Merge pull request #61 from plaresmedima/development

Bug fixes, model corrections and doc updates

README.rst

@@ -0,0 +1,79 @@
+mdreg
+=====
+
+.. image:: https://img.shields.io/badge/License-Apache_2.0-blue.svg
+  :target: https://opensource.org/licenses/Apache-2.0
+
+
+
+Model-driven motion correction for medical imaging
+--------------------------------------------------
+
+- **Documentation:** https://qib-sheffield.github.io/mdreg/
+- **Source code:** https://github.com/QIB-Sheffield/mdreg
+
+
+*Note:* mdreg is under construction. At this stage, the API may still change 
+and features may be deprecated without warning.
+
+
+Installation
+------------
+
+.. code-block:: console
+
+    pip install mdreg
+
+
+Typical usage
+-------------
+
+.. code-block:: python
+
+    import mdreg
+
+    # Get some test data (variable flip angle MRI)
+    data = mdreg.fetch('VFA')  
+
+    # Configure the signal model fit
+    fit_image = {
+        'func': mdreg.spgr_vfa_lin,     # VFA signal model
+        'FA': data['FA'],               # Flip angle in degress    
+        'progress_bar': True,           # Show a progress bar
+    }
+
+    # Configure the coregistration method
+    fit_coreg = {
+        'package': 'elastix',
+        'spacing': data['spacing'],           
+    } 
+
+    # Perform the motion correction
+    coreg, defo, fit, pars = mdreg.fit(
+        data['array'],                # Signal data to correct
+        fit_image = fit_image,        # Signal model fit
+        fit_coreg = fit_coreg,        # Coregistration
+        verbose = 2,                  # Show progress update
+    )
+
+    # Visualize the results
+    anim = mdreg.animation(
+        coreg, 
+        title = 'Motion corrected VFA', 
+        'interval' : 500,                   # Time between animation frames in ms
+        'vmin' : 0,                         # Minimum value of the colorbar
+        'vmax' : np.percentile(coreg, 99),  # Maximum value of the colorbar
+    )
+
+
+.. image:: https://qib-sheffield.github.io/mdreg/_images/sphx_glr_plot_3Dexample_vfa_002.gif
+  :width: 800
+
+
+License
+-------
+
+Released under the `Apache 2.0 <https://opensource.org/licenses/Apache-2.0>`_  
+license::
+
+  Copyright (C) 2023-2024 dcmri developers

dev/sops.txt

@@ -99,6 +99,7 @@ To make all autogenerated documentation from scratch, first delete all auto-gene
 
 Building release notes
 ----------------------
+
 - Get a personal token on https://github.com/settings/tokens (does not need any permissions)
 - Save the token in the environment variable GH_TOKEN. On windows:
 >>> $env:GH_TOKEN='token'

docs/examples/README.rst

@@ -6,4 +6,5 @@ Examples
 
 .. note::
 
-   `mdreg` is developed in public but is work in progress. As long as this notice is visible, backwards compatibility is not guaranteed and features may be deprecated without warning.
+   ``mdreg`` is under construction. At this stage, the API may still change and 
+   features may be deprecated without warning.

docs/examples/tutorials/plot_getting_started_defo.py

@@ -63,7 +63,6 @@
 molli = {
     'func': mdreg.abs_exp_recovery_2p,
     'TI': np.array(data['TI'])/1000,
-    'progress_bar': True,
 }
 
 # Perform model-driven coregistration