def testOnNumpyArray(self):
na = np.random.randn(4,4)
d = { 'k1' : 'v1',
'd2' : {'d2k1':0, 1:190, 'na':na,
'd2-3' : {'plop':'plip',435:'fr'}},
'k3' : 1098,
}
sd1 = dictToString(d)
#print sd1
naf = {'precision':2, 'max_line_width':100}
sd2 = dictToString(d, numpyArrayFormat=naf)
def append_common_treatment_options(parser):
parser.add_option('-s','--spm-mat-file', metavar='MATFILE', dest='spmFile',
default=None,
help='SPM.mat from which to extract paradigm data '\
'(onsets and stimulus durations) and TR. Note: if '\
'the option "-p/--paradigm" is also provided, then'\
' the latter is ignored.')
paradigms = ['loc_av', 'loc', 'loc_cp_only', 'loc_cpcd', 'language',
'loc_ainsi', 'loc_ainsi_cpcd']
parser.add_option('-p','--paradigm', dest='paradigm', default=paradigms[0],
metavar='STRING', type='choice', choices=paradigms,
help='Paradigm to use, choices are: '+ \
string.join(paradigms,',') + '. Default is %default.'\
' Note: ignored if option "-s/--spm-mat-file" is '\
'provided.')
parser.add_option('-r','--paradigm-csv', dest='paradigm_csv',
default=None,
metavar='CSVFILE',
help='Paradigm CSV file input')
parser.add_option('-I','--time-repetition', dest='tr',
default=None,
metavar='FLOAT',type='float',
help='Repetition time')
inputTypes = ['volume', 'surface', 'simulation']
parser.add_option('-d','--data-type', type='choice', choices=inputTypes,
metavar='STRING', dest='inputDataType', default='volume',
help='Define the type of input data, choices are: ' + \
string.join(inputTypes,',') + ' default is %default')
data_choices = ['default', 'small', 'realistic']
parser.add_option('-t', choices=data_choices, dest='data_scenario',
metavar='STRING', default='default',
help='Scenario for default data set: %s.' \
%', '.join(data_choices))
parser.add_option('-v','--verbose',dest='verbose',metavar='INTEGER',
type='int',default=0,
help=dictToString(pyhrf.verboseLevels))
parser.add_option('-f','--func-data-file', action='append',
dest='func_data_file',
metavar='FILE', default=None,
help='Functional data file (BOLD signal).')
parser.add_option('-k','--mask-file',dest='mask_file',
metavar='FILE', default=None,
help='Functional mask file '\
'(n-ary, may be a parcellation).')
parser.add_option('-g','--mesh-file',dest='mesh_file',
metavar='FILE', default=None,
help='Mesh file (only for surface analysis)')
def get_info(self, long=True):
s = ''
s += 'sessionDurations: %s\n' %str(self.sessionDurations)
allOns = []
for oc in self.stimOnsets.values(): #parse conditions
for o in oc: #parse sessions
allOns.extend(o)
allOns = np.array(allOns)
allOns.sort()
last = allOns.max()
meanISI = np.diff(allOns).mean()
stdISI = np.diff(allOns).std()
s += ' - onsets : ISI=%1.2f(%1.2f)sec' \
' - last event: %1.2fsec\n' %(meanISI, stdISI, last)
for stimName in self.stimOnsets.keys():
ntrials = [len(o) for o in self.stimOnsets[stimName]]
s += ' >> %s, trials per session: %s\n' %(stimName,str(ntrials))
if long:
s += dictToString(self.stimOnsets[stimName], prefix=' ')
s += dictToString(self.stimDurations[stimName], prefix=' ')
return s
def run_pyhrf_cmd_treatment(cfg_cmd, exec_cmd, default_cfg_file,
default_profile_file, label_for_cluster):
usage = 'usage: %%prog [options]'
description = 'Manage a joint detection-estimation treatment of fMRI data.' \
'This command runs the treatment defined in an xml '\
'parameter file. See pyhrf_jde_buildcfg command to build a'\
'template of such a file. If no xml file found, then runs a '\
'default example analysis.'
parser = OptionParser(usage=usage, description=description)
parser.add_option('-c','--input-cfg-file', metavar='XMLFILE', dest='cfgFile',
default=default_cfg_file,
help='Configuration file: XML file containing parameters'\
' defining input data and analysis to perform.')
parser.add_option('-r','--roi-data', metavar='PICKLEFILE', dest='roidata',
default=None, help='Input fMRI ROI data. The data '\
'definition part in the config file is ignored.')
parser.add_option('-t','--treatment_pck',
metavar='PICKLEFILE', dest='treatment_pck',
default=None, help='Input treatment as a pickle dump.' \
'The XML cfg file is ignored')
parser.add_option('-s','--stop-on-error', dest='stop_on_error',
action='store_true',
default=False, help='For debug: do not continue if error' \
' during one ROI analysis')
parser.add_option('-v','--verbose',dest='verbose',metavar='INTEGER',
type='int',default=0,
help=dictToString(pyhrf.verboseLevels))
parser.add_option('-p','--profile',action='store_true', default=False,
help='Enable profiling of treatment. Store profile data in '\
'%s. NOTE: not avalaible in parallel mode.'\
%default_profile_file)
parallel_choices = ['LAN','local','cluster']
parser.add_option('-x','--parallel', choices=parallel_choices,
help='Parallel processing. Choices are %s'\
%string.join(parallel_choices,', '))
(options,args) = parser.parse_args()
pyhrf.verbose.set_verbosity(options.verbose)
t0 = time.time()
if options.treatment_pck is not None:
f = open(options.treatment_pck)
treatment = cPickle.load(f)
f.close()
else:
if not os.path.exists(options.cfgFile):
print 'Error: could not find default configuration file "%s"\n'\
'Consider running "%s" to generate it.' \
%(options.cfgFile, cfg_cmd)
sys.exit(1)
else:
pyhrf.verbose(1, 'Loading configuration from: "%s" ...' \
%options.cfgFile)
f = open(options.cfgFile, 'r')
sXml = string.join(f.readlines())
f.close()
treatment = xmlio.fromXML(sXml)
if 0:
sXml = xmlio.toXML(treatment,
handler=xmlio.xmlnumpy.NumpyXMLHandler())
f = './treatment_cmd.xml'
fOut = open(f,'w')
fOut.write(sXml)
fOut.close()
#f = open(fOut, 'w')
#cPickle.dump(treatment, f)
#f.close()
treatment.analyser.set_pass_errors(not options.stop_on_error)
if options.parallel is not None:
# tmpDir = tempfile.mkdtemp(prefix='pyhrf',
# dir=pyhrf.cfg['global']['tmp_path'])
# pyhrf.verbose(1, 'Tmpdir: %s' %tmpDir)
treatment.run(parallel=options.parallel)
else:
if options.roidata is not None:
#treatment.set_roidata(options.roidata)
pyhrf.verbose(1, 'Loading ROI data from: "%s" ...' \
%options.roidata)
roidata = cPickle.load(open(options.roidata))
roidata.verbosity = pyhrf.verbose.verbosity
if pyhrf.verbose > 1:
print roidata.getSummary()
#TODO: enable profiling
pyhrf.verbose(1, 'Launching analysis ...')
if options.profile:
cProfile.runctx("result = treatment.analyser(roidata)",
globals(),
{'treatment':treatment,'roidata': roidata},
default_profile_file)
else:
result = treatment.analyser(roidata)
outPath = op.dirname(op.abspath(options.roidata))
fOut = op.join(outPath,"result_%04d.pck" %roidata.get_roi_id())
pyhrf.verbose(1, 'Dumping results to %s ...' %fOut)
f = open(fOut, 'w')
cPickle.dump(result, f)
f.close()
else:
pyhrf.verbose(1, 'ROI data is none')
if options.profile:
cProfile.runctx("treatment.run()", globals(),
{'treatment':treatment}, default_profile_file)
else:
#print 'treatment:', treatment
treatment.run()
pyhrf.verbose(1, 'Estimation done, took %s' %format_duration(time.time() - t0))
