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Doc update for v1.0

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# 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
---
hide:
- navigation
---
# Command line interface # 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. 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 ...@@ -7,7 +12,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
``` title="Command" ``` title="Command"
qim3d gui --data-explorer 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 ## Graphical User Interfaces
...@@ -50,7 +55,7 @@ The command line interface allows you to run graphical user interfaces directly ...@@ -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` 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 !!! Example
...@@ -82,7 +87,7 @@ The command line interface allows you to run graphical user interfaces directly ...@@ -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/` 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 ...@@ -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: 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" !!! Example "Example using k3d"
``` title="Command" ``` title="Command"
...@@ -152,7 +157,7 @@ You can launch volumetric visualizations directly from the command line. By defa ...@@ -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: 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: 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 ...@@ -196,32 +201,32 @@ File previewing can also be done directly from the command line interface to pre
qim3d preview blobs_256x256x256.tif qim3d preview blobs_256x256x256.tif
``` ```
![CLI k3d](assets/preview/default.png){ width="512" } ![CLI k3d](../../assets/preview/default.png){ width="512" }
!!! Example !!! Example
``` title="Command" ``` title="Command"
qim3d preview blobs_256x256x256.tif --resolution 30 qim3d preview blobs_256x256x256.tif --resolution 30
``` ```
![CLI k3d](assets/preview/res30.png){ width="512" } ![CLI k3d](../../assets/preview/res30.png){ width="512" }
!!! Example !!! Example
``` title="Command" ``` title="Command"
qim3d preview blobs_256x256x256.tif --resolution 50 --axis 1 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 !!! Example
``` title="Command" ``` title="Command"
qim3d preview blobs_256x256x256.tif --resolution 50 --axis 2 --slice 0 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 !!! Example
``` title="Command" ``` title="Command"
qim3d preview qim_logo.png --resolution 40 qim3d preview qim_logo.png --resolution 40
``` ```
![CLI k3d](assets/preview/qimLogo.png){ width="512" } ![CLI k3d](../../assets/preview/qimLogo.png){ width="512" }
# Synthetic data generation
::: qim3d.generate
options:
members:
- noise_object
- noise_object_collection
# 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
---
hide:
- navigation
---
# Graphical User Interfaces # Graphical User Interfaces
The `qim3d` library provides a set of custom made GUIs that ease the interaction with the available tools. 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). ...@@ -21,17 +26,17 @@ For details see [here](cli.md#qim3d-gui).
::: qim3d.gui.data_explorer ::: qim3d.gui.data_explorer
options: options:
members: False members: False
![Data explorer GUI](assets/screenshots/GUI-data_explorer.png) ![Data explorer GUI](../../assets/screenshots/GUI-data_explorer.png)
::: qim3d.gui.local_thickness ::: qim3d.gui.local_thickness
options: options:
members: False members: False
![Local thickness GUI](assets/screenshots/GUI-local_thickness.png) ![Local thickness GUI](../../assets/screenshots/GUI-local_thickness.png)
::: qim3d.gui.iso3d ::: qim3d.gui.iso3d
options: options:
members: False members: False
![Iso3d GUI](assets/screenshots/GUI-iso3d.png) ![Iso3d GUI](../../assets/screenshots/GUI-iso3d.png)
::: qim3d.gui.annotation_tool ::: qim3d.gui.annotation_tool
options: options:
......
File moved
File moved
File moved
::: qim3d.mesh
options:
members:
- from_volume
File moved
File moved
File moved
---
hide:
- navigation
- toc
---
# Machine learning models # Machine learning models
The `qim3d` library aims to ease the creation of ML models for volumetric images The `qim3d` library aims to ease the creation of ML models for volumetric images
......
---
hide:
- navigation
---
# Release History # Release History
[![PyPI version](https://badge.fury.io/py/qim3d.svg)](https://badge.fury.io/py/qim3d) [![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) [![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 ...@@ -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) ### 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) ### v0.4.3 (02/10/2024)
- Updated requirements - 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) ### v0.4.2 (30/09/2024)
- Export and import is now possible in the OME-Zarr standard, including multi-scale datasets. - 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) ### 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 ...@@ -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 - Loading and saving for Zarr files
- File convertion using the CLI, including Zarr - File convertion using the CLI, including Zarr
- Refactoring for the GUIs - 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` - 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) ### 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 ...@@ -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) ### v0.3.7 (17/06/2024)
- Performance improvements when importing - 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) ### v0.3.6 (30/05/2024)
- Refactoring for performance improvement - Refactoring for performance improvement
- Welcome message for the CLI - 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) ### v0.3.5 (27/05/2024)
- Added runtime and memory usage in the documentation - 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) - 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) - CLI refactoring, adding welcome message to the user ![CLI refactoring](../../assets/screenshots/releases/qim3d-CLI_welcome_message.png)
- Introduction of `preview` CLI 🎉 - Introduction of `preview` CLI 🎉
......
---
hide:
- navigation
---
# Data visualization # Data visualization
The `qim3d` library aims to provide easy ways to explore and get insights from volumetric data. The `qim3d` library aims to provide easy ways to explore and get insights from volumetric data.
......
---
hide:
- navigation
---
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css"> <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> <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 ...@@ -215,14 +220,16 @@ Below is a list of contributors to the project, arranged in chronological order
| Author | Commits | First commit | | Author | Commits | First commit |
|:----------------------------|----------:|-------------:| |:----------------------------|----------:|-------------:|
| Felipe Delestro | 231 | 2023-05-12 | | Felipe Delestro | 254 | 2023-05-12 |
| Stefan Engelmann Jensen | 29 | 2023-06-29 | | Stefan Engelmann Jensen | 29 | 2023-06-29 |
| Oskar Kristoffersen | 15 | 2023-07-05 | | Oskar Kristoffersen | 15 | 2023-07-05 |
| Christian Kento Rasmussen | 22 | 2024-02-01 | | Christian Kento Rasmussen | 23 | 2024-02-01 |
| Alessia Saccardo | 13 | 2024-02-19 | | Alessia Saccardo | 14 | 2024-02-19 |
| David Grundfest | 16 | 2024-04-12 | | David Grundfest | 19 | 2024-04-12 |
| Anna Bøgevang Ekner | 6 | 2024-04-18 | | Anna Bøgevang Ekner | 7 | 2024-04-18 |
| David Diamond Wang Johansen | 1 | 2024-10-31 | | David Diamond Wang Johansen | 2 | 2024-10-31 |
| Oscar Flensburg Clausen | 5 | 2024-11-20 |
| Hans Martin Kjer | 1 | 2024-12-02 |
## Support ## Support
......
# 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
...@@ -7,20 +7,22 @@ repo_name: Gitlab ...@@ -7,20 +7,22 @@ repo_name: Gitlab
nav: nav:
- qim3d: index.md - Data handling:
- Data handling: datahandling.md - Input and Output: doc/data_handling/io.md
- Visualization: viz.md - Synthetic data: doc/data_handling/generate.md
- Features: features.md - Visualization: doc/visualization/viz.md
- Filters: filters.md - Image analysis:
- Detection: detection.md - Features: doc/image_analysis/features.md
- Segmentation: segmentation.md - Filters: doc/image_analysis/filters.md
- Operations: operations.md - Detection: doc/image_analysis/detection.md
- Processing: processing.md - Segmentation: doc/image_analysis/segmentation.md
- ML Models: models.md - Operations: doc/image_analysis/operations.md
- GUIs: gui.md - Processing: doc/image_analysis/processing.md
- CLI: cli.md - Meshes: doc/image_analysis/mesh.md
- Machine Learning: doc/ml/models.md
- Release history: releases.md - Graphical User Interfaces: doc/gui/gui.md
- Command Line Interface: doc/cli/cli.md
- Release history: doc/releases/releases.md
theme: theme:
language: en language: en
...@@ -35,7 +37,7 @@ theme: ...@@ -35,7 +37,7 @@ theme:
- navigation.expand - navigation.expand
- navigation.instant - navigation.instant
# - navigation.tracking # - navigation.tracking
- toc.integrate # - toc.integrate
# - toc.follow # - toc.follow
- search.suggest - search.suggest
# - content.tabs.link # - content.tabs.link
...@@ -87,6 +89,6 @@ plugins: ...@@ -87,6 +89,6 @@ plugins:
show_source: true show_source: true
show_root_full_path: true show_root_full_path: true
show_object_full_path: true show_object_full_path: true
show_symbol_type_heading: true show_symbol_type_heading: false
show_symbol_type_toc: false show_symbol_type_toc: false
separate_signature: true separate_signature: true
\ No newline at end of file
...@@ -56,13 +56,13 @@ def blobs( ...@@ -56,13 +56,13 @@ def blobs(
# Visualize detected blobs # Visualize detected blobs
qim3d.viz.circles(blobs, vol, alpha=0.8, color='blue') 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 ```python
# Visualize binary binary_volume # Visualize binary binary_volume
qim3d.viz.slicer(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 from skimage.feature import blob_dog
......
...@@ -141,8 +141,8 @@ class Pipeline: ...@@ -141,8 +141,8 @@ class Pipeline:
# Show filtered # Show filtered
fig2 = qim3d.viz.slices_grid(vol_filtered, num_slices=5, display_figure=True) fig2 = qim3d.viz.slices_grid(vol_filtered, num_slices=5, display_figure=True)
``` ```
![original volume](assets/screenshots/filter_original.png) ![original volume](../../assets/screenshots/filter_original.png)
![filtered volume](assets/screenshots/filter_processed.png) ![filtered volume](../../assets/screenshots/filter_processed.png)
""" """
......
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