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v0.4.1 #60
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v0.4.1 #60
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* Setup gitignore to not track changes in the .vscode folder - The will not be useful between users
* Remove line creating flattened coregistered array * Code outputs each time point into array of shape matching (x,y,z,t)
* Varibale flip angle data added to give 4D data example - Flips angles of 2, 5, 10, 20, 25 deg used - (x,y,z,phi) ordering used when read in using numpy * Accessible via mdreg.fetch('VFA')
* New models added to src/mdreg/models.py module * Models added: - SGPR VFA (spoiled gradient echo varibale flip angle) * Non-linear fitting * Linear fitting - 2CFM (2 compartment filtration model) * Linear model
* Checked rendering in documentation * Added sphinxcontrib-video to docs requirements.txt to render .gifs properly * Signal fitting code corrected in models.py to use M and C parameters * Plotting functions adjusted to skip if no plotting required to show or save - Also keep animation open for long enough to render or no output into the example * Added docustrings for docs in models.py, plots.py
* Originally just as a page but now also within the examples section * Allows integrated download and shows run time
* Renders with links and photos of github information
* Docustring updated and expanded * Elastix freeform default parameters changed from Smoothing -> Recursive - Aligns with the defaults used in elastix example and provides very similar results
* Add plotting to the docs * Change to include template for autosummary to fix missing function docustrings in docs
Example VFA script and documentation update
- Added progress bar varaible to set visiblility according to verbose parameter - Added information to docustrings on specific size and dimensions of arrays - Add params example to docstring
- Added progress bar varaible to set visiblility according to verbose parameter - Added information to docustrings on specific size and dimensions of arrays
- Add docustring information - Harmonise all models to use signal rather than combination of ydata and signal - Adjust SPGR non-linear to convert from degrees to radians within function to keep readability of main code and usual usage
- Reformatted code to match elastix module with both _coreg_2d and _coreg_3d - optical flow extended for use with 3D spatial data
- Align progress bar from the main mdreg.fit into fit_pixels - set ddint to non-docs
- If 3D spatial data by deafult animation and plot_series will create figures showing the animation over all slices for in a grid. For plot series this creates 3 figures moving, fixed, coreg all with a grid of animated slices. For animation only one figure is produced. - If slice parameter is supplied the function will return as if 2D data is entered and plot_series show animation of moving, fixed, and coreg side by side. - Added protections if moving, fixed, and coreg array are not the same shape
- Non-linear fitting example extended to show poor fitting metrics (chi-squared) result in poor coregistration results. - Linear SPGR fitting included as main example for 3D data as before - New 3D plotting functions employed
- Added fix for ukat model (requires absolute values) - Fixed progress bars to stop displaying in notebook
- Updated contributor details page - Updated funding info
3D compatibility update and tutorials
…/jacobian_and_norm_def_fields
* Add in description tables for variable size and shape ect * Link these tables to models and main mdreg.fit function * Update default handling of fit_image, fit_pixel, fir_coreg - Now None by default and set up to default dictionaries at start of the function
Updates docs and main fit defaults
…ef_fields Deformation Field QA Functions
* update some docstrings in skimage * add source, target to variable description table * correct moving description * correct links for types
Small docs update
bug fix + force_2d option
update docs
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