From 2081a3c79b18b1b436e57ec80efa117d05bf5112 Mon Sep 17 00:00:00 2001
From: fima <fima@dtu.dk>
Date: Tue, 21 Jan 2025 13:43:26 +0100
Subject: [PATCH] Doc update for v1.0
---
docs/datahandling.md | 28 ---------------
docs/{ => doc/cli}/cli.md | 25 ++++++++------
docs/doc/data_handling/generate.md | 7 ++++
docs/doc/data_handling/io.md | 12 +++++++
docs/{ => doc/gui}/gui.md | 11 ++++--
docs/{ => doc/image_analysis}/detection.md | 0
docs/{ => doc/image_analysis}/features.md | 0
docs/{ => doc/image_analysis}/filters.md | 0
docs/doc/image_analysis/mesh.md | 4 +++
docs/{ => doc/image_analysis}/operations.md | 0
docs/{ => doc/image_analysis}/processing.md | 0
docs/{ => doc/image_analysis}/segmentation.md | 0
docs/{ => doc/ml}/models.md | 6 ++++
docs/{ => doc/releases}/releases.md | 24 ++++++++-----
docs/{ => doc/visualization}/viz.md | 5 +++
docs/index.md | 19 +++++++----
docs/utils.md | 8 -----
mkdocs.yml | 34 ++++++++++---------
qim3d/detection/_common_detection_methods.py | 4 +--
qim3d/filters/_common_filter_methods.py | 4 +--
qim3d/generate/_aggregators.py | 8 ++---
qim3d/generate/_generators.py | 6 ++--
qim3d/gui/annotation_tool.py | 2 +-
qim3d/gui/layers2d.py | 2 +-
qim3d/io/_downloader.py | 2 +-
.../operations/_common_operations_methods.py | 8 ++---
qim3d/processing/_layers.py | 4 +--
qim3d/processing/_local_thickness.py | 6 ++--
qim3d/processing/_structure_tensor.py | 4 +--
.../_common_segmentation_methods.py | 4 +--
qim3d/viz/_cc.py | 4 +--
qim3d/viz/_data_exploration.py | 14 ++++----
qim3d/viz/_detection.py | 2 +-
qim3d/viz/_local_thickness.py | 2 +-
qim3d/viz/_structure_tensor.py | 2 +-
qim3d/viz/colormaps/_qim_colors.py | 2 +-
qim3d/viz/colormaps/_segmentation.py | 6 ++--
37 files changed, 146 insertions(+), 123 deletions(-)
delete mode 100644 docs/datahandling.md
rename docs/{ => doc/cli}/cli.md (91%)
create mode 100644 docs/doc/data_handling/generate.md
create mode 100644 docs/doc/data_handling/io.md
rename docs/{ => doc/gui}/gui.md (81%)
rename docs/{ => doc/image_analysis}/detection.md (100%)
rename docs/{ => doc/image_analysis}/features.md (100%)
rename docs/{ => doc/image_analysis}/filters.md (100%)
create mode 100644 docs/doc/image_analysis/mesh.md
rename docs/{ => doc/image_analysis}/operations.md (100%)
rename docs/{ => doc/image_analysis}/processing.md (100%)
rename docs/{ => doc/image_analysis}/segmentation.md (100%)
rename docs/{ => doc/ml}/models.md (82%)
rename docs/{ => doc/releases}/releases.md (87%)
rename docs/{ => doc/visualization}/viz.md (95%)
delete mode 100644 docs/utils.md
diff --git a/docs/datahandling.md b/docs/datahandling.md
deleted file mode 100644
index 894f8fed..00000000
--- 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 c2f878cc..58fae7e2 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 00000000..6a414d16
--- /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 00000000..82c984bb
--- /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 ef996896..681041fc 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 00000000..bcedeb55
--- /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 a3e0f840..af961f70 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 abbd8177..dcc9c2e2 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 c5386089..0f22a927 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 eddb3a9b..2afac808 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 3becb903..00000000
--- 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 10c59f55..cfcd31f0 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 71a4b348..3049baef 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 bc4b02f0..4faf7365 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 0eb09086..c1d834c6 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 15578a67..ed54b8b4 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 a3cac14e..8f386da3 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 8b7ae441..5a25f6e9 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 3d7724bb..89e3759d 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 42932d5c..a83b25d2 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 7e7ef930..b77a4834 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 a38e9423..12d6f19b 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 f4343c97..de735212 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 6baff849..fc647459 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 24d047af..8ace8abf 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 c754604d..3544af79 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 200904de..5b0ad9fc 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 0f63c641..9336ee32 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 43fb8b58..13d45e1f 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 429151e1..3ac7a400 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 523714f8..715eb6da 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
--
GitLab