def createNewProject(self, file_name, pen_data):
PenDataSegmentCategory.clearSegmentCache()
self._project_settings = None
self._name = file_name
# Normalize pen sample times so first sample starts at 0.0 sec.
self._original_timebase_offset=pen_data[0]['time']
pen_data['time']-=self._original_timebase_offset
pen_data['time']=pen_data['time']/1000.0
# to flip data vertically by changing y pos values...
# Maybe better to see if pyqtgraph has a built in option
# to flip a plot vertically.
#
# pmax = pen_data['y'].max()
# pmin = pen_data['y'].min()
# pen_data['y'] = pmax-pen_data['y']+pmin
self._pendata = pen_data
self.nonzero_pressure_mask=self._pendata['pressure']>0
# nonzero_regions_ix will be a tuple of (starts, stops, lengths) arrays
self.nonzero_region_ix=contiguous_regions(self.nonzero_pressure_mask)
self._segmentset=PenDataSegmentCategory(name=self.name,project=self)
self._pendata['segment_id']=self._segmentset.id
if self._selectedtimeregion is None:
MarkWriteProject._selectedtimeregion = SelectedTimePeriodItem(project=self)
else:
MarkWriteProject._selectedtimeregion.project = self
MarkWriteProject._selectedtimeregion.setBounds(bounds=(self.pendata['time'][0], self.pendata['time'][-1]))
MarkWriteProject._selectedtimeregion.setRegion([self.pendata['time'][0], self.pendata['time'][0] + 1.0])
def createNewProject(self, file_name, pen_data, condvars=None, stime_var=None, etime_var=None, file_type=None):
PenDataSegmentCategory.clearSegmentCache()
self._project_settings = None
self._name = file_name
self._filetype = file_type
self._expcondvars = condvars
self._stimevar = stime_var
self._etimevar = etime_var
# go through each trial, select only the samples within
# the trial period, add the trials sample array to list of trial
# sample data.
samples_by_trial = []
trial_times = None
if self._expcondvars is not None and self._stimevar is not None and self._etimevar is not None:
trial_times = []
for t in self._expcondvars:
try:
trialstart = float(t[self._stimevar])
trialend = float(t[self._etimevar])
trial_times.append((trialstart,trialend))
trial_samples = pen_data[(pen_data['time'] >= trialstart) & (pen_data['time'] <= trialend)]
samples_by_trial.append(trial_samples)
#print "trial samples:",trial_samples.shape
except:
print("Error getting trial time period:")
import traceback
traceback.print_exc()
if samples_by_trial:
# make pen_data == concat'ed samples_by_trial
pen_data = np.concatenate(samples_by_trial)
# turn trial start, stop time list into np array
trial_times = np.asarray(trial_times)
# Normalize pen sample times so first sample starts at 0.0 sec.
self._original_timebase_offset=pen_data[0]['time']
pen_data['time']-=self._original_timebase_offset
if trial_times is not None:
trial_times-=self._original_timebase_offset
self._trialtimes = trial_times
# Change time stamps to sec.msec format, if needed
if file_type != 'hdf5':
# data from iohub hdf5 file is already in sec.msec format
pen_data['time']=pen_data['time']/1000.0
self._pendata = pen_data
self.nonzero_pressure_mask=self._pendata['pressure']>0
# nonzero_regions_ix will be a tuple of (starts, stops, lengths) arrays
self.nonzero_region_ix=contiguous_regions(self.nonzero_pressure_mask)
self._segmentset=PenDataSegmentCategory(name=self.name,project=self)
self._pendata['segment_id']=self._segmentset.id
if self._selectedtimeregion is None:
MarkWriteProject._selectedtimeregion = SelectedTimePeriodItem(project=self)
else:
MarkWriteProject._selectedtimeregion.project = self