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Merge pull request #14 from ofgulban/master
pep 8 & pep 257 style improvements and some cleanup
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| # Byte-compiled / optimized / DLL files | ||
| __pycache__/ | ||
| *.py[cod] | ||
| *$py.class | ||
|
|
||
| # C extensions | ||
| *.so | ||
|
|
||
| # Distribution / packaging | ||
| .Python | ||
| build/ | ||
| develop-eggs/ | ||
| dist/ | ||
| downloads/ | ||
| eggs/ | ||
| .eggs/ | ||
| lib/ | ||
| lib64/ | ||
| parts/ | ||
| sdist/ | ||
| var/ | ||
| wheels/ | ||
| *.egg-info/ | ||
| .installed.cfg | ||
| *.egg | ||
| MANIFEST | ||
|
|
||
| # PyInstaller | ||
| # Usually these files are written by a python script from a template | ||
| # before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
| *.manifest | ||
| *.spec | ||
|
|
||
| # Installer logs | ||
| pip-log.txt | ||
| pip-delete-this-directory.txt | ||
|
|
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| # Unit test / coverage reports | ||
| htmlcov/ | ||
| .tox/ | ||
| .coverage | ||
| .coverage.* | ||
| .cache | ||
| nosetests.xml | ||
| coverage.xml | ||
| *.cover | ||
| .hypothesis/ | ||
|
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||
| # Translations | ||
| *.mo | ||
| *.pot | ||
|
|
||
| # Django stuff: | ||
| *.log | ||
| .static_storage/ | ||
| .media/ | ||
| local_settings.py | ||
|
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| # Flask stuff: | ||
| instance/ | ||
| .webassets-cache | ||
|
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| # Scrapy stuff: | ||
| .scrapy | ||
|
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| # Sphinx documentation | ||
| docs/_build/ | ||
|
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| # PyBuilder | ||
| target/ | ||
|
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| # Jupyter Notebook | ||
| .ipynb_checkpoints | ||
|
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| # pyenv | ||
| .python-version | ||
|
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| # celery beat schedule file | ||
| celerybeat-schedule | ||
|
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| # SageMath parsed files | ||
| *.sage.py | ||
|
|
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| # Environments | ||
| .env | ||
| .venv | ||
| env/ | ||
| venv/ | ||
| ENV/ | ||
| env.bak/ | ||
| venv.bak/ | ||
|
|
||
| # Spyder project settings | ||
| .spyderproject | ||
| .spyproject | ||
|
|
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| # Rope project settings | ||
| .ropeproject | ||
|
|
||
| # mkdocs documentation | ||
| /site | ||
|
|
||
| # mypy | ||
| .mypy_cache/ |
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|---|---|---|
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| """ | ||
| util scripts for pydeface | ||
| """ | ||
| """Utility scripts for pydeface.""" | ||
|
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| import sys | ||
| import subprocess | ||
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| def run_shell_cmd(cmd,cwd=[]): | ||
| """ run a command in the shell using Popen | ||
| """ | ||
| 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) | ||
| 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() | ||
| print(line.strip()) | ||
| process.wait() | ||
|
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|
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| def usage(): | ||
| """ print the docstring and exit""" | ||
| """Print the docstring and exit.""" | ||
| sys.stdout.write(__doc__) | ||
| sys.exit(2) |
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| #!/usr/bin/env python | ||
| """ deface an image using FSL | ||
| USAGE: deface <filename to deface> <optional: outfilename> | ||
| """ | ||
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| ## Copyright 2011, Russell Poldrack. All rights reserved. | ||
|
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| ## Redistribution and use in source and binary forms, with or without modification, are | ||
| ## permitted provided that the following conditions are met: | ||
| """Deface an image using FSL. | ||
| ## 1. Redistributions of source code must retain the above copyright notice, this list of | ||
| ## conditions and the following disclaimer. | ||
|
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| ## 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. | ||
|
|
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| ## 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. | ||
| Usage: | ||
| ------ | ||
| pydeface.py <filename to deface> <optional: outfilename> | ||
| """ | ||
|
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| # 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. | ||
|
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| import nibabel | ||
| import os,sys | ||
| import numpy as N | ||
| import os | ||
| import sys | ||
| import tempfile | ||
| import subprocess | ||
| import inspect | ||
| from nipype.interfaces import fsl | ||
| from pkg_resources import resource_filename,Requirement | ||
|
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| 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 usage(): | ||
| """ print the docstring and exit""" | ||
| sys.stdout.write(__doc__) | ||
| sys.exit(2) | ||
| from pkg_resources import resource_filename, Requirement, require | ||
|
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| def main(): | ||
| cleanup=True | ||
| verbose=False | ||
| scriptdir=os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) # script directory | ||
|
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| template=resource_filename(Requirement.parse("pydeface"), 'pydeface/data/mean_reg2mean.nii.gz') | ||
| facemask=resource_filename(Requirement.parse("pydeface"), "pydeface/data/facemask.nii.gz") | ||
|
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| try: | ||
| assert os.path.exists(facemask) | ||
| except: | ||
| raise Exception('missing facemask: %s'%facemask) | ||
| cleanup, verbose = True, False | ||
|
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| try: | ||
| assert os.path.exists(template) | ||
| except: | ||
| raise Exception('missing template: %s'%template) | ||
| template = resource_filename(Requirement.parse("pydeface"), | ||
| "pydeface/data/mean_reg2mean.nii.gz") | ||
| facemask = resource_filename(Requirement.parse("pydeface"), | ||
| "pydeface/data/facemask.nii.gz") | ||
|
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| 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) | ||
|
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| if len(sys.argv)<2: | ||
| usage() | ||
| if len(sys.argv) < 2: | ||
| sys.stdout.write(__doc__) | ||
| sys.exit(2) | ||
| else: | ||
| infile=sys.argv[1] | ||
| infile = sys.argv[1] | ||
|
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| 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) | ||
| except: | ||
| raise Exception('%s already exists, remove it first'%outfile) | ||
|
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| if 'FSLDIR' in os.environ: | ||
| FSLDIR=os.environ['FSLDIR'] | ||
| if len(sys.argv) > 2: | ||
| outfile = sys.argv[2] | ||
| else: | ||
| print('FSL must be installed and FSLDIR environment variable must be defined') | ||
| sys.exit(2) | ||
| outfile = infile.replace('.nii', '_defaced.nii') | ||
|
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| if os.path.exists(outfile): | ||
| raise Exception('%s already exists, remove it first.' % outfile) | ||
|
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| if 'FSLDIR' not in os.environ: | ||
| raise Exception("FSL must be installed and " | ||
| "FSLDIR environment variable must be defined.") | ||
| sys.exit(2) | ||
|
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| foo,tmpmat=tempfile.mkstemp() | ||
| tmpmat=tmpmat+'.mat' | ||
| foo,tmpfile=tempfile.mkstemp() | ||
| tmpfile=tmpfile+'.nii.gz' | ||
| _, tmpmat = tempfile.mkstemp() | ||
| tmpmat = tmpmat + '.mat' | ||
| _, tmpfile = tempfile.mkstemp() | ||
| tmpfile = tmpfile + '.nii.gz' | ||
| if verbose: | ||
| print(tmpmat) | ||
| print(tmpfile) | ||
| foo,tmpfile2=tempfile.mkstemp() | ||
| foo,tmpmat2=tempfile.mkstemp() | ||
| _, tmpfile2 = tempfile.mkstemp() | ||
| _, tmpmat2 = tempfile.mkstemp() | ||
|
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| print(('defacing', infile)) | ||
| # register template to infile | ||
| print('Defacing...\n%s' % infile) | ||
|
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| 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 | ||
| # register template to infile | ||
| 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.run() | ||
|
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| # 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 = 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() | ||
|
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| # multiply mask by infile and save | ||
|
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| 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()) | ||
| 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) | ||
|
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| if cleanup: | ||
| os.remove(tmpfile) | ||
| os.remove(tmpfile2) | ||
| os.remove(tmpmat) | ||
|
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| print('Output saved as:\n%s' % outfile) | ||
|
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| if __name__ == "__main__": | ||
| welcome_str = 'pydeface ' + require("pydeface")[0].version | ||
| welcome_decor = '-' * len(welcome_str) | ||
| print(welcome_decor + '\n' + welcome_str + '\n' + welcome_decor) | ||
| main() |
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