Additional flags used to deface 7T data

README.md

@@ -1,4 +1,4 @@
-Defacing tool for nifti images.  
+Defacing tool for nifti images.
 
 ### Requirements:
 - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)
@@ -14,5 +14,10 @@ python setup.py install
 
 ### To use:
 ```
-pydeface.py infile.nii.gz
+pydeface infile.nii.gz
+```
+
+Also see the help for additional options:
+```
+pydeface --help
 ```

pydeface/__main__.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python
+"""Defacing utility for MRI images."""
+
+# Copyright 2011, Russell Poldrack. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#    1. Redistributions of source code must retain the above copyright notice,
+#       this list of conditions and the following disclaimer.
+#    2. Redistributions in binary form must reproduce the above copyright
+#       notice, this list of conditions and the following disclaimer in the
+#       documentation and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY RUSSELL POLDRACK ``AS IS'' AND ANY EXPRESS OR
+# IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+# EVENT SHALL RUSSELL POLDRACK OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+import argparse
+import os
+import tempfile
+from nipype.interfaces import fsl
+from nibabel import load, Nifti1Image
+from pkg_resources import require
+from pydeface.utils import initial_checks, output_checks
+
+
+def main():
+    """Command line call argument parsing."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        'infile', metavar='path',
+        help="Path to input nifti.")
+
+    parser.add_argument(
+        "--outfile", metavar='path', required=False,
+        help="If not provided adds '_defaced' suffix.")
+
+    parser.add_argument(
+        "--force", action='store_true',
+        help="Force to rewrite the output even if it exists.")
+
+    parser.add_argument(
+        '--applyto', nargs='+', required=False, metavar='',
+        help="Apply the created face mask to other images. Can take multiple "
+             "arguments.")
+
+    parser.add_argument(
+        "--cost", metavar='mutualinfo', required=False, default='mutualinfo',
+        help="FSL-FLIRT cost function. Default is 'mutualinfo'.")
+
+    parser.add_argument(
+        "--template", metavar='path', required=False,
+        help=("Optional template image that will be used as the registration "
+              "target instead of the default."))
+
+    parser.add_argument(
+        "--facemask", metavar='path', required=False,
+        help="Optional face mask image that will be used instead of the "
+             "default.")
+
+    parser.add_argument(
+        "--nocleanup", action='store_true',
+        help="Do not cleanup temporary files. Off by default.")
+
+    parser.add_argument(
+        "--verbose", action='store_true',
+        help="Show additional status prints. Off by default.")
+
+    welcome_str = 'pydeface ' + require("pydeface")[0].version
+    welcome_decor = '-' * len(welcome_str)
+    print(welcome_decor + '\n' + welcome_str + '\n' + welcome_decor)
+
+    args = parser.parse_args()
+    template, facemask = initial_checks(args.template, args.facemask)
+    infile = args.infile
+    outfile = output_checks(infile, args.outfile, args.force)
+
+    # temporary files
+    _, tmpmat = tempfile.mkstemp()
+    tmpmat = tmpmat + '.mat'
+    _, tmpfile = tempfile.mkstemp()
+    tmpfile = tmpfile + '.nii.gz'
+    if args.verbose:
+        print("Temporary files:\n  %s\n  %s" % (tmpmat, tmpfile))
+    _, tmpfile2 = tempfile.mkstemp()
+    _, tmpmat2 = tempfile.mkstemp()
+
+    print('Defacing...\n  %s' % args.infile)
+
+    # register template to infile
+    flirt = fsl.FLIRT()
+    flirt.inputs.cost_func = args.cost
+    flirt.inputs.in_file = template
+    flirt.inputs.out_matrix_file = tmpmat
+    flirt.inputs.out_file = tmpfile2
+    flirt.inputs.reference = infile
+    flirt.run()
+
+    # warp facemask to infile
+    flirt = fsl.FLIRT()
+    flirt.inputs.in_file = facemask
+    flirt.inputs.in_matrix_file = tmpmat
+    flirt.inputs.apply_xfm = True
+    flirt.inputs.reference = infile
+    flirt.inputs.out_file = tmpfile
+    flirt.inputs.out_matrix_file = tmpmat2
+    flirt.run()
+
+    # multiply mask by infile and save
+    infile_img = load(infile)
+    tmpfile_img = load(tmpfile)
+    outdata = infile_img.get_data() * tmpfile_img.get_data()
+    outfile_img = Nifti1Image(outdata, infile_img.get_affine(),
+                              infile_img.get_header())
+    outfile_img.to_filename(outfile)
+    print("Defaced image saved as:\n  %s" % outfile)
+
+    # apply mask to other given images
+    if args.applyto is not None:
+        print("Defacing mask also applied to:")
+        for applyfile in args.applyto:
+            applyfile_img = load(applyfile)
+            outdata = applyfile_img.get_data() * tmpfile_img.get_data()
+            applyfile_img = Nifti1Image(outdata, applyfile_img.get_affine(),
+                                        applyfile_img.get_header())
+            outfile = output_checks(applyfile)
+            applyfile_img.to_filename(outfile)
+            print('  %s' % applyfile)
+
+    if args.nocleanup:
+        pass
+    else:
+        os.remove(tmpfile)
+        os.remove(tmpfile2)
+        os.remove(tmpmat)
+
+    print('Finished.')
+
+
+if __name__ == "__main__":
+    main()

pydeface/utils.py

@@ -1,22 +1,43 @@
 """Utility scripts for pydeface."""
 
+import os
 import sys
-import subprocess
+from pkg_resources import resource_filename, Requirement
 
 
-def run_shell_cmd(cmd, cwd=[]):
-    """Run a command in the shell using Popen."""
-    if cwd:
-        process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
-                                   cwd=cwd)
-    else:
-        process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
-    for line in process.stdout:
-        print(line.strip())
-    process.wait()
+def initial_checks(template=None, facemask=None):
+    """Initial sanity checks."""
+    if template is None:
+        template = resource_filename(Requirement.parse("pydeface"),
+                                     "pydeface/data/mean_reg2mean.nii.gz")
+    if facemask is None:
+        facemask = resource_filename(Requirement.parse("pydeface"),
+                                     "pydeface/data/facemask.nii.gz")
+
+    if not os.path.exists(template):
+        raise Exception('Missing template: %s' % template)
+    if not os.path.exists(facemask):
+        raise Exception('Missing face mask: %s' % facemask)
+
+    if 'FSLDIR' not in os.environ:
+        raise Exception("FSL must be installed and "
+                        "FSLDIR environment variable must be defined.")
+        sys.exit(2)
+    return template, facemask
 
 
-def usage():
-    """Print the docstring and exit."""
-    sys.stdout.write(__doc__)
-    sys.exit(2)
+def output_checks(infile, outfile=None, force=False):
+    """Determine output file name."""
+    if force is None:
+        force = False
+    if outfile is None:
+        outfile = infile.replace('.nii', '_defaced.nii')
+
+    if os.path.exists(outfile) and force:
+        print('Previous output will be overwritten.')
+    elif os.path.exists(outfile):
+        raise Exception("%s already exists. Remove it first or use '--force' "
+                        "flag to overwrite." % outfile)
+    else:
+        pass
+    return outfile

setup.py

@@ -4,6 +4,8 @@
 #
 # Some portions were borrowed from:
 # https://github.com/mwaskom/lyman/blob/master/setup.py
+# and:
+# https://chriswarrick.com/blog/2014/09/15/python-apps-the-right-way-entry_points-and-scripts/
 
 import os
 from setuptools import setup
@@ -15,7 +17,7 @@
 LICENSE = 'MIT'
 URL = 'http://poldracklab.org'
 DOWNLOAD_URL = 'https://github.com/poldracklab/pydeface/'
-VERSION = '1.1'
+VERSION = '2.0'
 
 if os.path.exists('MANIFEST'):
     os.remove('MANIFEST')
@@ -33,12 +35,15 @@
       download_url=DOWNLOAD_URL,
       packages=['pydeface'],
       package_data=datafiles,
-      scripts=['scripts/pydeface.py'],
       classifiers=['Intended Audience :: Science/Research',
                    'Programming Language :: Python :: 2.7',
                    'License :: OSI Approved :: BSD License',
                    'Operating System :: POSIX',
                    'Operating System :: Unix',
                    'Operating System :: MacOS'],
       install_requires=['numpy', 'nibabel', 'nipype'],
+      entry_points={
+            'console_scripts': [
+                'pydeface = pydeface.__main__:main'
+                ]},
       )