From 3bca2d0ee473e45022b51bcda9adab5c686f612a Mon Sep 17 00:00:00 2001
From: Felipe Delestro Matos <fima@pop-os.localdomain>
Date: Wed, 14 Feb 2024 09:22:31 +0100
Subject: [PATCH] Initial setup for mkdocs
---
docs/assets/qim3d-icon.svg | 147 +++++++++++++++++++++++++++++++++++++
docs/assets/qim3d-logo.png | Bin 0 -> 25680 bytes
docs/assets/qim3d-logo.svg | 147 +++++++++++++++++++++++++++++++++++++
docs/gui.md | 3 +
docs/index.md | 76 +++++++++++++++++++
docs/io.md | 3 +
docs/models.md | 1 +
docs/releases.md | 50 +++++++++++++
docs/stylesheets/extra.css | 44 +++++++++++
docs/utils.md | 4 +
docs/version_history.md | 31 --------
docs/viz.md | 18 +++++
mkdocs.yml | 66 +++++++++++++++++
qim3d/io/load.py | 12 ++-
qim3d/viz/img.py | 17 +++--
15 files changed, 581 insertions(+), 38 deletions(-)
create mode 100644 docs/assets/qim3d-icon.svg
create mode 100644 docs/assets/qim3d-logo.png
create mode 100644 docs/assets/qim3d-logo.svg
create mode 100644 docs/gui.md
create mode 100644 docs/index.md
create mode 100644 docs/io.md
create mode 100644 docs/models.md
create mode 100644 docs/releases.md
create mode 100644 docs/stylesheets/extra.css
create mode 100644 docs/utils.md
delete mode 100644 docs/version_history.md
create mode 100644 docs/viz.md
create mode 100644 mkdocs.yml
diff --git a/docs/assets/qim3d-icon.svg b/docs/assets/qim3d-icon.svg
new file mode 100644
index 00000000..91283061
--- /dev/null
+++ b/docs/assets/qim3d-icon.svg
@@ -0,0 +1,147 @@
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diff --git a/docs/gui.md b/docs/gui.md
new file mode 100644
index 00000000..40e99eca
--- /dev/null
+++ b/docs/gui.md
@@ -0,0 +1,3 @@
+::: qim3d.gui.data_explorer
+::: qim3d.gui.iso3d
+::: qim3d.gui.local_thickness
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..b2d702e3
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,76 @@
+# <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
diff --git a/docs/io.md b/docs/io.md
new file mode 100644
index 00000000..f72aa9b9
--- /dev/null
+++ b/docs/io.md
@@ -0,0 +1,3 @@
+::: qim3d.io.load
+::: qim3d.io.save
+::: qim3d.io.downloader
\ No newline at end of file
diff --git a/docs/models.md b/docs/models.md
new file mode 100644
index 00000000..079b974a
--- /dev/null
+++ b/docs/models.md
@@ -0,0 +1 @@
+::: qim3d.models.unet
\ No newline at end of file
diff --git a/docs/releases.md b/docs/releases.md
new file mode 100644
index 00000000..5a72d14c
--- /dev/null
+++ b/docs/releases.md
@@ -0,0 +1,50 @@
+# 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
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
new file mode 100644
index 00000000..4b12b898
--- /dev/null
+++ b/docs/stylesheets/extra.css
@@ -0,0 +1,44 @@
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+.md-nav__item .md-nav__link--active, .md-nav__item .md-nav__link--active code {
+ color: orange}
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+.md-typeset a {
+ color: orange;
+ word-break: break-word;
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+ font-size: 1.0em;
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+ font-size: 2.0em;
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+ margin-left: auto;
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+
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+.md-header__source {
+ text-align: right;
+}
+
+.md-header__title {
+ margin-left: 0px !important;
+}
\ No newline at end of file
diff --git a/docs/utils.md b/docs/utils.md
new file mode 100644
index 00000000..a1b939ce
--- /dev/null
+++ b/docs/utils.md
@@ -0,0 +1,4 @@
+::: qim3d.utils.system
+ options:
+ members:
+ - Memory
\ No newline at end of file
diff --git a/docs/version_history.md b/docs/version_history.md
deleted file mode 100644
index 26318aa2..00000000
--- a/docs/version_history.md
+++ /dev/null
@@ -1,31 +0,0 @@
-# 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
diff --git a/docs/viz.md b/docs/viz.md
new file mode 100644
index 00000000..5a92ef56
--- /dev/null
+++ b/docs/viz.md
@@ -0,0 +1,18 @@
+# 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
+
+
+
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 00000000..ef07ca04
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,66 @@
+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:
+ - stylesheets/extra.css
+
+extra:
+ social:
+ - icon: fontawesome/brands/x-twitter
+ link: https://twitter.com/QIMCenter
+
+markdown_extensions:
+ - pymdownx.highlight:
+ anchor_linenums: true
+ - pymdownx.superfences
+
+plugins:
+ - tags
+ - search
+ - mkdocstrings:
+ handlers:
+ python:
+ options:
+ show_root_heading: true
+ show_source: true
+ show_root_full_path: true
+ show_object_full_path: true
+ show_symbol_type_heading: true
+ show_symbol_type_toc: true
+ separate_signature: true
\ No newline at end of file
diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index f6b11848..a761d328 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -1,4 +1,14 @@
-"""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 os
diff --git a/qim3d/viz/img.py b/qim3d/viz/img.py
index e3648f54..804cdd28 100644
--- a/qim3d/viz/img.py
+++ b/qim3d/viz/img.py
@@ -1,4 +1,6 @@
-""" Provides a collection of visualization functions."""
+"""
+Provides a collection of visualization functions.
+"""
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
from matplotlib import colormaps
@@ -25,18 +27,21 @@ def grid_overview(data, num_images=7, cmap_im="gray", cmap_segm="viridis", alpha
Raises:
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:
fig (matplotlib.figure.Figure): The figure with an overview of the images and their labels.
Example:
+ ```python
data = [(image1, label1, mask1), (image2, label2, mask2)]
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
--
GitLab