# -*- coding: utf-8 -*-
'''
Classes
=======
:class:`Popen`
--------------
Functions
=========
:func:`find_spm`
----------------
:func:`check_spm_configuration`
-------------------------------
:func:`check_configuration_values`
----------------------------------
:func:`auto_configuration`
--------------------------
:func:`spm_command`
-------------------
:func:`call`
------------
:func:`check_call`
------------------
:func:`check_output`
--------------------
'''
from __future__ import absolute_import
import os.path as osp
import glob
import soma.subprocess
from traits.api import Undefined
[docs]
def find_spm(spm_version='', matlab_exec='matlab', matlab_path=None):
""" Function to return the root directory of SPM.
Parameters
----------
spm_version: str (default='')
if given, the version to use when running spm<version> in Matlab.
matlab: str (default='matlab')
if given, is the path to the Matlab executable.
matlab_path: str (default None)
if given, is a Matlab expression fed to addpath.
Returns
-------
last_line: str
the SPM root directory
"""
# Script to execute with matlab in order to find SPM root dir
script = ("spm%s;"
"fprintf(1, '%%s', spm('dir'));"
"exit();") % spm_version
# Add matlab path if necessary
if matlab_path:
script = "addpath({0});".format(matlab_path) + script
# Generate the matlab command
command = [matlab_exec,
"-nodisplay", "-nosplash", "-nojvm",
"-r", script]
# Try to execute the command
try:
last_line = soma.subprocess.check_output(command).decode('utf-8')
except OSError:
raise Exception("Could not find SPM.")
# Do not consider weird data at the end of the line
if '\x1b' in last_line:
last_line = last_line[:last_line.index('\x1b')]
# If the last line is empty, SPM not found
if last_line == "":
raise Exception("Could not find SPM.")
return last_line
[docs]
def check_spm_configuration(study_config):
'''
Obsolete.
Check thas study_config configuration is valid to call SPM commands.
If not, try to automatically configure SPM. Finally raises an
EnvironmentError if configuration is still wrong.
'''
if getattr(study_config, '_spm_config_checked', False):
# Check SPM configuration only once
return
if 'SPMConfig' not in study_config.modules:
raise EnvironmentError('SPMConfig module is missing in StudyConfig.')
if study_config.use_spm is False:
raise EnvironmentError(
'Configuration is set not to use SPM. Set use_spm to True in '
'order to use SPM.')
# Configuration must be valid otherwise
# try to update configuration and recheck is validity
if check_configuration_values(study_config) is not None:
auto_configuration(study_config)
error_message = check_configuration_values(study_config)
if error_message:
raise EnvironmentError(error_message)
study_config.use_spm = True
study_config._spm_config_checked = True
[docs]
def check_configuration_values(study_config):
'''
Obsolete.
Check if the configuration is valid to run SPM and returns an error
message if there is an error or None if everything is good.
'''
if study_config.spm_directory is Undefined:
return 'No SPM directory defined'
if not osp.isdir(study_config.spm_directory):
return "'%s' is not a valid SPM directory" % study_config.spm_directory
if study_config.spm_standalone is Undefined:
return 'SPM standalone usage is undefined'
if study_config.spm_standalone:
if study_config.spm_exec is Undefined:
return 'spm_exec must be defined to use SPM standalone'
if not osp.isdir(study_config.spm_mcr_directory):
return '"%s" is not a valid mrc directory for SPM standalone' \
% study_config.spm_mcr_directory
else:
if not study_config.use_matlab:
return 'Matlab is disabled. Cannot use SPM via Matlab'
[docs]
def auto_configuration(study_config):
'''
Obsolete.
Try to automatically set the study_config configuration for SPM.
'''
if study_config.spm_directory is not Undefined and \
osp.exists(study_config.spm_directory):
spm_sh = glob.glob(osp.join(study_config.spm_directory, 'run_spm*.sh'))
if spm_sh:
if study_config.spm_standalone is Undefined:
study_config.spm_standalone = True
elif not study_config.spm_standalone:
raise EnvironmentError(
'Requested SPM non standalone but directory "%s" contains '
'SPM standalone' % study_config.spm_directory)
spm_version = spm_sh[0][:-3]
spm_version = spm_version[spm_version.rfind('run_spm')+7:]
if study_config.spm_version is Undefined:
study_config.spm_version = spm_version
elif study_config.spm_version != spm_version:
raise EnvironmentError(
'Requested SPM %s but directory "%s" contains SPM %s'
% (study_config.spm_version, study_config.spm_directory,
spm_version))
mcr_dir = glob.glob(osp.join(study_config.spm_directory, 'mcr',
'v*'))
if mcr_dir:
study_config.spm_mcr_directory = mcr_dir[0]
return
# Matlab
# determine SPM version (currently only 8 or 12 are supported)
if study_config.spm_directory is not Undefined \
and osp.isdir(osp.join(study_config.spm_directory, 'toolbox',
'OldNorm')):
spm_version = '12'
elif study_config.spm_directory is not Undefined \
and osp.isdir(osp.join(study_config.spm_directory, 'templates')):
spm_version = '8'
else:
spm_version = Undefined
if spm_version is not Undefined:
if study_config.spm_version is Undefined:
study_config.spm_version = spm_version
elif study_config.spm_version != spm_version:
raise EnvironmentError(
'Requested SPM %s but directory "%s" contains SPM %s'
% (study_config.spm_version, study_config.spm_directory,
spm_version))
def spm_command(study_config, batch_file):
if study_config.spm_standalone:
cmd = [study_config.spm_exec,
study_config.spm_mcr_directory,
'script',
batch_file]
return cmd
else:
raise NotImplementedError('Running SPM with matlab is not '
'implemented yet')
[docs]
class Popen(soma.subprocess.Popen):
'''
Equivalent to Python soma.subprocess.Popen for SPM batch
'''
def __init__(self, study_config, batch_file, **kwargs):
check_spm_configuration(study_config)
cmd = spm_command(study_config, batch_file)
super(Popen, self).__init__(cmd, **kwargs)
[docs]
def call(study_config, batch_file, **kwargs):
'''
Equivalent to Python soma.subprocess.call for SPM batch
'''
check_spm_configuration(study_config)
cmd = spm_command(study_config, batch_file)
return soma.subprocess.call(cmd, **kwargs)
[docs]
def check_call(study_config, batch_file, **kwargs):
'''
Equivalent to Python soma.subprocess.check_call for SPM batch
'''
check_spm_configuration(study_config)
cmd = spm_command(study_config, batch_file)
return soma.subprocess.check_call(cmd, **kwargs)
[docs]
def check_output(study_config, batch_file, **kwargs):
'''
Equivalent to Python soma.subprocess.check_output for SPM batch
'''
check_spm_configuration(study_config)
cmd = spm_command(study_config, batch_file)
return soma.subprocess.check_output(cmd, **kwargs)
if __name__ == '__main__':
from capsul.api import StudyConfig
from capsul.soma.subprocess.spm import check_call as call_spm
import tempfile
sc = StudyConfig(spm_directory='/home/yc176684/spm12-standalone-7219')
batch = tempfile.NamedTemporaryFile(suffix='.m')
batch.write("fprintf(1, '%s', spm('dir'));")
batch.flush()
call_spm(sc, batch.name)
