Merge ff61f5c into 2193729

setup.py

@@ -21,6 +21,7 @@
         'console_scripts': [
             "st_download_data=shimmingtoolbox.cli.download_data:download_data",
             "st_dicom_to_nifti=shimmingtoolbox.cli.dicom_to_nifti:dicom_to_nifti_cli",
+            "st_mask=shimmingtoolbox.cli.mask:mask",
         ]
     },
     packages=find_packages(exclude=["docs"]),

shimmingtoolbox/cli/mask.py

@@ -0,0 +1,186 @@
+#!/usr/bin/env python3
+
+import click
+import nibabel as nib
+import numpy as np
+import os
+import sys
+import subprocess
+
+sys.path.insert(1, 'C:/Users/heuss/spinalcordtoolbox')
+# from scripts.sct_create_mask import main as sct_mask
+
+from shimmingtoolbox.masking.threshold import threshold
+from shimmingtoolbox.masking.shapes import shape_square
+from shimmingtoolbox.masking.shapes import shape_cube
+
+CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS, help=f"Creates a cube, square or threshold mask.")
+def mask():
+    pass
+
+
+@mask.command(context_settings=CONTEXT_SETTINGS, help=f"Creates a SCT (SpinalCordToolbox) mask from the input file "
+                                                      f"with coordinates process. Returns an output nifti file with "
+                                                      f"SCT mask.")
+@click.option('-input', type=click.File('r'), required=True, help="Complete input path of the nifti file to mask.")
+@click.option('-output', type=click.Path(), default=os.curdir, help="Name of output mask, Example: data.nii.")
+@click.option('-size', default='41', help="Size of the mask in the axial plane, given in pixel (Example: 35) or in "
+                                          "millimeter (Example: 35mm). If shape=gaussian, size corresponds to sigma ("
+                                          "Example: 45).")
+@click.option('-shape', type=click.Choice(['cylinder', 'box', 'gaussian']), default='cylinder',
+              help="Shape of the mask: cylinder, box or gaussian.")
+@click.option('-remove', type=click.IntRange(0, 1), default=1, help="Remove temporary files.")
+@click.option('-verbose', type=click.IntRange(0, 2), default=1, help="Verbose: 0 = nothing, 1 = classic, 2 = expended.")
+@click.option('-process', required=True, help='<coord,XxY>: Center mask at the X,Y coordinates. (e.g. "coord,20x15")')
+def sct_coord(input, output, size, shape, remove, verbose, process):
+    """
+        Creates a SCT (SpinalCordToolbox) mask from the input file with coordinates process. Returns an output nifti
+        file with SCT mask.
+
+        Args:
+            input (file): Input nifti file to mask. Must be 3D. Example: data.nii.gz
+            output (str): Name of output mask, Example: data.nii.
+            size: Size of the mask in the axial plane, given in pixel (Example: 35) or in millimeter (Example:
+                    35mm). If shape=gaussian, size corresponds to sigma (Example: 45). (default: 41).
+            shape (str): Shape of the mask (default: cylinder).
+            remove (int): Remove temporary files (default: 1).
+            verbose (int): Verbose: 0 = nothing, 1 = classic, 2 = expended (default: 1).
+            process (str): Process to generate mask.
+                          <coord,XxY>: Center mask at the X,Y coordinates. (e.g.
+                          "coord,20x15")
+
+        Returns:
+            output (str): Output nifti file with SCT mask.
+        """
+    subprocess.run(['sct_create_mask', '-i', input, '-p', 'coord', process, '-size', size, '-f', shape, 'o', output,
+                    '-r', remove, '-v', verbose], check=True)
+    click.echo('The path to the output nifti file (mask.nii.gz) that contains the mask is: %s'
+               % os.path.abspath(output))
+    return output
+
+
+@mask.command(context_settings=CONTEXT_SETTINGS, help=f"Creates a SCT (SpinalCordToolbox) mask from the input file "
+                                                      f"with point process. Returns an output nifti file with "
+                                                      f"SCT mask.")
+@click.option('-input', type=click.File('r'), required=True, help="Complete input path of the nifti file to mask.")
+@click.option('-output', type=click.Path(), default=os.curdir, help="Name of output mask, Example: data.nii.")
+@click.option('-size', default='41', help="Size of the mask in the axial plane, given in pixel (Example: 35) or in "
+                                          "millimeter (Example: 35mm). If shape=gaussian, size corresponds to sigma ("
+                                          "Example: 45).")
+@click.option('-shape', type=click.Choice(['cylinder', 'box', 'gaussian']), default='cylinder',
+              help="Shape of the mask: cylinder, box or gaussian.")
+@click.option('-remove', type=click.IntRange(0, 1), default=1, help="Remove temporary files.")
+@click.option('-verbose', type=click.IntRange(0, 2), default=1, help="Verbose: 0 = nothing, 1 = classic, 2 = expended.")
+@click.option('-process', type=click.File('r'), required=True,
+              help='<point,FILE>: Center mask at the X,Y coordinates of the label defined in input volume FILE. ('
+                   'e.g."point,label.nii.gz")')
+def sct_point(input, output, size, shape, remove, verbose, process):
+    """
+        Creates a SCT (SpinalCordToolbox) mask from the input file with point process. Returns an output nifti file with
+         SCT mask.
+
+        Args:
+            input (file): Input nifti file to mask. Must be 3D. Example: data.nii.gz
+            output (str): Name of output mask, Example: data.nii.
+            size: Size of the mask in the axial plane, given in pixel (Example: 35) or in millimeter (Example:
+                    35mm). If shape=gaussian, size corresponds to sigma (Example: 45). (default: 41).
+            shape (str): Shape of the mask (default: cylinder).
+            remove (int): Remove temporary files (default: 1).
+            verbose (int): Verbose: 0 = nothing, 1 = classic, 2 = expended (default: 1).
+            process (str): Process to generate mask.
+                          <point,FILE>: Center mask at the X,Y coordinates of
+                          the label defined in input volume FILE. (e.g.
+                          "point,label.nii.gz")
+
+        Returns:
+            output (str): Output nifti file with SCT mask.
+        """
+    subprocess.run(['sct_create_mask', '-i', input, '-p', 'point', process, '-size', size, '-f', shape, 'o', output,
+                    '-r', remove, '-v', verbose], check=True)
+    click.echo('The path to the output nifti file (mask.nii.gz) that contains the mask is: %s'
+               % os.path.abspath(output))
+    return output
+
+
+@mask.command(context_settings=CONTEXT_SETTINGS, help=f"Creates a SCT (SpinalCordToolbox) mask from the input file "
+                                                      f"with center process. Returns an output nifti file with "
+                                                      f"SCT mask.")
+@click.option('-input', type=click.File('r'), required=True, help="Complete input path of the nifti file to mask.")
+@click.option('-output', type=click.Path(), default=os.curdir, help="Name of output mask, Example: data.nii.")
+@click.option('-size', default='41', help="Size of the mask in the axial plane, given in pixel (Example: 35) or in "
+                                          "millimeter (Example: 35mm). If shape=gaussian, size corresponds to sigma ("
+                                          "Example: 45).")
+@click.option('-shape', type=click.Choice(['cylinder', 'box', 'gaussian']), default='cylinder',
+              help="Shape of the mask: cylinder, box or gaussian.")
+@click.option('-remove', type=click.IntRange(0, 1), default=1, help="Remove temporary files.")
+@click.option('-verbose', type=click.IntRange(0, 2), default=1, help="Verbose: 0 = nothing, 1 = classic, 2 = expended.")
+def sct_center(input, output, size, shape, remove, verbose):
+    """
+        Creates a SCT (SpinalCordToolbox) mask from the input file with center process. Returns an output nifti file
+        with SCT mask.
+
+        Args:
+            input (file): Input nifti file to mask. Must be 3D. Example: data.nii.gz
+            output (str): Name of output mask, Example: data.nii.
+            size: Size of the mask in the axial plane, given in pixel (Example: 35) or in millimeter (Example:
+                    35mm). If shape=gaussian, size corresponds to sigma (Example: 45). (default: 41).
+            shape (str): Shape of the mask (default: cylinder).
+            remove (int): Remove temporary files (default: 1).
+            verbose (int): Verbose: 0 = nothing, 1 = classic, 2 = expended (default: 1).
+
+
+        Returns:
+            output (str): Output nifti file with SCT mask.
+        """
+    subprocess.run(['sct_create_mask', '-i', input, '-p', 'center', '-size', size, '-f', shape, 'o', output, '-r',
+                    remove, '-v', verbose], check=True)
+    click.echo('The path to the output nifti file (mask.nii.gz) that contains the mask is: %s'
+               % os.path.abspath(output))
+    return output
+
+
+@mask.command(context_settings=CONTEXT_SETTINGS, help=f"Creates a SCT (SpinalCordToolbox) mask from the input file "
+                                                      f"with centerline process. Returns an output nifti file with "
+                                                      f"SCT mask.")
+@click.option('-input', type=click.File('r'), required=True, help="Complete input path of the nifti file to mask.")
+@click.option('-output', type=click.Path(), default=os.curdir, help="Name of output mask, Example: data.nii.")
+@click.option('-size', default='41', help="Size of the mask in the axial plane, given in pixel (Example: 35) or in "
+                                          "millimeter (Example: 35mm). If shape=gaussian, size corresponds to sigma ("
+                                          "Example: 45).")
+@click.option('-shape', type=click.Choice(['cylinder', 'box', 'gaussian']), default='cylinder',
+              help="Shape of the mask: cylinder, box or gaussian.")
+@click.option('-remove', type=click.IntRange(0, 1), default=1, help="Remove temporary files.")
+@click.option('-verbose', type=click.IntRange(0, 2), default=1, help="Verbose: 0 = nothing, 1 = classic, 2 = expended.")
+@click.option('-process', type=click.File('r'), required=True,
+              help='<centerline,FILE>: At each slice, the mask is centered at the spinal cord centerline, defined by '
+                   'the input segmentation FILE. (e.g. "centerline,t2_seg.nii.gz")')
+def sct_centerline(input, output, size, shape, remove, verbose, process):
+    """
+        Creates a SCT (SpinalCordToolbox) mask from the input file with centerline process. Returns an output nifti file
+         with SCT mask.
+
+        Args:
+            input (file): Input nifti file to mask. Must be 3D. Example: data.nii.gz
+            output (str): Name of output mask, Example: data.nii.
+            size: Size of the mask in the axial plane, given in pixel (Example: 35) or in millimeter (Example:
+                    35mm). If shape=gaussian, size corresponds to sigma (Example: 45). (default: 41).
+            shape (str): Shape of the mask (default: cylinder).
+            remove (int): Remove temporary files (default: 1).
+            verbose (int): Verbose: 0 = nothing, 1 = classic, 2 = expended (default: 1).
+            process (str): Process to generate mask.
+                          <centerline,FILE>: At each slice, the mask is centered
+                          at the spinal cord centerline, defined by the input
+                          segmentation FILE. (e.g. "centerline,t2_seg.nii.gz")
+                          (default: center)
+
+        Returns:
+            output (str): Output nifti file with SCT mask.
+        """
+    subprocess.run(['sct_create_mask', '-i', input, '-p', 'centerline', process, '-size', size, '-f', shape, 'o',
+                    output, '-r', remove, '-v', verbose], check=True)
+    click.echo('The path to the output nifti file (mask.nii.gz) that contains the mask is: %s'
+               % os.path.abspath(output))
+    return output