Merge branch 'doc_update_for_v1.0' into 'main'

Doc update for v1.0

See merge request !149

docs/datahandling.md

-# 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

docs/cli.md → docs/doc/cli/cli.md

+---
+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
     ```
-    ![CLI Data Explorer](assets/screenshots/CLI-data_explorer.gif)
+    ![CLI Data Explorer](../../assets/screenshots/CLI-data_explorer.gif)
 
 
 ## 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`
 
-    ![Data explorer GUI](assets/screenshots/GUI-data_explorer.png)
+    ![Data explorer GUI](../../assets/screenshots/GUI-data_explorer.png)
 
 
 !!! 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/`
 
-    ![Local thickness GUI](assets/screenshots/GUI-local_thickness.png)
+    ![Local thickness GUI](../../assets/screenshots/GUI-local_thickness.png)
 
 
 
@@ -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:
 
-    ![itk-vtk-viewer](assets/screenshots/itk-vtk-viewer.gif)
+    ![itk-vtk-viewer](../../assets/screenshots/itk-vtk-viewer.gif)
 
 !!! 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:
 
-    ![CLI k3d](assets/screenshots/CLI-k3d.png){ width="512" }
+    ![CLI k3d](../../assets/screenshots/CLI-k3d.png){ 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 
     ```
 
-    ![CLI k3d](assets/preview/default.png){ width="512" }
+    ![CLI k3d](../../assets/preview/default.png){ width="512" }
 
 !!! Example
     ``` title="Command"
     qim3d preview blobs_256x256x256.tif --resolution 30
     ```
 
-    ![CLI k3d](assets/preview/res30.png){ width="512" }
+    ![CLI k3d](../../assets/preview/res30.png){ width="512" }
 
 !!! Example
     ``` title="Command"
     qim3d preview blobs_256x256x256.tif --resolution 50 --axis 1
     ```
 
-    ![CLI k3d](assets/preview/axis1.png){ width="512" }
+    ![CLI k3d](../../assets/preview/axis1.png){ width="512" }
 
 !!! Example
     ``` title="Command"
     qim3d preview blobs_256x256x256.tif --resolution 50 --axis 2 --slice 0
     ```
 
-    ![CLI k3d](assets/preview/relativeIntensity.png){ width="512" }
+    ![CLI k3d](../../assets/preview/relativeIntensity.png){ width="512" }
 
 !!! Example
     ``` title="Command"
     qim3d preview qim_logo.png --resolution 40
     ```
 
-    ![CLI k3d](assets/preview/qimLogo.png){ width="512" }
+    ![CLI k3d](../../assets/preview/qimLogo.png){ width="512" }

docs/doc/data_handling/generate.md

+# Synthetic data generation
+
+::: qim3d.generate
+    options:
+        members:
+            - noise_object
+            - noise_object_collection

docs/doc/data_handling/io.md

+# 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

docs/gui.md → docs/doc/gui/gui.md

+---
+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
-![Data explorer GUI](assets/screenshots/GUI-data_explorer.png)
+![Data explorer GUI](../../assets/screenshots/GUI-data_explorer.png)
 
 ::: qim3d.gui.local_thickness
     options:
         members: False
-![Local thickness GUI](assets/screenshots/GUI-local_thickness.png)
+![Local thickness GUI](../../assets/screenshots/GUI-local_thickness.png)
 
 ::: qim3d.gui.iso3d
     options:
         members: False
-![Iso3d GUI](assets/screenshots/GUI-iso3d.png)
+![Iso3d GUI](../../assets/screenshots/GUI-iso3d.png)
 
 ::: qim3d.gui.annotation_tool
     options:

docs/doc/image_analysis/mesh.md

+::: qim3d.mesh
+    options:
+        members:
+            - from_volume

docs/models.md → docs/doc/ml/models.md

+---
+hide:
+  - navigation
+  - toc
+---
+
 # Machine learning models
 
 The `qim3d` library aims to ease the creation of ML models for volumetric images

docs/releases.md → docs/doc/releases/releases.md

+---
+hide:
+  - navigation
+  
+---
+
 # Release History
 [![PyPI version](https://badge.fury.io/py/qim3d.svg)](https://badge.fury.io/py/qim3d)
 [![Downloads](https://static.pepy.tech/badge/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 🎉 ![itk-vtk-viewer](assets/screenshots/itk-vtk-viewer.gif)
+- Introduction of `itk-vtk-viewer` for OME-Zarr data visualization 🎉 ![itk-vtk-viewer](../../assets/screenshots/itk-vtk-viewer.gif)
 
 
 ### v0.4.3 (02/10/2024)
 
 - Updated requirements
-- Introduction of mesh generation, visualization, saving and loading 🎉  ![Mesh generation](assets/screenshots/releases/mesh_generation.png)
+- Introduction of mesh generation, visualization, saving and loading 🎉  ![Mesh generation](../../assets/screenshots/releases/mesh_generation.png)
 
 ### 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 with dask](assets/screenshots/releases/filters_with_dask.png)
+- Filters now have the option to use Dask when available ![Filters with dask](../../assets/screenshots/releases/filters_with_dask.png)
 
 
 ### 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](assets/screenshots/releases/qim3d-structure_tensor_with_colors.gif)
+- Color visualization for structure tensor ![Color visualization for structure tensor](../../assets/screenshots/releases/qim3d-structure_tensor_with_colors.gif)
 - Refactoring for synthetic data generation, from `utils` to `generate`
-- Introduction of `qim3d.generate.collection` 🎉 ![Introduction of `qim3d.generate.collection`](assets/screenshots/releases/qim3d-generate_collection.gif)
+- Introduction of `qim3d.generate.collection` 🎉 ![Introduction of `qim3d.generate.collection`](../../assets/screenshots/releases/qim3d-generate_collection.gif)
 
 ### 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](assets/screenshots/releases/qim3d-blob_detection_refactoring.gif)
+- Refactoring for blob detection ![Refactoring for blob detection](../../assets/screenshots/releases/qim3d-blob_detection_refactoring.gif)
 
 
 ### 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`](assets/screenshots/releases/qim3d-fade_viz.gif)
+- Introduction of `qim3d.processing.fade_mask` 🎉 ![Introduction of `qim3d.processing.fade_mask`](../../assets/screenshots/releases/qim3d-fade_viz.gif)
 
 
 
 ### v0.3.5 (27/05/2024)
 
 - Added runtime and memory usage in the documentation
-- Introduction of `qim3d.utils.generate_volume` 🎉 ![Introduction of `qim3d.utils.generate_volume`](assets/screenshots/releases/qim3d-synthetic_volume.gif)
-- CLI refactoring, adding welcome message to the user ![CLI refactoring](assets/screenshots/releases/qim3d-CLI_welcome_message.png)
+- Introduction of `qim3d.utils.generate_volume` 🎉 ![Introduction of `qim3d.utils.generate_volume`](../../assets/screenshots/releases/qim3d-synthetic_volume.gif)
+- CLI refactoring, adding welcome message to the user ![CLI refactoring](../../assets/screenshots/releases/qim3d-CLI_welcome_message.png)
 - Introduction of `preview` CLI 🎉
 
 

docs/viz.md → docs/doc/visualization/viz.md

+---
+hide:
+  - navigation
+---
+
 # Data visualization
 The `qim3d` library aims to provide easy ways to explore and get insights from volumetric data. 
 

docs/index.md

+---
+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

docs/utils.md

-# 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

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

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')
             ```
-            ![blob detection](assets/screenshots/blob_detection.gif)    
+            ![blob detection](../../assets/screenshots/blob_detection.gif)    
 
             ```python
             # Visualize binary binary_volume
             qim3d.viz.slicer(binary_volume)
             ```
-            ![blob detection](assets/screenshots/blob_get_mask.gif)
+            ![blob detection](../../assets/screenshots/blob_get_mask.gif)
     """
     from skimage.feature import blob_dog
 

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)
         ```
-        ![original volume](assets/screenshots/filter_original.png)
-        ![filtered volume](assets/screenshots/filter_processed.png)
+        ![original volume](../../assets/screenshots/filter_original.png)
+        ![filtered volume](../../assets/screenshots/filter_processed.png)
 
     """