Remove leftover unnecessary R| formatting (#3561)

* Remove "R|" from the help descriptions of CLI scripts
* Clean up SmartFormatter docstrings that reference "R|"

spinalcordtoolbox/scripts/sct_analyze_lesion.py

@@ -27,7 +27,7 @@
 
 def get_parser():
     parser = SCTArgumentParser(
-        description='R|Compute statistics on segmented lesions. The function assigns an ID value to each lesion (1, 2, '
+        description='Compute statistics on segmented lesions. The function assigns an ID value to each lesion (1, 2, '
                     '3, etc.) and then outputs morphometric measures for each lesion:\n'
                     '- volume [mm^3]\n'
                     '- length [mm]: length along the Superior-Inferior axis\n'

spinalcordtoolbox/scripts/sct_compute_snr.py

@@ -39,7 +39,7 @@ def get_parser():
     mandatoryArguments.add_argument(
         '-i',
         required=True,
-        help="R|Image to compute the SNR on. (Example: b0s.nii.gz)\n"
+        help="Image to compute the SNR on. (Example: b0s.nii.gz)\n"
              "- For '-method diff' and '-method mult', the image must be 4D, as SNR will be computed "
              "along the 4th dimension.\n"
              "- For '-method single', the image can either be 3D or 4D. If a 4D image is passed, a specific "
@@ -63,7 +63,7 @@ def get_parser():
         default='')
     optional.add_argument(
         '-method',
-        help='R|Method to use to compute the SNR (default: diff):\n'
+        help='Method to use to compute the SNR (default: diff):\n'
              "  - diff: Substract two volumes (defined by -vol) and estimate noise variance within the ROI "
              "(flag '-m' is required). Requires a 4D volume.\n"
              "  - mult: Estimate noise variance over time across volumes specified with '-vol'. Requires a 4D volume.\n"
@@ -78,7 +78,7 @@ def get_parser():
         default='diff')
     optional.add_argument(
         '-vol',
-        help="R|Volumes to compute SNR from. Separate with ',' (Example: '-vol 0,1'), or select range "
+        help="Volumes to compute SNR from. Separate with ',' (Example: '-vol 0,1'), or select range "
              "using ':' (Example: '-vol 2:50'). If this argument is not passed:\n"
              "  - For '-method mult', all volumes will be used.\n"
              "  - For '-method diff', the first two volumes will be used.\n"

spinalcordtoolbox/scripts/sct_create_mask.py

@@ -71,7 +71,7 @@ def get_parser():
         '-p',
         default=param_default.process,
         required=True,
-        help='R|Process to generate mask.\n'
+        help='Process to generate mask.\n'
              '  <coord,XxY>: Center mask at the X,Y coordinates. (e.g. "coord,20x15")\n'
              '  <point,FILE>: Center mask at the X,Y coordinates of the label defined in input volume FILE. (e.g. "point,label.nii.gz")\n'
              '  <center>: Center mask in the middle of the FOV (nx/2, ny/2).\n'

spinalcordtoolbox/scripts/sct_deepseg_lesion.py

@@ -37,7 +37,7 @@ def get_parser():
     mandatory.add_argument(
         "-c",
         required=True,
-        help='R|Type of image contrast.\n'
+        help='Type of image contrast.\n'
              ' t2: T2w scan with isotropic or anisotropic resolution.\n'
              ' t2_ax: T2w scan with axial orientation and thick slices.\n'
              ' t2s: T2*w scan with axial orientation and thick slices.',
@@ -53,7 +53,7 @@ def get_parser():
     )
     optional.add_argument(
         "-centerline",
-        help="R|Method used for extracting the centerline:\n"
+        help="Method used for extracting the centerline:\n"
              " svm: Automatic detection using Support Vector Machine algorithm.\n"
              " cnn: Automatic detection using Convolutional Neural Network.\n"
              " viewer: Semi-automatic detection using manual selection of a few points with an interactive viewer "

spinalcordtoolbox/scripts/sct_deepseg_sc.py

@@ -50,7 +50,7 @@ def get_parser():
         help="show this help message and exit")
     optional.add_argument(
         "-centerline",
-        help="R|Method used for extracting the centerline:\n"
+        help="Method used for extracting the centerline:\n"
              " svm: Automatic detection using Support Vector Machine algorithm.\n"
              " cnn: Automatic detection using Convolutional Neural Network.\n"
              " viewer: Semi-automatic detection using manual selection of a few points with an interactive viewer "

spinalcordtoolbox/scripts/sct_dmri_compute_dti.py

@@ -49,7 +49,7 @@ def get_parser():
         help="Show this help message and exit")
     optional.add_argument(
         '-method',
-        help='R|Type of method to calculate the diffusion tensor:\n'
+        help='Type of method to calculate the diffusion tensor:\n'
              ' standard: Standard equation [Basser, Biophys J 1994]\n'
              ' restore: Robust fitting with outlier detection [Chang, MRM 2005]',
         default='standard',

spinalcordtoolbox/scripts/sct_dmri_moco.py

@@ -101,7 +101,7 @@ def get_parser():
         '-param',
         metavar=Metavar.list,
         type=list_type(',', str),
-        help=f"R|Advanced parameters. Assign value with \"=\", and separate arguments with \",\".\n"
+        help=f"Advanced parameters. Assign value with \"=\", and separate arguments with \",\".\n"
              f"  - poly [int]: Degree of polynomial function used for regularization along Z. For no regularization "
              f"set to 0. Default={param_default.poly}.\n"
              f"  - smooth [mm]: Smoothing kernel. Default={param_default.smooth}.\n"

spinalcordtoolbox/scripts/sct_download_data.py

@@ -123,7 +123,7 @@ def get_parser():
         '-o',
         metavar=Metavar.folder,
         action=ActionCreateFolder,
-        help="R|Path to a directory to save the downloaded data.\n"
+        help="Path to a directory to save the downloaded data.\n"
              "(Defaults to ./${dataset-name}. Directory will be created if it does not exist. Warning: existing "
              "data in the directory will be erased unless -k is provided.)\n"
     )

spinalcordtoolbox/scripts/sct_extract_metric.py

@@ -125,7 +125,7 @@ def get_parser():
         '-method',
         choices=['ml', 'map', 'wa', 'bin', 'median', 'max'],
         default=param_default.method,
-        help="R|Method to extract metrics.\n"
+        help="Method to extract metrics.\n"
              "  - ml: maximum likelihood.\n"
              "    This method is recommended for large labels and low noise. Also, this method should only be used"
              " with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels"
@@ -160,7 +160,7 @@ def get_parser():
         '-o',
         metavar=Metavar.file,
         default=param_default.fname_output,
-        help="R|File name of the output result file collecting the metric estimation results. Include the '.csv' "
+        help="File name of the output result file collecting the metric estimation results. Include the '.csv' "
              "file extension in the file name. Example: extract_metric.csv"
     )
     optional.add_argument(
@@ -175,15 +175,15 @@ def get_parser():
         '-z',
         metavar=Metavar.str,
         default=param_default.slices_of_interest,
-        help="R|Slice range to estimate the metric from. First slice is 0. Example: 5:23\n"
+        help="Slice range to estimate the metric from. First slice is 0. Example: 5:23\n"
              "You can also select specific slices using commas. Example: 0,2,3,5,12'"
     )
     optional.add_argument(
         '-perslice',
         type=int,
         choices=(0, 1),
         default=param_default.perslice,
-        help="R|Whether to output one metric per slice instead of a single output metric. 0 = no, 1 = yes.\n"
+        help="Whether to output one metric per slice instead of a single output metric. 0 = no, 1 = yes.\n"
              "Please note that when methods ml or map are used, outputting a single metric per slice and then "
              "averaging them all is not the same as outputting a single metric at once across all slices."
     )
@@ -197,16 +197,16 @@ def get_parser():
         '-vertfile',
         metavar=Metavar.file,
         default="./label/template/PAM50_levels.nii.gz",
-        help="R|Vertebral labeling file. Only use with flag -vert.\n"
-            "The input Image and the vertebral labelling file must in the same voxel coordinate system "
-            "and must match the dimensions between each other."
+        help="Vertebral labeling file. Only use with flag -vert.\n"
+             "The input Image and the vertebral labelling file must in the same voxel coordinate system "
+             "and must match the dimensions between each other."
     )
     optional.add_argument(
         '-perlevel',
         type=int,
         metavar=Metavar.int,
         default=0,
-        help="R|Whether to output one metric per vertebral level instead of a single output metric. 0 = no, 1 = yes.\n"
+        help="Whether to output one metric per vertebral level instead of a single output metric. 0 = no, 1 = yes.\n"
              "Please note that this flag needs to be used with the -vert option."
     )
     optional.add_argument(
@@ -224,7 +224,7 @@ def get_parser():
         '-param',
         metavar=Metavar.str,
         default='',
-        help="R|Advanced parameters for the 'map' method. Separate with comma. All items must be listed (separated "
+        help="Advanced parameters for the 'map' method. Separate with comma. All items must be listed (separated "
              "with comma).\n"
              "  - #1: standard deviation of metrics across labels\n"
              "  - #2: standard deviation of the noise (assumed Gaussian)"
@@ -248,7 +248,7 @@ def get_parser():
         '-norm-method',
         choices=['sbs', 'whole'],
         default='',
-        help="R|Method to use for normalization:\n"
+        help="Method to use for normalization:\n"
              "  - sbs: normalization slice-by-slice\n"
              "  - whole: normalization by the metric value in the whole label for all slices."
     )

spinalcordtoolbox/scripts/sct_fmri_moco.py

@@ -72,7 +72,7 @@ def get_parser():
         '-param',
         metavar=Metavar.list,
         type=list_type(',', str),
-        help=f"R|Advanced parameters. Assign value with \"=\"; Separate arguments with \",\".\n"
+        help=f"Advanced parameters. Assign value with \"=\"; Separate arguments with \",\".\n"
              f"  - poly [int]: Degree of polynomial function used for regularization along Z. For no regularization "
              f"set to 0. Default={param_default.poly}.\n"
              f"  - smooth [mm]: Smoothing kernel. Default={param_default.smooth}.\n"

spinalcordtoolbox/scripts/sct_get_centerline.py

@@ -50,7 +50,7 @@ def get_parser():
         "-method",
         choices=['optic', 'viewer', 'fitseg'],
         default='optic',
-        help="R|Method used for extracting the centerline.\n"
+        help="Method used for extracting the centerline.\n"
              "  - optic: automatic spinal cord detection method\n"
              "  - viewer: manual selection a few points followed by interpolation\n"
              "  - fitseg: fit a regularized centerline on an already-existing cord segmentation. It will "

spinalcordtoolbox/scripts/sct_image.py

@@ -37,10 +37,10 @@ def get_parser():
         '-i',
         nargs='+',
         metavar=Metavar.file,
-        help='R|Input file(s). Example: "data.nii.gz"\n'
+        help='Input file(s). Example: "data.nii.gz"\n'
              'Note: Only "-concat" or "-omc" support multiple input files. In those cases, separate filenames using '
              'spaces. Example usage: "sct_image -i data1.nii.gz data2.nii.gz -concat"',
-        required = True)
+        required=True)
     optional = parser.add_argument_group('OPTIONAL ARGUMENTS')
     optional.add_argument(
         '-h',

spinalcordtoolbox/scripts/sct_label_utils.py

@@ -90,7 +90,7 @@ def get_parser():
         '-create-seg',
         metavar=Metavar.list,
         type=list_type(':', list_type(',', int)),
-        help="R|Create labels on a cord segmentation (or centerline) image defined by '-i'. Each label should be "
+        help="Create labels on a cord segmentation (or centerline) image defined by '-i'. Each label should be "
              "specified using the form 'v1,v2' where 'v1' is value of the slice index along the inferior-superior "
              "axis, and 'v2' is the value of the label. Separate each label with ':'. \n"
              "Example: '-create-seg 5,1:14,2:23,3' adds three labels at the axial slices 5, 14, and 23 (starting from "
@@ -101,7 +101,7 @@ def get_parser():
         '-create-seg-mid',
         metavar=Metavar.int,
         type=int,
-        help="R|Similar to '-create-seg'. This option takes a single label value, and will automatically select the "
+        help="Similar to '-create-seg'. This option takes a single label value, and will automatically select the "
              "mid-point slice in the inferior-superior direction (so there is no need for a slice index).\n"
              "This is useful for when you have centered the field of view of your data at a specific location. "
              "For example, if you already know that the C2-C3 disc is centered in the I-S direction, then "
@@ -144,7 +144,7 @@ def get_parser():
         '-vert-body',
         metavar=Metavar.list,
         type=list_type(',', int),
-        help="R|From vertebral labeling, create points that are centered at the mid-vertebral levels. Separate "
+        help="From vertebral labeling, create points that are centered at the mid-vertebral levels. Separate "
              "desired levels with ','. Example: 3,8\n"
              "To get all levels, enter 0."
     )

spinalcordtoolbox/scripts/sct_label_vertebrae.py

@@ -109,7 +109,7 @@ def get_parser():
         '-initz',
         metavar=Metavar.list,
         type=list_type(',', int),
-        help="R|Initialize using slice number and disc value. Example: 68,4 (slice 68 corresponds to disc C3/C4). "
+        help="Initialize using slice number and disc value. Example: 68,4 (slice 68 corresponds to disc C3/C4). "
              "Example: 125,3\n"
              "WARNING: Slice number should correspond to superior-inferior direction (e.g. Z in RPI orientation, but "
              "Y in LIP orientation)."
@@ -177,7 +177,7 @@ def get_parser():
         '-param',
         metavar=Metavar.list,
         type=list_type(',', str),
-        help=f"R|Advanced parameters. Assign value with \"=\"; Separate arguments with \",\"\n"
+        help=f"Advanced parameters. Assign value with \"=\"; Separate arguments with \",\"\n"
              f"  - shift_AP [mm]: AP shift of centerline for disc search. Default={param_default.shift_AP}.\n"
              f"  - size_AP [mm]: AP window size for disc search. Default={param_default.size_AP}.\n"
              f"  - size_RL [mm]: RL window size for disc search. Default={param_default.size_RL}.\n"

spinalcordtoolbox/scripts/sct_maths.py

@@ -109,7 +109,7 @@ def get_parser():
         "-adap",
         metavar=Metavar.list,
         type=list_type(',', int),
-        help="R|Threshold image using Adaptive algorithm (from skimage). Provide 2 values separated by ',' that "
+        help="Threshold image using Adaptive algorithm (from skimage). Provide 2 values separated by ',' that "
              "correspond to the parameters below. For example, '-adap 7,0' corresponds to a block size of 7 and an "
              "offset of 0.\n"
              "  - Block size: Odd size of pixel neighborhood which is used to calculate the threshold value. \n"
@@ -120,7 +120,7 @@ def get_parser():
         "-otsu-median",
         metavar=Metavar.list,
         type=list_type(',', int),
-        help="R|Threshold image using Median Otsu algorithm (from dipy). Provide 2 values separated by ',' that "
+        help="Threshold image using Median Otsu algorithm (from dipy). Provide 2 values separated by ',' that "
              "correspond to the parameters below. For example, '-otsu-median 3,5' corresponds to a filter size of 3 "
              "repeated over 5 iterations.\n"
              "  - Size: Radius (in voxels) of the applied median filter.\n"
@@ -164,7 +164,7 @@ def get_parser():
         required=False)
     mathematical.add_argument(
         '-shape',
-        help="R|Shape of the structuring element for the mathematical morphology operation. Default: ball.\n"
+        help="Shape of the structuring element for the mathematical morphology operation. Default: ball.\n"
              "If a 2D shape {'disk', 'square'} is selected, -dim must be specified.",
         required=False,
         choices=('square', 'cube', 'disk', 'ball'),
@@ -196,7 +196,7 @@ def get_parser():
         required=False)
     filtering.add_argument(
         '-denoise',
-        help='R|Non-local means adaptative denoising from P. Coupe et al. as implemented in dipy. Separate with ". Example: p=1,b=3\n'
+        help='Non-local means adaptative denoising from P. Coupe et al. as implemented in dipy. Separate with ". Example: p=1,b=3\n'
              ' p: (patch radius) similar patches in the non-local means are searched for locally, inside a cube of side 2*p+1 centered at each voxel of interest. Default: p=1\n'
              ' b: (block radius) the size of the block to be used (2*b+1) in the blockwise non-local means implementation. Default: b=5 '
              '    Note, block radius must be smaller than the smaller image dimension: default value is lowered for small images)\n'

spinalcordtoolbox/scripts/sct_process_segmentation.py

@@ -142,7 +142,7 @@ def get_parser():
         '-vertfile',
         metavar=Metavar.str,
         default='./label/template/PAM50_levels.nii.gz',
-        help="R|Vertebral labeling file. Only use with flag -vert.\n"
+        help="Vertebral labeling file. Only use with flag -vert.\n"
         "The input and the vertebral labelling file must in the same voxel coordinate system "
         "and must match the dimensions between each other. "
     )
@@ -213,7 +213,7 @@ def get_parser():
         metavar=Metavar.list,
         action=SeparateNormArgs,
         nargs="+",
-        help="R|Normalize CSA values ('MEAN(area)').\n"
+        help="Normalize CSA values ('MEAN(area)').\n"
              "Two models are available:\n"
              "    1. sex, brain-volume, thalamus-volume.\n"
              "    2. sex, brain-volume.\n"

spinalcordtoolbox/scripts/sct_propseg.py

@@ -278,7 +278,7 @@ def get_parser():
     optional.add_argument(
         '-init-centerline',
         metavar=Metavar.file,
-        help="R|Filename of centerline to use for the propagation. Use format .txt or .nii; see file structure in "
+        help="Filename of centerline to use for the propagation. Use format .txt or .nii; see file structure in "
              "documentation.\n"
              "Replace filename by 'viewer' to use interactive viewer for providing centerline. Example: "
              "-init-centerline viewer"
@@ -292,7 +292,7 @@ def get_parser():
     optional.add_argument(
         '-init-mask',
         metavar=Metavar.file,
-        help="R|Mask containing three center of the spinal cord, used to initiate the propagation.\n"
+        help="Mask containing three center of the spinal cord, used to initiate the propagation.\n"
              "Replace filename by 'viewer' to use interactive viewer for providing mask. Example: -init-mask viewer"
     )
     optional.add_argument(

spinalcordtoolbox/scripts/sct_register_multimodal.py

@@ -157,7 +157,7 @@ def get_parser():
         '-param',
         metavar=Metavar.list,
         type=list_type(':', str),
-        help=(f"R|Parameters for registration. Separate arguments with \",\". Separate steps with \":\".\n"
+        help=(f"Parameters for registration. Separate arguments with \",\". Separate steps with \":\".\n"
               f"Example: step=1,type=seg,algo=slicereg,metric=MeanSquares:step=2,type=im,algo=syn,metric=MI,iter=5,"
               f"shrink=2\n"
               f"  - step: <int> Step number (starts at 1, except for type=label).\n"