def extract_stats_fsl(data, mask, gmmask, threshold=0.3):
""" uses fsl tools to extract data values in mask,
masks 'mask' with gmmask thresholded at 'threshold' (default 0.3)
returns mean, std, nvoxels
NOTE: generates some tmp files in tempdir, but also removes them"""
tmpdir = tempfile.mkdtemp()
startdir = os.getcwd()
os.chdir(tmpdir)
# first mask mask with thresholded gmmask
pth, nme = os.path.split(mask)
outfile = fname_presuffix(mask, prefix='gmask_', newpath=tmpdir)
c1 = CommandLine('fslmaths %s -thr %2.2f -nan -mul %s %s' %
(gmmask, threshold, mask, outfile)).run()
if not c1.runtime.returncode == 0:
print 'gm masking of mask failed for %s' % (mask)
print 'tmp dir', tmpdir
print c1.runtime.stderr
return None
#first mask data
cmd = 'fslmaths %s -nan -mas %s masked_data' % (data, outfile)
mask_out = CommandLine(cmd).run()
if not mask_out.runtime.returncode == 0:
print 'masking failed for %s' % (data)
return None, None, None
masked = find_single_file('masked*')
# get stats
mean_out = CommandLine('fslstats %s -M' % (masked)).run()
mean = mean_out.runtime.stdout.strip('\n').strip()
std_out = CommandLine('fslstats %s -S' % (masked)).run()
std = std_out.runtime.stdout.strip('\n').strip()
vox_out = CommandLine('fslstats %s -V' % (masked)).run()
vox = vox_out.runtime.stdout.split()[0]
os.chdir(startdir)
rmtree(tmpdir)
return mean, std, vox
def make_cerebellum(aseg):
cwd = os.getcwd()
pth, nme = os.path.split(aseg)
os.chdir(pth)
cl = CommandLine('fslmaths %s -thr 47 -uthr 47 right_cerebellum'% (aseg))
cout = cl.run()
if not cout.runtime.returncode == 0:
os.chdir(cwd)
print 'Unable to create right cerebellum for %s'%(aseg)
return None
cl2 = CommandLine('fslmaths %s -thr 8 -uthr 8 left_cerebellum'% (aseg))
cout2 = cl2.run()
if not cout2.runtime.returncode == 0:
os.chdir(cwd)
print 'Unable to create left cerebellum for %s'%(aseg)
return None
cl3 = CommandLine('fslmaths left_cerebellum -add right_cerebellum -bin grey_cerebellum')
cout3 = cl3.run()
if not cout3.runtime.returncode == 0:
print 'Unable to create whole cerebellum for %s'%(aseg)
print cout3.runtime.stderr
print cout3.runtime.stdout
return None
cmd = 'rm right_cerebellum.* left_cerebellum.*'
cl4 = CommandLine(cmd)
cout4 = cl4.run()
os.chdir(cwd)
cerebellum = glob('%s/grey_cerebellum.*'%(pth))
return cerebellum[0]
def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
show_connectinfo=False, dotfilename='graph.dot', format='png',
simple_form=True):
""" Displays the graph layout of the pipeline
This function requires that pygraphviz and matplotlib are available on
the system.
Parameters
----------
show : boolean
Indicate whether to generate pygraphviz output fromn
networkx. default [False]
use_execgraph : boolean
Indicates whether to use the specification graph or the
execution graph. default [False]
show_connectioninfo : boolean
Indicates whether to show the edge data on the graph. This
makes the graph rather cluttered. default [False]
"""
graph = deepcopy(graph_in)
if use_execgraph:
graph = generate_expanded_graph(graph)
logger.debug('using execgraph')
else:
logger.debug('using input graph')
if base_dir is None:
base_dir = os.getcwd()
if not os.path.exists(base_dir):
os.makedirs(base_dir)
outfname = fname_presuffix(dotfilename,
suffix='_detailed.dot',
use_ext=False,
newpath=base_dir)
logger.info('Creating detailed dot file: %s' % outfname)
_write_detailed_dot(graph, outfname)
cmd = 'dot -T%s -O %s' % (format, outfname)
res = CommandLine(cmd).run()
if res.runtime.returncode:
logger.warn('dot2png: %s', res.runtime.stderr)
pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form)
outfname = fname_presuffix(dotfilename,
suffix='.dot',
use_ext=False,
newpath=base_dir)
nx.write_dot(pklgraph, outfname)
logger.info('Creating dot file: %s' % outfname)
cmd = 'dot -T%s -O %s' % (format, outfname)
res = CommandLine(cmd).run()
if res.runtime.returncode:
logger.warn('dot2png: %s', res.runtime.stderr)
if show:
pos = nx.graphviz_layout(pklgraph, prog='dot')
nx.draw(pklgraph, pos)
if show_connectinfo:
nx.draw_networkx_edge_labels(pklgraph, pos)
def fs_extract_label_rois(subdir, pet, dat, labels):
"""
Uses freesurfer tools to extract
Parameters
-----------
subdir : subjects freesurfer directory
pet : filename of subjects PET volume coreg'd to mri space
dat : filename of dat generated by tkregister mapping pet to mri
labels : filename of subjects aparc+aseg.mgz
Returns
-------
stats_file: file that contains roi stats
label_file : file of volume with label rois in pet space
you can check dat with ...
'tkmedit %s T1.mgz -overlay %s -overlay-reg %s
-fthresh 0.5 -fmid1'%(subject, pet, dat)
"""
pth, nme, ext = split_filename(pet)
pth_lbl, nme_lbl, ext_lbl = split_filename(labels)
stats_file = os.path.join(pth, '%s_%s_stats' % (nme, nme_lbl))
label_file = os.path.join(pth, '%s_%s_.nii.gz' % (nme, nme_lbl))
# Gen label file
cmd = [
'mri_label2vol',
'--seg %s/mri/%s' % (subdir, labels),
'--temp %s' % (pet),
'--reg' % (dat),
'--o %s' % (label_file)
]
cmd = ' '.join(cmd)
cout = CommandLine(cmd).run()
if not cout.runtime.returncode == 0:
print 'mri_label2vol failed for %s' % (pet)
return None, None
## Get stats
cmd = [
'mri_segstats',
'--seg %s' % (label_file),
'--sum %s' % (stats_file),
'--in %s' % (pet), '--nonempty --ctab',
'/usr/local/freesurfer_x86_64-4.5.0/FreeSurferColorLUT.txt'
]
cmd = ' '.join(cmd)
cout = CommandLine(cmd).run()
if not cout.runtime.returncode == 0:
print 'mri_segstats failed for %s' % (pet)
return None, None
return stats_file, label_file
def dicom2nrrd(dicomdir, experiment_dir, out_prefix, out_suffix):
import os
import shutil
dirnames = os.listdir(dicomdir)
for d_i in range(len(dirnames)):
fileName, fileExtension = os.path.splitext(dirnames[d_i])
if fileExtension == '.gz':
os.remove(dirnames[d_i])
if fileExtension == '.bval':
os.remove(dirnames[d_i])
if fileExtension == '.bvec':
os.remove(dirnames[d_i])
from nipype.interfaces.base import CommandLine
basename = experiment_dir + '/' + out_prefix + '/' + out_prefix + out_suffix
cmd = CommandLine(
'/Users/eija/Documents/osx/dcm2nii -a Y -d N -e N -i N -p N -o %s %s' %
(basename, dicomdir))
print "DICOM->NII:" + cmd.cmd
cmd.run()
dirnames = os.listdir(dicomdir)
filename_nii = ''
filename_bvec = ''
filename_bval = ''
for d_i in range(len(dirnames)):
fileName, fileExtension = os.path.splitext(dirnames[d_i])
if fileExtension == '.gz':
if len(filename_nii) > 0:
raise "multiple copies of .nii.gz was found"
filename_nii = fileName
if fileExtension == '.bval':
if len(filename_nii) > 0:
raise "multiple copies of .bval was found"
filename_bval = fileName
if fileExtension == '.bvec':
if len(filename_nii) > 0:
raise "multiple copies of .bvec was found"
filename_bvec = fileName
move_to_results((dicomdir + '/' + filename_nii + '.gz'), experiment_dir,
out_prefix)
move_to_results((dicomdir + '/' + filename_bval + '.bval'), experiment_dir,
out_prefix)
move_to_results((dicomdir + '/' + filename_bvec + '.bvec'), experiment_dir,
out_prefix)
cmd = CommandLine(
'DWIConvert --inputVolume %s.nii.gz --outputVolume %s.nrrd --conversionMode FSLToNrrd --inputBValues %s.bval --inputBVectors %s.bvec'
% (basename, basename, basename, basename))
print "NII->NRRD:" + cmd.cmd
cmd.run()
return os.path.abspath('%s.nrrd' % (basename))
def remove_files(files):
"""removes files """
if not hasattr(files, '__iter__'):
cl = CommandLine('rm %s'% files)
out = cl.run()
if not out.runtime.returncode == 0:
print 'failed to delete %s' % files
print out.runtime.stderr
return
for f in files:
cl = CommandLine('rm %s'% f)
out = cl.run()
if not out.runtime.returncode == 0:
print 'failed to delete %s' % f
print out.runtime.stderr
def geodesic_depth(command, surface_file):
"""
Measure "travel depth" of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : travel depth C++ executable command
surface_file : ``vtk file``
Returns
-------
depth_file: string
vtk file with geodesic depth per vertex of mesh
"""
import os
from nipype.interfaces.base import CommandLine
depth_file = os.path.join(
os.getcwd(),
os.path.splitext(os.path.basename(surface_file))[0] +
'.geodesic_depth.vtk')
cli = CommandLine(command=command)
cli.inputs.args = ' '.join([surface_file, depth_file])
cli.cmdline
cli.run()
if not os.path.exists(depth_file):
raise (IOError(depth_file + " not found"))
return depth_file
def area(command, surface_file):
"""
Measure area of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
Voronoi-based surface area C++ executable command
surface_file : string
vtk file with surface mesh
Returns
-------
area_file: string
vtk file with surface area per vertex of mesh
"""
import os
from nipype.interfaces.base import CommandLine
area_file = os.path.join(
os.getcwd(),
os.path.splitext(os.path.basename(surface_file))[0] + '.area.vtk')
cli = CommandLine(command=command)
cli.inputs.args = ' '.join([surface_file, area_file])
cli.cmdline
cli.run()
if not os.path.exists(area_file):
raise (IOError(area_file + " not found"))
return area_file
def fs_generate_dat(pet, subdir):
""" use freesurfer tkregister to generate a dat file used in
extracting PET counts with a labelled mri mask in freesurfer
Parameters
----------
pet : pet file that is registered to the subjects mri
subdir : subjects freesurfer directory
Returns
-------
dat : dat file generated , or None if failes
you can check dat with ...
'tkmedit %s T1.mgz -overlay %s -overlay-reg %s
-fthresh 0.5 -fmid1'%(subject, pet, dat)
"""
pth, nme, ext = split_filename(pet)
dat = os.path.join(pth, '%s_2_FS.dat' % (nme))
cmd = 'tkregister2 --mov %s --s %s --regheader --reg %s --noedit' % (
pet, subdir, dat)
cout = CommandLine(cmd).run()
if not cout.runtime.returncode == 0:
print 'tkregister failed for %s' % (pet)
return None
return dat
def dicom2mhd(dicomdir, experiment_dir, out_prefix):
from nipype.utils.filemanip import split_filename
from nipype.interfaces.base import CommandLine
import os
_, name, _ = split_filename(dicomdir)
outfile_mhd = experiment_dir + '/' + out_prefix + '/' + name + '_tmp/' + 'output' + '.mhd'
outfile_raw = experiment_dir + '/' + out_prefix + '/' + name + '_tmp/' + 'output' + '.raw'
outfile_txt = experiment_dir + '/' + out_prefix + '/' + name + '_tmp/' + 'output' + '_info.txt'
outdir = experiment_dir + '/' + out_prefix + '/' + name + '_tmp'
cmd = CommandLine((
mcverter_basedir +
'mcverter %s -r -f meta -o %s -F-PatientName-SeriesDate-SeriesDescription-StudyId-SeriesNumber'
% (dicomdir, outdir)))
print "DICOM->NII:" + cmd.cmd
cmd.run()
# Move to results folder
outfile_mhd = move_to_results(outfile_mhd, experiment_dir, out_prefix)
outfile_raw = move_to_results(outfile_raw, experiment_dir, out_prefix)
outfile_txt = move_to_results(outfile_txt, experiment_dir, out_prefix)
os.rmdir(outdir)
# Rename basename, and reference in mhd header
outfile_mhd = rename_basename_to(outfile_mhd, name)
outfile_raw = rename_basename_to(outfile_raw, name)
outfile_txt = rename_basename_to(outfile_txt, name)
replace_inplace(outfile_mhd, ('output.raw'), (name + '.raw'))
return outfile_mhd, outfile_raw, outfile_txt
def get_doc(cmd, opt_map, help_flag=None, trap_error=True):
"""Get the docstring from our command and options map.
Parameters
----------
cmd : string
The command whose documentation we are fetching
opt_map : dict
Dictionary of flags and option attributes.
help_flag : string
Provide additional help flag. e.g., -h
trap_error : boolean
Override if underlying command returns a non-zero returncode
Returns
-------
doc : string
The formated docstring
"""
res = CommandLine('which %s' % cmd.split(' ')[0],
terminal_output='allatonce').run()
cmd_path = res.runtime.stdout.strip()
if cmd_path == '':
raise Exception('Command %s not found'%cmd.split(' ')[0])
if help_flag:
cmd = ' '.join((cmd,help_flag))
doc = grab_doc(cmd,trap_error)
opts = reverse_opt_map(opt_map)
return build_doc(doc, opts)
def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True):
"""Auto-generate option map from command line help
Parameters
----------
cmd : string
The command whose documentation we are fetching
style : string default ['--']
The help command style (--, -). Multiple styles can be provided in a
list e.g. ['--','-'].
help_flag : string
Provide additional help flag. e.g., -h
trap_error : boolean
Override if underlying command returns a non-zero returncode
Returns
-------
optmap : dict
Contains a mapping from input to command line variables
"""
res = CommandLine('which %s' % cmd.split(' ')[0],
terminal_output='allatonce').run()
cmd_path = res.runtime.stdout.strip()
if cmd_path == '':
raise Exception('Command %s not found'%cmd.split(' ')[0])
if help_flag:
cmd = ' '.join((cmd,help_flag))
doc = grab_doc(cmd,trap_error)
return _parse_doc(doc,style)
def _grab_xml(self, module):
cmd = CommandLine(command="Slicer3", args="--launch %s --xml" % module)
ret = cmd.run()
if ret.runtime.returncode == 0:
return xml.dom.minidom.parseString(ret.runtime.stdout)
else:
raise Exception(cmd.cmdline + " failed:\n%s" % ret.runtime.stderr)
def version():
"""Check for RATS version on system
Parameters
----------
None
Returns
-------
version : str
Version number as string or None if RATS not found
"""
try:
clout = CommandLine(command='RATS_MM --version',
resource_monitor=False).run()
except IOError:
# If rats_vcheck is not present, return None
LOGGER.warn('RATS_MM executable not found.')
return None
version_stamp = clout.runtime.stdout.split('\n')[1].split(
'version ')[0]
if version_stamp.startswith('RATS_MM'):
version_stamp = version_stamp.split('version: ')[1]
else:
return None
return version_stamp
def run_palm(cope_file,
design_file,
contrast_file,
group_file,
mask_file,
cluster_threshold=3.09):
import os
from glob import glob
from nipype.interfaces.base import CommandLine
#cmd = ("palm -i {cope_file} -m {mask_file} -d {design_file} -t {contrast_file} -eb {group_file} -T "
# "-C {cluster_threshold} -Cstat extent -fdr -noniiclass -twotail -logp -zstat")
#cl = CommandLine(cmd.format(cope_file=cope_file, mask_file=mask_file, design_file=design_file,
# contrast_file=contrast_file,
# group_file=group_file, cluster_threshold=cluster_threshold))
# XXX: ideally we should make it more fancy, but since we're only doing
# 1-sample t-tests we need to omit the design, contrast, and group files
# as for PALM's FAQs
cmd = (
"palm -i {cope_file} -m {mask_file} -T "
"-C {cluster_threshold} -Cstat extent -fdr -noniiclass -twotail -logp -zstat"
)
cl = CommandLine(
cmd.format(cope_file=cope_file,
mask_file=mask_file,
cluster_threshold=cluster_threshold))
results = cl.run(terminal_output='file')
return [os.path.join(os.getcwd(), val) for val in sorted(glob('palm*'))]
def DICOM2animatedGIF_sidebyside(dcmdir_l, dcmdir_r, outputpath, slice_i, suffix):
dcmio = DicomIO.DicomIO()
dwidcm_l = dcmio.ReadDICOM_frames(dcmdir_l)
dwidcm_r = dcmio.ReadDICOM_frames(dcmdir_r)
# Write all frames of slice into set of png files
for frame_i in range(len(dwidcm_l)):
slice_l = dwidcm_l[frame_i][slice_i].pixel_array.T
slice_r = dwidcm_r[frame_i][slice_i].pixel_array.T
dimx = slice_l.shape[0]
dimy = slice_l.shape[1]
newImg1 = PIL.Image.new('L', (dimx*2, dimy))
pixels1 = newImg1.load()
for i in range (0, dimx):
for j in range (0, dimy):
pixels1[i, j] = float(slice_l[i, j])
pixels1[dimx+i, j] = float(slice_r[i, j])
#pixels1[i, j] = float(slice[i, j]) * dwidcm[frame_i][slice_i].RescaleSlope + dwidcm[frame_i][slice_i].RescaleIntercept
newImg1.save((outputpath + '_' + ('%02d' % frame_i) + '.png'),'PNG')
cmd = CommandLine('convert -delay 25 -loop 0 %s_*.png %s_%s.gif' % (outputpath, outputpath, suffix))
cmd.run()
for frame_i in range(len(dwidcm_l)):
os.remove((outputpath + '_' + ('%02d' % frame_i) + '.png'))
print "convert (ImageMagick):" + cmd.cmd
return (outputpath + '.gif')
def _submit_batchtask(self, scriptfile, node):
cmd = CommandLine('qsub', environ=os.environ.data,
terminal_output='allatonce')
path = os.path.dirname(scriptfile)
qsubargs = ''
if self._qsub_args:
qsubargs = self._qsub_args
if 'qsub_args' in node.plugin_args:
if 'overwrite' in node.plugin_args and \
node.plugin_args['overwrite']:
qsubargs = node.plugin_args['qsub_args']
else:
qsubargs += (" " + node.plugin_args['qsub_args'])
if '-o' not in qsubargs:
qsubargs = '%s -o %s' % (qsubargs, path)
if '-e' not in qsubargs:
qsubargs = '%s -e %s' % (qsubargs, path)
if node._hierarchy:
jobname = '.'.join((os.environ.data['LOGNAME'],
node._hierarchy,
node._id))
else:
jobname = '.'.join((os.environ.data['LOGNAME'],
node._id))
jobnameitems = jobname.split('.')
jobnameitems.reverse()
jobname = '.'.join(jobnameitems)
jobname = qsub_sanitize_job_name(jobname)
cmd.inputs.args = '%s -N %s %s' % (qsubargs,
jobname,
scriptfile)
oldlevel = iflogger.level
iflogger.setLevel(logging.getLevelName('CRITICAL'))
tries = 0
result = list()
while True:
try:
result = cmd.run()
except Exception as e:
if tries < self._max_tries:
tries += 1
time.sleep(
self._retry_timeout) # sleep 2 seconds and try again.
else:
iflogger.setLevel(oldlevel)
raise RuntimeError('\n'.join((('Could not submit sge task'
' for node %s') % node._id,
str(e))))
else:
break
iflogger.setLevel(oldlevel)
# retrieve sge taskid
lines = [line for line in result.runtime.stdout.split('\n') if line]
taskid = int(re.match("Your job ([0-9]*) .* has been submitted",
lines[-1]).groups()[0])
self._pending[taskid] = node.output_dir()
self._refQstatSubstitute.add_startup_job(taskid, cmd.cmdline)
logger.debug('submitted sge task: %d for node %s with %s' %
(taskid, node._id, cmd.cmdline))
return taskid
def run_rand(cope_file,
design_file,
contrast_file,
group_file,
mask_file,
cluster_threshold=2.3,
n=10000):
import os
from glob import glob
from nipype.interfaces.base import CommandLine
cmd = (
"randomise -i {cope_file} -m {mask_file} -d {design_file} -t {contrast_file} -e {group_file} -T "
"-c {cluster_threshold} -x -n {n}")
cl = CommandLine(
cmd.format(cope_file=cope_file,
mask_file=mask_file,
design_file=design_file,
contrast_file=contrast_file,
group_file=group_file,
cluster_threshold=cluster_threshold,
n=n))
results = cl.run(terminal_output='file')
return [os.path.join(os.getcwd(), val) for val in sorted(glob('rand*'))]
def _submit_batchtask(self, scriptfile, node):
cmd = CommandLine('bsub',
environ=os.environ.data,
terminal_output='allatonce')
path = os.path.dirname(scriptfile)
bsubargs = ''
if self._bsub_args:
bsubargs = self._bsub_args
if 'bsub_args' in node.plugin_args:
if 'overwrite' in node.plugin_args and\
node.plugin_args['overwrite']:
bsubargs = node.plugin_args['bsub_args']
else:
bsubargs += (" " + node.plugin_args['bsub_args'])
if '-o' not in bsubargs: # -o outfile
bsubargs = '%s -o %s' % (bsubargs, scriptfile + ".log")
if '-e' not in bsubargs:
bsubargs = '%s -e %s' % (bsubargs, scriptfile + ".log"
) # -e error file
if node._hierarchy:
jobname = '.'.join(
(os.environ.data['LOGNAME'], node._hierarchy, node._id))
else:
jobname = '.'.join((os.environ.data['LOGNAME'], node._id))
jobnameitems = jobname.split('.')
jobnameitems.reverse()
jobname = '.'.join(jobnameitems)
cmd.inputs.args = '%s -J %s sh %s' % (bsubargs, jobname, scriptfile
) # -J job_name_spec
logger.debug('bsub ' + cmd.inputs.args)
oldlevel = iflogger.level
iflogger.setLevel(logging.getLevelName('CRITICAL'))
tries = 0
while True:
try:
result = cmd.run()
except Exception as e:
if tries < self._max_tries:
tries += 1
sleep(
self._retry_timeout) # sleep 2 seconds and try again.
else:
iflogger.setLevel(oldlevel)
raise RuntimeError('\n'.join(
(('Could not submit lsf task'
' for node %s') % node._id, str(e))))
else:
break
iflogger.setLevel(oldlevel)
# retrieve lsf taskid
match = re.search('<(\d*)>', result.runtime.stdout)
if match:
taskid = int(match.groups()[0])
else:
raise ScriptError("Can't parse submission job output id: %s" %
result.runtime.stdout)
self._pending[taskid] = node.output_dir()
logger.debug('submitted lsf task: %d for node %s' % (taskid, node._id))
return taskid
def area(command, surface_file, verbose=False):
"""
Measure area of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
Voronoi-based surface area C++ executable command
surface_file : string
vtk file with surface mesh
verbose : bool
print statements?
Returns
-------
area_file: string
vtk file with surface area per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import area
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'area', 'PointAreaMain')
>>> area_file = area(command, surface_file, verbose)
>>>
>>> scalars, name = read_scalars(area_file)
>>> np.allclose(scalars[0:8],
... [0.48270401731, 0.39661528543, 0.57813454792, 0.70574099571,
... 0.84318527207, 0.57642554119, 0.66942016035, 0.70629953593])
True
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
area_file = os.path.join(os.getcwd(), basename + '.area.vtk')
args = ' '.join([surface_file, area_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.terminal_output = 'file'
cli.run()
if not os.path.exists(area_file):
raise IOError(area_file + " not found")
return area_file
def dicom2nrrd(dicomdir, out_prefix):
import os
from nipype.interfaces.base import CommandLine
cmd = CommandLine(
'DWIConvert --inputDicomDirectory %s --outputVolume %s.nrrd' %
(dicomdir, out_prefix))
cmd.run()
return os.path.abspath('%s.nrrd' % out_prefix)
def test_provenance():
ps = ProvStore()
from nipype.interfaces.base import CommandLine
results = CommandLine('echo hello').run()
ps.add_results(results)
provn = ps.g.get_provn()
prov_json = ps.g.serialize(format='json')
yield assert_true, 'echo hello' in provn
def test_provenance(tmpdir):
from nipype.interfaces.base import CommandLine
tmpdir.chdir()
ps = ProvStore()
results = CommandLine('echo hello').run()
ps.add_results(results)
provn = ps.g.get_provn()
assert 'echo hello' in provn
def convert_audio_file(old_file,
new_file,
command='ffmpeg',
input_args='-i',
output_args='-ac 2'):
"""
Convert audio file to new format.
Parameters
----------
old_file : string
full path to the input file
new_file : string
full path to the output file
command : string
executable command without arguments
input_args : string
arguments preceding input file name in command
output_args : string
arguments preceding output file name in command
Returns
-------
new_file : string
full path to the output file
Examples
--------
>>> from mhealthx.xio import convert_audio_file
>>> old_file = '/Users/arno/mhealthx_cache/mhealthx/feature_files/test.m4a'
>>> new_file = 'test.wav'
>>> command = 'ffmpeg'
>>> input_args = '-y -i'
>>> output_args = '-ac 2'
>>> new_file = convert_audio_file(old_file, new_file, command, input_args, output_args)
"""
import os
from nipype.interfaces.base import CommandLine
if not os.path.isfile(old_file):
raise IOError("{0} does not exist.".format(old_file))
new_file = None
else:
input_args = ' '.join([input_args, old_file, output_args, new_file])
try:
# Nipype command line wrapper:
cli = CommandLine(command=command)
cli.inputs.args = input_args
cli.cmdline
cli.run()
except:
import traceback
traceback.print_exc()
print("'{0} {1}' unsuccessful".format(command, input_args))
new_file = None
return new_file
def _submit_batchtask(self, scriptfile, node):
"""
This is more or less the _submit_batchtask from sge.py with flipped variable
names, different command line switches, and different output formatting/processing
"""
cmd = CommandLine('sbatch',
environ=os.environ.data,
terminal_output='allatonce')
path = os.path.dirname(scriptfile)
sbatch_args = ''
if self._sbatch_args:
sbatch_args = self._sbatch_args
if 'sbatch_args' in node.plugin_args:
if 'overwrite' in node.plugin_args and\
node.plugin_args['overwrite']:
sbatch_args = node.plugin_args['sbatch_args']
else:
sbatch_args += (" " + node.plugin_args['sbatch_args'])
if '-o' not in sbatch_args:
sbatch_args = '%s -o %s' % (sbatch_args,
os.path.join(path, 'slurm-%j.out'))
if '-e' not in sbatch_args:
sbatch_args = '%s -e %s' % (sbatch_args,
os.path.join(path, 'slurm-%j.out'))
if '-p' not in sbatch_args:
sbatch_args = '%s -p normal' % (sbatch_args)
if '-n' not in sbatch_args:
sbatch_args = '%s -n 16' % (sbatch_args)
if '-t' not in sbatch_args:
sbatch_args = '%s -t 1:00:00' % (sbatch_args)
if node._hierarchy:
jobname = '.'.join(
(os.environ.data['LOGNAME'], node._hierarchy, node._id))
else:
jobname = '.'.join((os.environ.data['LOGNAME'], node._id))
jobnameitems = jobname.split('.')
jobnameitems.reverse()
jobname = '.'.join(jobnameitems)
cmd.inputs.args = '%s -J %s %s' % (sbatch_args, jobname, scriptfile)
oldlevel = iflogger.level
iflogger.setLevel(logging.getLevelName('CRITICAL'))
tries = 0
while True:
try:
result = cmd.run()
except Exception, e:
if tries < self._max_tries:
tries += 1
sleep(
self._retry_timeout) # sleep 2 seconds and try again.
else:
iflogger.setLevel(oldlevel)
raise RuntimeError('\n'.join(
(('Could not submit sbatch task'
' for node %s') % node._id, str(e))))
else:
break
def travel_depth(command, surface_file, verbose=False):
"""
Measure "travel depth" of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
travel depth C++ executable command
surface_file : string
vtk file
verbose : bool
print statements?
Returns
-------
depth_file: string
vtk file with travel depth per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import travel_depth
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'travel_depth', 'TravelDepthMain')
>>> depth_file = travel_depth(command, surface_file, verbose)
>>> scalars, name = read_scalars(depth_file)
>>> print(np.array_str(np.array(scalars[0:8]), precision=5,
... suppress_small=True))
[ 0.02026 0.06009 0.12859 0.04564 0.00774 0.05284 0.05354 0.01316]
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
depth_file = os.path.join(os.getcwd(), basename + '.travel_depth.vtk')
args = ' '.join([surface_file, depth_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.cmdline
cli.run()
if not os.path.exists(depth_file):
raise IOError(depth_file + " not found")
return depth_file
def tar_cmd(infile):
""" given a ipped tar archive, untars"""
cwd = os.getcwd()
pth, nme = os.path.split(infile)
os.chdir(pth)
cl = CommandLine('tar xfvz %s'%(infile))
cout = cl.run()
os.chdir(cwd)
return pth
def unzip(infile):
gunzipfile, gz = os.path.splitext(infile)
if not 'gz' in gz:
#when running gunzip on file when
return infile
else:
c3 = CommandLine('gunzip %s'%(infile))
c3.run()
return gunzipfile
def travel_depth(command, surface_file, verbose=False):
"""
Measure "travel depth" of each vertex in a surface mesh.
(Calls Joachim Giard's C++ code)
Parameters
----------
command : string
travel depth C++ executable command
surface_file : string
vtk file
verbose : bool
print statements?
Returns
-------
depth_file: string
vtk file with travel depth per vertex of mesh
Examples
--------
>>> import os
>>> import numpy as np
>>> from mindboggle.shapes.surface_shapes import travel_depth
>>> from mindboggle.mio.vtks import read_scalars
>>> from mindboggle.mio.fetch_data import prep_tests
>>> urls, fetch_data = prep_tests()
>>> surface_file = fetch_data(urls['left_pial'], '', '.vtk')
>>> verbose = False
>>> ccode_path = os.environ['vtk_cpp_tools']
>>> command = os.path.join(ccode_path, 'travel_depth', 'TravelDepthMain')
>>> depth_file = travel_depth(command, surface_file, verbose)
>>> scalars, name = read_scalars(depth_file)
>>> np.allclose(scalars[0:8], [0.020259869839, 0.06009166489, 0.12858575442, 0.045639221313, 0.007742772964, 0.052839111255, 0.053538904296, 0.013158746337])
True
"""
import os
from nipype.interfaces.base import CommandLine
basename = os.path.splitext(os.path.basename(surface_file))[0]
depth_file = os.path.join(os.getcwd(), basename + '.travel_depth.vtk')
args = ' '.join([surface_file, depth_file])
if verbose:
print("{0} {1}".format(command, args))
cli = CommandLine(command=command)
cli.inputs.args = args
cli.terminal_output = 'file'
cli.run()
if not os.path.exists(depth_file):
raise IOError(depth_file + " not found")
return depth_file
def dicom2nii(dicomdir, experiment_dir, out_prefix, out_suffix):
import os
import shutil
from nipype.interfaces.base import CommandLine
dirnames = os.listdir(dicomdir)
for d_i in range(len(dirnames)):
fileName, fileExtension = os.path.splitext(dirnames[d_i])
if fileExtension == '.gz':
os.remove(os.path.join(dicomdir, dirnames[d_i]))
if fileExtension == '.bval':
os.remove(os.path.join(dicomdir, dirnames[d_i]))
if fileExtension == '.bvec':
os.remove(os.path.join(dicomdir, dirnames[d_i]))
from nipype.interfaces.base import CommandLine
basename = experiment_dir + '/' + out_prefix + '/' + out_prefix + out_suffix
cmd = CommandLine(
'/Users/eija/Documents/osx/dcm2nii -a Y -d N -e N -i N -p N -o %s %s' %
(basename, dicomdir))
print "DICOM->NII:" + cmd.cmd
cmd.run()
dirnames = os.listdir(dicomdir)
filename_nii = ''
filename_bvec = ''
filename_bval = ''
for d_i in range(len(dirnames)):
fileName, fileExtension = os.path.splitext(dirnames[d_i])
if fileExtension == '.gz':
if len(filename_nii) > 0:
raise "multiple copies of .nii.gz was found"
filename_nii = fileName
if fileExtension == '.bval':
if len(filename_nii) > 0:
raise "multiple copies of .bval was found"
filename_bval = fileName
if fileExtension == '.bvec':
if len(filename_nii) > 0:
raise "multiple copies of .bvec was found"
filename_bvec = fileName
outfile = move_to_results((dicomdir + '/' + filename_nii + '.gz'),
experiment_dir, out_prefix)
outfile_bval = ''
outfile_bvec = ''
if len(filename_bval) > 0:
outfile_bval = move_to_results(
(dicomdir + '/' + filename_bval + '.bval'), experiment_dir,
out_prefix)
if len(filename_bvec) > 0:
outfile_bvec = move_to_results(
(dicomdir + '/' + filename_bvec + '.bvec'), experiment_dir,
out_prefix)
return outfile, outfile_bval, outfile_bvec
