Merge 655eaf4 into 6170cf3

shimming-toolbox · Jan 25, 2024 · d01b24a · d01b24a
2 parents 6170cf3 + 655eaf4
commit d01b24a
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Showing 3 changed files with 17 additions and 16 deletions.
diff --git a/shimmingtoolbox/cli/b0shim.py b/shimmingtoolbox/cli/b0shim.py
@@ -1108,7 +1108,7 @@ def _initial_in_bounds(coefs: dict, bounds: dict):
     # If the scanner coefficients are valid, update the initial coefficients
     if scanner_shim_settings['has_valid_settings']:
         if scanner_shim_settings['0'] is not None and 0 in orders:
-            initial_coefs['0'] = np.array([scanner_shim_settings['0']])
+            initial_coefs['0'] = np.array(scanner_shim_settings['0'])
         if scanner_shim_settings['1'] is not None and 1 in orders:
             initial_coefs['1'] = scanner_shim_settings['1']
         if scanner_shim_settings['2'] is not None and 2 in orders:

diff --git a/shimmingtoolbox/shim/shim_utils.py b/shimmingtoolbox/shim/shim_utils.py
@@ -232,7 +232,7 @@ def get_scanner_shim_settings(bids_json_dict):
 
     # get_imaging_frequency
     if bids_json_dict.get('ImagingFrequency'):
-        scanner_shim['0'] = int(bids_json_dict.get('ImagingFrequency') * 1e6)
+        scanner_shim['0'] = [int(bids_json_dict.get('ImagingFrequency') * 1e6)]
 
     # get_shim_orders
     if bids_json_dict.get('ShimSetting'):
@@ -311,18 +311,13 @@ def concatenate_shim_settings(self, orders=[2]):
             logger.warning("Invalid Shim Settings")
             return coefs
 
-        if self.shim_settings.get('0') is not None and any(order>=0 for order in orders):
-            # Concatenate 2 lists
-            coefs = [self.shim_settings.get('0')]
-        else:
-            coefs = [0]
-
-        for order in orders:
-            if self.shim_settings.get(order) is not None:
-                # Concatenate 2 lists
-                coefs.extend(self.shim_settings.get(order))
-            else:
-                n_coefs = (order + 1) * 2
-                coefs.extend([0] * n_coefs)
+        if any(order >= 0 for order in orders):
+            for order in sorted(orders):
+                if self.shim_settings.get(str(order)) is not None:
+                    # Concatenate 2 lists
+                    coefs.extend(self.shim_settings.get(str(order)))
+                else:
+                    n_coefs = (order + 1) * 2
+                    coefs.extend([0] * n_coefs)
 
         return coefs
diff --git a/test/cli/test_cli_b0shim.py b/test/cli/test_cli_b0shim.py
@@ -449,13 +449,19 @@ def test_cli_dynamic_absolute(self, nii_fmap, nii_anat, nii_mask, fm_data, anat_
                                              '--fmap', fname_fmap,
                                              '--anat', fname_anat,
                                              '--mask', fname_mask,
-                                             '--scanner-coil-order', '2',
+                                             '--scanner-coil-order', '0, 2',
                                              '--output-value-format', 'absolute',
                                              '--output', tmp],
                                 catch_exceptions=False)
 
             assert res.exit_code == 0
             assert os.path.isfile(os.path.join(tmp, "coefs_coil0_Prisma_fit.txt"))
+            with open(os.path.join(tmp, "coefs_coil0_Prisma_fit.txt"), 'r') as file:
+                lines = file.readlines()
+                line = lines[8].strip().split(',')
+                values = [float(val) for val in line if val.strip()]
+
+            assert values == [123259067.330864, -718.069583, 138.656751, -110.517759, 24.97596, -4.888655]
 
     def test_cli_2d_fmap(self, nii_fmap, nii_anat, nii_mask, fm_data, anat_data):