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v0.4.1 #60

Merged
merged 44 commits into from
Dec 3, 2024
Merged

v0.4.1 #60

merged 44 commits into from
Dec 3, 2024

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plaresmedima
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plaresmedima and others added 30 commits August 6, 2024 14:20
* 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
EShalom and others added 14 commits November 29, 2024 14:13
* 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
@plaresmedima plaresmedima merged commit 9bd0cbf into main Dec 3, 2024
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3 participants