MT/ihMT scripts: cleanup and adding B1+ correction

scilpy/reconst/tests/test_mti.py

@@ -6,36 +6,46 @@ def test_py_fspecial_gauss():
     pass
 
 
-def test_compute_contrasts_maps():
+def test_process_contrast_map():
     # toDO
     pass
 
 
-def test_compute_saturation():
+def test_compute_saturation_map():
     # toDO
     pass
 
 
-def test_compute_ihMT_maps():
+def test_compute_ratio_map():
     # toDO
     pass
 
 
-def test_compute_MT_maps_from_ihMT():
+def test_threshold_map():
     # toDO
     pass
 
 
-def test_compute_MT_maps():
+def test_adjust_B1_map_intensities():
     # toDO
     pass
 
 
-def test_threshold_maps():
+def test_smooth_B1_map():
     # toDO
     pass
 
 
-def test_apply_B1_correction():
+def test_apply_B1_corr_empiric():
+    # toDO
+    pass
+
+
+def test_apply_B1_corr_model_based():
+    # toDO
+    pass
+
+
+def test_adjust_B1_map_header():
     # toDO
     pass

scripts/scil_mti_adjust_B1_header.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Correct B1 map header problem.
+
+"""
+
+import argparse
+import json
+import logging
+
+import nibabel as nib
+
+from scilpy.io.utils import (add_overwrite_arg,
+                             add_verbose_arg,
+                             assert_inputs_exist,
+                             assert_outputs_exist)
+from scilpy.reconst.mti import (adjust_B1_map_header)
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    p.add_argument('in_B1_map',
+                   help='Path to input B1 map file.')
+    p.add_argument('out_B1_map',
+                   help='Path to output B1 map file.')
+    p.add_argument('in_B1_json',
+                   help='Json file of the B1 map.')
+
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
+
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
+
+    assert_outputs_exist(parser, args, args.out_B1_map)
+    assert_inputs_exist(parser, (args.in_B1_map, args.in_B1_json))
+
+    with open(args.in_B1_json) as curr_json:
+        b1_json = json.load(curr_json)
+        if 'PhilipsRescaleSlope' in b1_json.keys():
+            slope = b1_json['PhilipsRescaleSlope']
+        else:
+            raise ValueError('Rescale slope not in Json file.')
+
+    b1_img = nib.load(args.in_B1_map)
+
+    new_b1_img = adjust_B1_map_header(b1_img, slope)
+
+    nib.save(new_b1_img, args.out_B1_map)
+
+
+if __name__ == '__main__':
+    main()