From 78d3f2a89bdf296939ae71b6fc40bd2710dc7685 Mon Sep 17 00:00:00 2001
From: s214735 <s214735@dtu.dk>
Date: Thu, 9 Jan 2025 10:46:30 +0100
Subject: [PATCH] addition of headers and some warning handling
---
docs/cli.md | 16 ++++-----------
docs/datahandling.md | 28 +++++++++++++++++++++++++++
docs/detection.md | 8 ++++++++
docs/features.md | 10 ++++++++++
docs/filters.md | 17 ++++++++++++++++
docs/generate.md | 9 ---------
docs/io.md | 15 ---------------
docs/operations.md | 10 ++++++++++
docs/processing.md | 45 +------------------------------------------
docs/releases.md | 2 +-
docs/segmentation.md | 9 +++++++++
mkdocs.yml | 13 ++++++++-----
qim3d/cli/__init__.py | 10 +++++++++-
13 files changed, 105 insertions(+), 87 deletions(-)
create mode 100644 docs/datahandling.md
create mode 100644 docs/detection.md
create mode 100644 docs/features.md
create mode 100644 docs/filters.md
delete mode 100644 docs/generate.md
delete mode 100644 docs/io.md
create mode 100644 docs/operations.md
create mode 100644 docs/segmentation.md
diff --git a/docs/cli.md b/docs/cli.md
index 9f59091e..c2f878cc 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -11,6 +11,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
## Graphical User Interfaces
+The command line interface allows you to run graphical user interfaces directly from the terminal.
### `qim3d gui`
!!! quote "Reference"
@@ -38,7 +39,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
!!! Example
- Here's an example of how to open the [Data Explorer](gui.md#data_explorer)
+ Here's an example of how to open the [Data Explorer](gui.md#qim3d.gui.data_explorer)
``` title="Command"
qim3d gui --data-explorer
@@ -85,16 +86,6 @@ This offers quick interactions, making it ideal for tasks that require efficienc
-
-
-
-
-
-
-
-
-
-
## Data visualization
The command line interface also allows you to easily visualize data.
@@ -190,7 +181,8 @@ Or an specific path for destination can be used. We can also choose to not open
This writes to disk the `my_plot.html` file.
## File preview
-Command line interface, which allows users to preview 3D structers or 2D images directly in command line.
+File previewing can also be done directly from the command line interface to preview 3D structure or 2D images.
+
### `qim3d preview`
| Arguments | Description |
| --------- | ----------- |
diff --git a/docs/datahandling.md b/docs/datahandling.md
new file mode 100644
index 00000000..894f8fed
--- /dev/null
+++ b/docs/datahandling.md
@@ -0,0 +1,28 @@
+# 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/detection.md b/docs/detection.md
new file mode 100644
index 00000000..8f22020e
--- /dev/null
+++ b/docs/detection.md
@@ -0,0 +1,8 @@
+# Detection in volumetric data
+
+The `qim3d` library provides a set of detection methods for volumes.
+
+::: qim3d.detection
+ options:
+ members:
+ - blobs
\ No newline at end of file
diff --git a/docs/features.md b/docs/features.md
new file mode 100644
index 00000000..7f5b33ec
--- /dev/null
+++ b/docs/features.md
@@ -0,0 +1,10 @@
+# Feature extraction
+
+The `qim3d` library provides a set of methods for feature extraction on volumetric data
+
+::: qim3d.features
+ options:
+ members:
+ - area
+ - volume
+ - sphericity
diff --git a/docs/filters.md b/docs/filters.md
new file mode 100644
index 00000000..147aa5e8
--- /dev/null
+++ b/docs/filters.md
@@ -0,0 +1,17 @@
+# Filtering data
+
+The `qim3d` library provides a set of methods for filtering volumes.
+
+::: qim3d.filters
+ options:
+ members:
+ - gaussian
+ - median
+ - maximum
+ - minimum
+ - tophat
+
+::: qim3d.filters.Pipeline
+ options:
+ members:
+ - append
\ No newline at end of file
diff --git a/docs/generate.md b/docs/generate.md
deleted file mode 100644
index fb74f1f8..00000000
--- a/docs/generate.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# Generating synthetic data
-
-The `qim3d` library provides a set of methods for generating volumes consisting of a single synthetic blob or a collection of multiple synthetic blobs.
-
-::: qim3d.generate
- options:
- members:
- - noise_object
- - noise_object_collection
diff --git a/docs/io.md b/docs/io.md
deleted file mode 100644
index cbb1eb20..00000000
--- a/docs/io.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# Data input and output
-Dealing with volumetric data can be done by `qim3d` for the most common image formats available.
-
-Currently, it is possible to directly load `tiff`, `h5`, `nii`,`txm`, `vol` and common `PIL` formats using one single function.
-
-::: qim3d.io
- options:
- members:
- - load
- - load_mesh
- - save
- - save_mesh
- - Downloader
- - export_ome_zarr
- - import_ome_zarr
\ No newline at end of file
diff --git a/docs/operations.md b/docs/operations.md
new file mode 100644
index 00000000..8023f31d
--- /dev/null
+++ b/docs/operations.md
@@ -0,0 +1,10 @@
+# Operations on volumetric data
+
+The `qim3d` library provides a set of methods for different operations on volumes.
+
+::: qim3d.operations
+ options:
+ members:
+ - remove_background
+ - fade_mask
+ - overlay_rgb_images
\ No newline at end of file
diff --git a/docs/processing.md b/docs/processing.md
index dc50ac45..93d0e9b5 100644
--- a/docs/processing.md
+++ b/docs/processing.md
@@ -8,47 +8,4 @@ Here, we provide functionalities designed specifically for 3D image analysis and
- structure_tensor
- local_thickness
- get_lines
- - segment_layers
-
-::: qim3d.mesh
- options:
- members:
- - from_volume
-
-::: qim3d.detection
- options:
- members:
- - blobs
-
-::: qim3d.operations
- options:
- members:
- - remove_background
- - fade_mask
- - overlay_rgb_images
-
-::: qim3d.segmentation
- options:
- members:
- - watershed
- - get_3d_cc
-
-::: qim3d.filters
- options:
- members:
- - gaussian
- - median
- - maximum
- - minimum
- - tophat
-::: qim3d.filters.Pipeline
- options:
- members:
- - append
-
-::: qim3d.features
- options:
- members:
- - area
- - volume
- - sphericity
\ No newline at end of file
+ - segment_layers
\ No newline at end of file
diff --git a/docs/releases.md b/docs/releases.md
index cee2d6a4..abbd8177 100644
--- a/docs/releases.md
+++ b/docs/releases.md
@@ -7,7 +7,7 @@ Below, you'll find details about the version history of `qim3d`.
As the library is still in its early development stages, **there may be breaking changes** before `v1.0` without prior deprecation warnings. Therefore, it's advisable to review the release history for more information if you encounter any issues.
-And remember to keep your pip installation [up to date](/qim3d/#get-the-latest-version) so that you have the latest features!
+And remember to keep your pip installation [up to date](index.md/#get-the-latest-version) so that you have the latest features!
### v0.4.5 (21/11/2024)
diff --git a/docs/segmentation.md b/docs/segmentation.md
new file mode 100644
index 00000000..4ac23eba
--- /dev/null
+++ b/docs/segmentation.md
@@ -0,0 +1,9 @@
+# Segmenting data
+
+The `qim3d` library provides a set of methods for data segmentation.
+
+::: qim3d.segmentation
+ options:
+ members:
+ - watershed
+ - get_3d_cc
diff --git a/mkdocs.yml b/mkdocs.yml
index 18670519..10c59f55 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -7,14 +7,17 @@ repo_name: Gitlab
nav:
-
- qim3d: index.md
- - Input & Output: io.md
- - Data Generation: generate.md
- - Processing: processing.md
+ - Data handling: datahandling.md
- Visualization: viz.md
- - GUIs: gui.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
diff --git a/qim3d/cli/__init__.py b/qim3d/cli/__init__.py
index ef60bdb8..5646925a 100644
--- a/qim3d/cli/__init__.py
+++ b/qim3d/cli/__init__.py
@@ -6,7 +6,15 @@ import qim3d
import os
QIM_TITLE = ouf.rainbow(
- f"\n _ _____ __ \n ____ _(_)___ ___ |__ /____/ / \n / __ `/ / __ `__ \ /_ </ __ / \n/ /_/ / / / / / / /__/ / /_/ / \n\__, /_/_/ /_/ /_/____/\__,_/ \n /_/ v{qim3d.__version__}\n\n",
+ rf"""
+ _ _____ __
+ ____ _(_)___ ___ |__ /____/ /
+ / __ `/ / __ `__ \ /_ </ __ /
+ / /_/ / / / / / / /__/ / /_/ /
+ \__, /_/_/ /_/ /_/____/\__,_/
+ /_/ v{qim3d.__version__}
+
+ """,
return_str=True,
cmap="hot",
)
--
GitLab