def __init__(self, data_type, root_dir=None, data_name=None, savefile=None, logfile=None, shell=False):
if 'SSH_CONNECTION' in os.environ:
shell = True
if root_dir is None:
root_dir = userIO.get_filedirs('Select %s directory' % data_type,
shell=shell)
if root_dir is None or not os.path.isdir(root_dir):
raise NotADirectoryError('Must provide a valid root directory for the %s' % data_type)
if root_dir.endswith('/'):
root_dir = root_dir[:-1]
if data_name is None:
data_name = userIO.get_user_input('Enter name for %s' % data_type,
os.path.basename(root_dir), shell)
if savefile is None:
savefile = os.path.join(root_dir, '%s_%s.p'
% (data_name, data_type))
if logfile is None:
logfile = os.path.join(root_dir, '%s_%s.log'
% (data_name, data_type))
self.root_dir = root_dir
self.data_type = data_type
self.data_name = data_name
self.save_file = savefile
self.log_file = logfile
def load_data(data_type, file_dir=None, shell=False):
'''Loads a data_object .p file and returns the object
Parameters
----------
data_type : str
type of data_object extension do you want
dataset, experiment or object
file_dir : str (optional)
path to file dir that the .p file is saved in
or path to .p file
Returns
-------
blechpy.data_object
Raises
------
NotADirectoryError
'''
if 'SSH_CONNECTION' in os.environ:
shell = True
if file_dir is None:
file_dir = userIO.get_filedirs('Select %s directory or .p file' %
data_type,
shell=shell)
if os.path.isfile(file_dir) and f'{data_type}.p' in file_dir:
data_file = [file_dir]
file_dir = os.path.dirname(file_dir)
elif not os.path.isdir(file_dir):
raise NotADirectoryError('%s not found.' % file_dir)
else:
data_file = [
x for x in os.listdir(file_dir) if x.endswith('%s.p' % data_type)
]
if len(data_file) == 0:
return None
elif len(data_file) > 1:
tmp = userIO.select_from_list('Multiple %s files found.'
'Select the one you want to load.' %
data_type,
data_file,
shell=shell)
if tmp is None:
return None
else:
data_file = tmp
else:
data_file = data_file[0]
data_file = os.path.join(file_dir, data_file)
with open(data_file, 'rb') as f:
out = pickle.load(f)
return out
def _change_root(self, new_root=None):
if 'SSH_CONNECTION' in os.environ:
shell = True
else:
shell = False
if new_root is None:
new_root = userIO.get_filedirs('Select new location of %s' % self.root_dir, shell=shell)
old_root = self.root_dir
self.root_dir = self.root_dir.replace(old_root, new_root)
self.save_file = self.save_file.replace(old_root, new_root)
self.log_file = self.log_file.replace(old_root, new_root)
return new_root
def __init__(self, proj_dir=None, proj_name=None, exp_dirs=None,
exp_groups=None, params=None, shell=False):
if 'SSH_CONNECTION' in os.environ:
shell = True
# Setup basics
super().__init__('project', data_name=proj_name,
root_dir=proj_dir, shell=shell)
if exp_dirs is None:
exp_dirs = userIO.get_filedirs('Select experiment directories',
multi=True, shell=shell)
exp_names = []
for ed in exp_dirs:
exp = load_experiment(ed)
if exp is None:
raise FileNotFoundError('No experiment.p file found for %s' % ed)
exp_names.append(exp.data_name)
# Get experiment groups
if exp_groups is None:
exp_groups = userIO.get_labels(exp_names, 'Label Experiment Groups')
self._exp_info = pd.DataFrame({'exp_name': exp_names,
'exp_group': exp_groups,
'exp_dir': exp_dirs})
# Make list of all major files managed by this object
self._files = {'params':
os.path.join(self.root_dir,
self.data_name+'_analysis_params.json')}
# Check which files exist
status = self._file_check()
if status['params'] and params is None:
self._params = wt.read_dict_from_json(self._files['params'])
elif params is not None:
self._params = params
wt.write_dict_to_json(params, self._files['params'])
else:
# TODO: Load defaults and allow user edit
pass
self.save()
def add_recording(self, new_dir=None, shell=None):
'''Add recording directory to experiment
Parameters
----------
new_dir : str (optional)
full path to new directory to add to recording dirs
shell : bool (optional)
True for command-line interface for user input
False (default) for GUI
If not passed then the preference set upon object creation is used
'''
if 'SSH_CONNECTION' in os.environ:
shell = True
elif shell is None:
shell = False
if new_dir is None:
new_dir = userIO.get_filedirs('Select recoring directory',
root=self.root_dir,
shell=shell)
if not os.path.isdir(new_dir):
raise NotADirectoryError('%s must be a valid directory' % new_dir)
if not any([x.endswith('.h5') for x in os.listdir(new_dir)]):
raise FileNotFoundError('No .h5 file found in %s' % new_dir)
if not any([x.endswith('dataset.p') for x in os.listdir(new_dir)]):
raise FileNotFoundError('*_dataset.p file not found in %s' %
new_dir)
if new_dir.endswith('/'):
new_dir = new_dir[:-1]
label = userIO.get_user_input('Enter label for recording %s' %
os.path.basename(new_dir),
shell=shell)
self.recording_dirs.append(new_dir)
self.rec_labels[label] = new_dir
self._order_dirs(shell=shell)
self._setup_taste_map()
print('Added recording: %s')
self.save()
def port_in_dataset(rec_dir=None, shell=False):
'''Import an existing dataset into this framework
'''
if rec_dir is None:
rec_dir = userIO.get_filedirs('Select recording directory',
shell=shell)
if rec_dir is None:
return None
dat = dataset(rec_dir, shell=shell)
# Check files that will be overwritten: log_file, save_file
if os.path.isfile(dat.save_file):
prompt = '%s already exists. Continuing will overwrite this. Continue?' % dat.save_file
q = userIO.ask_user(prompt, shell=shell)
if q == 0:
print('Aborted')
return None
# if os.path.isfile(dat.h5_file):
# prompt = '%s already exists. Continuinlg will overwrite this. Continue?' % dat.h5_file
# q = userIO.ask_user(prompt, shell=shell)
# if q == 0:
# print('Aborted')
# return None
if os.path.isfile(dat.log_file):
prompt = '%s already exists. Continuing will append to this. Continue?' % dat.log_file
q = userIO.ask_user(prompt, shell=shell)
if q == 0:
print('Aborted')
return None
with open(dat.log_file, 'a') as f:
print(
'\n==========\nPorting dataset into blechpy format\n==========\n',
file=f)
print(dat, file=f)
status = dat.process_status
dat.initParams(shell=shell)
user_status = status.copy()
user_status = userIO.fill_dict(user_status,
'Which processes have already been '
'done to the data?',
shell=shell)
status.update(user_status)
# if h5 exists data must have been extracted
if not os.path.isfile(dat.h5_file) or status['extract_data'] == False:
dat.save()
return dat
# write eletrode map and digital input & output maps to hf5
dio.h5io.write_electrode_map_to_h5(dat.h5_file, dat.electrode_mapping)
if dat.rec_info.get('dig_in') is not None:
dio.h5io.write_digital_map_to_h5(dat.h5_file, dat.dig_in_mapping, 'in')
if dat.rec_info.get('dig_out') is not None:
dio.h5io.write_digital_map_to_h5(dat.h5_file, dat.dig_out_mapping,
'out')
node_list = dio.h5io.get_node_list(dat.h5_file)
if (status['create_trial_list'] == False) and ('digital_in' in node_list):
dat.create_trial_list()
dat.save()
return dat
