs/segmentation.md b/docs/doc/image_analysis/segmentation.md
similarity index 100%
rename from docs/segmentation.md
rename to docs/doc/image_analysis/segmentation.md
diff --git a/docs/models.md b/docs/doc/ml/models.md
similarity index 82%
rename from docs/models.md
rename to docs/doc/ml/models.md
index a3e0f8409ecd3d32a03b799e4ad1fe21c90f2114..af961f700a70d2ea4861519fc1c931476b324c52 100644
--- a/docs/models.md
+++ b/docs/doc/ml/models.md
@@ -1,3 +1,9 @@
+---
+hide:
+ - navigation
+ - toc
+---
+
# Machine learning models
The `qim3d` library aims to ease the creation of ML models for volumetric images
diff --git a/docs/releases.md b/docs/doc/releases/releases.md
similarity index 87%
rename from docs/releases.md
rename to docs/doc/releases/releases.md
index abbd81777bb6de085c81fa7689bb3cc879cc50fc..dcc9c2e2f5c107377ab3d7a89c00d74112739c4a 100644
--- a/docs/releases.md
+++ b/docs/doc/releases/releases.md
@@ -1,3 +1,9 @@
+---
+hide:
+ - navigation
+
+---
+
# Release History
[](https://badge.fury.io/py/qim3d)
[](https://pepy.tech/project/qim3d)
@@ -19,18 +25,18 @@ And remember to keep your pip installation [up to date](index.md/#get-the-latest
### v0.4.4 (11/10/2024)
-- Introduction of `itk-vtk-viewer` for OME-Zarr data visualization 🎉 
+- Introduction of `itk-vtk-viewer` for OME-Zarr data visualization 🎉 
### v0.4.3 (02/10/2024)
- Updated requirements
-- Introduction of mesh generation, visualization, saving and loading 🎉 
+- Introduction of mesh generation, visualization, saving and loading 🎉 
### v0.4.2 (30/09/2024)
- Export and import is now possible in the OME-Zarr standard, including multi-scale datasets.
-- Filters now have the option to use Dask when available 
+- Filters now have the option to use Dask when available 
### v0.4.1 (30/07/2024)
@@ -50,9 +56,9 @@ And remember to keep your pip installation [up to date](index.md/#get-the-latest
- Loading and saving for Zarr files
- File convertion using the CLI, including Zarr
- Refactoring for the GUIs
-- Color visualization for structure tensor 
+- Color visualization for structure tensor 
- Refactoring for synthetic data generation, from `utils` to `generate`
-- Introduction of `qim3d.generate.collection` 🎉 
+- Introduction of `qim3d.generate.collection` 🎉 
### v0.3.8 (20/06/2024)
@@ -61,22 +67,22 @@ And remember to keep your pip installation [up to date](index.md/#get-the-latest
### v0.3.7 (17/06/2024)
- Performance improvements when importing
-- Refactoring for blob detection 
+- Refactoring for blob detection 
### v0.3.6 (30/05/2024)
- Refactoring for performance improvement
- Welcome message for the CLI
-- Introduction of `qim3d.processing.fade_mask` 🎉 
+- Introduction of `qim3d.processing.fade_mask` 🎉 
### v0.3.5 (27/05/2024)
- Added runtime and memory usage in the documentation
-- Introduction of `qim3d.utils.generate_volume` 🎉 
-- CLI refactoring, adding welcome message to the user 
+- Introduction of `qim3d.utils.generate_volume` 🎉 
+- CLI refactoring, adding welcome message to the user 
- Introduction of `preview` CLI 🎉
diff --git a/docs/viz.md b/docs/doc/visualization/viz.md
similarity index 95%
rename from docs/viz.md
rename to docs/doc/visualization/viz.md
index c538608987668f683db7b0a2f10db41bdf937836..0f22a927ac31aaab6a0940fdbaa075caab389d0f 100644
--- a/docs/viz.md
+++ b/docs/doc/visualization/viz.md
@@ -1,3 +1,8 @@
+---
+hide:
+ - navigation
+---
+
# Data visualization
The `qim3d` library aims to provide easy ways to explore and get insights from volumetric data.
diff --git a/docs/index.md b/docs/index.md
index eddb3a9b05946c1ca79cf8a294b77de142c0c7bd..2afac8087c0ac759d13747921ed587f8e428df5e 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,3 +1,8 @@
+---
+hide:
+ - navigation
+---
+
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css">
<audio id="audio" src="assets/qim3d.mp3"></audio>
@@ -215,14 +220,16 @@ Below is a list of contributors to the project, arranged in chronological order
| Author | Commits | First commit |
|:----------------------------|----------:|-------------:|
-| Felipe Delestro | 231 | 2023-05-12 |
+| Felipe Delestro | 254 | 2023-05-12 |
| Stefan Engelmann Jensen | 29 | 2023-06-29 |
| Oskar Kristoffersen | 15 | 2023-07-05 |
-| Christian Kento Rasmussen | 22 | 2024-02-01 |
-| Alessia Saccardo | 13 | 2024-02-19 |
-| David Grundfest | 16 | 2024-04-12 |
-| Anna Bøgevang Ekner | 6 | 2024-04-18 |
-| David Diamond Wang Johansen | 1 | 2024-10-31 |
+| Christian Kento Rasmussen | 23 | 2024-02-01 |
+| Alessia Saccardo | 14 | 2024-02-19 |
+| David Grundfest | 19 | 2024-04-12 |
+| Anna Bøgevang Ekner | 7 | 2024-04-18 |
+| David Diamond Wang Johansen | 2 | 2024-10-31 |
+| Oscar Flensburg Clausen | 5 | 2024-11-20 |
+| Hans Martin Kjer | 1 | 2024-12-02 |
## Support
diff --git a/docs/utils.md b/docs/utils.md
deleted file mode 100644
index 3becb903d07477d8b310bfb201aa842d47c17334..0000000000000000000000000000000000000000
--- a/docs/utils.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# Utils
-
-A set of tools to ease managment of the system, with the common needs for large data in mind.
-
-::: qim3d.utils
- options:
- members:
- - Memory
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 10c59f55d3dfb2a5ce75b8754e9fd98d48f7b347..cfcd31f08b8d744486e4516fd7e7a989a4e3f90f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -7,20 +7,22 @@ repo_name: Gitlab
nav:
- - qim3d: index.md
- - Data handling: datahandling.md
- - Visualization: viz.md
- - Features: features.md
- - Filters: filters.md
- - Detection: detection.md
- - Segmentation: segmentation.md
- - Operations: operations.md
- - Processing: processing.md
- - ML Models: models.md
- - GUIs: gui.md
- - CLI: cli.md
-
- - Release history: releases.md
+ - Data handling:
+ - Input and Output: doc/data_handling/io.md
+ - Synthetic data: doc/data_handling/generate.md
+ - Visualization: doc/visualization/viz.md
+ - Image analysis:
+ - Features: doc/image_analysis/features.md
+ - Filters: doc/image_analysis/filters.md
+ - Detection: doc/image_analysis/detection.md
+ - Segmentation: doc/image_analysis/segmentation.md
+ - Operations: doc/image_analysis/operations.md
+ - Processing: doc/image_analysis/processing.md
+ - Meshes: doc/image_analysis/mesh.md
+ - Machine Learning: doc/ml/models.md
+ - Graphical User Interfaces: doc/gui/gui.md
+ - Command Line Interface: doc/cli/cli.md
+ - Release history: doc/releases/releases.md
theme:
language: en
@@ -35,7 +37,7 @@ theme:
- navigation.expand
- navigation.instant
# - navigation.tracking
- - toc.integrate
+ # - toc.integrate
# - toc.follow
- search.suggest
# - content.tabs.link
@@ -87,6 +89,6 @@ plugins:
show_source: true
show_root_full_path: true
show_object_full_path: true
- show_symbol_type_heading: true
+ show_symbol_type_heading: false
show_symbol_type_toc: false
separate_signature: true
\ No newline at end of file
diff --git a/qim3d/detection/_common_detection_methods.py b/qim3d/detection/_common_detection_methods.py
index 71a4b348a417c4a13a74edd25615681c6c8a00ee..3049baef5dbfee1e9f053cd19e8e8c2f79a01a0a 100644
--- a/qim3d/detection/_common_detection_methods.py
+++ b/qim3d/detection/_common_detection_methods.py
@@ -56,13 +56,13 @@ def blobs(
# Visualize detected blobs
qim3d.viz.circles(blobs, vol, alpha=0.8, color='blue')
```
- 
+ 
```python
# Visualize binary binary_volume
qim3d.viz.slicer(binary_volume)
```
- 
+ 
"""
from skimage.feature import blob_dog
diff --git a/qim3d/filters/_common_filter_methods.py b/qim3d/filters/_common_filter_methods.py
index bc4b02f0de5e94eb3e41a17786a04b950a36696d..4faf7365216885eecce388e129fc8cb11ca0a6ab 100644
--- a/qim3d/filters/_common_filter_methods.py
+++ b/qim3d/filters/_common_filter_methods.py
@@ -141,8 +141,8 @@ class Pipeline:
# Show filtered
fig2 = qim3d.viz.slices_grid(vol_filtered, num_slices=5, display_figure=True)
```
- 
- 
+ 
+ 
"""
diff --git a/qim3d/generate/_aggregators.py b/qim3d/generate/_aggregators.py
index 0eb09086de627446ea00279df2064167b2695d29..c1d834c6d9317abd445900ac703a4cb5fb673de4 100644
--- a/qim3d/generate/_aggregators.py
+++ b/qim3d/generate/_aggregators.py
@@ -199,14 +199,14 @@ def noise_object_collection(
```python
qim3d.viz.slicer(synthetic_collection)
```
- 
+ 
```python
# Visualize labels
cmap = qim3d.viz.colormaps.segmentation(num_labels=num_objects)
qim3d.viz.slicer(labels, color_map=cmap, value_max=num_objects)
```
- 
+ 
Example:
```python
@@ -257,7 +257,7 @@ def noise_object_collection(
# Visualize slices
qim3d.viz.slices_grid(vol, num_slices=15)
```
- 
+ 
Example:
```python
@@ -287,7 +287,7 @@ def noise_object_collection(
# Visualize slices
qim3d.viz.slices_grid(vol, num_slices=15, slice_axis=1)
```
- 
+ 
"""
if verbose:
original_log_level = log.getEffectiveLevel()
diff --git a/qim3d/generate/_generators.py b/qim3d/generate/_generators.py
index 15578a67e341790a4433a6b0069d1273c87f007b..ed54b8b4de9fef663caea00fd75429524c7c5f0e 100644
--- a/qim3d/generate/_generators.py
+++ b/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)
```
- 
+ 
Example:
```python
@@ -78,7 +78,7 @@ def noise_object(
# Visualize slices
qim3d.viz.slices_grid(vol, num_slices=15, slice_axis=1)
```
- 
+ 
Example:
```python
@@ -102,7 +102,7 @@ def noise_object(
# Visualize
qim3d.viz.slices_grid(vol, num_slices=15)
```
- 
+ 
"""
if not isinstance(final_shape, tuple) or len(final_shape) != 3:
diff --git a/qim3d/gui/annotation_tool.py b/qim3d/gui/annotation_tool.py
index a3cac14e168316c34408e9304f7e05266370c8b8..8f386da385ab9e26c089a99670fb972f2afc17bd 100644
--- a/qim3d/gui/annotation_tool.py
+++ b/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])
```
-
+
"""
diff --git a/qim3d/gui/layers2d.py b/qim3d/gui/layers2d.py
index 8b7ae4419f2fc388c8e020d2b39556c83d585ff4..5a25f6e975a084b263fc5a3657aa72eed01ed94a 100644
--- a/qim3d/gui/layers2d.py
+++ b/qim3d/gui/layers2d.py
@@ -13,7 +13,7 @@ import qim3d
layers = qim3d.gui.layers2d.Interface()
app = layers.launch()
```
-
+
"""
diff --git a/qim3d/io/_downloader.py b/qim3d/io/_downloader.py
index 3d7724bb1ed0b3cdcccc841fdcf535a1f199cb83..89e3759d9a2c30a9eb557ba45d8a5dc0152165f3 100644
--- a/qim3d/io/_downloader.py
+++ b/qim3d/io/_downloader.py
@@ -54,7 +54,7 @@ class Downloader:
qim3d.viz.slicer_orthogonal(data, color_map="magma")
```
- 
+ 
"""
def __init__(self):
diff --git a/qim3d/operations/_common_operations_methods.py b/qim3d/operations/_common_operations_methods.py
index 42932d5c292686903ccc4a3a3d23858e4d25612d..a83b25d26f223c2ad20ad2b383044f4a45a0ad38 100644
--- a/qim3d/operations/_common_operations_methods.py
+++ b/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)
```
- 
+ 
```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)
```
- 
+ 
"""
# 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.
- 
+ 
```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.
- 
+ 
"""
if 0 > axis or axis >= vol.ndim:
diff --git a/qim3d/processing/_layers.py b/qim3d/processing/_layers.py
index 7e7ef93058cd58b678965cedbdb43d9924c01b22..b77a4834120fedf31b757b23d9a631c709cfc1f6 100644
--- a/qim3d/processing/_layers.py
+++ b/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)
```
- 
- 
+ 
+ 
"""
if isinstance(data, np.ndarray):
diff --git a/qim3d/processing/_local_thickness.py b/qim3d/processing/_local_thickness.py
index a38e9423599d30370a4f02f1f3de97f8b222eb15..12d6f19b664d61bb6bd8e0bc8db1347e8cd1c9a0 100644
--- a/qim3d/processing/_local_thickness.py
+++ b/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)
```
- 
+ 
```python
import qim3d
@@ -56,10 +56,10 @@ def local_thickness(
lt_blobs = qim3d.processing.local_thickness(slice, visualize=True)
```
- 
+ 
!!! info "Runtime and memory usage of the local thickness method for different volume sizes"
- 
+ 
Performance computed on Intel(R) Xeon(R) Gold 6226 CPU @ 2.70GHz.
diff --git a/qim3d/processing/_structure_tensor.py b/qim3d/processing/_structure_tensor.py
index f4343c972118decd9aa37a2405f448f77233fc1f..de73521274a1879ae02edf4ab9f459409f370cd2 100644
--- a/qim3d/processing/_structure_tensor.py
+++ b/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)
```
- 
+ 
!!! info "Runtime and memory usage of the structure tensor method for different volume sizes"
- 
+ 
Performance computed on Intel(R) Xeon(R) Gold 6226 CPU @ 2.70GHz.
diff --git a/qim3d/segmentation/_common_segmentation_methods.py b/qim3d/segmentation/_common_segmentation_methods.py
index 6baff849b112504bef23936cf99111608b21ff3e..fc6474597a34246f31ddcbc9634f0be803b831ed 100644
--- a/qim3d/segmentation/_common_segmentation_methods.py
+++ b/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)
```
- 
+ 
```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)
```
- 
+ 
"""
import skimage
diff --git a/qim3d/viz/_cc.py b/qim3d/viz/_cc.py
index 24d047afbb9442f1a05d847dbe836ae84058f520..8ace8abf830f3cc3e0cc7eb5219f90c90f378242 100644
--- a/qim3d/viz/_cc.py
+++ b/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])
```
- 
- 
+ 
+ 
"""
# if no components are given, plot the first max_cc_to_plot=32 components
if component_indexs is None:
diff --git a/qim3d/viz/_data_exploration.py b/qim3d/viz/_data_exploration.py
index c754604d44df47437ee7ea3e33deee751ce3681d..3544af79a28cd96bbe2608f81ed55e2d715ecd94 100644
--- a/qim3d/viz/_data_exploration.py
+++ b/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)
```
- 
+ 
"""
if image_size:
image_height = image_size
@@ -354,7 +354,7 @@ def slicer(
vol = qim3d.examples.bone_128x128x128
qim3d.viz.slicer(vol)
```
- 
+ 
"""
if image_size:
@@ -427,7 +427,7 @@ def slicer_orthogonal(
vol = qim3d.examples.fly_150x256x256
qim3d.viz.slicer_orthogonal(vol, color_map="magma")
```
- 
+ 
"""
if image_size:
@@ -484,7 +484,7 @@ def fade_mask(
vol = qim3d.examples.cement_128x128x128
qim3d.viz.fade_mask(vol)
```
- 
+ 
"""
@@ -623,7 +623,7 @@ def chunks(zarr_path: str, **kwargs)-> widgets.interactive:
# Explore chunks
qim3d.viz.chunks("Escargot.zarr")
```
- 
+ 
"""
# Load the Zarr dataset
@@ -904,7 +904,7 @@ def histogram(
vol = qim3d.examples.bone_128x128x128
qim3d.viz.histogram(vol)
```
- 
+ 
```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)
```
- 
+ 
"""
if not (0 <= axis < volume.ndim):
diff --git a/qim3d/viz/_detection.py b/qim3d/viz/_detection.py
index 200904de308604cb30888057c49007f353595f37..5b0ad9fc7059636f5d49a5d6ef4aac02c12fac2b 100644
--- a/qim3d/viz/_detection.py
+++ b/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')
```
- 
+ 
"""
def _slicer(z_slice):
diff --git a/qim3d/viz/_local_thickness.py b/qim3d/viz/_local_thickness.py
index 0f63c64165c965c58db59df7aa0ff986c677f0e4..9336ee32acb23ac4b9e9a43df2c5a1e045b3ea23 100644
--- a/qim3d/viz/_local_thickness.py
+++ b/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)
```
- 
+ 
"""
diff --git a/qim3d/viz/_structure_tensor.py b/qim3d/viz/_structure_tensor.py
index 43fb8b58b90d43de0104491643a7c8cc65ca0581..13d45e1f252e139c5a9cd2518280136a821e9443 100644
--- a/qim3d/viz/_structure_tensor.py
+++ b/qim3d/viz/_structure_tensor.py
@@ -69,7 +69,7 @@ def vectors(
# Visualize the structure tensor
qim3d.viz.vectors(vol, vec, axis = 2, interactive = True)
```
- 
+ 
"""
diff --git a/qim3d/viz/colormaps/_qim_colors.py b/qim3d/viz/colormaps/_qim_colors.py
index 429151e1664ac911a2d07d9a8c27059153e55fec..3ac7a4005ee2d92f12a00a3588acb482fe308dc5 100644
--- a/qim3d/viz/colormaps/_qim_colors.py
+++ b/qim3d/viz/colormaps/_qim_colors.py
@@ -19,6 +19,6 @@ Example:
display(qim3d.viz.colormaps.qim)
```
- 
+ 
"""
colormaps.register(qim)
diff --git a/qim3d/viz/colormaps/_segmentation.py b/qim3d/viz/colormaps/_segmentation.py
index 523714f849cef17f39a2cb855df305334728d844..715eb6da5cbdac3c7a50487782e24a40c028b0bd 100644
--- a/qim3d/viz/colormaps/_segmentation.py
+++ b/qim3d/viz/colormaps/_segmentation.py
@@ -71,7 +71,7 @@ def segmentation(
display(cmap_earth)
display(cmap_ocean)
```
- 
+ 
```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)
```
- 
+ 
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.
- 
+ 
"""
from skimage import color