# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.preproc.connectomist.complete_preprocessing",
names=["complete_preprocessing"])
bredala.register("clindmri.preproc.connectomist.import_and_qspace_model",
names=["dwi_data_import_and_qspace_sampling"])
bredala.register("clindmri.preproc.connectomist.mask",
names=["dwi_rough_mask_extraction"])
bredala.register("clindmri.preproc.connectomist.outliers",
names=["dwi_outlier_detection"])
bredala.register("clindmri.preproc.connectomist.susceptibility",
names=["dwi_susceptibility_artifact_correction"])
bredala.register("clindmri.preproc.connectomist.registration",
names=["dwi_to_anatomy"])
bredala.register("clindmri.preproc.connectomist.eddy_current_and_motion",
names=[
"dwi_eddy_current_and_motion_correction",
"export_eddy_motion_results_to_nifti"
])
# First activate brainvisa env:
# /neurospin/brainvisa/build/Ubuntu-14.04-x86_64/bug_fix/bin/bv_env
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.morphologist",
names=["morphologist_all"])
bredala.register("clindmri.extensions.morphologist", names=["set_bvenv"])
except:
pass
# Clindmri import
from clindmri.segmentation.morphologist import morphologist_all
from clindmri.extensions.morphologist import set_bvenv
# Parameters to keep trace
__hopla__ = ["t1file", "subjectdir", "wffile", "wfid", "wfstatus", "spmrun",
"spmdir"]
# Script documentation
Credit: A Grigis
The proposed module display function signatures and by default function
line profiles. The latest option can be disabled::
import bredala
bredala.USE_PROFILER = False
At the beginning of your script import the project and select which specific
functions/methods have to be profiled/signed (it must be done before any
import):
"""
import bredala
bredala.register("bredala.demo.myfunctions",
names=["addition", "substraction"])
from bredala.demo.myfunctions import addition, substraction, factorial
addition(2, 1)
substraction(2, 1)
factorial(5)
#############################################################################
# For classes we can select to follow all the methods of a class:
bredala.register("bredala.demo.myclasses", names=["Square"])
from bredala.demo.myclasses import Square, Triangle
o = Square("my_square")
o.area(2)
o = Triangle("my_square")
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer",
names=["aparcstats2table", "asegstats2table"])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import aparcstats2table
from clindmri.segmentation.freesurfer import asegstats2table
# Parameters to keep trace
__hopla__ = ["fsdir", "statfiles"]
# Script documentation
doc = """
Freesurfer statistics
~~~~~~~~~~~~~~~~~~~~~
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import os
import shutil
import argparse
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("pyfreesurfer.conversions.voltools",
names=["mri_convert"])
bredala.register("pyfreesurfer.conversions.surftools",
names=["resample_cortical_surface", "surf_convert"])
bredala.register("pyfreesurfer.utils.regtools",
names=["conformed_to_native_space"])
except:
pass
# Pyfreesurfer import
from pyfreesurfer import __version__ as version
from pyfreesurfer import DEFAULT_FREESURFER_PATH
from pyfreesurfer.conversions.voltools import mri_convert
from pyfreesurfer.conversions.surftools import resample_cortical_surface
from pyfreesurfer.utils.regtools import conformed_to_native_space
from pyfreesurfer.conversions.surftools import surf_convert
##########################################################################
"""
"""
# System import
from __future__ import print_function
import os
import shutil
import argparse
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer",
names=["aparcstats2table", "asegstats2table"])
except:
pass
# Wrappers of FreeSurfer's tabs
from pyfreesurfer.utils.datatools import aparcstats2table
from pyfreesurfer.utils.datatools import asegstats2table
# Parameters to keep trace
__hopla__ = ["fsdir", "statfiles"]
# Script documentation
doc = """
Freesurfer statistics
============================================
Credit: A Grigis
The proposed module display function signatures and by default function
line profiles. The latest option can be disabled::
import bredala
bredala.USE_PROFILER = False
At the beginning of your script import the project and select all the
functions/methods of a module that must be profiled/signed (it must be done
before any import):
"""
import bredala
bredala.USE_PROFILER = False
bredala.register("bredala.demo.myfunctions")
bredala.register("bredala.demo.myclasses")
from bredala.demo.myfunctions import addition, substraction, factorial
from bredala.demo.myclasses import Square, Triangle
addition(2, 1)
substraction(2, 1)
factorial(2)
o = Square("my_square")
o.area(2)
o = Triangle("my_square")
o.area(2, 3)
#! /usr/bin/env python
##########################################################################
# Hopla - Copyright (C) AGrigis, 2015
# Distributed under the terms of the CeCILL-B license, as published by
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("os.path", names=["listdir"])
except:
pass
# System import
from datetime import datetime
import argparse
import os
# Parameters to keep trace
__hopla__ = ["runtime", "inputs", "outputs"]
def is_directory(dirarg):
""" Type for argparse - checks that directory exists.
"""
if not os.path.isdir(dirarg):
raise argparse.ArgumentError(
# for details.
##########################################################################
# System imports
from __future__ import print_function
import os
import argparse
import shutil
import glob
import numpy
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.connectivity.fsl",
names=["get_profile", "qc_profile"])
bredala.register("clindmri.tractography.fsl", names=["probtrackx2"])
bredala.register("clindmri.registration.fsl", names=["flirt"])
bredala.register("clindmri.segmentation.freesurfer",
names=["mri_vol2surf"])
except:
pass
# Clindmri imports
from clindmri.connectivity.fsl import get_profile
from clindmri.connectivity.fsl import qc_profile
from clindmri.extensions.freesurfer.reader import TriSurface
from clindmri.extensions.freesurfer.reader import apply_affine_on_mesh
from clindmri.registration.fsl import flirt
from clindmri.extensions.fsl import flirt2aff
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register(
"clindmri.tractography.connectomist.complete_tractography",
names=["complete_tractography"])
bredala.register(
"clindmri.tractography.connectomist.dwi_local_modeling",
names=["dwi_local_modeling"])
bredala.register(
"clindmri.tractography.connectomist.mask",
names=["tractography_mask"])
bredala.register(
"clindmri.tractography.connectomist.tractography",
names=["tractography"])
except:
pass
# Clindmri import
from clindmri.tractography.connectomist.complete_tractography import (
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
import numpy
import nibabel
import copy
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer",
names=["population_statistic", "parse_fs_lut"])
bredala.register("clindmri.plot.slicer", names=["xyz_mosaics"])
bredala.register("clindmri.plot.polar", names=["polarplot"])
bredala.register("clindmri.segmentation.fsl", names=["fslreorient2std"])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import population_statistic
from clindmri.segmentation.freesurfer import parse_fs_lut
from clindmri.plot.slicer import xyz_mosaics
from clindmri.plot.polar import polarplot
from clindmri.segmentation.fsl import fslreorient2std
from clindmri.extensions.freesurfer.reader import TriSurface
# Parameters to keep trace
# for details.
##########################################################################
# System imports
from __future__ import print_function
import os
import argparse
import shutil
import glob
import numpy
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.connectivity.fsl",
names=["get_profile", "qc_profile"])
bredala.register("clindmri.tractography.fsl", names=["probtrackx2"])
bredala.register("clindmri.registration.fsl", names=["flirt"])
bredala.register("clindmri.segmentation.freesurfer",
names=["mri_vol2surf"])
except:
pass
# Clindmri imports
from clindmri.connectivity.fsl import get_profile
from clindmri.connectivity.fsl import qc_profile
from clindmri.extensions.freesurfer.reader import TriSurface
from clindmri.extensions.freesurfer.reader import apply_affine_on_mesh
from clindmri.registration.fsl import flirt
from clindmri.extensions.fsl import flirt2aff
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer", names=["recon_all"])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import recon_all
# Parameters to keep trace
__hopla__ = ["fsdir", "subjectid", "anatfile"]
# Script documentation
doc = """
Freesurfer segmentation
~~~~~~~~~~~~~~~~~~~~~~~
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer",
names=[
"mri_convert", "resample_cortical_surface",
"conformed_to_native_space", "surf_convert", "qc"
])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import mri_convert
from clindmri.segmentation.freesurfer import resample_cortical_surface
from clindmri.segmentation.freesurfer import conformed_to_native_space
from clindmri.segmentation.freesurfer import surf_convert
from clindmri.segmentation.freesurfer import qc
# Script documentation
doc = """
Freesurfer inspection
# for details.
##########################################################################
# python modules
import os
import glob
import numpy
import shutil
import argparse
import textwrap
# bredala module
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.fsl", names=["bet2"])
bredala.register("clindmri.tractography.fsl",
names=["bedpostx", "bedpostx_datacheck"])
bredala.register("clindmri.registration.utils", names=["extract_image"])
bredala.register("clindmri.plot.slicer", names=["plot_image"])
except:
pass
# clindmri modules
from clindmri.segmentation.fsl import bet2
from clindmri.tractography.fsl import bedpostx
from clindmri.registration.utils import extract_image
from clindmri.tractography.fsl import bedpostx_datacheck
# parameters to keep trace
__hopla__ = [
line profiles. The latest option can be disabled::
import bredala
bredala.USE_PROFILER = False
At the beginning of your script import the project and select all the
functions/methods of a module that must be profiled/signed (it must be done
before any import).
In this example we want to add or substract only integer values and we show
only the 'addition' function signature:
"""
import bredala
bredala.USE_PROFILER = False
bredala.register("bredala.demo.myfunctions", names=["addition"])
bredala.itype("bredala.demo.myfunctions",
name="addition",
input_types=(int, int))
bredala.otype("bredala.demo.myfunctions",
name="addition",
output_types=(int, ))
bredala.itype("bredala.demo.myfunctions",
name="substraction",
input_types=(int, int))
bredala.otype("bredala.demo.myfunctions",
name="substraction",
output_types=(int, ))
from bredala.demo.myfunctions import addition, substraction
addition(2, 1)
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
import numpy
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("qap.viz.plotting", names=["plot_mosaic"])
bredala.register("capsul.process", names=["get_process_instance"])
bredala.register("mmutils.adapters.io", names=["gzip_file"])
except:
pass
# Mmutils import
from mmutils.adapters.io import gzip_file
# CAPSUL import
from capsul.study_config import StudyConfig
from capsul.process import get_process_instance
# Qap import
from qap.viz.plotting import plot_mosaic
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from nilearn import plotting
import nibabel
import argparse
import os
from clindmri.registration.fsl import flirt
from glob import glob
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.registration.fsl.flirt")
bredala.register("nilearn.plotting")
except:
pass
doc = """
Perform unit registration of T2 on T1 image using fsl/flirt command.
Use mutual info and trigger sinc resampling
Create results according to path and prepare QC plots (from nilearn)
Command:
========
python register_pitie.py -r AxT1enhanced.nii.gz -i AxT2.nii.gz -o rAxT2.nii.gz
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register(
"clindmri.tractography.connectomist.complete_tractography",
names=["complete_tractography"])
bredala.register("clindmri.tractography.connectomist.dwi_local_modeling",
names=["dwi_local_modeling"])
bredala.register("clindmri.tractography.connectomist.mask",
names=["tractography_mask"])
bredala.register("clindmri.tractography.connectomist.tractography",
names=["tractography"])
except:
pass
# Clindmri import
from clindmri.tractography.connectomist.complete_tractography import (
complete_tractography)
# Parameters to keep trace
##########################################################################
# System imports
from __future__ import print_function
import argparse
import os
import shutil
import nibabel
import numpy
import json
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clinfmri.quality_control.movement_quantity",
names=["time_serie_mq"])
bredala.register("nipype.algorithms.misc", names=["TSNR.run"])
bredala.register("qap.temporal_qc", names=["fd_jenkinson"])
bredala.register(
"qap.qap_workflows_utils",
names=["qap_functional_spatial", "qap_functional_temporal"])
bredala.register("qap.spatial_qc",
names=[
"snr", "cnr", "fber", "efc", "artifacts", "fwhm",
"ghost_direction", "ghost_all", "summary_mask",
"get_background", "check_datatype",
"convert_negatives"
])
bredala.register("mmqa.fmri.fmri_spikes", names=["spike_detector"])
bredala.register("mmqa.fmri.movement_quantity", names=["get_rigid_matrix"])
bredala.register("qap.temporal_qc",
##########################################################################
# Bredala - Copyright (C) AGrigis, 2015
# Distributed under the terms of the CeCILL-B license, as published by
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
import unittest
# Bredala import
import bredala
bredala.USE_PROFILER = True
bredala.register("bredala.demo.myfunctions", names=["addition", "factorial"])
bredala.register("bredala.demo.myclasses", names=["Square.area", "Triangle.area"])
from bredala.demo.myfunctions import addition, substraction, factorial
from bredala.demo.myclasses import Square, Triangle
class TestBredala(unittest.TestCase):
""" Test the module functionalities.
"""
def test_specific_functions(self):
""" Test functions execution follow up.
"""
addition(2, 1)
substraction(2, 1)
factorial(5)
##########################################################################
"""
"""
# System import
from __future__ import print_function
import os
import shutil
import argparse
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer",
names=["textures2table", "mri_surf2surf"])
except:
pass
# Wrappers of FreeSurfer's tabs
from pyfreesurfer.utils.datatools import textures2table
# Parameters to keep trace
__hopla__ = ["fsdir", "ico_order", "fsconfig", "textures_regex",
"textures_files"]
# Script documentation
doc = """
Freesurfer textures
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
import numpy
import nibabel
import copy
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer",
names=["population_statistic", "parse_fs_lut"])
bredala.register("clindmri.plot.slicer", names=["xyz_mosaics"])
bredala.register("clindmri.plot.polar", names=["polarplot"])
bredala.register("clindmri.segmentation.fsl", names=["fslreorient2std"])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import population_statistic
from clindmri.segmentation.freesurfer import parse_fs_lut
from clindmri.segmentation.freesurfer import mri_binarize
from clindmri.plot.slicer import xyz_mosaics
from clindmri.plot.polar import polarplot
from clindmri.segmentation.fsl import fslreorient2std
from clindmri.extensions.freesurfer.reader import TriSurface
# System imports
from __future__ import print_function
import argparse
import os
import shutil
import nibabel
import numpy
import json
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clinfmri.quality_control.movement_quantity",
names=["time_serie_mq"])
bredala.register("nipype.algorithms.misc", names=["TSNR.run"])
bredala.register("qap.temporal_qc", names=["fd_jenkinson"])
bredala.register("qap.qap_workflows_utils",
names=["qap_functional_spatial",
"qap_functional_temporal"])
bredala.register("qap.spatial_qc", names=["snr", "cnr", "fber", "efc",
"artifacts", "fwhm",
"ghost_direction", "ghost_all",
"summary_mask", "get_background",
"check_datatype",
"convert_negatives"])
bredala.register("mmqa.fmri.fmri_spikes", names=["spike_detector"])
bredala.register("mmqa.fmri.movement_quantity", names=["get_rigid_matrix"])
bredala.register("qap.temporal_qc", names=["mean_dvars_wrapper",
"mean_outlier_timepoints",
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register(
"clindmri.segmentation.freesurfer",
names=["mri_convert", "resample_cortical_surface",
"conformed_to_native_space", "surf_convert", "qc"])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import mri_convert
from clindmri.segmentation.freesurfer import resample_cortical_surface
from clindmri.segmentation.freesurfer import conformed_to_native_space
from clindmri.segmentation.freesurfer import surf_convert
from clindmri.segmentation.freesurfer import qc
# Script documentation
doc = """
Freesurfer inspection
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.freesurfer", names=["recon_all"])
except:
pass
# Clindmri import
from clindmri.segmentation.freesurfer import recon_all
# Parameters to keep trace
__hopla__ = ["fsdir", "subjectid", "anatfile"]
# Script documentation
doc = """
Freesurfer segmentation
~~~~~~~~~~~~~~~~~~~~~~~
Performs all the FreeSurfer cortical reconstruction process.
# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
# for details.
##########################################################################
# python modules
import os
import glob
import numpy
import shutil
import argparse
# bredala module
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("clindmri.segmentation.fsl", names=["bet2"])
bredala.register("clindmri.tractography.fsl",
names=["bedpostx", "bedpostx_datacheck"])
bredala.register("clindmri.registration.utils", names=["extract_image"])
bredala.register("clindmri.plot.slicer", names=["plot_image"])
except:
pass
# clindmri modules
from clindmri.segmentation.fsl import bet2
from clindmri.tractography.fsl import bedpostx
from clindmri.registration.utils import extract_image
from clindmri.tractography.fsl import bedpostx_datacheck
# parameters to keep trace
##########################################################################
# System import
from __future__ import print_function
import argparse
import os
import shutil
import numpy
import nibabel
import copy
# Bredala import
try:
import bredala
bredala.USE_PROFILER = False
bredala.register("pyfreesurfer.utils.stattools",
names=["population_summary"])
bredala.register("pyfreesurfer.plots.slicer",
names=["slice_aparc_overlay"])
bredala.register("pyfreesurfer.plots.polar", names=["polar_plot"])
bredala.register("pyfreesurfer.utils.filetools", names=["surf2ctm"])
except:
pass
# Clindmri import
from pyfreesurfer import __version__ as version
from pyfreesurfer.utils.stattools import population_summary
from pyfreesurfer.plots.slicer import slice_aparc_overlay
from pyfreesurfer.plots.slicer import AXIS_NAME
from pyfreesurfer.plots.polar import polar_plot
from pyfreesurfer import DEFAULT_FREESURFER_PATH
from pyfreesurfer.utils.filetools import surf2ctm
