Blur face

README.md

@@ -5,12 +5,12 @@ Requirements:
 - nibabel
 - nipype
 
-####To install:
+#### To install:
 
 * git clone https://github.com/poldracklab/pydeface.git
 * cd pydeface
 * python setup.py install
 
-####To use:
+#### To use:
 
 pydeface.py infile.nii.gz

scripts/pydeface.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
-""" deface an image using FSL
-USAGE:  deface <filename to deface> <optional: outfilename>
+"""
+deface an image using FSL
+USAGE:  deface -i <filename to deface> -o [output filename]
 """
 
 ## Copyright 2011, Russell Poldrack. All rights reserved.
@@ -26,118 +27,154 @@
 ## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 
-
-import nibabel
-import os,sys
-import numpy as N
+import os
+import sys
 import tempfile
 import subprocess
 import inspect
+import argparse
+import nibabel
+from scipy import ndimage as nd
 from nipype.interfaces import fsl
-from pkg_resources import resource_filename,Requirement
+from pkg_resources import resource_filename, Requirement
+
 
 def run_shell_cmd(cmd,cwd=[]):
-    """ run a command in the shell using Popen
+    """
+    Run a command in the shell using Popen
     """
     if cwd:
-        process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,cwd=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()
+        print(line.strip())
 
-def usage():
-    """ print the docstring and exit"""
-    sys.stdout.write(__doc__)
-    sys.exit(2)
+    process.wait()
 
 
 def main():
-    cleanup=True
-    verbose=False
-    scriptdir=os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) # script directory
 
-    template=resource_filename(Requirement.parse("pydeface"), 'pydeface/data/mean_reg2mean.nii.gz')
-    facemask=resource_filename(Requirement.parse("pydeface"), "pydeface/data/facemask.nii.gz")
+    # T1w template and face mask locations
+    T1w_template = resource_filename(Requirement.parse("pydeface"), 'pydeface/data/T1w_template.nii.gz')
+    facemask = resource_filename(Requirement.parse("pydeface"), "pydeface/data/facemask.nii.gz")
 
-    try:
-        assert os.path.exists(facemask)
-    except:
-        raise Exception('missing facemask: %s'%facemask)
 
     try:
-        assert os.path.exists(template)
+        assert os.path.exists(T1w_template)
     except:
-        raise Exception('missing template: %s'%template)
-
-
-
-    if len(sys.argv)<2:
-        usage()
-        sys.exit(2)
-    else:
-        infile=sys.argv[1]
+        raise Exception('*** Missing template : %s'%T1w_template)
 
-    if len(sys.argv)>2:
-        outfile=sys.argv[2]
-    else:
-        outfile=infile.replace('.nii.gz','_defaced.nii.gz')
     try:
-        assert not os.path.exists(outfile)
+        assert os.path.exists(facemask)
     except:
-        raise Exception('%s already exists, remove it first'%outfile)
+        raise Exception('*** Missing facemask : %s'%facemask)
 
+    # Check that FSLDIR is set
     if 'FSLDIR' in os.environ:
         FSLDIR=os.environ['FSLDIR']
     else:
         print('FSL must be installed and FSLDIR environment variable must be defined')
         sys.exit(2)
 
+    # Command line argument parser
+    parser = argparse.ArgumentParser(description='Remove facial structure from MRI images')
+    parser.add_argument('-i', '--infile', required=True, help='T1w input image')
+    parser.add_argument('-o', '--outfile', required=False, help='Defaced output image [<infile>_defaced.nii.gz]')
+    parser.add_argument('-s', '--scalefactor', required=False, help='Voxelation scale factor [8.0]')
+
+    # Parse command line arguments
+    args = parser.parse_args()
+
+    # Input T1w image filename
+    T1w_fname = args.infile
+
+    # Create output filename if not supplied
+    if args.outfile:
+        T1w_defaced_fname = args.outfile
+    else:
+        T1w_defaced_fname = T1w_fname.replace('.nii.gz','_defaced.nii.gz')
+
+    if args.scalefactor:
+        vox_sf = float(args.scalefactor)
+    else:
+        vox_sf = 8.0
+
+    # Check if output file already exists
+    if os.path.isfile(T1w_defaced_fname):
+        print('%s already exists - remove it first' % T1w_defaced_fname)
+        sys.exit(1)
 
-    foo,tmpmat=tempfile.mkstemp()
-    tmpmat=tmpmat+'.mat'
-    foo,tmpfile=tempfile.mkstemp()
-    tmpfile=tmpfile+'.nii.gz'
-    if verbose:
-        print(tmpmat)
-        print(tmpfile)
-    foo,tmpfile2=tempfile.mkstemp()
-    foo,tmpmat2=tempfile.mkstemp()
+    # Temporary template to individual affine transform matrix
+    _, temp2ind_mat_fname = tempfile.mkstemp()
+    temp2ind_mat_fname += '.mat'
 
-    print(('defacing', infile))
-    # register template to infile
+    # Temporal face mask in individual space
+    _, indmask_fname_fname = tempfile.mkstemp()
+    indmask_fname_fname += '.nii.gz'
 
-    flirt=fsl.FLIRT()
+    # Dummy output data
+    _, dummy_img_fname = tempfile.mkstemp()
+    _, dummy_mat_fname = tempfile.mkstemp()
+
+    print('Defacing %s' % T1w_fname)
+
+    # Register template to infile
+    print('Registering template to individual space')
+    flirt = fsl.FLIRT()
     flirt.inputs.cost_func='mutualinfo'
-    flirt.inputs.in_file=template
-    flirt.inputs.out_matrix_file=tmpmat
-    flirt.inputs.out_file=tmpfile2
-    flirt.inputs.reference=infile
+    flirt.inputs.in_file = T1w_template
+    flirt.inputs.out_matrix_file = temp2ind_mat_fname
+    flirt.inputs.reference = T1w_fname
+    flirt.inputs.out_file = dummy_img_fname
     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
+    # Affine transform facemask to infile
+    print('Resampling face mask to individual space')
+    flirt = fsl.FLIRT()
+    flirt.inputs.in_file = facemask
+    flirt.inputs.in_matrix_file = temp2ind_mat_fname
+    flirt.inputs.apply_xfm = True
+    flirt.inputs.reference = T1w_fname
+    flirt.inputs.out_file = indmask_fname_fname
+    flirt.inputs.out_matrix_file = dummy_mat_fname
     flirt.run()
 
-    # multiply mask by infile and save
-
-    infile_img=nibabel.load(infile)
-    tmpfile_img=nibabel.load(tmpfile)
-    outdata=infile_img.get_data()*tmpfile_img.get_data()
-    outfile_img=nibabel.Nifti1Image(outdata,infile_img.get_affine(),infile_img.get_header())
-    outfile_img.to_filename(outfile)
+    # Load T1w input image
+    print('Loading T1w image : %s' % T1w_fname)
+    T1w_nii = nibabel.load(T1w_fname)
+    T1w_img = T1w_nii.get_data()
+
+    # Voxelate T1w image
+    # 1. Cubic downsample
+    # 2. Nearest neighbor upsample
+    print('Voxelating T1w image : scale factor %0.1f' % vox_sf)
+    print('  Spline downsampling')
+    T1w_vox_img = nd.interpolation.zoom(T1w_img, zoom=1.0/vox_sf, order=3)
+    print('  Nearest neighbor upsampling')
+    T1w_vox_img = nd.interpolation.zoom(T1w_vox_img, zoom=vox_sf, order=0)
+
+    # Load individual space face mask
+    indmask_nii = nibabel.load(indmask_fname_fname)
+    indmask_img = indmask_nii.get_data()
+
+    # Replace face area with voxelated version
+    # Note that the face mask is 0 in the face region, 1 elsewhere.
+    print('Anonymizing face area')
+    T1w_defaced_img = T1w_img * indmask_img + T1w_vox_img * (1 - indmask_img)
+
+    # Save defaced image
+    print('Saving defaced image : %s' % T1w_defaced_fname)
+    outfile_img = nibabel.Nifti1Image(T1w_defaced_img, T1w_nii.get_affine(), T1w_nii.get_header())
+    outfile_img.to_filename(T1w_defaced_fname)
+
+    # Cleanup temporary files
+    print('Cleaning up')
+    os.remove(temp2ind_mat_fname)
+    os.remove(indmask_fname_fname)
+    os.remove(dummy_img_fname)
+    os.remove(dummy_mat_fname)
 
-    if cleanup:
-        os.remove(tmpfile)
-        os.remove(tmpfile2)
-        os.remove(tmpmat)
 
 if __name__ == "__main__":
     main()

setup.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
 #
 # Copyright (C) 2013-2015 Russell Poldrack <[email protected]>
 # some portions borrowed from https://github.com/mwaskom/lyman/blob/master/setup.py
@@ -17,13 +17,13 @@
 LICENSE='MIT'
 URL='http://poldracklab.org'
 DOWNLOAD_URL='https://github.com/poldracklab/pydeface/'
-VERSION='1.0'
+VERSION='1.1'
 
 def check_dependencies():
 
     # Just make sure dependencies exist, I haven't rigorously
     # tested what the minimal versions that will work are
-    needed_deps = ["numpy", "nibabel","nipype"]
+    needed_deps = ["numpy", "nibabel", "nipype"]
     missing_deps = []
     for dep in needed_deps:
         try:
@@ -47,7 +47,7 @@ def check_dependencies():
                             'clean'))):
         check_dependencies()
 
-    datafiles = {'pydeface': ['data/facemask.nii.gz','data/mean_reg2mean.nii.gz']}
+    datafiles = {'pydeface': ['data/facemask.nii.gz','data/T1w_template.nii.gz', 'ident.mat']}
 
     setup(name=DISTNAME,
         maintainer=MAINTAINER,