def load_centre_stage_file(self, yaml_name):
"""
Load in centrer-specific annotation parameter list
Parameters
----------
yaml_name: str
basename of annotation parameter file
Returns
-------
dict
"""
path = join(OPTIONS_DIR, yaml_name)
opts = load_yaml(path)
# Rename the param_1, param_2 keys with IMPC parameter key
renamed = {}
for k in list(opts['parameters']):
new_key = opts['parameters'][k]['impc_id']
renamed[new_key] = opts['parameters'][k]
opts['parameters'] = renamed
return opts['parameters']
def load_centre_stage_file(self, yaml_name):
"""
Load in centrer-specific annotation parameter list
Parameters
----------
yaml_name: str
basename of annotation parameter file
Returns
-------
dict
"""
path = join(OPTIONS_DIR, yaml_name)
opts = load_yaml(path)
# Rename the param_1, param_2 keys with IMPC parameter key
renamed = {}
for k in list(opts['parameters']):
new_key = opts['parameters'][k]['impc_id']
renamed[new_key] = opts['parameters'][k]
opts['parameters'] = renamed
return opts['parameters']
def __init__(self):
# Add assert for default in options
try:
opts = load_yaml(OPTIONS_CONFIG_PATH)
except OSError:
logging.warning('could not open the annotations yaml file {}'.format(OPTIONS_CONFIG_PATH))
raise
self.opts = opts
self.available_options = self.opts['available_options']
for center in opts['centers']:
for stage_id, stage_data in opts['centers'][center]['stages'].items():
stage_file = stage_data['file_']
# now add the parameters from each individual centre/stage file to the main options config
opts['centers'][center]['stages'][stage_id]['parameters'] = self.load_centre_stage_file(stage_file)
def __init__(self):
self.using_appdata = True # Set to false if we weren't able to find a sirectory to save the appdata
appname = 'vpv_viewer'
appdata_dir = appdirs.user_data_dir(appname)
if not os.path.isdir(appdata_dir):
try:
os.mkdir(appdata_dir)
except WindowsError:
#Can't find the AppData directory. So just make one in home directory
appdata_dir = os.path.join(expanduser("~"), '.' + appname)
if not os.path.isdir(appdata_dir):
os.mkdir(appdata_dir)
self.app_data_file = os.path.join(appdata_dir, 'vpv_viewer.yaml')
if os.path.isfile(self.app_data_file):
self.data = common.load_yaml(self.app_data_file)
if not self.data:
logging.error(
f'Warning: could not load app data file\nTry deleting {self.app_data_file}'
)
self.data = {}
else:
self.data = {}
# Appdata versioning was not always in place. If a we find some appdata without a version, reset the data
# Also reset the data if we find a previous version
# This breaks for JIm on v2.02. Complains about NoneType not having a get(). Catch attribute error
try:
if self.data.get('version') is None or self.data[
'version'] < VPV_APPDATA_VERSION:
print("resetting appdata")
self.data = {}
except AttributeError:
self.data = {}
if self.data == {}:
self.data['version'] = VPV_APPDATA_VERSION
if 'recent_files' not in self.data:
self.data['recent_files'] = collections.deque(maxlen=10)
def __init__(self):
self.using_appdata = True # Set to false if we weren't able to find a sirectory to save the appdata
appname = 'vpv'
appdata_dir = appdirs.user_data_dir(appname)
if not os.path.isdir(appdata_dir):
try:
os.mkdir(appdata_dir)
except WindowsError:
#Can't find the AppData directory. So just make one in home directory
appdata_dir = os.path.join(expanduser("~"), '.' + appname)
if not os.path.isdir(appdata_dir):
os.mkdir(appdata_dir)
self.app_data_file = os.path.join(appdata_dir, 'vpv.yaml')
if os.path.isfile(self.app_data_file):
self.app_data = common.load_yaml(self.app_data_file)
if not self.app_data:
logging('Warning: could not load app data file')
self.app_data = {}
else:
self.app_data = {}
# Appdata versioning was not always in place. If a we find some appdata without a version, reset the data
# Also reset the data if we find a previous version
# This breaks for JIm on v2.02. Complains about NoneType not having a get(). Catch attribute error
try:
if self.app_data.get('version') is None or self.app_data['version'] < VPV_APPDATA_VERSION:
print("resetting appdata")
self.app_data = {}
except AttributeError:
self.app_data = {}
if self.app_data == {}:
self.app_data['version'] = VPV_APPDATA_VERSION
if 'recent_files' not in self.app_data:
self.app_data['recent_files'] = collections.deque(maxlen=10)
def __init__(self):
# Add assert for default in options
try:
opts = load_yaml(OPTIONS_CONFIG_PATH)
except OSError:
logging.warning('could not open the annotations yaml file {}'.format(OPTIONS_CONFIG_PATH))
raise
self.opts = opts
self.available_options = self.opts['available_options']
# Get the centre/stage-specific parameters
for centre_id, centre_data in opts['centers'].items():
for proc_id, proc_data in centre_data['procedures'].items():
param_file_ = proc_data['file_']
# now add the parameters from each individual centre/stage file to the main options config
try:
opts['centers'][centre_id]['procedures'][proc_id]['parameters'] = self.load_centre_stage_file(param_file_)
except KeyError as e:
raise
def _load_done_status(self):
"""
Load in the doneList.yaml which specifies which parameters have been loked at. This is used to populate the
'done' checkboxes, which is just a guide for the user. Has no other effect
"""
if self.annotation_dir:
done_file = join(self.annotation_dir, ANNOTATION_DONE_METADATA_FILE)
if not isfile(done_file):
return
done_status = load_yaml(done_file)
if not done_status:
return
self.index = len(self.annotations) # bodge. Need to reset the annotations iterator
for ann in self:
done = done_status.get(ann.term, 'notpresent')
if done is 'notpresent':
logging.warning('Cannot find term in done metadata\n{}'.format(done_file))
else:
ann.looked_at = done
def _load_done_status(self):
"""
Load in the doneList.yaml which specifies which parameters have been loked at. This is used to populate the
'done' checkboxes, which is just a guide for the user. Has no other effect
"""
if self.annotation_dir:
done_file = join(self.annotation_dir, ANNOTATION_DONE_METADATA_FILE)
if not isfile(done_file):
return
done_status = load_yaml(done_file)
if not done_status:
return
self.index = len(self.annotations) # bodge. Need to reset the annotations iterator
for ann in self:
done = done_status.get(ann.term, 'notpresent')
if done is 'notpresent':
logging.warning('Cannot find term in done metadata\n{}'.format(done_file))
else:
ann.looked_at = done
def _load_options_and_metadata(self):
"""
The volume has been loaded. Now see if there is an associated annotation folder that will contain the IMPC
metadata parameter file. Also load in any partially completed xml annotation files
Returns
-------
"""
if not self.annotation_dir:
return
self.metadata_parameter_file = join(self.annotation_dir, PROCEDURE_METADATA)
if not isfile(self.metadata_parameter_file):
self.metadata_parameter_file = None
return
cso = centre_stage_options.opts
metadata_params = load_yaml(self.metadata_parameter_file)
if not metadata_params:
return
# proc_id = metadata_params['procedure_id']
proc_id = metadata_params['procedure_id'] = ANNOTATIONS_PROC_VERSION
center_id = metadata_params['centre_id']
stage_id = get_stage_from_proc_id(proc_id, center_id)
self.stage = stage_id
self.center = center_id
# Get the procedure parameters for the given center/stage
center_stage_default_params = cso['centers'][center_id]['stages'][stage_id]['parameters']
for _, param_info in center_stage_default_params.items():
try:
options = centre_stage_options.opts['available_options'][param_info['options']]
except TypeError as e:
logging.error('Falied to load annotation parameter file {}'.format(e))
return
if param_info['default_option'] not in options:
logging.error(
"""Annotation parameter list load error
default option: {} not in available options:{}
Centre:, stage:{}""".format(param_info['default_option'], options, center_id, stage_id))
error_dialog(None, 'Annotation options load error', "See log file - 'info/show log'")
return
default = param_info['default_option']
self.add_impc_annotation(None,
None,
None,
param_info['impc_id'],
param_info['name'],
options,
default,
self.stage,
param_info['order'],
param_info['mandatory'],
self.dims
)
# Sort the list and set the interator index
self.annotations.sort(key=lambda x: x.order, reverse=True)
self.index = len(self.annotations)
def _load_options_and_metadata(self):
"""
The volume has been loaded. Now see if there is an associated annotation folder that will contain the IMPC
metadata parameter file. Also load in any partially completed xml annotation files.
"""
if not self.annotation_dir:
return
self.metadata_parameter_file = join(self.annotation_dir, PROCEDURE_METADATA)
if not isfile(self.metadata_parameter_file):
self.metadata_parameter_file = None
return
cso = centre_stage_options.opts
metadata_params = load_yaml(self.metadata_parameter_file)
if not metadata_params:
return
proc_id = metadata_params['procedure_id']
# Temp fix 030320 to increment procedures to 002 so they vallidate correctly
proc_id = proc_id.replace('_001', '_002')
self.proc_id = proc_id
center_id = metadata_params['centre_id']
stage_id, modality = get_stage_and_modality(proc_id, center_id)
self.stage = stage_id
self.center = center_id
self.modality = modality
# Get the procedure parameters for the given center/stage
try:
cso['centers'][center_id]['procedures'][proc_id]
except KeyError:
logging.error(f'Procedure id {proc_id} not in the annotation_conf')
return
center_stage_default_params = cso['centers'][center_id]['procedures'][proc_id]['parameters']
# opts['centers'][center]['procedures'][proc_id]['parameters'] = self.load_centre_stage_file(param_file_)
for _, param_info in center_stage_default_params.items():
try:
options = centre_stage_options.opts['available_options'][param_info['options']]
except TypeError as e:
logging.error('Falied to load annotation parameter file {}'.format(e))
return
if param_info['default_option'] not in options:
logging.error(
"""Annotation parameter list load error
default option: {} not in available options:{}
Centre:, stage:{}""".format(param_info['default_option'], options, center_id, stage_id))
error_dialog(None, 'Annotation options load error', "See log file - 'info/show log'")
return
default = param_info['default_option']
self.add_impc_annotation(None,
None,
None,
param_info['impc_id'],
param_info['name'],
options,
default,
self.stage,
param_info['order'],
param_info['mandatory'],
self.dims
)
# Sort the list and set the interator index
self.annotations.sort(key=lambda x: x.order, reverse=True)
self.index = len(self.annotations)