some modifications to code formating

shimmingtoolbox/cli/mask.py

@@ -305,22 +305,24 @@ def sct(fname_input, fname_output, contrast, centerline, file_centerline, brain,
 
 
 @mask_cli.command(context_settings=CONTEXT_SETTINGS,
-                  help="Create a mask to shim single voxel MRS."
-                       "voxel position and size can be directly given or these info can be read "
-                       "from the twix raw-data."
+                  help="Create a mask to shim single voxel MRS. "
+                       "Voxel position and size can be directly given or these info can be read "
+                       "from the twix raw-data. "
                        "The mask is stored by default under the name 'mask_mrs.nii.gz' in the output "
                        "folder. Return an output nifti file to be used as a mask for MRS shimming.")
-@click.option('-i', '--input', 'fname_input',  type=click.Path(), required=True,
+@click.option('-i', '--input', 'fname_input', type=click.Path(), required=True,
                help="Input path of the fieldmap to be shimmed.")
 @click.option('-r', '--raw_data', type=click.Path(),
-              help="Input path of the of the twix raw-data (supported extention .dat) [optional]")
-@click.option('-o', '--output', type=click.Path(), default=os.path.join(os.curdir, 'mask_mrs.nii.gz'), show_default=True,
-              help="Name of the output mask. Supported extensions are .nii or .nii.gz. (default: "
+              help="Input path of the of the twix raw-data (supported extention .dat)")
+@click.option('-o', '--output', type=click.Path(), default=os.path.join(os.curdir, 'mask_mrs.nii.gz'),
+              show_default=True, help="Name of the output mask. Supported extensions are .nii or .nii.gz. (default: "
                    "(os.curdir, 'mask_mrs.nii.gz'))")
-@click.option('-c', '--center', nargs=3, type=click.FLOAT, help="voxel's center position in mm of the x, y and z of the scanner's coordinate [optional]")
-@click.option('-s', '--size', nargs=3, type=click.FLOAT, help="voxel size in mm of the x, y and z of the scanner's coordinate")
+@click.option('-c', '--center', nargs=3, type=click.FLOAT, help="Voxel's center position in mm of the x, y and z of "
+              "the scanner's coordinate")
+@click.option('-s', '--size', nargs=3, type=click.FLOAT, help="Voxel size in mm of the x, y and z of the scanner's "
+              "coordinate")
 @click.option('--verbose', type=click.Choice(['info', 'debug']), default='info', help="Be more verbose")
-def mrs_mask(fname_input, output, raw_data, center, size, verbose):
+def mrs(fname_input, output, raw_data, center, size, verbose):
 
     # Set all loggers
     set_all_loggers(verbose)

shimmingtoolbox/masking/mask_mrs.py

@@ -19,11 +19,10 @@ def mask_mrs(fname_input, raw_data, center, size):
     Create a mask to shim single voxel MRS
 
     Args:
-        fname_input (str): Input path of the fieldmap to be shimmed (supported extention .nii and .nii.gz) [required]
-        raw_data (str): Input path of the of the twix raw-data (supported extention .dat) [optional]
-        center (float): voxel's center position in mm of the x, y and z of the scanner's coordinate [optional]
-        size (float): voxel size in mm of the x, y and z of the scanner's coordinate [optional]
-
+        fname_input (str): Input path of the fieldmap to be shimmed (supported extention .nii and .nii.gz)
+        raw_data (str): Input path of the of the twix raw-data (supported extention .dat)
+        center (float): voxel's center position in mm of the x, y and z of the scanner's coordinate
+        size (float): voxel size in mm of the x, y and z of the scanner's coordinate
     Returns:
         numpy.ndarray: Cubic mask with same dimensions as MRS voxel.
     """
@@ -34,29 +33,28 @@ def mask_mrs(fname_input, raw_data, center, size):
     if raw_data is None:
         logger.info(" The raw_data is not provided, creating the mask with the given voxel position and size info")
         if center is None or size is None:
-             raise TypeError('As the raw_data is not provided, the voxel position and size must be given to create the mask (See: st_mask mrs-mask -h)')
+             raise TypeError('The raw_data is not provided; the voxel position and size are required to proceed')
         else:
             mrs_voxel_size = size
-            logger.debug('center:',center )
+            logger.debug('center:', center)
             scanner_coordinate = np.array(center + (1,))
             logger.debug(f"Scanner position is: {scanner_coordinate}")
 
     else:
-            logger.info("Reading the twix raw_data")
-            run_subprocess(['spec2nii', 'twix', raw_data, '-e', 'image'])
-            name_nii, ext = splitext(raw_data)
-            nii = nib.load(name_nii + '.nii.gz')
-            header_twix = nii.header
-            affine = nii.affine
-            position_sag = header_twix['qoffset_x']
-            position_cor = header_twix['qoffset_y']
-            position_tra = header_twix['qoffset_z']
-            logger.debug(f"twix header: {header_twix}")
-            logger.debug(f"affine: {affine}")
-            scanner_coordinate = np.array([position_sag, position_cor, position_tra, 1])
-            logger.debug(f"Scanner position is: {scanner_coordinate}")
-            mrs_voxel_size = header_twix['pixdim'][1:4]
-
+        logger.info("Reading the twix raw_data")
+        run_subprocess(['spec2nii', 'twix', raw_data, '-e', 'image'])
+        name_nii, ext = splitext(raw_data)
+        nii = nib.load(name_nii + '.nii.gz')
+        header_twix = nii.header
+        affine = nii.affine
+        position_sag = header_twix['qoffset_x']
+        position_cor = header_twix['qoffset_y']
+        position_tra = header_twix['qoffset_z']
+        logger.debug(f"twix header: {header_twix}")
+        logger.debug(f"affine: {affine}")
+        scanner_coordinate = np.array([position_sag, position_cor, position_tra, 1])
+        logger.debug(f"Scanner position is: {scanner_coordinate}")
+        mrs_voxel_size = header_twix['pixdim'][1:4]
 
     logger.debug('mrs_voxel_size is:', mrs_voxel_size)
     fmap_nii = nib.load(fname_input)
@@ -69,17 +67,17 @@ def mask_mrs(fname_input, raw_data, center, size):
     voxel_position = np.round(voxel_position)
     logger.debug('voxel_position:', voxel_position)
 
-      # The given coordinate (I, J, K) is the voxel's center position.
-    I, J, K = map(int, voxel_position[:3])
+    # The given coordinate (i, j, k) is the voxel's center position.
+    i, j, k = map(int, voxel_position[:3])
     fmap_resolution = fmap_header['pixdim'][1:4]
 
-    # To create a mask, the distance from the center of the MRS voxel to it's edges should be calculated based on number of fieldmap voxels.
+    # The distance from the center of the MRS voxel to it's edges is calculated based on number of fieldmap voxels.
     half_voxel_distances = np.ceil(np.divide(mrs_voxel_size, 2 * fmap_resolution)).astype(int)
     sd = half_voxel_distances
 
     # create a zero mask with the same size as the input fieldmap to be shimmed.
     mask = np.zeros(fmap_array.shape)
 
     # Change the MRS voxel position to have 1 value.
-    mask[I - sd[0]:I + sd[0], J - sd[1]:J + sd[1], K - sd[2]:K + sd[2]] = 1
+    mask[i - sd[0]:i + sd[0], j - sd[1]:j + sd[1], k - sd[2]:k + sd[2]] = 1
     return mask