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Commit ef46affa authored by s214735's avatar s214735
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addition of headers and some warning handling

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...@@ -11,6 +11,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc ...@@ -11,6 +11,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
## Graphical User Interfaces ## Graphical User Interfaces
The command line interface allows you to run graphical user interfaces directly from the terminal.
### `qim3d gui` ### `qim3d gui`
!!! quote "Reference" !!! quote "Reference"
...@@ -38,7 +39,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc ...@@ -38,7 +39,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
!!! Example !!! 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" ``` title="Command"
qim3d gui --data-explorer qim3d gui --data-explorer
...@@ -85,16 +86,6 @@ This offers quick interactions, making it ideal for tasks that require efficienc ...@@ -85,16 +86,6 @@ This offers quick interactions, making it ideal for tasks that require efficienc
## Data visualization ## Data visualization
The command line interface also allows you to easily visualize data. 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 ...@@ -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. This writes to disk the `my_plot.html` file.
## File preview ## 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` ### `qim3d preview`
| Arguments | Description | | Arguments | Description |
| --------- | ----------- | | --------- | ----------- |
......
# Data input and output # Data handling
Dealing with volumetric data can be done by `qim3d` for the most common image formats available. 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. 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 ::: qim3d.io
options: options:
members: members:
- load - load
- load_mesh
- save - save
- save_mesh
- Downloader - Downloader
- export_ome_zarr - export_ome_zarr
- import_ome_zarr - import_ome_zarr
- save_mesh
- load_mesh
::: qim3d.mesh
options:
members:
- from_volume
::: qim3d.generate
options:
members:
- noise_object
- noise_object_collection
# 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
# Feature extraction
The `qim3d` library provides a set of methods for feature extraction on volumetric data
::: qim3d.features
options:
members:
- area
- volume
- sphericity
# 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
# 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
# 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
...@@ -9,46 +9,3 @@ Here, we provide functionalities designed specifically for 3D image analysis and ...@@ -9,46 +9,3 @@ Here, we provide functionalities designed specifically for 3D image analysis and
- local_thickness - local_thickness
- get_lines - get_lines
- segment_layers - 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
...@@ -7,7 +7,7 @@ Below, you'll find details about the version history of `qim3d`. ...@@ -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. 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) ### v0.4.5 (21/11/2024)
......
# Segmenting data
The `qim3d` library provides a set of methods for data segmentation.
::: qim3d.segmentation
options:
members:
- watershed
- get_3d_cc
...@@ -7,14 +7,17 @@ repo_name: Gitlab ...@@ -7,14 +7,17 @@ repo_name: Gitlab
nav: nav:
- qim3d: index.md - qim3d: index.md
- Input & Output: io.md - Data handling: datahandling.md
- Data Generation: generate.md
- Processing: processing.md
- Visualization: viz.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 - ML Models: models.md
- GUIs: gui.md
- CLI: cli.md - CLI: cli.md
- Release history: releases.md - Release history: releases.md
......
...@@ -6,7 +6,15 @@ import qim3d ...@@ -6,7 +6,15 @@ import qim3d
import os import os
QIM_TITLE = ouf.rainbow( QIM_TITLE = ouf.rainbow(
f"\n _ _____ __ \n ____ _(_)___ ___ |__ /____/ / \n / __ `/ / __ `__ \ /_ </ __ / \n/ /_/ / / / / / / /__/ / /_/ / \n\__, /_/_/ /_/ /_/____/\__,_/ \n /_/ v{qim3d.__version__}\n\n", rf"""
_ _____ __
____ _(_)___ ___ |__ /____/ /
/ __ `/ / __ `__ \ /_ </ __ /
/ /_/ / / / / / / /__/ / /_/ /
\__, /_/_/ /_/ /_/____/\__,_/
/_/ v{qim3d.__version__}
""",
return_str=True, return_str=True,
cmap="hot", cmap="hot",
) )
......
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