Slix

Added

Changed

Fixed
- Added `SLIX.parameters` to the `__init__.py` file.
- Fixed an issue where vectors were misaligned when using both vector options of SLIXVisualizeParameter.
- Fixed an issue where a white border would be shown in the output vector images when using the latest SLIX versions.

Added
- Added inclination sign map in SLIXParameterGenerator
- Added `SLIX.parameters` which contains all the parameters for the operations of the toolbox.
- Added `SLIX._logging` to replace the print statements in SLIX. This is a private variable and should not be used.
- Added `SLIX._decorators` for additional checks of the toolbox. This should ensure that the toolbox is not used in a wrong way.

Changed
- Added check for write operations before actually trying to generate any content reducing the computing time if the program would fail anyways.
- Changed the memory management between CPU and GPU in SLIXParameterGenerator which might reduce computing time.
- Changed print statements in SLIX to logging statements where possible. The tqdm progress bar is still used.
- `SLIX.GPU` now uses more than 1 thread for the GPU. The current value is 16x16 threads per block.
- Replaced `uint8` with `int8` in `_centroid_correction_bases`. This shouldn't affect the toolbox itself but ensures that the correct data type is used.
- Refactored some methods throughout the toolbox to improve maintainability. This will not affect the functionality of the toolbox.
- The inclination sign map will now be written by default.

Fixed
- Fixed out-of-bounds issues in `SLIX.GPU` when using more than 1x1 threads per block.
- Fixed issue in centroid calculation on the GPU where the normalized image wasn't stored in the GPU memory resulting in additional transfers through the CPU and GPU.
- Fixed an issue with `SLIX.attributemanager` where the method `set_reference_modality_to` was not working because it got overwritten.
- Fixed an issue where you could use any amount of arguments after the `--smoothing` flag in SLIXParameterGenerator resulting in weird behaviour for the users.
- Fixed an issue where the GPU would still be used to calculate the centroids even though the GPU execution was disabled.

Added
- Added vector weighting option available for SLIXVisualizeParameter with the parameter `--weight_map`. This parameter is used to weight the length of the shown vectors in both the unit vector visualization as well as the vector distribution.
- Added new options to SLIXVisualizeParameter to allow the user to customize the appearance of the resulting parameter maps such as the vector maps and the FOM.
- Added a new interface to SLIX.visualize called Colormaps. This class contains basic colormaps that can be used to visualize the results of the SLIX.visualize methods.
- Currently this class holds the following color maps:
- Colomaps.rgb
- Colormaps.hsv_black
- Colormaps.hsv_white
- Colormaps.hsv_black_reverse
- Colormaps.hsv_white_reverse
- Colormaps.rgb_reverse
- Added command line parameters for the user to choose the color maps when calling SLIXVisualizeParameter (`-c, --colormap`).
- Added a new color_bubble method to SLIX.visualize.
- Added an inclination parameter to SLIXVisualizeParameter [...] fom to allow the user to choose the inclination of the FOM.
-
Changed
- When calling SLIXVisualizeParameter, a color bubble associated with the written image will be written as well. This can be disabled by using the `--disable_colorbubble` option.
- Added a new method to SLIX.toolbox to get unit vectors from both direction and inclination images (3D instead of 2D only).
- Added the name of the color map to the filename.
- Added optional paramer name for the directions in SLIXVisualizeParameter (`--direction`).
-
Fixed
- Fixed a bug in SLIXVisualizeParameter and SLIX.visualize.unit_vectors which caused the unit vectors to be drawn in the wrong direction.

Added
- Added `SLIXCluster`, a tool which can be used to separate regions based on classification data through SLI measurements. The parameters aren't final yet and might change in the future.
- Added `SLIX.classification` which includes the classification methods of generated parameter maps.
- Added a new parameter to `SLIXVisualizeParameter [...] vector` named `--distribution` which allows to plot all vectors in a selected threshold region. This allows to see which regions have a high confidence in their reported orientation and which regions might not give any information. Please note that the performance for full measurements isn't that high in the current state.
- Added `SLIX.visualization.unit_vector_distribution` which is used for the creating of the image described in the last bullet point.
- Added DPI option to SLIXVisualizeParameter. The default was 1000 dpi but images with a lower dpi value might be interesting when presenting the image for a paper or presentation.
- Added `--value` and `--saturation` to `SLIXVisualizeParameter [...] fom` which allows the user to set two images to weight the FOM.

Changed
- Restructured some of the hidden methods to other Python files to make the basic package infrastructure easier to read.
- Renamed methods in `SLIX.visualization` to prevent the repetition of `visualize`
- The README.md will now use GitHub asset links instead of the old repository used during the first implementation of SLIX.
- Changed the structure for the command line programs from `_cmd.py` to a package named `_cmd` containing all programs in separate files. Both solutions work but the new solution allows SLIX to scale more easily in the future.
- When using the smoothing parameter in `SLIXParameterGenerator`, the resulting files will include the chosen algorithm as well as their respective parameters.
- Rework of `SLIXLineplotParameterGenerator`. The tool will now generate way more detailed parameters when called with default parameters. You can use the `--simple` option to reduce the information to average values (just like before). The CSV structure was also altered to make parsing the results easier.
- `SLIXLineplotParameterGenerator` now also supports the smoothing options from `SLIXParameterGenerator`
- Multiple line profiles will be calculated in parallel when using `SLIXLineplotParameterGenerator`
- When reading multiple files from a folder with `SLIXParameterGenerator` the filename will now not match the folder name but will instead use the file pattern in the read files instead.
- Disabled the GPU usage for unit vectors in SLIXVisualizeParameter until a better solution for large input files has been found.
- When using SLIXVisualizeParameter, a warning will now be shown when the background image dimensions do not match the image dimensions of the direction.
- When using SLIXVisualizeParameter, the background image will only be rotated when it would match the orientation of the direction images

Fixed
- Fixed a bug in the tests of the visualization images where the Matplotlib figure wasn't cleared as expected. The tests did check the right things though. It only resulted in a problem when adding another test for the new parameter.
- Fixed a bug where a 3D stack with the shape (1, 1, x) would not be processed correctly with SLIXParameterGenerator
- Fixed a bug in SLIXVisualizeParameter which could occur when the thinout is exactly the image size

Added

Changed

Fixed
- Fixed a visualization issue which could result in a wrong vector because the median of all vectors within that region was not chosen correctly.

Added

Changed

Fixed
- Fixed an error regarding the mask caluclation which sometimes would not create a mask because of an error when using the average histogram