def get_saccades_for_group(self, group, configuration):
""" Returns the saccades for the given group and configuration.
If configuration is not passed, we use the default.
"""
if self.use_flydra_db:
table = 'groupsaccades_%s' % configuration
if self.flydra_db.has_sample(group) and \
self.flydra_db.has_table(group, table):
t = self.flydra_db.get_table(group, table)
#value = t.copy()
value = t
#self.flydra_db.release_table(t)
return value
if self.use_cache:
key = str(('get_saccades_for_group', group, configuration))
if key in self.shelve:
return self.shelve[key]
filename = self.groups[group].configurations[configuration]
saccades = saccades_read_mat(filename)
if self.use_flydra_db:
if not self.flydra_db.has_sample(group):
self.flydra_db.add_sample(group)
self.flydra_db.set_table(group, table, saccades)
if self.use_cache:
self.shelve[key] = saccades
return saccades
def __init__(self, data, verbose=False):
''' data: base directory '''
if not os.path.exists(data) or not os.path.isdir(data):
raise Exception('Could not open directory %s' % data)
self.data = data
# self.use_cache = True
self.use_cache = False
self.use_flydra_db = True
if self.use_cache:
self.open_shelve()
if self.use_flydra_db:
self.open_flydra_db()
self.groups = {}
#self.group2samples = {}
# maps id to .mat file
self.sample2expmat = {}
# maps id to .pickle file
self.sample2exppickle = {}
# list of all configurations
self.configurations = set()
# maps sample -> group
self.sample2group = {}
#print "Loading data in %s" % data
for group in os.listdir(data):
group_dir = os.path.join(data, group)
if not os.path.isdir(group_dir):
continue
# print "Reading group %s" % group
group_record = Group()
for file in [file for file in os.listdir(group_dir)
if file.startswith('data_') and file.endswith('.mat')]:
id = file[5:-4]
group_record.samples.add(id)
self.sample2expmat[id] = os.path.join(group_dir,file)
self.sample2group[id] = group
for file in [file for file in os.listdir(group_dir)
if file.startswith('data_') and file.endswith('.pickle')]:
id = file[5:-7]
group_record.samples.add(id)
self.sample2exppickle[id] = os.path.join(group_dir,file)
self.sample2group[id] = group
group_record.has_experimental_data = len(group_record.samples) > 0
processed_dir = os.path.join(group_dir, 'processed')
if not os.path.exists(processed_dir):
if verbose:
print "No processed data found for %s." % group
pass
else:
for conf in os.listdir(processed_dir):
saccades = os.path.join(processed_dir, conf, 'saccades.mat')
if os.path.exists(saccades):
group_record.configurations[conf] = saccades
# add to general list
self.configurations.add(conf)
# else:
# conf_dir = os.path.join(processed_dir, conf)
# for file in [file for file in os.listdir(conf_dir)
# if file.startswith('processed_data_') and file.endswith('.mat')]:
# id = file[5:-7]
# if we don't have exp data, get list of samples from
# processed data
if group_record.configurations and \
not group_record.has_experimental_data:
saccades = saccades_read_mat(saccades)
group_record.samples = set(numpy.unique(saccades['sample']))
for sample in group_record.samples:
self.sample2group[sample] = group
if len(group_record.samples)> 0:
self.groups[group] = group_record
print "has it", group, group_record.has_experimental_data
def main():
parser = OptionParser(usage=description)
parser.add_option("--saccade_data", help="Main data directory",
default='saccade_data')
parser.add_option("--db", help="FlydraDB directory")
parser.add_option("--verbose", help='Verbose output',
default=False, action="store_true")
(options, args) = parser.parse_args() #@UnusedVariable
if not options.db:
raise Exception('Please define FlydraDB directory using `--db`.')
def printv(s):
if options.verbose:
print(s)
flydra_db = FlydraDB(options.db, create=True)
matlab_dir = options.saccade_data
for group in os.listdir(matlab_dir):
group_dir = os.path.join(matlab_dir, group)
if not os.path.isdir(group_dir):
continue
printv("Opening {0}".format(group))
#
#
# exp_data, attributes = read_raw_data(filename)
#
# consider_importing_processed(flydra_db, sample, exp_data, attributes)
#
# flydra_db.set_attr(sample, 'species', attributes['species'])
# flydra_db.set_attr(sample, 'background', attributes['background'])
#
# flydra_db.set_table(sample, EXP_DATA_TABLE, exp_data)
# flydra_db.add_sample_to_group(sample, group)
# flydra_db.add_sample_to_group(sample, 'ros')
#
processed_dir = os.path.join(group_dir, 'processed')
if not os.path.exists(processed_dir):
printv("No processed data found for group %r." % group)
continue
for conf in os.listdir(processed_dir):
# first look for saccades.mat
saccades_file = os.path.join(processed_dir, conf, 'saccades.mat')
if os.path.exists(saccades_file):
printv('Loading from file %r.' % saccades_file)
saccades = saccades_read_mat(saccades_file)
samples = numpy.unique(saccades['sample'])
for sample in samples:
if not flydra_db.has_sample(sample):
flydra_db.add_sample(sample)
flydra_db.add_sample_to_group(sample, group)
sample_saccades = saccades[saccades[:]['sample'] == sample]
flydra_db.set_table(sample=sample, table=SACCADES_TABLE,
version=conf, data=sample_saccades)
# else:
# prefix = 'data_'
# suffix = '.mat'
# for file in [file for file in os.listdir(group_dir)
# if (file.startswith(prefix)) and file.endswith(suffix)]:
#
# sample = file[len(prefix):file.index('.')]
#
# if verbose:
# print(" - Considering sample {0}".format(sample.__repr__()))
#
# if not flydra_db.has_sample(sample):
# flydra_db.add_sample(sample)
#
# filename = os.path.join(group_dir, file)
#
#
#
# else:
# for conf in os.listdir(processed_dir):
# saccades = os.path.join(processed_dir, conf, 'saccades.mat')
# if os.path.exists(saccades):
# group_record.configurations[conf] = saccades
# # add to general list
# self.configurations.add(conf)
## else:
## conf_dir = os.path.join(processed_dir, conf)
## for file in [file for file in os.listdir(conf_dir)
## if file.startswith('processed_data_') and file.endswith('.mat')]:
## id = file[5:-7]
#
# # if we don't have exp data, get list of samples from
# # processed data
# if group_record.configurations and \
# not group_record.has_experimental_data:
# saccades = saccades_read_mat(saccades)
# group_record.samples = set(numpy.unique(saccades['sample']))
# for sample in group_record.samples:
# self.sample2group[sample] = group
#
# if len(group_record.samples)> 0:
# self.groups[group] = group_record
#
# print "has it", group, group_record.has_experimental_data
#
flydra_db.close()
