# 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
# 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