def _run_interface(self, runtime):
from pyacwereg import viz
if self.inputs.view == 'all':
view = ['axial', 'coronal', 'sagittal']
else:
view = np.atleast_1d(self.inputs.view).tolist()
label = None
if isdefined(self.inputs.label):
label = self.inputs.label
slices = None
if isdefined(self.inputs.slices):
slices = self.inputs.slices
if self.inputs.split:
self._out_file = []
for i, v in enumerate(view):
o = op.abspath('%s%04d.pdf' % (self.inputs.out_file, i))
viz.slices_gridplot(self.inputs.in_files, view=v,
out_file=o, label=label[i],
slices=slices)
self._out_file.append(o)
else:
self._out_file = [op.abspath(self.inputs.out_file + '.pdf')]
viz.slices_gridplot(self.inputs.in_files, view=view,
out_file=self._out_file, label=label,
slices=slices)
return runtime
def _check_mlab_inputs(self):
if not isdefined(self.inputs.matlab_cmd) and self._matlab_cmd:
self.inputs.matlab_cmd = self._matlab_cmd
if not isdefined(self.inputs.paths) and self._paths:
self.inputs.paths = self._paths
if not isdefined(self.inputs.use_mcr) and self._use_mcr:
self.inputs.use_mcr = self._use_mcr
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = self.inputs.out_file
if not isdefined(outputs['out_file']) and isdefined(self.inputs.in_file):
outputs['out_file']=self._gen_fname(self.inputs.in_file,
suffix='_sigloss')
return outputs
def _list_outputs(self):
"""Execute this module.
"""
outdir = self.inputs.base_directory
if not isdefined(outdir):
outdir = os.path.abspath('.')
if isdefined(self.inputs.container):
print "container defined", self.inputs.container
outdir = os.path.join(outdir, self.inputs.container)
print outdir
cwd = os.getcwd()
dst = self._get_dst(os.path.join(cwd,self.inputs.json_name+'.json'))
print "dst = ", dst
outdir = os.path.join(outdir,dst)
print "new outdir = ", outdir
outdir = self._substitute(outdir)
print "substituted outdir = ", outdir
if not os.path.exists(outdir):
try:
os.makedirs(outdir)
except OSError, inst:
if 'File exists' in inst:
pass
else:
raise(inst)
def _run_interface(self, runtime):
mask_erode_mm = self.inputs.mask_erode_mm
if not isdefined(mask_erode_mm):
mask_erode_mm = None
erode_mm = self.inputs.erode_mm
if not isdefined(erode_mm):
erode_mm = None
mask_erode_prop = self.inputs.mask_erode_prop
if not isdefined(mask_erode_prop):
mask_erode_prop = None
erode_prop = self.inputs.erode_prop
if not isdefined(erode_prop):
erode_prop = None
roi_file, eroded_mask = _tpm2roi(
self.inputs.in_tpm,
self.inputs.in_mask,
mask_erode_mm,
erode_mm,
mask_erode_prop,
erode_prop,
self.inputs.prob_thresh,
newpath=runtime.cwd,
)
self._results['roi_file'] = roi_file
self._results['eroded_mask'] = eroded_mask
return runtime
def _list_outputs(self):
outputs = self.output_spec().get()
#if isdefined(self.inputs.output_csv_file):
#write to a csv file and assign a value to self.coherence_file (a
#file name + path)
#Always defined (the arrays):
outputs['coherence_array']=self.coherence
outputs['timedelay_array']=self.delay
#Conditional
if isdefined(self.inputs.output_csv_file) and hasattr(self,'coherence'):
# we need to make a function that we call here that writes the
# coherence values to this file "coherence_csv" and makes the
# time_delay csv file??
self._make_output_files()
outputs['coherence_csv']=fname_presuffix(self.inputs.output_csv_file,suffix='_coherence')
outputs['timedelay_csv']=fname_presuffix(self.inputs.output_csv_file,suffix='_delay')
if isdefined(self.inputs.output_figure_file) and hasattr(self,
'coherence'):
self._make_output_figures()
outputs['coherence_fig'] = fname_presuffix(self.inputs.output_figure_file,suffix='_coherence')
outputs['timedelay_fig'] = fname_presuffix(self.inputs.output_figure_file,suffix='_delay')
return outputs
def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.join(os.getcwd(),
self.inputs.out_base + '.nii.gz')
if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg) and isdefined(self.inputs.fmap):
outputs['out_1vol'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_1vol.nii.gz')
outputs['fmap2str_mat'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fieldmap2str.mat')
outputs['fmap2epi_mat'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fieldmaprads2epi.mat')
outputs['fmap_epi'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
outputs['fmap_str'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fieldmaprads2str.ni `i.gz')
outputs['fmapmag_str'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fieldmap2str.nii.gz')
outputs['shiftmap'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
outputs['fullwarp'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_warp.nii.gz')
outputs['epi2str_inv'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_inv.mat')
outputs['epi2str_mat'] = os.path.join(os.getcwd(),
self.inputs.out_base + '.mat')
outputs['wmedge'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fast_wmedge.nii.gz')
outputs['wmseg'] = os.path.join(os.getcwd(),
self.inputs.out_base + '_fast_wmseg.nii.gz')
return outputs
def _run_interface(self, runtime):
in_file_ref = Path(self.inputs.in_file)
if isdefined(self.inputs.out_file):
in_file_ref = Path(self.inputs.out_file)
fname = in_file_ref.name.rstrip(
''.join(in_file_ref.suffixes))
out_file = (Path(runtime.cwd) / ('plot_%s_contours.svg' % fname)).resolve()
self._results['out_file'] = str(out_file)
vmax = None if not isdefined(self.inputs.vmax) else self.inputs.vmax
vmin = None if not isdefined(self.inputs.vmin) else self.inputs.vmin
plot_segmentation(
self.inputs.in_file,
self.inputs.in_contours,
out_file=str(out_file),
cut_coords=self.inputs.cut_coords,
display_mode=self.inputs.display_mode,
levels=self.inputs.levels,
colors=self.inputs.colors,
saturate=self.inputs.saturate,
vmin=vmin, vmax=vmax)
return runtime
def modify_paths(object, relative=True, basedir=None):
"""Modify filenames in a data structure to either full paths or relative paths
"""
if not basedir:
basedir = os.getcwd()
if isinstance(object, dict):
out = {}
for key, val in sorted(object.items()):
if isdefined(val):
out[key] = modify_paths(val, relative=relative,
basedir=basedir)
elif isinstance(object, (list,tuple)):
out = []
for val in object:
if isdefined(val):
out.append(modify_paths(val, relative=relative,
basedir=basedir))
if isinstance(object, tuple):
out = tuple(out)
else:
if isdefined(object):
if isinstance(object, str) and os.path.isfile(object):
if relative:
if config.getboolean('execution','use_relative_paths'):
out = relpath(object,start=basedir)
else:
out = object
else:
out = os.path.abspath(os.path.join(basedir,object))
if not os.path.exists(out):
raise FileNotFoundError('File %s not found'%out)
else:
out = object
return out
def _list_outputs(self):
outputs = self._outputs().get()
jobtype = self.inputs.jobtype
if jobtype.startswith('est'):
outputs['normalization_parameters'] = []
for imgf in filename_to_list(self.inputs.source):
outputs['normalization_parameters'].append(fname_presuffix(imgf, suffix='_sn.mat', use_ext=False))
outputs['normalization_parameters'] = list_to_filename(outputs['normalization_parameters'])
if self.inputs.jobtype == "estimate":
if isdefined(self.inputs.apply_to_files):
outputs['normalized_files'] = self.inputs.apply_to_files
outputs['normalized_source'] = self.inputs.source
elif 'write' in self.inputs.jobtype:
outputs['normalized_files'] = []
if isdefined(self.inputs.apply_to_files):
for imgf in filename_to_list(self.inputs.apply_to_files):
outputs['normalized_files'].append(fname_presuffix(imgf, prefix='w'))
if isdefined(self.inputs.source):
outputs['normalized_source'] = []
for imgf in filename_to_list(self.inputs.source):
outputs['normalized_source'].append(fname_presuffix(imgf, prefix='w'))
return outputs
def _format_arg(self, opt, spec, val):
if opt == 'moving_image':
retval = []
for ii in range(len(self.inputs.moving_image)):
retval.append('--metric "%s[%s,%s,%d,%d]"' % (self.inputs.metric, self.inputs.fixed_image[ii], self.inputs.moving_image[ii],self.inputs.metric_weight,self.inputs.radius))
return " ".join(retval)
elif opt == 'moving_image_mask':
return '--masks "[%s,%s]"' % (self.inputs.fixed_image_mask, self.inputs.moving_image_mask)
elif opt == 'initial_moving_transform':
if isdefined(self.inputs.invert_initial_moving_transform) and self.inputs.invert_initial_moving_transform:
return '--initial-moving-transform "[%s,1]"' % self.inputs.initial_moving_transform
else:
return '--initial-moving-transform "[%s,0]"' % self.inputs.initial_moving_transform
elif opt == "number_of_iterations":
convergence_iter = "x".join([str(i) for i in self.inputs.number_of_iterations])
return '--convergence "[%s,%g,%d]"' % (convergence_iter,
self.inputs.convergence_threshold,
self.inputs.convergence_window_size)
elif opt == 'output_transform_prefix':
if isdefined(self.inputs.output_inverse_warped_image) and self.inputs.output_inverse_warped_image:
return '--output "[%s,%s,%s]"' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image, self.inputs.output_inverse_warped_image )
elif isdefined(self.inputs.output_warped_image) and self.inputs.output_warped_image:
return '--output "[%s,%s]"' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image )
else:
return '--output %s' % self.inputs.output_transform_prefix
return super(antsRegistration, self)._format_arg(opt, spec, val)
def _list_outputs(self):
outputs = self._outputs().get()
outputs["out_file"] = self.inputs.out_file
if not isdefined(outputs["out_file"]):
source = self.inputs.source_file
# Some recon-all files don't have a proper extension (e.g. "lh.thickness")
# so we have to account for that here
bad_extensions = [".%s" % e for e in ["area", "mid", "pial", "avg_curv", "curv", "inflated",
"jacobian_white", "orig", "nofix", "smoothwm", "crv",
"sphere", "sulc", "thickness", "volume", "white"]]
use_ext = True
if split_filename(source)[2] in bad_extensions:
source = source + ".stripme"
use_ext = False
ext = ""
if isdefined(self.inputs.target_type):
ext = "." + filemap[self.inputs.target_type]
use_ext = False
outputs["out_file"] = fname_presuffix(source,
suffix=".%s%s" % (self.inputs.target_subject, ext),
newpath=os.getcwd(),
use_ext=use_ext)
else:
outputs["out_file"] = os.path.abspath(self.inputs.out_file)
return outputs
def _format_arg(self, name, trait_spec, value):
if name == 'syn_file':
if (isdefined(self.inputs.bvec_file) == False) or (isdefined(self.inputs.b0_file) == False):
return ""
else:
return trait_spec.argstr % value
return super(DwiTool, self)._format_arg(name, trait_spec, value)
def _gen_outfilename(self): out_file = self.inputs.out_file if not isdefined(out_file) and isdefined(self.inputs.in_file): out_file = self._gen_fname(self.inputs.in_file, suffix="_surf") #out_file = self._gen_fname(self.inputs.in_file, suffix="_surf") return out_file
def _parse_inputs( self, skip=None ):
if skip is None:
skip = []
if not isdefined(self.inputs.out_base ):
self.inputs.out_base = './nipypetu'
self.inputs.out_base = os.path.abspath(self.inputs.out_base)
if isdefined( self.inputs.encoding_file ):
skip.append( 'encoding_direction' )
skip.append( 'readout_times' )
else:
encdir = 'y'
enctimes = None
if isdefined( self.inputs.encoding_direction ):
encdir = self.inputs.encoding_direction
if isdefined( self.inputs.readout_times ):
enctimes = self.inputs.readout_times
self.inputs.encoding_file = self._generate_encfile( encdir, enctimes )
return super(TOPUP, self)._parse_inputs(skip=skip)
def _list_outputs(self):
outputs = self._outputs().get()
jobtype = self.inputs.jobtype
if jobtype.startswith("est"):
outputs["normalization_parameters"] = []
for imgf in filename_to_list(self.inputs.source):
outputs["normalization_parameters"].append(fname_presuffix(imgf, suffix="_sn.mat", use_ext=False))
outputs["normalization_parameters"] = list_to_filename(outputs["normalization_parameters"])
if self.inputs.jobtype == "estimate":
if isdefined(self.inputs.apply_to_files):
outputs["normalized_files"] = self.inputs.apply_to_files
outputs["normalized_source"] = self.inputs.source
elif "write" in self.inputs.jobtype:
outputs["normalized_files"] = []
if isdefined(self.inputs.apply_to_files):
for imgf in filename_to_list(self.inputs.apply_to_files):
outputs["normalized_files"].append(fname_presuffix(imgf, prefix="w"))
if isdefined(self.inputs.source):
outputs["normalized_source"] = []
for imgf in filename_to_list(self.inputs.source):
outputs["normalized_source"].append(fname_presuffix(imgf, prefix="w"))
return outputs
def _list_outputs(self):
outputs = self.output_spec().get()
_in = self.inputs
if isdefined(_in.out_reg_file):
outputs["out_reg_file"] = op.abspath(_in.out_reg_file)
elif _in.source_file:
suffix = "_bbreg_%s.dat" % _in.subject_id
outputs["out_reg_file"] = fname_presuffix(_in.source_file, suffix=suffix, use_ext=False)
if isdefined(_in.registered_file):
if isinstance(_in.registered_file, bool):
outputs["registered_file"] = fname_presuffix(_in.source_file, suffix="_bbreg")
else:
outputs["registered_file"] = op.abspath(_in.registered_file)
if isdefined(_in.out_fsl_file):
if isinstance(_in.out_fsl_file, bool):
suffix = "_bbreg_%s.mat" % _in.subject_id
out_fsl_file = fname_presuffix(_in.source_file, suffix=suffix, use_ext=False)
outputs["out_fsl_file"] = out_fsl_file
else:
outputs["out_fsl_file"] = op.abspath(_in.out_fsl_file)
outputs["min_cost_file"] = outputs["out_reg_file"] + ".mincost"
return outputs
def _run_interface(self, runtime):
out_file = op.abspath(self._gen_outfilename())
settings = dict(mask=None,
rician=(self.inputs.noise_model == 'rician'))
if isdefined(self.inputs.in_mask):
settings['mask'] = nb.load(self.inputs.in_mask).get_data()
if isdefined(self.inputs.patch_radius):
settings['patch_radius'] = self.inputs.patch_radius
if isdefined(self.inputs.block_radius):
settings['block_radius'] = self.inputs.block_radius
noise_mask = None
if isdefined(self.inputs.in_mask):
noise_mask = nb.load(self.inputs.noise_mask).get_data()
_, s = nlmeans_proxy(self.inputs.in_file,
settings,
noise_mask=noise_mask,
out_file=out_file)
iflogger.info(('Denoised image saved as {i}, estimated '
'sigma={s}').format(i=out_file, s=s))
return runtime
def _list_outputs(self):
outputs = self.output_spec().get()
if not isdefined(self.inputs.out_dir):
out_dir = self._gen_filename("out_dir")
else:
out_dir = self.inputs.out_dir
outputs['log'] = os.path.abspath(os.path.join(out_dir, 'probtrackx.log'))
#utputs['way_total'] = os.path.abspath(os.path.join(out_dir, 'waytotal'))
if isdefined(self.inputs.opd == True):
if isinstance(self.inputs.seed, list) and isinstance(self.inputs.seed[0], list):
outputs['fdt_paths'] = []
for seed in self.inputs.seed:
outputs['fdt_paths'].append(
os.path.abspath(
self._gen_fname("fdt_paths_%s" % ("_".join([str(s) for s in seed])),
cwd=out_dir, suffix='')))
else:
outputs['fdt_paths'] = os.path.abspath(self._gen_fname("fdt_paths",
cwd=out_dir, suffix=''))
# handle seeds-to-target output files
if isdefined(self.inputs.target_masks):
outputs['targets'] = []
for target in self.inputs.target_masks:
outputs['targets'].append(os.path.abspath(
self._gen_fname('seeds_to_' + os.path.split(target)[1],
cwd=out_dir,
suffix='')))
if isdefined(self.inputs.verbose) and self.inputs.verbose == 2:
outputs['particle_files'] = [os.path.abspath(
os.path.join(out_dir, 'particle%d' % i))
for i in range(self.inputs.n_samples)]
return outputs
def _post_run_hook(self, runtime):
outputs = self.aggregate_outputs(runtime=runtime)
mri_dir = None
if isdefined(self.inputs.subject_id):
mri_dir = os.path.join(self.inputs.subjects_dir,
self.inputs.subject_id, 'mri')
if isdefined(self.inputs.reference_file):
target_file = self.inputs.reference_file
else:
target_file = os.path.join(mri_dir, 'brainmask.mgz')
# Apply transform for simplicity
mri_vol2vol = fs.ApplyVolTransform(
source_file=self.inputs.source_file,
target_file=target_file,
lta_file=outputs.out_lta_file,
interp='nearest')
res = mri_vol2vol.run()
self._fixed_image = target_file
self._moving_image = res.outputs.transformed_file
if mri_dir is not None:
self._contour = os.path.join(mri_dir, 'ribbon.mgz')
NIWORKFLOWS_LOG.info(
'Report - setting fixed (%s) and moving (%s) images',
self._fixed_image, self._moving_image)
return super(MRICoregRPT, self)._post_run_hook(runtime)
def _run_interface(self, runtime):
mask = None
if isdefined(self.inputs.in_mask):
mask = self.inputs.in_mask
title = self.inputs.title
if isdefined(self.inputs.subject):
title += ', subject %s' % self.inputs.subject
if isdefined(self.inputs.metadata):
title += ' (' + '_'.join(self.inputs.metadata) + ')'
if isdefined(self.inputs.figsize):
fig = plot_mosaic(
self.inputs.in_file,
title=title,
overlay_mask=mask,
figsize=self.inputs.figsize)
else:
fig = plot_mosaic(
self.inputs.in_file,
title=title,
overlay_mask=mask)
fig.savefig(self.inputs.out_file, dpi=self.inputs.dpi)
return runtime
def _list_outputs(self):
outputs = self._outputs().get()
outputs['outlier_files'] = []
outputs['intensity_files'] = []
outputs['statistic_files'] = []
if isdefined(self.inputs.use_norm) and self.inputs.use_norm:
outputs['norm_files'] = []
if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
outputs['plot_files'] = []
for i, f in enumerate(filename_to_list(self.inputs.realigned_files)):
outlierfile, intensityfile, statsfile, normfile, plotfile = self._get_output_filenames(f, os.getcwd())
outputs['outlier_files'].insert(i, outlierfile)
outputs['intensity_files'].insert(i, intensityfile)
outputs['statistic_files'].insert(i, statsfile)
if isdefined(self.inputs.use_norm) and self.inputs.use_norm:
outputs['norm_files'].insert(i, normfile)
if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
outputs['plot_files'].insert(i, plotfile)
'''
outputs['outlier_files'] = list_to_filename(outputs['outlier_files'])
outputs['intensity_files'] = list_to_filename(outputs['intensity_files'])
outputs['statistic_files'] = list_to_filename(outputs['statistic_files'])
if isdefined(self.inputs.use_norm) and self.inputs.use_norm:
outputs['norm_files'] = list_to_filename(outputs['norm_files'])
if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
outputs['plot_files'] = list_to_filename(outputs['plot_files'])
'''
return outputs
def _get_dst(self, src):
path, fname = os.path.split(src)
if self.inputs.parameterization:
dst = path
if isdefined(self.inputs.strip_dir):
dst = dst.replace(self.inputs.strip_dir, '')
if not isdefined(self.inputs.container):
folders = [folder for folder in dst.split(os.path.sep) if
folder.startswith('_')]
else:
folders = [folder for folder in dst.split(os.path.sep) if
(folder.startswith('_') and not self.inputs.container in folder)]
dst = os.path.sep.join(folders).replace('_','')
else:
if fname:
dst = fname
else:
dst = path.split(os.path.sep)[-1]
try:
if dst[0] == os.path.sep(dst):
dst = dst[1:]
except:
pass
return dst
def _list_outputs(self):
outputs = self.output_spec().get()
outputs["out_reg_file"] = self.inputs.out_reg_file
if not isdefined(self.inputs.out_reg_file) and self.inputs.source_file:
outputs["out_reg_file"] = fname_presuffix(self.inputs.source_file, suffix="_robustreg.lta", use_ext=False)
prefices = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
suffices = dict(
registered_file=("src", "_robustreg", True),
weights_file=("src", "_robustweights", True),
half_source=("src", "_halfway", True),
half_targ=("trg", "_halfway", True),
half_weights=("src", "_halfweights", True),
half_source_xfm=("src", "_robustxfm.lta", False),
half_targ_xfm=("trg", "_robustxfm.lta", False),
)
for name, sufftup in suffices.items():
value = getattr(self.inputs, name)
if isdefined(value):
if isinstance(value, bool):
outputs[name] = fname_presuffix(
prefices[sufftup[0]], suffix=sufftup[1], newpath=os.getcwd(), use_ext=sufftup[2]
)
else:
outputs[name] = value
return outputs
def _generate_design(self, infolist=None):
"""Generate design specification for a typical fmri paradigm
"""
realignment_parameters = []
if isdefined(self.inputs.realignment_parameters):
for parfile in self.inputs.realignment_parameters:
realignment_parameters.append(np.loadtxt(parfile))
outliers = []
if isdefined(self.inputs.outlier_files):
for filename in self.inputs.outlier_files:
try:
outindices = np.loadtxt(filename, dtype=int)
except IOError:
outliers.append([])
else:
if outindices.size == 1:
outliers.append([outindices.tolist()])
else:
outliers.append(outindices.tolist())
if infolist is None:
if isdefined(self.inputs.subject_info):
infolist = self.inputs.subject_info
else:
infolist = gen_info(self.inputs.event_files)
self._sessinfo = self._generate_standard_design(
infolist,
functional_runs=self.inputs.functional_runs,
realignment_parameters=realignment_parameters,
outliers=outliers,
)
def _run_interface(self, runtime):
if not isdefined(self.inputs.screenshot_stem):
stem = "%s_%s_%s" % (
self.inputs.subject_id, self.inputs.hemi, self.inputs.surface)
else:
stem = self.inputs.screenshot_stem
stem_args = self.inputs.stem_template_args
if isdefined(stem_args):
args = tuple([getattr(self.inputs, arg) for arg in stem_args])
stem = stem % args
# Check if the DISPLAY variable is set -- should avoid crashes (might not?)
if not "DISPLAY" in os.environ:
raise RuntimeError("Graphics are not enabled -- cannot run tksurfer")
runtime.environ["_SNAPSHOT_STEM"] = stem
self._write_tcl_script()
runtime = super(SurfaceSnapshots, self)._run_interface(runtime)
# If a display window can't be opened, this will crash on
# aggregate_outputs. Let's try to parse stderr and raise a
# better exception here if that happened.
errors = ["surfer: failed, no suitable display found",
"Fatal Error in tksurfer.bin: could not open display"]
for err in errors:
if err in runtime.stderr:
self.raise_exception(runtime)
# Tksurfer always (or at least always when you run a tcl script)
# exits with a nonzero returncode. We have to force it to 0 here.
runtime.returncode = 0
return runtime
def _run_interface(self, runtime):
print 'in plot_coclass'
coclass_matrix_file = self.inputs.coclass_matrix_file
labels_file = self.inputs.labels_file
list_value_range = self.inputs.list_value_range
print 'loading coclass'
coclass_mat = np.load(coclass_matrix_file)
if isdefined(labels_file):
print 'loading labels'
labels = [line.strip() for line in open(labels_file)]
else :
labels = []
if not isdefined(list_value_range):
list_value_range = [np.amin(coclass_mat),np.amax(coclass_mat)]
print 'plotting heatmap'
path,fname,ext = split_f(coclass_matrix_file)
plot_coclass_matrix_file = os.path.abspath('heatmap_' + fname + '.eps')
plot_ranged_cormat(plot_coclass_matrix_file,coclass_mat,labels,fix_full_range = list_value_range)
return runtime
def _list_outputs(self):
outputs = self._outputs().get()
jobtype = self.inputs.jobtype
if jobtype.startswith('est'):
outputs['normalization_parameters'] = []
for imgf in filename_to_list(self.inputs.source):
outputs['normalization_parameters'].append(fname_presuffix(imgf, suffix='_sn.mat', use_ext=False))
outputs['normalization_parameters'] = list_to_filename(outputs['normalization_parameters'])
if self.inputs.jobtype == "estimate":
if isdefined(self.inputs.apply_to_files):
outputs['normalized_files'] = self.inputs.apply_to_files
outputs['normalized_source'] = self.inputs.source
elif 'write' in self.inputs.jobtype:
outputs['normalized_files'] = []
if isdefined(self.inputs.apply_to_files):
filelist = filename_to_list(self.inputs.apply_to_files)
for f in filelist:
if isinstance(f, list):
run = [fname_presuffix(in_f, prefix=self.inputs.out_prefix) for in_f in f]
else:
run = [fname_presuffix(f, prefix=self.inputs.out_prefix)]
outputs['normalized_files'].extend(run)
if isdefined(self.inputs.source):
outputs['normalized_source'] = fname_presuffix(self.inputs.source, prefix=self.inputs.out_prefix)
return outputs
def _run_interface(self, runtime):
tracks, header = trk.read(self.inputs.in_file)
if not isdefined(self.inputs.data_dims):
data_dims = header['dim']
else:
data_dims = self.inputs.data_dims
if not isdefined(self.inputs.voxel_dims):
voxel_size = header['voxel_size']
else:
voxel_size = self.inputs.voxel_dims
affine = header['vox_to_ras']
streams = ((ii[0]) for ii in tracks)
data = density_map(streams, data_dims, voxel_size)
if data.max() < 2**15:
data = data.astype('int16')
img = nb.Nifti1Image(data,affine)
out_file = op.abspath(self.inputs.out_filename)
nb.save(img, out_file)
iflogger.info('Track density map saved as {i}'.format(i=out_file))
iflogger.info('Data Dimensions {d}'.format(d=data_dims))
iflogger.info('Voxel Dimensions {v}'.format(v=voxel_size))
return runtime
def _list_outputs(self):
outputs = self.output_spec().get()
outfile = self.inputs.binary_file
if not isdefined(outfile):
if isdefined(self.inputs.out_type):
outfile = fname_presuffix(self.inputs.in_file,
newpath=os.getcwd(),
suffix='.'.join(('_thresh',
self.inputs.out_type)),
use_ext=False)
else:
outfile = fname_presuffix(self.inputs.in_file,
newpath=os.getcwd(),
suffix='_thresh')
outputs['binary_file'] = outfile
value = self.inputs.count_file
if isdefined(value):
if isinstance(value, bool):
if value:
outputs['count_file'] = fname_presuffix(self.inputs.in_file,
suffix='_count.txt',
newpath=os.getcwd(),
use_ext=False)
else:
outputs['count_file'] = value
return outputs
def _post_run_hook(self, runtime):
""" generates a report showing slices from each axis """
brain_extraction_mask = self.aggregate_outputs(
runtime=runtime).BrainExtractionMask
if (isdefined(self.inputs.keep_temporary_files)
and self.inputs.keep_temporary_files == 1):
self._anat_file = self.aggregate_outputs(
runtime=runtime).N4Corrected0
else:
self._anat_file = self.inputs.anatomical_image
self._mask_file = brain_extraction_mask
self._seg_files = [brain_extraction_mask]
self._masked = False
NIWORKFLOWS_LOG.info(
'Generating report for ANTS BrainExtraction. file "%s", mask "%s"',
self._anat_file,
self._mask_file,
)
return super(BrainExtractionRPT, self)._post_run_hook(runtime)
def _generate_segment(self):
if not isdefined(self.inputs.subjects_dir):
freesurfer_status = 'Not run'
else:
recon = fs.ReconAll(subjects_dir=self.inputs.subjects_dir,
subject_id=self.inputs.subject_id,
T1_files=self.inputs.t1w,
flags='-noskullstrip')
if recon.cmdline.startswith('echo'):
freesurfer_status = 'Pre-existing directory'
else:
freesurfer_status = 'Run by sMRIPrep'
t2w_seg = ''
if self.inputs.t2w:
t2w_seg = '(+ {:d} T2-weighted)'.format(len(self.inputs.t2w))
return SUBJECT_TEMPLATE.format(subject_id=self.inputs.subject_id,
n_t1s=len(self.inputs.t1w),
t2w=t2w_seg,
output_spaces=', '.join(
self.inputs.output_spaces),
freesurfer_status=freesurfer_status)
def _check_len(self, name, new):
if name == "keys":
nitems = len(new)
if len(set(new)) != nitems:
raise ValueError(
'Found duplicated entries in the index of ordered keys')
if not isdefined(self.inputs.keys):
return
if name == "key" and new not in self.inputs.keys:
raise ValueError('Selected key "%s" not found in the index' % new)
if name in self._fields:
if isinstance(new, str) or len(new) < 1:
raise ValueError(
'Trying to set an invalid value (%s) for input "%s"' %
(new, name))
if len(new) != len(self.inputs.keys):
raise ValueError(
'Length of value (%s) for input field "%s" does not match '
'the length of the indexing list.' % (new, name))
def _list_outputs(self):
"""Create a Bunch which contains all possible files generated
by running the interface. Some files are always generated, others
depending on which ``inputs`` options are set.
Returns
-------
outputs : Bunch object
Bunch object containing all possible files generated by
interface object.
If None, file was not generated
Else, contains path, filename of generated outputfile
"""
outputs = self._outputs().get()
ext = Info.output_type_to_ext(self.inputs.output_type)
outbase = 'vol*'
if isdefined(self.inputs.out_base_name):
outbase = '%s*' % self.inputs.out_base_name
outputs['out_files'] = sorted(glob(os.path.join(os.getcwd(),
outbase + ext)))
return outputs
def _run_interface(self, runtime):
sub = self.inputs.sub
ses = self.inputs.ses
task = self.inputs.task
fwhm = self.inputs.fwhm
run = self.inputs.run
rec = self.inputs.rec
acq = self.inputs.acq
df = pd.DataFrame([], columns=metric_columns)
for metric_name, metric_function in pvc_metrics.items():
mse = pvc_mse(self.inputs.pvc, self.inputs.pve, fwhm)
temp = pd.DataFrame(
[['pvc', sub, ses, task, run, acq, rec, 02, metric_name, mse]],
columns=metric_columns)
df = pd.concat([df, temp])
df.fillna(0, inplace=True)
if not isdefined(self.inputs.out_file):
self.inputs.out_file = self._gen_output(
self.inputs.sub, self.inputs.ses, self.inputs.task,
self.inputs.run, self.inputs.acq, self.inputs.rec)
df.to_csv(self.inputs.out_file, index=False)
return runtime
def _run_interface(self, runtime):
self._merged_file = None
if not isdefined(self.inputs.in_files):
return runtime
in_imgs = [nib.load(in_file) for in_file in self.inputs.in_files]
if len(in_imgs) == 0:
return runtime
outshape = first(in_imgs).shape
assert all(in_img.shape == outshape for in_img in in_imgs)
in_data = [np.asanyarray(in_img.dataobj).astype(np.bool) for in_img in in_imgs]
outarr = np.logical_and.reduce(in_data)
outimg = new_img_like(first(in_imgs), outarr)
self._merged_file = op.abspath(f"merged.nii.gz")
nib.save(outimg, self._merged_file)
return runtime
def _post_run_hook(self, runtime):
self._fixed_image = self.inputs.after
self._moving_image = self.inputs.before
if self.inputs.base == 'before':
resampled_after = nli.resample_to_img(self._fixed_image, self._moving_image)
fname = fname_presuffix(self._fixed_image, suffix='_resampled', newpath=runtime.cwd)
resampled_after.to_filename(fname)
self._fixed_image = fname
else:
resampled_before = nli.resample_to_img(self._moving_image, self._fixed_image)
fname = fname_presuffix(self._moving_image, suffix='_resampled', newpath=runtime.cwd)
resampled_before.to_filename(fname)
self._moving_image = fname
self._contour = self.inputs.wm_seg if isdefined(self.inputs.wm_seg) else None
NIWORKFLOWS_LOG.info(
'Report - setting before (%s) and after (%s) images',
self._fixed_image, self._moving_image)
runtime = super(ResampleBeforeAfterRPT, self)._post_run_hook(runtime)
NIWORKFLOWS_LOG.info('Successfully created report (%s)', self._out_report)
os.unlink(fname)
return runtime
def _run_interface(self, runtime):
models = self.inputs.model
if not isinstance(models, list):
layout = gb.BIDSLayout(self.inputs.bids_dir)
if not isdefined(models):
models = layout.get(type='model')
if not models:
raise ValueError("No models found")
elif models == 'default':
models = ba.auto_model(layout)
models = [_ensure_model(m) for m in models]
if self.inputs.selectors:
# This is almost certainly incorrect
models = [model for model in models
if all(val in model['input'].get(key, [val])
for key, val in self.inputs.selectors.items())]
self._results['model_spec'] = models
return runtime
def _run_interface(self, runtime):
function_handle = create_function_from_source(self.inputs.function_str)
args = {}
for name in self._input_names:
value = getattr(self.inputs, name)
if isdefined(value):
args[name] = value
out = function_handle(**args)
if len(self._output_names) == 1:
self._out[self._output_names[0]] = out
else:
if isinstance(out,
tuple) and (len(out) != len(self._output_names)):
raise RuntimeError('Mismatch in number of expected outputs')
else:
for idx, name in enumerate(self._output_names):
self._out[name] = out[idx]
return runtime
def _list_outputs(self):
outputs = self.output_spec().get()
includelist = [
re.match(self.inputs.pattern, in_value) is None
for in_value in self.inputs.keys
]
for field in self._fields:
valuelist = getattr(self.inputs, field)
if not isdefined(valuelist): # require all inputs
return outputs
for field in self._fields:
valuelist = getattr(self.inputs, field)
if not isinstance(valuelist, list):
valuelist = [valuelist]
outputs[field] = [
value for include, value in zip(includelist, valuelist)
if include
]
return outputs
def set_mapnode_substitutions(self, n_runs):
"""Find mapnode names and add datasink substitutions to sort by run."""
# First determine top-level mapnode names
mapnode_names = find_mapnodes(self.wf)
# Then determine mapnode names for each nested workflow
# Note that this currently only works for one level of nesting
nested_workflows = find_nested_workflows(self.wf)
for wf in nested_workflows:
mapnode_names.extend(find_mapnodes(wf))
# Build a list of substitution tuples
substitutions = []
for r in reversed(range(n_runs)):
for name in mapnode_names:
substitutions.append(("_%s%d" % (name, r), "run_%d" % (r + 1)))
# Set the substitutions attribute on the DataSink node
if isdefined(self.sink_node.inputs.substitutions):
self.sink_node.inputs.substitutions.extend(substitutions)
else:
self.sink_node.inputs.substitutions = substitutions
def _run_interface(self, runtime):
from scipy.ndimage.morphology import binary_dilation
from nilearn.masking import compute_epi_mask
orig_file_nii = nb.load(self.inputs.in_file)
in_file_data = orig_file_nii.get_fdata()
# pad the data to avoid the mask estimation running into edge effects
in_file_data_padded = np.pad(in_file_data, (1, 1),
"constant",
constant_values=(0, 0))
padded_nii = nb.Nifti1Image(in_file_data_padded, orig_file_nii.affine,
orig_file_nii.header)
mask_nii = compute_epi_mask(padded_nii, exclude_zeros=True)
mask_data = np.asanyarray(mask_nii.dataobj).astype(np.uint8)
if isdefined(self.inputs.dilation):
mask_data = binary_dilation(mask_data).astype(np.uint8)
# reverse image padding
mask_data = mask_data[1:-1, 1:-1, 1:-1]
# exclude zero and NaN voxels
mask_data[in_file_data == 0] = 0
mask_data[np.isnan(in_file_data)] = 0
better_mask = nb.Nifti1Image(mask_data, orig_file_nii.affine,
orig_file_nii.header)
better_mask.set_data_dtype(np.uint8)
better_mask.to_filename("mask_file.nii.gz")
self._mask_file = os.path.join(runtime.cwd, "mask_file.nii.gz")
runtime.returncode = 0
return super(ComputeEPIMask, self)._run_interface(runtime)
def _run_interface(self, runtime):
# Create function handle
if self.as_module:
import importlib
pieces = self.inputs.function_str.split('.')
module = '.'.join(pieces[:-1])
function = pieces[-1]
try:
function_handle = getattr(importlib.import_module(module),
function)
except ImportError:
raise RuntimeError('Could not import module: %s' %
self.inputs.function_str)
else:
function_handle = create_function_from_source(
self.inputs.function_str, self.imports)
# Get function args
args = {}
for name in self._input_names:
value = getattr(self.inputs, name)
if isdefined(value):
args[name] = value
out = function_handle(**args)
if len(self._output_names) == 1:
self._out[self._output_names[0]] = out
else:
if isinstance(out, tuple) and \
(len(out) != len(self._output_names)):
raise RuntimeError('Mismatch in number of expected outputs')
else:
for idx, name in enumerate(self._output_names):
self._out[name] = out[idx]
return runtime
def _generate_segment(self):
dof = self.inputs.registration_dof
stc = {
True: 'Applied',
False: 'Not applied',
'TooShort': 'Skipped (too few volumes)'
}[self.inputs.slice_timing]
reg = {
'FSL': [
'FSL <code>flirt</code> with boundary-based registration'
' (BBR) metric - %d dof' % dof,
'FSL <code>flirt</code> rigid registration - 6 dof'
],
'FreeSurfer': [
'FreeSurfer <code>bbregister</code> '
'(boundary-based registration, BBR) - %d dof' % dof,
'FreeSurfer <code>mri_coreg</code> - %d dof' % dof
],
}[self.inputs.registration][self.inputs.fallback]
if self.inputs.pe_direction is None:
pedir = 'MISSING - Assuming Anterior-Posterior'
else:
pedir = {
'i': 'Left-Right',
'j': 'Anterior-Posterior'
}[self.inputs.pe_direction[0]]
if isdefined(self.inputs.confounds_file):
with open(self.inputs.confounds_file) as cfh:
conflist = cfh.readline().strip('\n').strip()
return FUNCTIONAL_TEMPLATE.format(
pedir=pedir,
stc=stc,
sdc=self.inputs.distortion_correction,
registration=reg,
confounds=re.sub(r'[\t ]+', ', ', conflist),
tr=self.inputs.tr)
def prepare_contrasts(contrasts, all_regressors):
"""Make mutable copy of contrast list, and
generate contrast design_matrix from dictionary weight mapping
Each value in the contrasts list is a ContrastInfo object:
ContrastInfo = namedtuple(
'ContrastInfo', ('name', 'conditions', 'weights', 'test', 'entities')
)
"""
if not isdefined(contrasts):
return []
out_contrasts = []
for contrast_info in contrasts:
conds = contrast_info["conditions"]
in_weights = np.atleast_2d(contrast_info["weights"])
# Are any necessary values missing for contrast estimation?
missing = len(conds) != in_weights.shape[1] or any(
cond not in all_regressors for cond in conds)
if missing:
continue
weights = np.zeros((in_weights.shape[0], len(all_regressors)),
dtype=in_weights.dtype)
# Find indices of input conditions in all_regressors list
sorter = np.argsort(all_regressors)
indices = sorter[np.searchsorted(all_regressors, conds, sorter=sorter)]
weights[:, indices] = in_weights
out_contrasts.append((
contrast_info['name'],
weights,
contrast_info['entities'].copy(),
contrast_info['test'],
))
return out_contrasts
def _run_interface(self, runtime):
df = pd.read_csv(self.inputs.in_file)
out_columns = [
'sub', 'ses', 'task', 'roi', 'metric', 'measure', 'value'
]
df_out = pd.DataFrame(columns=out_columns)
for ses, ses_df in df.groupby(['ses']):
for task, task_df in ses_df.groupby(['task']):
for measure, measure_name in zip(outlier_measures.values(),
outlier_measures.keys()):
for metric_name, metric_df in task_df.groupby(['metric']):
metricValues = metric_df.value.values
if len(metricValues.shape) == 1:
metricValues = metricValues.reshape(-1, 1)
if 'cdf' in inspect.getargspec(measure).args:
if 'coreg' or 'pvc' in metric_df.analysis:
cdf = True
else:
cdf = False
m = np.array(measure(metricValues, cdf=cdf))
else:
m = np.array(measure(metricValues))
if len(m.shape) > 1: m = m.flatten()
r = pd.Series(m)
#Get column number of the current outlier measure Reindex the test_df from 0 to the number of rows it has
#Get the series with the calculate the distance measure for the current measure
df.index = range(df.shape[0])
df['value'] = r
df['measure'] = [measure_name] * df.shape[0]
df_out = pd.concat([df_out, df], axis=0)
if not isdefined(self.inputs.out_file):
self.inputs.out_file = self._gen_output()
df_out.to_csv(self.inputs.out_file, index=False)
return runtime
def _list_outputs(self):
outputs = self.output_spec().get()
self._set_outputs()
if isdefined(self.inputs.warped_image):
outputs["warped_image"] = self.inputs.warped_image
if isdefined(self.inputs.inverse_warped_image):
outputs["inverse_warped_image"] = self.inputs.inverse_warped_image
if isdefined(self.inputs.composite_transform):
outputs["composite_transform"] = self.inputs.composite_transform
if isdefined(self.inputs.out_matrix):
outputs["out_matrix"] = self.inputs.out_matrix
if isdefined(self.inputs.out_matrix_inverse):
outputs["out_matrix_inverse"] = self.inputs.out_matrix_inverse
if isdefined(self.inputs.inverse_composite_transform):
outputs[
"inverse_composite_transform"] = self.inputs.inverse_composite_transform
return outputs
def aggregate_outputs(self, runtime=None, needed_outputs=None):
outputs = self._outputs()
info = runtime.stdout
# Modified file
if isdefined(self.inputs.copy_sform2qform) or isdefined(self.inputs.copy_qform2sform) or isdefined(self.inputs.delete_orient) or isdefined(self.inputs.force_radiological) or isdefined(self.inputs.force_neurological) or isdefined(self.inputs.swap_orient):
outputs.out_file = self.inputs.in_file
#outputs['out_file'] = self.inputs.in_file
# Get information
if isdefined(self.inputs.get_orient):
outputs.orient = info
if isdefined(self.inputs.get_sform):
outputs.sform = info
if isdefined(self.inputs.get_qform):
outputs.qform= info
if isdefined(self.inputs.get_sformcode):
outputs.sformcode = info
if isdefined(self.inputs.get_qformcode):
outputs.qformcode = info
return outputs
def _run_interface(self, runtime):
"""Generate a reportlet."""
if isdefined(self.inputs.mif_file):
odf_img, directions = mif2amps(self.inputs.mif_file, runtime.cwd)
elif isdefined(self.inputs.fib_file):
odf_img, directions = fib2amps(self.inputs.fib_file,
self.inputs.background_image,
runtime.cwd)
elif isdefined(self.inputs.odf_file) and isdefined(
self.inputs.directions_file):
odf_img = nb.load(self.inputs.odf_file)
directions = np.load(self.inputs.directions_file)
else:
raise Exception('Requires either a mif file or fib file')
odf_4d = odf_img.get_fdata()
sphere = HemiSphere(xyz=directions.astype(np.float))
if not isdefined(self.inputs.background_image
) or self.inputs.background_image is None:
background_data = odf_4d.mean(3)
else:
background_data = nb.load(self.inputs.background_image).get_fdata()
peak_report = op.join(runtime.cwd, 'peak_report.png')
peak_slice_series(odf_4d,
sphere,
background_data,
peak_report,
n_cuts=self._ncuts,
mask_image=self.inputs.mask_file,
padding=self._padding)
self._results['out_report'] = peak_report
# Plot ODFs in interesting regions
if isdefined(self.inputs.odf_rois):
odf_report = op.join(runtime.cwd, 'odf_report.png')
odf_roi_plot(odf_4d,
sphere,
background_data,
odf_report,
self.inputs.odf_rois,
subtract_iso=self.inputs.subtract_iso,
mask=self.inputs.mask_file)
self._results['odf_report'] = odf_report
return runtime
def _cond_to_regress(self, info, nscans):
"""Converts condition information to full regressors
"""
reg = []
regnames = []
for i, cond in enumerate(info.conditions):
if hasattr(info, 'amplitudes') and info.amplitudes:
amplitudes = info.amplitudes[i]
else:
amplitudes = None
regnames.insert(len(regnames), cond)
scaled_onsets = scale_timings(info.onsets[i],
self.inputs.input_units, 'secs',
self.inputs.time_repetition)
scaled_durations = scale_timings(info.durations[i],
self.inputs.input_units, 'secs',
self.inputs.time_repetition)
regressor = self._gen_regress(scaled_onsets, scaled_durations,
amplitudes, nscans)
if isdefined(self.inputs.use_temporal_deriv) and \
self.inputs.use_temporal_deriv:
reg.insert(len(reg), regressor[0])
regnames.insert(len(regnames), cond + '_D')
reg.insert(len(reg), regressor[1])
else:
reg.insert(len(reg), regressor)
# need to deal with temporal and parametric modulators
# for sparse-clustered acquisitions enter T1-effect regressors
nvol = self.inputs.volumes_in_cluster
if nvol > 1:
for i in range(nvol - 1):
treg = np.zeros((nscans / nvol, nvol))
treg[:, i] = 1
reg.insert(len(reg), treg.ravel().tolist())
regnames.insert(len(regnames), 'T1effect_%d' % i)
return reg, regnames
def _run_interface(self, runtime):
if not isdefined(self.inputs.out_file):
fname = os.path.splitext(os.path.basename(self.inputs.in_file))[0]
dname = dname = os.getcwd()
self.inputs.out_file = dname + os.sep + fname + self._suffix + '.mnc'
temp_fn="/tmp/tmp_mnc_"+ strftime("%Y%m%d%H%M%S", gmtime())+str(np.random.randint(9999999999))+".mnc"
shutil.copy(self.inputs.in_file, temp_fn)
infile = volumeFromFile(self.inputs.in_file)
for view in ['xspace','yspace','zspace']:
#start = -1*infile.separations[infile.dimnames.index(view)]*infile.sizes[infile.dimnames.index(view)]/2
dim = infile.dimnames.index( view )
start = infile.starts[dim]
run_modifHrd=ModifyHeaderCommand()
run_modifHrd.inputs.in_file = temp_fn
run_modifHrd.inputs.dinsert = True;
run_modifHrd.inputs.opt_string = view+":start="+str(start);
run_modifHrd.run()
node_name="fixIrregularDimension"
fixIrregular = ModifyHeaderCommand()
#-dinsert xspace:direction_cosines=1,0,0 -dinsert yspace:direction_cosines=0,1,0 -dinsert zspace:direction_cosines=0,0,1
fixIrregular.inputs.opt_string = " -sinsert time:spacing=\"regular__\" -sinsert time-width:spacing=\"regular__\" -sinsert xspace:spacing=\"regular__\" -sinsert yspace:spacing=\"regular__\" -sinsert zspace:spacing=\"regular__\""
fixIrregular.inputs.in_file = temp_fn
print( fixIrregular.cmdline )
fixIrregular.run()
fixCosine = FixCosinesCommand()
fixCosine.inputs.in_file = fixIrregular.inputs.out_file
fixCosine.inputs.keep_real_range=True
fixCosine.inputs.dircos=True
fixCosine.run()
print(fixCosine.cmdline)
shutil.copy(fixCosine.inputs.out_file, self.inputs.out_file)
return runtime
def _list_outputs(self):
outputs = self._outputs().get()
outputs['annotated_trackvis_file'] = os.path.abspath(
self.inputs.out_tracks)
outputs['max_maps'] = []
outputs['mean_maps'] = []
if isdefined(self.inputs.stat_labels) and len(
self.inputs.stat_labels) == len(self.inputs.stat_files):
for label in self.inputs.stat_labels:
outputs['max_maps'].append(
os.path.abspath(self.inputs.out_max_map_prefix +
"_%s" % label + '.nii'))
outputs['mean_maps'].append(
os.path.abspath(self.inputs.out_mean_map_prefix +
"_%s" % label + '.nii'))
else:
for i in range(len(self.inputs.stat_files)):
outputs['max_maps'].append(
os.path.abspath(self.inputs.out_max_map_prefix + str(i) +
'.nii'))
outputs['mean_maps'].append(
os.path.abspath(self.inputs.out_mean_map_prefix + str(i) +
'.nii'))
return outputs
def _list_outputs(self):
outputs = self._outputs().get()
outfile = self.inputs.out_file
if not isdefined(outfile):
_, infile1, _ = split_filename(self.inputs.in_file)
if self.inputs.invert_xfm:
outfile = fname_presuffix(infile1,
suffix="_inv.mat",
newpath=os.getcwd(),
use_ext=False)
else:
if self.inputs.concat_xfm:
_, infile2, _ = split_filename(self.inputs.in_file2)
outfile = fname_presuffix("%s_%s" % (infile1, infile2),
suffix=".mat",
newpath=os.getcwd(),
use_ext=False)
else:
outfile = fname_presuffix(infile1,
suffix="_fix.mat",
newpath=os.getcwd(),
use_ext=False)
outputs["out_file"] = os.path.abspath(outfile)
return outputs
def _run_interface(self, runtime):
if not isdefined(self.inputs.out_file):
self.inputs.out_file = self._gen_output(self.inputs.in_file)
temp_fn = os.getcwd()+"/tmp_mnc_"+ strftime("%Y%m%d%H%M%S", gmtime())+str(np.random.randint(9999999999))+".mnc"
convert = nii2mnc_shCommand()
convert.inputs.in_file=self.inputs.in_file
convert.inputs.out_file=temp_fn
convert.inputs.dfloat = self.inputs.dfloat
convert.inputs.dint = self.inputs.dint
print(convert.cmdline)
convert.run()
minc2 = mincconvertCommand()
minc2.inputs.in_file=temp_fn
minc2.inputs.out_file=self.inputs.out_file
minc2.inputs.two=True
print(minc2.cmdline)
minc2.run()
move(minc2.inputs.out_file, self.inputs.out_file)
os.remove(temp_fn)
return runtime
def _checkinitxfm(in_bval, excl_nodiff, in_xfms=None):
from nipype.interfaces.base import isdefined
import numpy as np
import os.path as op
bvals = np.loadtxt(in_bval)
gen_id = ((in_xfms is None) or (not isdefined(in_xfms))
or (len(in_xfms) != len(bvals)))
init_xfms = []
if excl_nodiff:
dws = np.where(bvals != 0)[0].tolist()
else:
dws = range(len(bvals))
if gen_id:
for i in dws:
xfm_file = op.abspath('init_%04d.mat' % i)
np.savetxt(xfm_file, np.eye(4))
init_xfms.append(xfm_file)
else:
init_xfms = [in_xfms[i] for i in dws]
return init_xfms
def _list_outputs(self):
exclude = None
if self.inputs.strict:
exclude = ['derivatives/', 'code/', 'sourcedata/']
if bids_ver < version.parse('0.5'):
raise ImportError("pybids must be >= 0.5")
elif bids_ver >= version.parse('0.5') and bids_ver < version.parse('0.6'):
layout = bidslayout.BIDSLayout(self.inputs.base_dir, config=self.inputs.domains, exclude=exclude)
else:
if self.inputs.domains is None:
self.inputs.domains = ['bids']
layout = bidslayout.BIDSLayout((self.inputs.base_dir, self.inputs.domains), exclude=exclude)
# If infield is not given nm input value, silently ignore
filters = {}
for key in self._infields:
value = getattr(self.inputs, key)
if isdefined(value):
filters[key] = value
outputs = {}
for key, query in self.inputs.output_query.items():
args = query.copy()
args.update(filters)
filelist = layout.get(return_type=self.inputs.return_type, **args)
if len(filelist) == 0:
msg = 'Output key: %s returned no files' % key
if self.inputs.raise_on_empty:
raise IOError(msg)
else:
iflogger.warning(msg)
filelist = Undefined
outputs[key] = filelist
return outputs
def _get_dst(self, src):
# If path is directory with trailing os.path.sep,
# then remove that for a more robust behavior
src = src.rstrip(os.path.sep)
path, fname = os.path.split(src)
if self.inputs.parameterization:
dst = path
if isdefined(self.inputs.strip_dir):
dst = dst.replace(self.inputs.strip_dir, '')
folders = [
folder for folder in dst.split(os.path.sep)
if folder.startswith('_')
]
dst = os.path.sep.join(folders)
if fname:
dst = os.path.join(dst, fname)
else:
if fname:
dst = fname
else:
dst = path.split(os.path.sep)[-1]
if dst[0] == os.path.sep:
dst = dst[1:]
return dst
def cmdline(self):
cmd = super(MakeMidthickness, self).cmdline
if not isdefined(self.inputs.graymid) or len(self.inputs.graymid) < 1:
return cmd
# Possible graymid values inclue {l,r}h.{graymid,midthickness}
# Prefer midthickness to graymid, require to be of the same hemisphere
# as input
source = None
in_base = Path(self.inputs.in_file).name
mt = self._associated_file(in_base, "midthickness")
gm = self._associated_file(in_base, "graymid")
for surf in self.inputs.graymid:
if Path(surf).name == mt:
source = surf
break
if Path(surf).name == gm:
source = surf
if source is None:
return cmd
return "cp {} {}".format(source, self._list_outputs()["out_file"])
def _transform(self, array):
design = np.loadtxt(self.inputs.design_file, dtype=np.float64, ndmin=2)
filter_all = self.inputs.filter_all
if filter_all is not True:
filter_columns = self.inputs.filter_columns
else:
filter_columns = list(range(1, design.shape[1] + 1))
calculate_mask = isdefined(
self.inputs.mask) and self.inputs.mask is True
np.nan_to_num(array,
copy=False) # nans create problems further down the line
array2 = regfilt(array,
design,
filter_columns,
calculate_mask=calculate_mask,
aggressive=self.inputs.aggressive)
return array2
def _run_interface(self, runtime):
if not isdefined(self.inputs.out_file):
self.inputs.out_file = self._gen_output(self.inputs.in_file)
beast = mincbeastCommand()
beast.inputs.out_file = "/tmp/" + str(np.random.randint(
0, 9999999)) + "_" + os.path.basename(self.inputs.out_file)
beast.inputs.in_file = self.inputs.in_file
beast.inputs.library_dir = self.inputs.library_dir
beast.inputs.voxel_size = self.inputs.voxel_size
beast.inputs.same_resolution = self.inputs.same_resolution
beast.inputs.median = self.inputs.median
beast.inputs.fill = self.inputs.fill
beast.inputs.configuration = self.inputs.configuration
beast.run()
resample = FixCosinesCommand()
resample.inputs.two = True
resample.inputs.in_file = beast.inputs.out_file
resample.inputs.out_file = self.inputs.out_file
print(resample.cmdline)
resample.run()
return runtime