def __init__(self, pathDict):
# Parse L_modified file
self.pathLmod = os.path.join(pathDict['Preferences'], 'L_modified.mat')
prepcommon._testfile(self.pathLmod)
self.allen = pymatreader.read_mat(self.pathLmod)['L']
# Parse sessions file
pathSessions = os.path.join(pathDict['Preferences'],
'sessions_aud.csv')
self.dfSession = pd.read_csv(pathSessions, sep='\t')
# Find parse TGT files
self.dataPaths = pd.DataFrame(columns=[
'mouse',
'day',
'session',
'sessionPath', #'trialIndPath',
'trialStructPath',
'pathActivePassive',
'pathMovementVectors'
])
self.pathT1 = defaultdict(dict)
self.find_parse_data_paths(pathDict['AUD'])
# Find parse Overlay
# self.pathRef = {}
self.pathT2 = {}
self.find_parse_overlay(pathDict['Overlay'])
def __init__(self, pathDict):
# Parse L_modified file
self.pathLmod = os.path.join(pathDict['Preferences'], 'L_modified.mat')
prepcommon._testfile(self.pathLmod)
self.allen = pymatreader.read_mat(self.pathLmod)['L']
# Parse sessions file
pathSessions = os.path.join(pathDict['Preferences'], 'sessions_tex.csv')
self.dfSession = pd.read_csv(pathSessions, sep='\t')
# with open(pathSessions, 'r') as json_file:
# self.sessions = json.load(json_file)
# Find parse TGT files
self.dataPaths = pd.DataFrame(
columns=['mouse', 'day', 'session', 'sessionPath',
'trialIndPath', 'trialStructPathMat', 'trialStructPathLabview',
'pathActivePassive', 'pathMovementVectors'])
self.pathT1 = defaultdict(dict)
if 'TDT' in pathDict:
self.find_parse_tdt(pathDict['TDT'])
# Find parse Overlay
self.pathRef = {}
self.pathT2 = {}
if 'Overlay' in pathDict:
self.find_parse_overlay(pathDict['Overlay'])
def find_parse_overlay(self, pathOverlay):
for mouseName, dfMouse in self.dfSession.groupby(['mousename']):
pathMouse = os.path.join(pathOverlay, mouseName)
# pathRef = os.path.join(pathMouse, 'refImg_ROIs.mat')
pathT2 = os.path.join(pathMouse, 't2str.mat')
prepcommon._testdir(pathMouse)
# self._testfile(pathRef)
prepcommon._testfile(pathT2)
# self.pathRef[mouseName] = pathRef
self.pathT2[mouseName] = pathT2
def find_parse_data_paths(self, pathAUD):
for mouseName, dfMouse in self.dfSession.groupby(['mousename']):
pathMouse = os.path.join(pathAUD, mouseName)
prepcommon._testdir(pathMouse)
for dayName, dfDay in dfMouse.groupby(['dateKey']):
print(mouseName, dayName)
pathDay = os.path.join(pathMouse, dayName, 'widefield_labview')
pathAllen = os.path.join(pathDay, 'ROI_Allen',
'registration_transform_1510.mat')
haveDir = prepcommon._testdir(pathDay, critical=False)
haveFile = prepcommon._testfile(pathAllen, critical=False)
if haveDir and haveFile:
self.pathT1[mouseName][dayName] = pathAllen
for idx, row in dfDay.iterrows():
sessionSuffix = row['sessionKey']
pathSession = os.path.join(pathDay, sessionSuffix)
pathMat = os.path.join(pathSession, 'Matt_files')
# pathTrialInd = os.path.join(pathMat, 'trials_ind.mat')
matFiles = [
f for f in os.listdir(pathMat)
if os.path.splitext(f)[1] == '.mat'
and f[:9] == 'Behavior_'
]
assert len(matFiles) == 1
pathTrialStruct = os.path.join(pathMat, matFiles[0])
pathActivePassive = os.path.join(
pathMat,
'trials_with_and_wo_initial_moves_OCIA_from_movie.mat'
)
pathMovementVectors = os.path.join(
pathMat, 'move_vectors_from_movie.mat')
prepcommon._testdir(pathSession)
prepcommon._testdir(pathMat)
# prepcommon._testfile(pathTrialInd)
prepcommon._testfile(pathTrialStruct)
prepcommon._testfile(pathActivePassive)
prepcommon._testfile(pathMovementVectors,
critical=False)
self.dataPaths = pd_append_row(
self.dataPaths,
[
mouseName,
dayName,
sessionSuffix,
pathSession, #pathTrialInd,
pathTrialStruct,
pathActivePassive,
pathMovementVectors
])
def find_parse_tdt(self, pathTDT):
print('Parsing TDT:')
for mouseName, dfMouse in self.dfSession.groupby(['mousename']):
pathMouse = os.path.join(pathTDT, mouseName)
prepcommon._testdir(pathMouse)
for dayName, dfDay in dfMouse.groupby(['dateKey']):
print('--', mouseName, dayName)
pathDay = os.path.join(pathMouse, 'TDT', dayName, 'widefield_labview')
pathAllen = os.path.join(pathDay, 'ROI_Allen', 'registration_transform_1510.mat')
prepcommon._testdir(pathDay)
prepcommon._testfile(pathAllen)
self.pathT1[mouseName][dayName] = pathAllen
for idx, row in dfDay.iterrows():
sessionSuffix = row['sessionKey']
pathSession = os.path.join(pathDay, sessionSuffix)
pathMat = os.path.join(pathSession, 'Matt_files')
pathTrialInd = os.path.join(pathMat, 'trials_ind.mat')
if mouseName == 'mou_5':
matFiles = [f for f in os.listdir(pathMat) if os.path.isfile(os.path.join(pathMat, f))]
matFiles = [f for f in matFiles if '.mat' in f]
matFiles = [f for f in matFiles if dayName[:4] in f]
assert len(matFiles) == 1
pathTrialStructMat = os.path.join(pathMat, matFiles[0])
else:
pathTrialStructMat = os.path.join(pathMat, dayName + sessionSuffix + '.mat')
if mouseName == 'mou_5':
sessionKeyLabview = '_s' + sessionSuffix[-1]
elif mouseName == 'mou_6':
sessionKeyLabview = '_s' + str(self._letters_to_sessions(sessionSuffix))
else:
sessionKeyLabview = '_' + sessionSuffix
pathTrialStructLabview = os.path.join(pathSession, mouseName + sessionKeyLabview + ''.join(dayName.split('_')) + '.txt')
pathActivePassive = os.path.join(pathMat, 'trials_with_and_wo_initial_moves_OCIA_from_movie.mat')
pathMovementVectors = os.path.join(pathMat, 'move_vectors_from_movie.mat')
prepcommon._testdir(pathSession)
prepcommon._testdir(pathMat)
prepcommon._testfile(pathTrialInd)
prepcommon._testfile(pathTrialStructMat)
prepcommon._testfile(pathTrialStructLabview, critical=False)
prepcommon._testfile(pathActivePassive, critical=False)
prepcommon._testfile(pathMovementVectors, critical=False)
self.dataPaths = pd_append_row(self.dataPaths, [
mouseName, dayName, sessionSuffix, pathSession,
pathTrialInd, pathTrialStructMat, pathTrialStructLabview,
pathActivePassive, pathMovementVectors
])