#! /usr/bin/env python
##########################################################################
# CAPS - Copyright (C) CEA, 2013
# 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.
##########################################################################
# Trait import
try:
from traits.trait_base import _Undefined
from traits.api import (File, List, Directory, Str, Int, Enum, Float,
Dict, Any)
except ImportError:
from enthought.traits.api import (File, List, Directory, Str, Int, Enum,
Float, Dict, Any)
# Caps import
from matlab_utils import ConnProcess
[docs]class Results(ConnProcess):
""" Second-lvel analyses with CONN
"""
jobname = "Results"
def __init__(self):
super(Results, self).__init__()
self.add_trait("done", Int(
_Undefined(),
optional=True,
output=False,
field="done",
desc=("1/0, [0]. 0: only edits Results fields (do not run "
"Results->'Done'); 1: run Results->'Done'")))
self.add_trait("overwrite", Enum(
["Yes", "No"],
optional=True,
output=False,
field="overwrite",
desc="overwrite existing results if they exist ['Yes']"))
# PERFORMS FIRST-LEVEL ANALYSES (ROI-to-ROI and seed-to-voxel)
self.add_trait("analysis_number", List(Int(),
optional=True,
output=False,
field="analysis_number",
desc=("sequential indexes identifying each set of independent "
"analyses (set this variable to 0 to identify "
"voxel-to-voxel analyses) [1] ")))
self.add_trait("foldername", Directory(
optional=True,
output=False,
field="foldername",
desc=("folder to store the results ")))
self.add_trait("between_subjects_effect_names", List(Str(),
optional=True,
output=False,
field="between_subjects.effect_names",
desc=("second-level effect names ")))
self.add_trait("between_subjects_contrast", List(Float(),
optional=True,
output=False,
field="between_subjects.contrast",
desc=("between_subjects contrast vector (same size as "
"between_subjects_effect_names) ")))
self.add_trait("between_conditions_effect_names", List(Str(),
optional=True,
output=False,
field="between_conditions.effect_names",
desc=("condition names (as in Setup.conditions.names) [defaults "
"to multiple analyses, one per condition]. ")))
self.add_trait("between_conditions_contrast", List(Float(),
optional=True,
output=False,
field="between_conditions.contrast",
desc=("between_conditions contrast vector (same size as "
"between_conditions_effect_names) ")))
self.add_trait("between_sources_effect_names", List(Str(),
optional=True,
output=False,
field="between_sources.effect_names",
desc=("sources names. (as in Analysis.regressors, typically "
"appended with _1_1; generally they are appended with "
"_N_M -where N is an index ranging from 1 to 1+derivative "
"order, and M is an index ranging from 1 to the number of "
"dimensions specified for each ROI; for example "
"ROINAME_2_3 corresponds to the first derivative of the "
"third PCA component extracted from the roi ROINAME) "
"[defaults to multiple analyses, one per source]. ")))
self.add_trait("between_sources_contrast", List(Float(),
optional=True,
output=False,
field="between_sources.contrast",
desc=("between_sources contrast vector (same size as "
"between_sources_effect_names) ")))
def _run_process(self):
""" Method to acess the Matlab script of the CONN module.
"""
# Force some default parameters to be added in the batch
if isinstance(self.done, _Undefined):
self.done = 0
return self.run()
if __name__ == '__main__':
from manager import InputDataManager
from spatial_preproc import SpatialPreproc
from setup import Setup
from temporal_preproc import TemporalPreproc
from analysis import Analysis
import numpy
manager = InputDataManager()
manager.data_path = "/volatile/new/salma/NYU_TRT_session1a/"
manager.functional_dir_name = "func"
manager.anatomical_dir_name = "anat"
manager()
spreproc = SpatialPreproc()
spreproc.execute_mfile = False
# Setup step
setup = Setup()
setup.batch_header = spreproc.batch
setup.matlab_paths = ["/i2bm/local/spm8-5236",
"/volatile/new/salma/conn"]
setup.output_directory = "/volatile/new/salma/test_NSAP_NYU_NOspreproc"
setup.functional_paths = manager.functional_paths
setup.anatomical_paths = manager.anatomical_paths
setup.sp_functional_prefixes = ["swralfo*.nii"]
setup.sp_anatomical_prefix = "wmmprage_a*.nii"
setup.Grey_masks_prefix = "mwc1mprage_a*.nii"
setup.White_masks_prefix = "mwc2mprage_a*.nii"
setup.CSF_masks_prefix = "mwc3mprage_a*.nii"
setup.covariates_names = ["Realignment"]
setup.covariates_prefixes = [["rp_alfo*.txt"]]
setup.conditions_names = ["Condition1"]
setup.conditions_onsets = [[[numpy.nan if nsess != ncond else 0
for nsess in range(setup.nconditions)] for nsub in xrange(setup.nsubjects
)] for ncond in range(setup.nconditions)] # TODO: move it to manager?
setup.conditions_durations = [[[numpy.nan if nsess != ncond else numpy.inf
for nsess in range(setup.nconditions)] for nsub in xrange(setup.nsubjects
)]for ncond in range(setup.nconditions)] # TODO: move it to manager?
setup.overwrite = "Yes"
setup.done = 1
setup.isnew = 1
setup.execute_mfile = False
# Temporal preproc step
tpreproc = TemporalPreproc()
tpreproc.batch_header = setup.batch
tpreproc.execute_mfile = False
tpreproc.overwrite = "Yes"
tpreproc.done = 1
# Analysis
analysis = Analysis()
analysis.batch_header = tpreproc.batch
analysis.execute_mfile = False
analysis.overwrite = "Yes"
analysis.done = 1
# Results
results = Results()
results.matlab_paths = setup.matlab_paths
results.batch_header = analysis.batch
results.output_directory = setup.output_directory
results.execute_mfile = True
results.done = 1
runtime = results._run_process()
print runtime[0]
print runtime[1]
print runtime[2]
print results.mlabcmdline
