STYLE: multiply_stack_with_mask -> multiply application

niftymic/application/multiply.py

@@ -0,0 +1,47 @@
+##
+# \file multiply.py
+# \brief      Script multiply images with each other.
+#
+# \author     Michael Ebner (michael.ebner.14@ucl.ac.uk)
+# \date       October 2017
+#
+
+import os
+import SimpleITK as sitk
+
+import pysitk.python_helper as ph
+
+import niftymic.base.data_writer as dw
+from niftymic.utilities.input_arparser import InputArgparser
+
+
+def main():
+
+    input_parser = InputArgparser(
+        description="Multiply images. "
+        "Pixel type is determined by first given image.",
+    )
+
+    input_parser.add_filenames(required=True)
+    input_parser.add_output(required=True)
+    input_parser.add_verbose(default=0)
+
+    args = input_parser.parse_args()
+    input_parser.print_arguments(args)
+
+    if len(args.filenames) < 2:
+        raise IOError("At least two images must be provided")
+
+    out_sitk = sitk.ReadImage(args.filenames[0])
+    for f in args.filenames[1:]:
+        im_sitk = sitk.Cast(sitk.ReadImage(f), out_sitk.GetPixelIDValue())
+        out_sitk = out_sitk * im_sitk
+
+    dw.DataWriter.write_image(out_sitk, args.output)
+
+    if args.verbose:
+        args.filenames.insert(0, args.output)
+        ph.show_niftis(args.filenames)
+
+if __name__ == '__main__':
+    main()

niftymic/application/run_reconstruction_pipeline.py

@@ -193,7 +193,7 @@ def main():
             dir_motion_correction = os.path.join(
                 dir_output_recon_subject_space, "motion_correction")
             cmd_args = ["niftymic_reconstruct_volume_from_slices"]
-            cmd_args.append("--filenames %s" % (" ").join(args.filenames_masks))
+            cmd_args.append("--filenames %s" % " ".join(args.filenames_masks))
             cmd_args.append("--dir-input-mc %s" % dir_motion_correction)
             cmd_args.append("--output %s" % srr_subject_mask)
             cmd_args.append("--reconstruction-space %s" % srr_subject)
@@ -280,7 +280,7 @@ def main():
             dir_motion_correction = os.path.join(
                 dir_output_recon_template_space, "motion_correction")
             cmd_args = ["niftymic_reconstruct_volume_from_slices"]
-            cmd_args.append("--filenames %s" % (" ").join(args.filenames_masks))
+            cmd_args.append("--filenames %s" % " ".join(args.filenames_masks))
             cmd_args.append("--dir-input-mc %s" % dir_motion_correction)
             cmd_args.append("--output %s" % srr_template_mask)
             cmd_args.append("--reconstruction-space %s" % srr_template)
@@ -305,13 +305,16 @@ def main():
             raise RuntimeError("Copy of SRR to output directory failed")
 
         # Multiply template mask with reconstruction
-        cmd_args = []
-        cmd_args.append("--filename %s" % path_to_output)
-        cmd_args.append("--gestational-age %d" % gestational_age)
-        cmd_args.append("--verbose %s" % args.verbose)
-        cmd_args.append("--dir-input-templates %s " % args.dir_input_templates)
-        cmd = "niftymic_multiply_stack_with_mask %s" % (
-            " ").join(cmd_args)
+        cmd_args = ["niftymic_multiply"]
+        fnames = [
+            srr_template,
+            srr_template_mask,
+        ]
+        output_masked = "Masked_%s" % output
+        path_to_output_masked = os.path.join(args.dir_output, output_masked)
+        cmd_args.append("--filenames %s" % " ".join(fnames))
+        cmd_args.append("--output %s" % path_to_output_masked)
+        cmd = (" ").join(cmd_args)
         exit_code = ph.execute_command(cmd)
         if exit_code != 0:
             raise RuntimeError("SRR brain masking failed")

niftymic_multiply_stack_with_mask.py → niftymic_multiply.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 import sys
 
-from niftymic.application.multiply_stack_with_mask import main
+from niftymic.application.multiply import main
 
 if __name__ == "__main__":
     sys.exit(main())

setup.py

@@ -100,7 +100,7 @@ def install_requires(fname="requirements.txt"):
               'niftymic_reconstruct_volume = niftymic.application.reconstruct_volume:main',
               'niftymic_reconstruct_volume_from_slices = niftymic.application.reconstruct_volume_from_slices:main',
               'niftymic_register_image = niftymic.application.register_image:main',
-              'niftymic_multiply_stack_with_mask = niftymic.application.multiply_stack_with_mask:main',
+              'niftymic_multiply = niftymic.application.multiply:main',
               'niftymic_run_reconstruction_parameter_study = niftymic.application.run_reconstruction_parameter_study:main',
               'niftymic_run_reconstruction_pipeline = niftymic.application.run_reconstruction_pipeline:main',
               'niftymic_nifti2dicom = niftymic.application.nifti2dicom:main',