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Commit caede17f authored by fima's avatar fima :beers:
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Merge branch 'mkdocs' into 'main'

Initial setup for mkdocs

See merge request !50
parents f0d5b631 3bca2d0e
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1 merge request!50Initial setup for mkdocs
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::: qim3d.gui.data_explorer
::: qim3d.gui.iso3d
::: qim3d.gui.local_thickness
\ No newline at end of file
# <img src="assets/qim3d-logo.png" width="300px">
`qim3d` is a Python library for quantitative imaging analysis in 3D. It provides functionality for handling data, as well as tools for visualization and analysis.
## Installation
Install the latest stable version by using pip:
```
pip install qim3d
```
## Getting started
Some basic funtionalites are descibred here. The full documentation is still under development.
### Loading Data
To load image data from a file, use `qim.io.load()`
```python
import qim3d
# Load a file
vol = qim3d.io.load("path/to/file.tif")
# Load a file as a virtual stack
vol = qim3d.io.load("path/to/file.tif", virtual_stack=True)
```
### Visualize data
You can easily check slices from your volume using `slice_viz`
```python
import qim3d
img = qim3d.examples.fly_150x256x256
# By default shows the middle slice
qim3d.viz.slice_viz(img)
# Or we can specifly positions
qim3d.viz.slice_viz(img, position=[0,32,128])
# Parameters for size and colormap are also possible
qim3d.viz.slice_viz(img, img_width=6, img_height=6, cmap="inferno")
```
### GUI Components
The library also provides GUI components for interactive data analysis and exploration.
The `qim3d.gui` module contains various classes for visualization and analysis:
```python
import qim3d
app = qim3d.gui.iso3d.Interface()
app.launch()
```
GUIs can also be launched using the Qim3D CLI:
```
$ qim3d gui --data-explorer
```
## Contributing
Contributions to `qim3d` are welcome! If you find a bug, have a feature request, or would like to contribute code, please open an issue or submit a pull request.
You can find us at Gitlab:
https://lab.compute.dtu.dk/QIM/tools/qim3d
## License
This project is licensed under the MIT License.
\ No newline at end of file
::: qim3d.io.load
::: qim3d.io.save
::: qim3d.io.downloader
\ No newline at end of file
::: qim3d.models.unet
\ No newline at end of file
# Release history
Here you can fin details about the version history of `qim3d`
## v0.3.1 (February 1, 2024)
- Save functionality for all file formats
### Just for tests
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
## v0.3.0 (January 23, 2024)
- Introduction of qim3d CLI
- Data Explorer GUI
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
## v0.2.0 (Sept 18, 2023)
Includes new develoments toward the usability of the library, as well as its integration with the QIM platform.
- Refactored code for the graphical interfaces
- For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
- Improved data loader
- Now the extensions `tif`, `h5` and `txm` are supported.
- Added `qim3d.viz.slice_viz` for easy slice visualization.
- U-net model creation
- Model availabe from `qim3d.models.UNet`
- Data augmentation class at `qim3d.utils.Augmentation`
- Notebook with full pipeline at `docs/notebooks/Unet.ipynb`
- Image examples accessible from `qim3d.examples`
## v0.1.3 (May 17, 2023)
First stable release.
- Simple Tiff data loader
- Graphical interfaces
- Local thickness
- 3D Isosurfaces
- Data exploration tool
\ No newline at end of file
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background-color: #f0f0f0 !important;
}
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border-radius: 0px !important;
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::: qim3d.utils.system
options:
members:
- Memory
\ No newline at end of file
# Release history
Here you can fin details about the version history of `qim3d`
## v0.2.0 (Sept 18, 2023)
```pip install qim3d==0.2.0```
Includes new develoments toward the usability of the library, as well as its integration with the QIM platform.
- Refactored code for the graphical interfaces
- For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
- Improved data loader
- Now the extensions `tif`, `h5` and `txm` are supported.
- Added `qim3d.viz.slice_viz` for easy slice visualization.
- U-net model creation
- Model availabe from `qim3d.models.UNet`
- Data augmentation class at `qim3d.utils.Augmentation`
- Notebook with full pipeline at `docs/notebooks/Unet.ipynb`
- Image examples accessible from `qim3d.examples`
## v0.1.3 (May 17, 2023)
```pip install qim3d==0.1.3```
First stable release.
- Simple Tiff data loader
- Graphical interfaces
- Local thickness
- 3D Isosurfaces
- Data exploration tool
\ No newline at end of file
# Data visualization
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent non dolor non justo pharetra elementum porttitor at quam. Duis quam ligula, consequat vitae dolor non, facilisis tincidunt justo. Aliquam congue ex ac nibh tristique, et fringilla odio hendrerit. Cras sit amet dui mauris. Curabitur vitae nibh ut dui luctus cursus at id orci. Proin quam lacus, finibus in porttitor sed, ultrices vel ante. Phasellus ut rhoncus diam. Vestibulum vel ultricies orci, ut vehicula libero. Sed bibendum velit sed volutpat maximus. Maecenas non euismod ipsum. Donec eu tempor lorem. Donec lectus turpis, interdum eget commodo sed, euismod id sapien. Fusce malesuada tortor est.
Example:
```python
import qim3d
```
::: qim3d.viz.img
options:
members:
- grid_overview
- grid_pred
- slice_viz
site_name: qim3d documentation
site_url: https://platform.qim.dk/qim3d/
site_author: Qim3d contributors
site_description: Documentation for the Qim3d python library
repo_url: https://lab.compute.dtu.dk/QIM/tools/qim3d
repo_name: Source code at Gitlab
nav:
- 📦 qim3d: index.md
- 📥 Input & Output: io.md
- 📊 Visualization: viz.md
- 🔧 Utils: utils.md
- 🖥️ GUIs: gui.md
- 🧠 ML Models: models.md
- 📋 Release history: releases.md
theme:
language: en
name: material
nav_position: top
logo: assets/qim3d-icon.svg
favicon: assets/qim3d-icon.svg
features:
- navigation.tabs
# - navigation.expand
# - navigation.instant
- toc.integrate
- toc.follow
- search.suggest
# - content.tabs.link
# - content.code.annotation
- content.code.copy
palette:
primary: white
accent: orange
extra_css:
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extra:
social:
- icon: fontawesome/brands/x-twitter
link: https://twitter.com/QIMCenter
markdown_extensions:
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.superfences
plugins:
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- mkdocstrings:
handlers:
python:
options:
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show_root_full_path: true
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show_symbol_type_heading: true
show_symbol_type_toc: true
separate_signature: true
\ No newline at end of file
"""Provides functionality for loading data from various file formats.""" """
Provides functionality for loading data from various file formats.
Example:
```
import qim3d
data = qim3d.io.load("image.tif")
```
"""
import difflib import difflib
import os import os
......
""" Provides a collection of visualization functions.""" """
Provides a collection of visualization functions.
"""
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap from matplotlib.colors import LinearSegmentedColormap
from matplotlib import colormaps from matplotlib import colormaps
...@@ -25,18 +27,21 @@ def grid_overview(data, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha ...@@ -25,18 +27,21 @@ def grid_overview(data, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha
Raises: Raises:
ValueError: If the data elements are not tuples. ValueError: If the data elements are not tuples.
Notes:
- If the image data is RGB, the color map is ignored and the user is informed.
- The number of displayed images is limited to the minimum between `num_images`
and the length of the data.
- The grid layout and dimensions vary based on the presence of a mask.
Returns: Returns:
fig (matplotlib.figure.Figure): The figure with an overview of the images and their labels. fig (matplotlib.figure.Figure): The figure with an overview of the images and their labels.
Example: Example:
```python
data = [(image1, label1, mask1), (image2, label2, mask2)] data = [(image1, label1, mask1), (image2, label2, mask2)]
grid_overview(data, num_images=5, cmap_im='viridis', cmap_segm='hot', alpha=0.8) grid_overview(data, num_images=5, cmap_im='viridis', cmap_segm='hot', alpha=0.8)
```
Notes:
- If the image data is RGB, the color map is ignored and the user is informed.
- The number of displayed images is limited to the minimum between `num_images`
and the length of the data.
- The grid layout and dimensions vary based on the presence of a mask.
""" """
# Check if data has a mask # Check if data has a mask
......
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