def read_image(model, expect_missing_file):
try:
image = skimage.io.imread(model.path)
model.load(image)
except Exception as e:
terminal_error("Could not load image file: %s because: %s" % (model.path, str(e)))
else:
return True
def version(self, value):
version_regex = re.compile(r"""\d+\.\d+\.\d+""")
if version_regex.match(value):
self._version = value
else:
log.critical(
"Change the value in the VERSION file in the root directory of fylm_critic to 'x.y.z'."
)
terminal_error("Invalid version number! %s" % value)
def load(self, data):
try:
self._last_state, self._last_state_time_period = self._parse_state(data[0])
if len(data) > 1:
# We have some annotations already
for line in data[1:]:
self._parse_line(line)
except Exception as e:
terminal_error("Could not parse line for Channel Locator because of: %s" % e)
def load(self, data):
try:
header = data[0]
self._top_left, self._bottom_right = self._parse_header(header)
for line in data[1:]:
channel_number, locations = self._parse_line(line)
self._channels[channel_number] = locations
except Exception as e:
terminal_error("Could not parse line for Channel Locator because of: %s" % e)
def load(self, data):
try:
header = data[0]
self._top_left, self._bottom_right = self._parse_header(header)
for line in data[1:]:
channel_number, locations = self._parse_line(line)
self._channels[channel_number] = locations
except Exception as e:
terminal_error(
"Could not parse line for Channel Locator because of: %s" % e)
def read_text(model, expect_missing_file):
try:
with open(model.path) as f:
# strip raw data to remove trailing newlines, so splitting on newline can't produce an empty value
data = f.read(-1).strip().split("\n")
model.load(data)
except Exception as e:
if expect_missing_file:
return None
else:
terminal_error("Could not load text file: %s because: %s" % (model.path, str(e)))
else:
return True
def _get_nd2_attributes(self, experiment):
"""
Determine several attributes of the ND2s used in this experiment.
:type experiment: model.experiment.Experiment()
"""
experiment_log = self._load_experiment_log(experiment)
found_an_nd2 = False
for n, nd2_filename in enumerate(experiment.nd2s):
try:
nd2 = nd2reader.Nd2(nd2_filename)
except IOError:
pass
else:
# We need to know the absolute time that an experiment began so we can figure out the gap between
# different files (as that could be any amount of time).
timestamp = self._utc_timestamp(nd2.absolute_start)
time_period = n + 1
experiment.set_time_period_start_time(time_period, timestamp)
experiment_log['start_unix_timestamps'][str(
time_period)] = timestamp
experiment.field_of_view_count = nd2.field_of_view_count
experiment_log['field_of_view_count'] = nd2.field_of_view_count
experiment_log['has_fluorescent_channels'] = False
for channel in nd2.channels:
if channel.name != "":
log.info("Experiment has fluorescent channels.")
experiment.has_fluorescent_channels = True
experiment_log['has_fluorescent_channels'] = True
break
else:
log.info("Experiment does not have fluorescent channels.")
self._save_experiment_log(experiment, experiment_log)
found_an_nd2 = True
if not found_an_nd2:
# There are no ND2s so we load all the information we need from the log.
if 'field_of_view_count' not in experiment_log.keys(
) or 'has_fluorescent_channels' not in experiment_log.keys():
terminal_error(
"No ND2s found and no attributes saved. It seems like you haven't even started this experiment."
)
experiment.field_of_view_count = int(
experiment_log['field_of_view_count'])
experiment.has_fluorescent_channels = experiment_log[
'has_fluorescent_channels']
for time_period, timestamp in experiment_log[
'start_unix_timestamps'].items():
experiment.set_time_period_start_time(time_period, timestamp)
def _get_nd2_attributes(self, experiment):
"""
Determine several attributes of the ND2s used in this experiment.
:type experiment: model.experiment.Experiment()
"""
experiment_log = self._load_experiment_log(experiment)
found_an_nd2 = False
for n, nd2_filename in enumerate(experiment.nd2s):
try:
nd2 = nd2reader.Nd2(nd2_filename)
except IOError:
pass
else:
# We need to know the absolute time that an experiment began so we can figure out the gap between
# different files (as that could be any amount of time).
timestamp = self._utc_timestamp(nd2.absolute_start)
time_period = n + 1
experiment.set_time_period_start_time(time_period, timestamp)
experiment_log['start_unix_timestamps'][str(time_period)] = timestamp
experiment.field_of_view_count = nd2.field_of_view_count
experiment_log['field_of_view_count'] = nd2.field_of_view_count
experiment_log['has_fluorescent_channels'] = False
for channel in nd2.channels:
if channel.name != "":
log.info("Experiment has fluorescent channels.")
experiment.has_fluorescent_channels = True
experiment_log['has_fluorescent_channels'] = True
break
else:
log.info("Experiment does not have fluorescent channels.")
self._save_experiment_log(experiment, experiment_log)
found_an_nd2 = True
if not found_an_nd2:
# There are no ND2s so we load all the information we need from the log.
if 'field_of_view_count' not in experiment_log.keys() or 'has_fluorescent_channels' not in experiment_log.keys():
terminal_error("No ND2s found and no attributes saved. It seems like you haven't even started this experiment.")
experiment.field_of_view_count = int(experiment_log['field_of_view_count'])
experiment.has_fluorescent_channels = experiment_log['has_fluorescent_channels']
for time_period, timestamp in experiment_log['start_unix_timestamps'].items():
experiment.set_time_period_start_time(time_period, timestamp)
def _find_time_periods(self, experiment):
"""
Finds the time_periods of all available ND2 files associated with the experiment.
"""
regex = re.compile(r"""FYLM-%s-0(?P<time_period>\d+)\.nd2""" % experiment.start_date.clean_date)
found = False
for filename in sorted(self._os.listdir(experiment.base_dir)):
match = regex.match(filename)
if match:
found = True
time_period = int(match.group("time_period"))
log.debug("time_period: %s" % time_period)
experiment.add_time_period(time_period)
experiment_log = self._load_experiment_log(experiment)
for time_period in experiment_log['time_periods']:
found = True
experiment.add_time_period(time_period)
if not found:
terminal_error("No ND2s found!")
def get_experiment(self, experiment_start_date, base_dir, version, review):
experiment = ExperimentModel()
experiment.version = version
experiment.review_annotations = review
# set start date
experiment.start_date = experiment_start_date
if not experiment.start_date.is_valid:
terminal_error("Invalid start date: %s (use the format: YYMMDD)" % experiment_start_date)
log.debug("Experiment start date: %s" % experiment.start_date.clean_date)
# set the base directory
if not self._os.path.isdir(base_dir):
terminal_error("Base directory does not exist: %s" % base_dir)
experiment.base_dir = base_dir
log.debug("Experiment base directory: %s" % experiment.base_dir)
self._build_directories(experiment)
self._find_time_periods(experiment)
self._get_nd2_attributes(experiment)
return experiment
def _find_time_periods(self, experiment):
"""
Finds the time_periods of all available ND2 files associated with the experiment.
"""
regex = re.compile(r"""FYLM-%s-0(?P<time_period>\d+)\.nd2""" %
experiment.start_date.clean_date)
found = False
for filename in sorted(self._os.listdir(experiment.base_dir)):
match = regex.match(filename)
if match:
found = True
time_period = int(match.group("time_period"))
log.debug("time_period: %s" % time_period)
experiment.add_time_period(time_period)
experiment_log = self._load_experiment_log(experiment)
for time_period in experiment_log['time_periods']:
found = True
experiment.add_time_period(time_period)
if not found:
terminal_error("No ND2s found!")
def get_experiment(self, experiment_start_date, base_dir, version, review):
experiment = ExperimentModel()
experiment.version = version
experiment.review_annotations = review
# set start date
experiment.start_date = experiment_start_date
if not experiment.start_date.is_valid:
terminal_error("Invalid start date: %s (use the format: YYMMDD)" %
experiment_start_date)
log.debug("Experiment start date: %s" %
experiment.start_date.clean_date)
# set the base directory
if not self._os.path.isdir(base_dir):
terminal_error("Base directory does not exist: %s" % base_dir)
experiment.base_dir = base_dir
log.debug("Experiment base directory: %s" % experiment.base_dir)
self._build_directories(experiment)
self._find_time_periods(experiment)
self._get_nd2_attributes(experiment)
return experiment