Slix

Latest version: v2.4.2

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2.2.0

Added
- Added SLIXVisualizeParameter to the toolbox which enables visualizing directions either as a fiber orientation map or as vectors seen before in the example Jupyter notebook
- Added a new paragraph to the README.md to explain the new SLIXVisualizeParameter
- Added a new method in visualization.py to generate a fiber orientation map from a direction.
- Added a `--correctdir` option to SLIXParameterGenerator to accommodate for a camera shift during the measurement which impacts the resulting direction angle.
- Added a `--smoothing` option to SLIXParameterGenerator as there are now two methods to smooth the line profiles of a measurement (Savitzky-Golay and Fourier)
- Added a `--output_type` option to SLIXParameterGenerator. SLIX now generally supports TIFF, HDF5 and NIfTI files. HDF5 files require that the image is locaed at `/Image`
- Added a `--unit_vector` option to write unit vectors (as `.nii`). The functionality was implemented already but there wasn't a parameter for users.
- Added attributemanager.py which handles the newly added attributes in HDF5 files.
- Added the option to read an entire folder of 2D image files instead of an image stack when following the following regex syntax: `.*_+p[0-9]+_?.*\.(tif{1,2}|jpe*g|nii|h5|png)`
- Added `imwrite_rgb` to io.py for writing fiber orientation maps as TIFF or HDF5.
- .nii.gz files can now be read. While this was technically possible before this change, a if clause prevented the usage of the right library

Changed
- Added compression to all available data types (.tiff, .nii.gz, .h5). nii files will only be written as a compressed file if you use --output_type .nii.gz. Other data types will be compressed automatically.
- Overhaul of the documentation. The path changed from /doc to /docs. The documentation is now hosted on https://3d-pli.github.io/SLIX/
and isn't solely in the GitHub wiki anymore.
- Changed the datatype for the detected number of peaks from `int` to `uint16` because there shouldn't be more than 65535 peaks in a measurement.
- There is now only a single `_cmd.py` instead of two `cmd_[...].py` which cleans up the package a bit.
- Added documentation to missing methods.
- Changed how the `background_threshold` parameter works. Now, you define a fraction. If the fraction of background pixels lies above this defined threshold,
background pixels will not be considered for computing the median for visualizing a downscaled vector image.
- The CPU and GPU separation of the SLIX toolbox are now protected as users should only use the main methods.
- Changed the error message when the GPU cannot be used due to errors with Numba. Previously the same message shown when CuPy couldn't be initialized was shown.
- Changed the background mask algorithm when using `SLIXParameterGenerator`. Instead of a fix value it is not based on the average image histogram. The parameter remains disabled by default.
- Removed the `--mask_threshold` parameter from `SLIXParameterGenerator` in process of the previously bullet point.

Fixed
- Fixed a bug where the direction of a line profile with two peaks wasn't generated when the distance between the peaks was outside of 180° +- 35°.
- Fixed a few bugs regarding image orientations when reading / writing different data types
- When importing a module from SLIX, the underlying modules were visible. This is now resolved.
- Fixed a bug which could result in white pixels inside of the visualized direciton.
- Fixed the missing parallelization of the peak generation when using only the GPU. Previously an issue with Numba prevented this. A change in the code structure now allowed to implement parallelization.

2.0

Added
- The parameter `--detailed` got added to SLIXParameterGenerator. When using this parameter, 3 dimensional parameter maps get created which give a more detailed look at the analysis of the underlying data.
- Added a method to thin out the measurement by using either a plain thin out, median thin out or average thin out.
- Added support for reading HDF5 files in the API.

Changed
- The entire package was overhauled to include support for GPUs and support for Windows. The toolbox will now use Numba and CuPY instead of PyMP.
- General performance improvements were made to ensure that large measurements can be evaluated.
- Restructuring of the whole toolbox. Now instead of toolbox.py and visualization.py there are also preparation.py and io.py.
- The unit vector method is now in toolbox.py instead of visualization.py

Fixed

1.2.2

Added

Changed
- This issue fixes some typos in the README.md and tutorial.
- Introduced a troubleshooting section for line profiles with 3/5 peaks.
- Further explanations in README.md, paper.md and tutorial.

Fixed

1.2.1

Added
Included GitHub Actions workflow to publish the repository on PyPI when creating a tag.

Changed
The example Jupyter Notebook was expanded to include how you could transfer the generated parameter maps to unit vector maps which could be used for tractography applications.

Fixed

1.2.0

Added
- Added GitHub workflow for automated testing
- Added CONTRIBUTING.md
- Greatly expanded README.md to include more examples, tutorials and generally more information on how to use the toolbox.
- Added progress bars to most methods so that the user can see how long each task will take approximately
- Added visualization to SLIX. Now parameter maps and unit vectors can be visualized using Matplotlib. A tutorial was added under examples.
- Added API documentation to the repository and in form of markdown documents in /doc

Changed
- Added two new parameters in SLIXParameterGenerator

Fixed
- Fixed a bug where the program could crash if the user did use the toolbox and did not set an upper prominence bound
- Fixed a bug where some methods could cause a crash because of a left over parameter that wasn't used anymore
- Fixed a bug where the NUMBER_OF_SAMPLES parameter would not be correctly applied to the sampling algorithm if the number of samples got changed.
- Wrong datatypes when calling the program will now result in an error message instead of a crash because of tifffile
- Fixed a bug where the crossing direction could not be correctly reshaped by the toolbox
- Fixed some smaller bugs in both programs in /bin

1.1.1

Added

Changed
- Additional updates to the documentation of the package and README.md

Fixed
- Fixed a bug where the generation of the parameter map for the mean prominence of an image would result in a type error in SLIXParameterGenerator.

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