def main():
#------------------------------------------------------------------------------------------------------------------------------------
#----------------------------------------------Begin setup of scan parameters--------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
# set up lasers
channel_labels = ["405", "488", "561", "635", "730"]
channel_states = [False, False, True, False,
False] # true -> active, false -> inactive
channel_powers = [50, 10, 90, 100, 95] # (0 -> 100%)
do_ind = [0, 1, 2, 3,
4] # digital output line corresponding to each channel
# parse which channels are active
active_channel_indices = [
ind for ind, st in zip(do_ind, channel_states) if st
]
n_active_channels = len(active_channel_indices)
print("%d active channels: " % n_active_channels, end="")
for ind in active_channel_indices:
print("%s " % channel_labels[ind], end="")
print("")
# exposure time
exposure_ms = 50.0
# excess scan positions
excess_scan_positions = 10
# galvo voltage at neutral
galvo_neutral_volt = -0.15 # unit: volts
# scan axis limits. Use stage positions reported by MM
scan_axis_start_um = 8680. #unit: um
scan_axis_end_um = 8800. #unit: um
# tile axis limits. Use stage positions reported by MM
tile_axis_start_um = -3841.28 #unit: um
tile_axis_end_um = -3841.28 #unit: um
# height axis limits. Use stage positions reported by MM
height_axis_start_um = 13128.63 #unit: um
height_axis_end_um = 13128.63 #unit: um
# number of timepoints to execute
# TO DO: add in control for rate of experiment
timepoints = 1
# FOV parameters
# ONLY MODIFY IF NECESSARY
# ROI = [0, 1152, 2304, 512] #unit: pixels
# setup file name
save_directory = Path('D:/20210831')
save_name = 'stage_scan'
#------------------------------------------------------------------------------------------------------------------------------------
#----------------------------------------------End setup of scan parameters----------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
# connect to Micromanager instance
bridge = Bridge()
core = bridge.get_core()
# turn off lasers
core.set_config('Laser', 'Off')
core.wait_for_config('Laser', 'Off')
# set camera to fast readout mode
core.set_config('Camera-Setup', 'ScanMode3')
core.wait_for_config('Camera-Setup', 'ScanMode3')
# set camera to START mode upon input trigger
core.set_config('Camera-TriggerType', 'START')
core.wait_for_config('Camera-TriggerType', 'START')
# set camera to positive input trigger
core.set_config('Camera-TriggerPolarity', 'POSITIVE')
core.wait_for_config('Camera-TriggerPolarity', 'POSITIVE')
# set camera to internal control
core.set_config('Camera-TriggerSource', 'INTERNAL')
core.wait_for_config('Camera-TriggerSource', 'INTERNAL')
# set camera to output positive triggers on all lines for exposure
core.set_property('OrcaFusionBT', 'OUTPUT TRIGGER KIND[0]', 'EXPOSURE')
core.set_property('OrcaFusionBT', 'OUTPUT TRIGGER KIND[1]', 'EXPOSURE')
core.set_property('OrcaFusionBT', 'OUTPUT TRIGGER KIND[2]', 'EXPOSURE')
core.set_property('OrcaFusionBT', 'OUTPUT TRIGGER POLARITY[0]', 'POSITIVE')
core.set_property('OrcaFusionBT', 'OUTPUT TRIGGER POLARITY[1]', 'POSITIVE')
core.set_property('OrcaFusionBT', 'OUTPUT TRIGGER POLARITY[2]', 'POSITIVE')
# change core timeout for long stage moves
core.set_property('Core', 'TimeoutMs', 100000)
time.sleep(1)
# set exposure
core.set_exposure(exposure_ms)
# determine image size
core.snap_image()
y_pixels = core.get_image_height()
x_pixels = core.get_image_width()
# grab exposure
true_exposure = core.get_exposure()
# get actual framerate from micromanager properties
actual_readout_ms = true_exposure + float(
core.get_property('OrcaFusionBT', 'ReadoutTime')) #unit: ms
# camera pixel size
pixel_size_um = .115 # unit: um
# scan axis setup
scan_axis_step_um = 0.4 # unit: um
scan_axis_step_mm = scan_axis_step_um / 1000. #unit: mm
scan_axis_start_mm = scan_axis_start_um / 1000. #unit: mm
scan_axis_end_mm = scan_axis_end_um / 1000. #unit: mm
scan_axis_range_um = np.abs(scan_axis_end_um -
scan_axis_start_um) # unit: um
scan_axis_range_mm = scan_axis_range_um / 1000 #unit: mm
actual_exposure_s = actual_readout_ms / 1000. #unit: s
scan_axis_speed = np.round(scan_axis_step_mm / actual_exposure_s,
4) #unit: mm/s
scan_axis_positions = np.rint(scan_axis_range_mm /
scan_axis_step_mm).astype(
int) #unit: number of positions
# tile axis setup
tile_axis_overlap = 0.2 #unit: percentage
tile_axis_range_um = np.abs(tile_axis_end_um -
tile_axis_start_um) #unit: um
tile_axis_range_mm = tile_axis_range_um / 1000 #unit: mm
tile_axis_ROI = x_pixels * pixel_size_um #unit: um
tile_axis_step_um = np.round((tile_axis_ROI) * (1 - tile_axis_overlap),
2) #unit: um
tile_axis_step_mm = tile_axis_step_um / 1000 #unit: mm
tile_axis_positions = np.rint(
tile_axis_range_mm /
tile_axis_step_mm).astype(int) + 1 #unit: number of positions
# if tile_axis_positions rounded to zero, make sure we acquire at least one position
if tile_axis_positions == 0:
tile_axis_positions = 1
# height axis setup
height_axis_overlap = 0.2 #unit: percentage
height_axis_range_um = np.abs(height_axis_end_um -
height_axis_start_um) #unit: um
height_axis_range_mm = height_axis_range_um / 1000 #unit: mm
height_axis_ROI = y_pixels * pixel_size_um * np.sin(
30. * np.pi / 180.) #unit: um
height_axis_step_um = np.round(
(height_axis_ROI) * (1 - height_axis_overlap), 2) #unit: um
height_axis_step_mm = height_axis_step_um / 1000 #unit: mm
height_axis_positions = np.rint(
height_axis_range_mm /
height_axis_step_mm).astype(int) + 1 #unit: number of positions
# if height_axis_positions rounded to zero, make sure we acquire at least one position
if height_axis_positions == 0:
height_axis_positions = 1
# get handle to xy and z stages
xy_stage = core.get_xy_stage_device()
z_stage = core.get_focus_device()
# galvo voltage at neutral
galvo_neutral_volt = -.15 # unit: volts
# set the galvo to the neutral position if it is not already
try:
taskAO_first = daq.Task()
taskAO_first.CreateAOVoltageChan("/Dev1/ao0", "", -4.0, 4.0,
daq.DAQmx_Val_Volts, None)
taskAO_first.WriteAnalogScalarF64(True, -1, galvo_neutral_volt, None)
taskAO_first.StopTask()
taskAO_first.ClearTask()
except:
print("DAQmx Error %s" % err)
# Setup Tiger controller to pass signal when the scan stage cross the start position to the PLC
plcName = 'PLogic:E:36'
propPosition = 'PointerPosition'
propCellConfig = 'EditCellConfig'
#addrOutputBNC3 = 35 # BNC3 on the PLC front panel
addrOutputBNC1 = 33 # BNC1 on the PLC front panel
addrStageSync = 46 # TTL5 on Tiger backplane = stage sync signal
# connect stage sync signal to BNC output
core.set_property(plcName, propPosition, addrOutputBNC1)
core.set_property(plcName, propCellConfig, addrStageSync)
# turn on 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub', 'OnlySendSerialCommandOnChange', 'No')
# set tile axis speed for all moves
command = 'SPEED Y=.1'
core.set_property('TigerCommHub', 'SerialCommand', command)
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand', command)
ready = core.get_property('TigerCommHub', 'SerialResponse')
time.sleep(.500)
# set scan axis speed for large move to initial position
command = 'SPEED X=.1'
core.set_property('TigerCommHub', 'SerialCommand', command)
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand', command)
ready = core.get_property('TigerCommHub', 'SerialResponse')
time.sleep(.500)
# turn off 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub', 'OnlySendSerialCommandOnChange', 'Yes')
# move scan scan stage to initial position
core.set_xy_position(scan_axis_start_um, tile_axis_start_um)
core.wait_for_device(xy_stage)
core.set_position(height_axis_start_um)
core.wait_for_device(z_stage)
# turn on 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub', 'OnlySendSerialCommandOnChange', 'No')
# set scan axis speed to correct speed for continuous stage scan
# expects mm/s
command = 'SPEED X=' + str(scan_axis_speed)
core.set_property('TigerCommHub', 'SerialCommand', command)
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand', command)
ready = core.get_property('TigerCommHub', 'SerialResponse')
time.sleep(.500)
# set scan axis to true 1D scan with no backlash
command = '1SCAN X? Y=0 Z=9 F=0'
core.set_property('TigerCommHub', 'SerialCommand', command)
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand', command)
ready = core.get_property('TigerCommHub', 'SerialResponse')
time.sleep(.500)
# set range and return speed (5% of max) for scan axis
# expects mm
command = '1SCANR X=' + str(scan_axis_start_mm) + ' Y=' + str(
scan_axis_end_mm) + ' R=10'
core.set_property('TigerCommHub', 'SerialCommand', command)
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand', command)
ready = core.get_property('TigerCommHub', 'SerialResponse')
time.sleep(.500)
# turn off 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub', 'OnlySendSerialCommandOnChange', 'Yes')
# set all laser to external triggering
core.set_config('Modulation-405', 'External-Digital')
core.wait_for_config('Modulation-405', 'External-Digital')
core.set_config('Modulation-488', 'External-Digital')
core.wait_for_config('Modulation-488', 'External-Digital')
core.set_config('Modulation-561', 'External-Digital')
core.wait_for_config('Modulation-561', 'External-Digital')
core.set_config('Modulation-637', 'External-Digital')
core.wait_for_config('Modulation-637', 'External-Digital')
core.set_config('Modulation-730', 'External-Digital')
core.wait_for_config('Modulation-730', 'External-Digital')
# turn all lasers on
core.set_config('Laser', 'AllOn')
core.wait_for_config('Laser', 'AllOn')
# set lasers to user defined power
core.set_property('Coherent-Scientific Remote',
'Laser 405-100C - PowerSetpoint (%)', channel_powers[0])
core.set_property('Coherent-Scientific Remote',
'Laser 488-150C - PowerSetpoint (%)', channel_powers[1])
core.set_property('Coherent-Scientific Remote',
'Laser OBIS LS 561-150 - PowerSetpoint (%)',
channel_powers[2])
core.set_property('Coherent-Scientific Remote',
'Laser 637-140C - PowerSetpoint (%)', channel_powers[3])
core.set_property('Coherent-Scientific Remote',
'Laser 730-30C - PowerSetpoint (%)', channel_powers[4])
# setup DAQ
samples_per_ch = 2
DAQ_sample_rate_Hz = 10000
num_DI_channels = 8
# set the galvo to neutral
taskAO_last = daq.Task()
taskAO_last.CreateAOVoltageChan("/Dev1/ao0", "", -4.0, 4.0,
daq.DAQmx_Val_Volts, None)
taskAO_last.WriteAnalogScalarF64(True, -1, galvo_neutral_volt, None)
taskAO_last.StopTask()
taskAO_last.ClearTask()
# output experiment info
print('Number of X positions: ' + str(scan_axis_positions))
print('Number of Y tiles: ' + str(tile_axis_positions))
print('Number of Z slabs: ' + str(height_axis_positions))
print('Number of channels: ' + str(n_active_channels))
# flags for metadata and processing
setup_processing = True
setup_metadata = True
# create events to execute scan
events = []
for x in range(scan_axis_positions + excess_scan_positions):
evt = {'axes': {'z': x}}
events.append(evt)
for t_idx in range(timepoints):
for y_idx in range(tile_axis_positions):
# calculate tile axis position
tile_position_um = tile_axis_start_um + (tile_axis_step_um * y_idx)
# move XY stage to new tile axis position
core.set_xy_position(scan_axis_start_um, tile_position_um)
core.wait_for_device(xy_stage)
for z_idx in range(height_axis_positions):
# calculate height axis position
height_position_um = height_axis_start_um + (
height_axis_step_um * z_idx)
# move Z stage to new height axis position
core.set_position(height_position_um)
core.wait_for_device(z_stage)
for ch_idx in active_channel_indices:
# create DAQ pattern for laser strobing controlled via rolling shutter
dataDO = np.zeros((samples_per_ch, num_DI_channels),
dtype=np.uint8)
dataDO[0, ch_idx] = 1
dataDO[1, ch_idx] = 0
#print(dataDO)
# update save_name with current tile information
save_name_tyzc = save_name + '_t' + str(t_idx).zfill(
4) + '_y' + str(y_idx).zfill(4) + '_z' + str(
z_idx).zfill(4) + '_ch' + str(ch_idx).zfill(4)
# turn on 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub',
'OnlySendSerialCommandOnChange', 'No')
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand',
command)
ready = core.get_property('TigerCommHub',
'SerialResponse')
time.sleep(.500)
# turn off 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub',
'OnlySendSerialCommandOnChange', 'Yes')
# save actual stage positions
xy_pos = core.get_xy_stage_position()
stage_x = xy_pos.x
stage_y = xy_pos.y
stage_z = core.get_position()
current_stage_data = [{
'stage_x': stage_x,
'stage_y': stage_y,
'stage_z': stage_z
}]
df_current_stage = pd.DataFrame(current_stage_data)
# setup DAQ for laser strobing
try:
# ----- DIGITAL input -------
taskDI = daq.Task()
taskDI.CreateDIChan("/Dev1/PFI0", "",
daq.DAQmx_Val_ChanForAllLines)
## Configure change detection timing (from wave generator)
taskDI.CfgInputBuffer(
0
) # must be enforced for change-detection timing, i.e no buffer
taskDI.CfgChangeDetectionTiming(
"/Dev1/PFI0", "/Dev1/PFI0",
daq.DAQmx_Val_ContSamps, 0)
## Set where the starting trigger
taskDI.CfgDigEdgeStartTrig("/Dev1/PFI0",
daq.DAQmx_Val_Rising)
## Export DI signal to unused PFI pins, for clock and start
taskDI.ExportSignal(daq.DAQmx_Val_ChangeDetectionEvent,
"/Dev1/PFI2")
taskDI.ExportSignal(daq.DAQmx_Val_StartTrigger,
"/Dev1/PFI1")
# ----- DIGITAL output ------
taskDO = daq.Task()
taskDO.CreateDOChan("/Dev1/port0/line0:7", "",
daq.DAQmx_Val_ChanForAllLines)
## Configure timing (from DI task)
taskDO.CfgSampClkTiming("/Dev1/PFI2",
DAQ_sample_rate_Hz,
daq.DAQmx_Val_Rising,
daq.DAQmx_Val_ContSamps,
samples_per_ch)
## Write the output waveform
samples_per_ch_ct_digital = ct.c_int32()
taskDO.WriteDigitalLines(
samples_per_ch, False, 10.0,
daq.DAQmx_Val_GroupByChannel, dataDO,
ct.byref(samples_per_ch_ct_digital), None)
## ------ Start digital input and output tasks ----------
taskDO.StartTask()
taskDI.StartTask()
except daq.DAQError as err:
print("DAQmx Error %s" % err)
# set camera to external control
# DCAM sets the camera back to INTERNAL mode after each acquisition
core.set_config('Camera-TriggerSource', 'EXTERNAL')
core.wait_for_config('Camera-TriggerSource', 'EXTERNAL')
# verify that camera actually switched back to external trigger mode
trigger_state = core.get_property('OrcaFusionBT',
'TRIGGER SOURCE')
# if not in external control, keep trying until camera changes settings
while not (trigger_state == 'EXTERNAL'):
time.sleep(2.0)
core.set_config('Camera-TriggerSource', 'EXTERNAL')
core.wait_for_config('Camera-TriggerSource',
'EXTERNAL')
trigger_state = core.get_property(
'OrcaFusionBT', 'TRIGGER SOURCE')
print('T: ' + str(t_idx) + ' Y: ' + str(y_idx) + ' Z: ' +
str(z_idx) + ' C: ' + str(ch_idx))
# run acquisition for this tyzc combination
with Acquisition(directory=save_directory,
name=save_name_tyzc,
post_camera_hook_fn=camera_hook_fn,
show_display=False,
max_multi_res_index=0,
saving_queue_size=5000) as acq:
acq.acquire(events)
# clean up acquisition so that AcqEngJ releases directory.
# NOTE: This currently does not work.
acq = None
acq_deleted = False
while not (acq_deleted):
try:
del acq
except:
time.sleep(0.1)
acq_deleted = False
else:
gc.collect()
acq_deleted = True
# stop DAQ and make sure it is at zero
try:
## Stop and clear both tasks
taskDI.StopTask()
taskDO.StopTask()
taskDI.ClearTask()
taskDO.ClearTask()
except daq.DAQError as err:
print("DAQmx Error %s" % err)
# save experimental info after first tile.
# we do it this way so that Pycromanager can manage the directories.
if (setup_metadata):
# save stage scan parameters
scan_param_data = [{
'root_name':
str(save_name),
'scan_type':
str('stage'),
'theta':
float(30.0),
'scan_step':
float(scan_axis_step_um * 1000.),
'pixel_size':
float(pixel_size_um * 1000.),
'num_t':
int(timepoints),
'num_y':
int(tile_axis_positions),
'num_z':
int(height_axis_positions),
'num_ch':
int(n_active_channels),
'scan_axis_positions':
int(scan_axis_positions),
'excess_scan_positions':
int(excess_scan_positions),
'y_pixels':
int(y_pixels),
'x_pixels':
int(x_pixels),
'405_active':
bool(channel_states[0]),
'488_active':
bool(channel_states[1]),
'561_active':
bool(channel_states[2]),
'635_active':
bool(channel_states[3]),
'730_active':
bool(channel_states[4])
}]
# df_stage_scan_params = pd.DataFrame(scan_param_data)
# save_name_stage_params = save_directory / 'scan_metadata.csv'
# df_stage_scan_params.to_csv(save_name_stage_params)
data_io.write_metadata(
scan_param_data[0],
save_directory / Path('scan_metadata.csv'))
setup_metadata = False
# save stage scan positions after each tile
save_name_stage_positions = Path('t' +
str(t_idx).zfill(4) +
'_y' +
str(y_idx).zfill(4) +
'_z' +
str(z_idx).zfill(4) +
'_ch' +
str(ch_idx).zfill(4) +
'_stage_positions.csv')
save_name_stage_positions = save_directory / save_name_stage_positions
# todo: use data_io instead
df_current_stage.to_csv(save_name_stage_positions)
# turn on 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub',
'OnlySendSerialCommandOnChange', 'No')
# check to make sure Tiger is not busy
ready = 'B'
while (ready != 'N'):
command = 'STATUS'
core.set_property('TigerCommHub', 'SerialCommand',
command)
ready = core.get_property('TigerCommHub',
'SerialResponse')
time.sleep(.500)
# turn off 'transmit repeated commands' for Tiger
core.set_property('TigerCommHub',
'OnlySendSerialCommandOnChange', 'Yes')
'''
# if first tile, make parent directory on NAS and start reconstruction script on the server
if setup_processing:
# make home directory on NAS
save_directory_path = Path(save_directory)
remote_directory = Path('y:/') / Path(save_directory_path.parts[1])
cmd='mkdir ' + str(remote_directory)
status_mkdir = subprocess.run(cmd, shell=True)
# copy full experiment metadata to NAS
src= Path(save_directory) / Path('scan_metadata.csv')
dst= Path(remote_directory) / Path('scan_metadata.csv')
Thread(target=shutil.copy, args=[str(src), str(dst)]).start()
setup_processing=False
# copy current tyzc metadata to NAS
save_directory_path = Path(save_directory)
remote_directory = Path('y:/') / Path(save_directory_path.parts[1])
src= Path(save_directory) / Path(save_name_stage_positions.parts[2])
dst= Path(remote_directory) / Path(save_name_stage_positions.parts[2])
Thread(target=shutil.copy, args=[str(src), str(dst)]).start()
# copy current tyzc data to NAS
save_directory_path = Path(save_directory)
remote_directory = Path('y:/') / Path(save_directory_path.parts[1])
src= Path(save_directory) / Path(save_name_tyzc+ '_1')
dst= Path(remote_directory) / Path(save_name_tyzc+ '_1')
Thread(target=shutil.copytree, args=[str(src), str(dst)]).start()
'''
# set lasers to zero power
channel_powers = [0., 0., 0., 0., 0.]
core.set_property('Coherent-Scientific Remote',
'Laser 405-100C - PowerSetpoint (%)', channel_powers[0])
core.set_property('Coherent-Scientific Remote',
'Laser 488-150C - PowerSetpoint (%)', channel_powers[1])
core.set_property('Coherent-Scientific Remote',
'Laser OBIS LS 561-150 - PowerSetpoint (%)',
channel_powers[2])
core.set_property('Coherent-Scientific Remote',
'Laser 637-140C - PowerSetpoint (%)', channel_powers[3])
core.set_property('Coherent-Scientific Remote',
'Laser 730-30C - PowerSetpoint (%)', channel_powers[4])
# turn all lasers off
core.set_config('Laser', 'Off')
core.wait_for_config('Laser', 'Off')
# set all lasers back to software control
core.set_config('Modulation-405', 'CW (constant power)')
core.wait_for_config('Modulation-405', 'CW (constant power)')
core.set_config('Modulation-488', 'CW (constant power)')
core.wait_for_config('Modulation-488', 'CW (constant power)')
core.set_config('Modulation-561', 'CW (constant power)')
core.wait_for_config('Modulation-561', 'CW (constant power)')
core.set_config('Modulation-637', 'CW (constant power)')
core.wait_for_config('Modulation-637', 'CW (constant power)')
core.set_config('Modulation-730', 'CW (constant power)')
core.wait_for_config('Modulation-730', 'CW (constant power)')
# set camera to internal control
core.set_config('Camera-TriggerSource', 'INTERNAL')
core.wait_for_config('Camera-TriggerSource', 'INTERNAL')
bridge.close()
viewer = napari.Viewer(ndisplay=2)
# initialize napari viewer with stack view and random data, reslice view
scale = [(z_range[1] - z_range[0]) / z_range[2] * z_scale, size_um[1],
size_um[0]]
layers = [
viewer.add_image(data,
name=layer_names[c],
colormap=cmap[c],
interpolation='nearest',
blending='additive',
rendering='attenuated_mip',
scale=scale,
contrast_limits=clim) for c in range(channels[0])
]
viewer.dims._roll()
# set sliders to the middle of the stack for all three dimensions.
# doesn't work anymore after fixing scaling
# would have to be done for both layers
#for dd, dim in enumerate(layers[0].data.shape):
# viewer.dims.set_point(dd, dim*scale[2-dd]//2)
# define start stop buttons and add to napari gui
# these will break when upgrading to magicgui v0.2.0
gui_start = start_acq.Gui()
gui_stop = stop_acq.Gui()
viewer.window.add_dock_widget(gui_start)
viewer.window.add_dock_widget(gui_stop)
bridge.close()
class MainWindow(NewWindow):
def __init__(self,
app,
args=None,
parent=None,
spatial_subsampling=4,
time_subsampling=1):
"""
Intrinsic Imaging GUI
"""
self.app = app
super(MainWindow, self).__init__(i=1, title='intrinsic imaging')
# some initialisation
self.running, self.stim, self.STIM = False, None, None
self.datafolder, self.img, self.vasculature_img = '', None, None
self.t0, self.period = 0, 1
### trying the camera
try:
# we initialize the camera
self.bridge = Bridge()
self.core = self.bridge.get_core()
self.exposure = self.core.get_exposure()
self.demo = False
auto_shutter = self.core.get_property('Core', 'AutoShutter')
self.core.set_property('Core', 'AutoShutter', 0)
except BaseException as be:
print(be)
print('')
print(' /!\ Problem with the Camera /!\ ')
print(' --> no camera found ')
print('')
self.exposure = -1 # flag for no camera
self.demo = True
########################
##### building GUI #####
########################
self.minView = False
self.showwindow()
# layout (from NewWindow class)
self.init_basic_widget_grid(wdgt_length=3, Ncol_wdgt=20, Nrow_wdgt=20)
# -- A plot area (ViewBox + axes) for displaying the image ---
self.view = self.graphics_layout.addViewBox(lockAspect=True,
invertY=True)
self.view.setMenuEnabled(False)
self.view.setAspectLocked()
self.pimg = pg.ImageItem()
# --- setting subject information ---
self.add_widget(QtWidgets.QLabel('subjects file:'))
self.subjectFileBox = QtWidgets.QComboBox(self)
self.subjectFileBox.addItems([
f for f in os.listdir(subjects_path)[::-1] if f.endswith('.json')
])
self.subjectFileBox.activated.connect(self.get_subject_list)
self.add_widget(self.subjectFileBox)
self.add_widget(QtWidgets.QLabel('subject:'))
self.subjectBox = QtWidgets.QComboBox(self)
self.get_subject_list()
self.add_widget(self.subjectBox)
self.add_widget(QtWidgets.QLabel(20 * ' - '))
self.vascButton = QtWidgets.QPushButton(
" - = save Vasculature Picture = - ", self)
self.vascButton.clicked.connect(self.take_vasculature_picture)
self.add_widget(self.vascButton)
self.add_widget(QtWidgets.QLabel(20 * ' - '))
# --- data acquisition properties ---
self.add_widget(QtWidgets.QLabel('data folder:'), spec='small-left')
self.folderB = QtWidgets.QComboBox(self)
self.folderB.addItems(FOLDERS.keys())
self.add_widget(self.folderB, spec='large-right')
self.add_widget(QtWidgets.QLabel(' - protocol:'), spec='small-left')
self.protocolBox = QtWidgets.QComboBox(self)
self.protocolBox.addItems(['ALL', 'up', 'down', 'left', 'right'])
self.add_widget(self.protocolBox, spec='large-right')
self.add_widget(
QtWidgets.QLabel(' - exposure: %.0f ms (from Micro-Manager)' %
self.exposure))
self.add_widget(QtWidgets.QLabel(' - Nrepeat :'), spec='large-left')
self.repeatBox = QtWidgets.QLineEdit()
self.repeatBox.setText('10')
self.add_widget(self.repeatBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - stim. period (s):'),
spec='large-left')
self.periodBox = QtWidgets.QLineEdit()
self.periodBox.setText('10')
self.add_widget(self.periodBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - bar size (degree):'),
spec='large-left')
self.barBox = QtWidgets.QLineEdit()
self.barBox.setText('6')
self.add_widget(self.barBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - spatial sub-sampling (px):'),
spec='large-left')
self.spatialBox = QtWidgets.QLineEdit()
self.spatialBox.setText(str(spatial_subsampling))
self.add_widget(self.spatialBox, spec='small-right')
self.add_widget(QtWidgets.QLabel(' - acq. freq. (Hz):'),
spec='large-left')
self.freqBox = QtWidgets.QLineEdit()
self.freqBox.setText('10')
self.add_widget(self.freqBox, spec='small-right')
# self.add_widget(QtWidgets.QLabel(' - flick. freq. (Hz) /!\ > acq:'),
# spec='large-left')
# self.flickBox = QtWidgets.QLineEdit()
# self.flickBox.setText('10')
# self.add_widget(self.flickBox, spec='small-right')
self.demoBox = QtWidgets.QCheckBox("demo mode")
self.demoBox.setStyleSheet("color: gray;")
self.add_widget(self.demoBox, spec='large-left')
self.demoBox.setChecked(self.demo)
self.camBox = QtWidgets.QCheckBox("cam.")
self.camBox.setStyleSheet("color: gray;")
self.add_widget(self.camBox, spec='small-right')
self.camBox.setChecked(True)
# --- launching acquisition ---
self.liveButton = QtWidgets.QPushButton("-- live view -- ", self)
self.liveButton.clicked.connect(self.live_view)
self.add_widget(self.liveButton)
# --- launching acquisition ---
self.acqButton = QtWidgets.QPushButton("-- RUN PROTOCOL -- ", self)
self.acqButton.clicked.connect(self.launch_protocol)
self.add_widget(self.acqButton, spec='large-left')
self.stopButton = QtWidgets.QPushButton(" STOP ", self)
self.stopButton.clicked.connect(self.stop_protocol)
self.add_widget(self.stopButton, spec='small-right')
# --- launching analysis ---
self.add_widget(QtWidgets.QLabel(20 * ' - '))
self.analysisButton = QtWidgets.QPushButton(" - = Analysis GUI = - ",
self)
self.analysisButton.clicked.connect(self.open_analysis)
self.add_widget(self.analysisButton, spec='large-left')
self.pimg.setImage(0 * self.get_frame())
self.view.addItem(self.pimg)
self.view.autoRange(padding=0.001)
self.analysisWindow = None
def take_vasculature_picture(self):
filename = generate_filename_path(FOLDERS[self.folderB.currentText()],
filename='vasculature-%s' %
self.subjectBox.currentText(),
extension='.tif')
# save HQ image as tiff
img = self.get_frame(force_HQ=True)
np.save(filename.replace('.tif', '.npy'), img)
img = np.array(255 * (img - img.min()) / (img.max() - img.min()),
dtype=np.uint8)
im = PIL.Image.fromarray(img)
im.save(filename)
print('vasculature image, saved as:')
print(filename)
# then keep a version to store with imaging:
self.vasculature_img = self.get_frame()
self.pimg.setImage(img) # show on displayn
def open_analysis(self):
self.analysisWindow = runAnalysis(self.app, parent=self)
def get_subject_list(self):
with open(
os.path.join(subjects_path,
self.subjectFileBox.currentText())) as f:
self.subjects = json.load(f)
self.subjectBox.clear()
self.subjectBox.addItems(self.subjects.keys())
def init_visual_stim(self, demo=True):
with open(
os.path.join(
pathlib.Path(__file__).resolve().parents[1], 'intrinsic',
'vis_stim', 'up.json'), 'r') as fp:
protocol = json.load(fp)
if self.demoBox.isChecked():
protocol['demo'] = True
self.stim = visual_stim.build_stim(protocol)
self.parent = dummy_parent()
def get_patterns(self, protocol, angle, size, Npatch=30):
patterns = []
if protocol in ['left', 'right']:
z = np.linspace(-self.stim.screen['resolution'][1],
self.stim.screen['resolution'][1], Npatch)
for i in np.arange(len(z) - 1)[(1 if self.flip else 0)::2]:
patterns.append(
visual.Rect(win=self.stim.win,
size=(self.stim.angle_to_pix(size),
z[1] - z[0]),
pos=(self.stim.angle_to_pix(angle), z[i]),
units='pix',
fillColor=1))
if protocol in ['up', 'down']:
x = np.linspace(-self.stim.screen['resolution'][0],
self.stim.screen['resolution'][0], Npatch)
for i in np.arange(len(x) - 1)[(1 if self.flip else 0)::2]:
patterns.append(
visual.Rect(win=self.stim.win,
size=(x[1] - x[0],
self.stim.angle_to_pix(size)),
pos=(x[i], self.stim.angle_to_pix(angle)),
units='pix',
fillColor=1))
return patterns
def run(self):
self.flip = False
self.stim = visual_stim(
{
"Screen": "Dell-2020",
"presentation-prestim-screen": -1,
"presentation-poststim-screen": -1
},
demo=self.demoBox.isChecked())
self.Nrepeat = int(self.repeatBox.text()) #
self.period = float(self.periodBox.text()) # degree / second
self.bar_size = float(self.barBox.text()) # degree / second
# self.dt_save, self.dt = 1./float(self.freqBox.text()), 1./float(self.flickBox.text())
self.dt_save, self.dt = 1. / float(self.freqBox.text()), 1. / float(
self.freqBox.text())
xmin, xmax = 1.15 * np.min(self.stim.x), 1.15 * np.max(self.stim.x)
zmin, zmax = 1.3 * np.min(self.stim.z), 1.3 * np.max(self.stim.z)
self.angle_start, self.angle_max, self.protocol, self.label = 0, 0, '', ''
self.Npoints = int(self.period / self.dt_save)
if self.protocolBox.currentText() == 'ALL':
self.STIM = {
'angle_start': [zmin, xmax, zmax, xmin],
'angle_stop': [zmax, xmin, zmin, xmax],
'label': ['up', 'left', 'down', 'right'],
'xmin': xmin,
'xmax': xmax,
'zmin': zmin,
'zmax': zmax
}
self.label = 'up' # starting point
else:
self.STIM = {
'label': [self.protocolBox.currentText()],
'xmin': xmin,
'xmax': xmax,
'zmin': zmin,
'zmax': zmax
}
if self.protocolBox.currentText() == 'up':
self.STIM['angle_start'] = [zmin]
self.STIM['angle_stop'] = [zmax]
if self.protocolBox.currentText() == 'down':
self.STIM['angle_start'] = [zmax]
self.STIM['angle_stop'] = [zmin]
if self.protocolBox.currentText() == 'left':
self.STIM['angle_start'] = [xmax]
self.STIM['angle_stop'] = [xmin]
if self.protocolBox.currentText() == 'right':
self.STIM['angle_start'] = [xmin]
self.STIM['angle_stop'] = [xmax]
self.label = self.protocolBox.currentText()
for il, label in enumerate(self.STIM['label']):
self.STIM[label + '-times'] = np.arange(
self.Npoints * self.Nrepeat) * self.dt_save
self.STIM[label + '-angle'] = np.concatenate([
np.linspace(self.STIM['angle_start'][il],
self.STIM['angle_stop'][il], self.Npoints)
for n in range(self.Nrepeat)
])
# initialize one episode:
self.iEp, self.iTime, self.t0_episode = 0, 0, time.time()
self.img, self.nSave = self.new_img(), 0
self.save_metadata()
print('acquisition running [...]')
self.update_dt() # while loop
def new_img(self):
return np.zeros(self.imgsize, dtype=np.float64)
def save_img(self):
if self.nSave > 0:
self.img /= self.nSave
if True: # live display
self.pimg.setImage(self.img)
# NEED TO STORE DATA HERE
self.FRAMES.append(self.img)
# re-init time step of acquisition
self.img, self.nSave = self.new_img(), 0
def update_dt(self):
self.tSave = time.time()
while (time.time() - self.tSave) <= self.dt_save:
self.t = time.time()
# show image
patterns = self.get_patterns(
self.STIM['label'][self.iEp % len(self.STIM['label'])],
self.STIM[self.STIM['label'][self.iEp %
len(self.STIM['label'])] +
'-angle'][self.iTime], self.bar_size)
for pattern in patterns:
pattern.draw()
try:
self.stim.win.flip()
except BaseException:
pass
if self.camBox.isChecked():
# # fetch image
self.img += self.get_frame()
self.nSave += 1.0
# time.sleep(max([self.dt-(time.time()-self.t), 0]))
# self.flip = (False if self.flip else True) # flip the flag
self.flip = (False if self.flip else True) # flip the flag
if self.camBox.isChecked():
self.save_img() # re-init image here
self.iTime += 1
# checking if not episode over
if not (self.iTime < len(self.STIM[self.STIM['label'][
self.iEp % len(self.STIM['label'])] + '-angle'])):
if self.camBox.isChecked():
self.write_data() # writing data when over
self.t0_episode, self.img, self.nSave = time.time(), self.new_img(
), 0
self.FRAMES = [] # re init data
self.iTime = 0
self.iEp += 1
# continuing ?
if self.running:
QtCore.QTimer.singleShot(1, self.update_dt)
def write_data(self):
filename = '%s-%i.nwb' % (self.STIM['label'][self.iEp % len(
self.STIM['label'])], int(self.iEp / len(self.STIM['label'])) + 1)
nwbfile = pynwb.NWBFile(
'Intrinsic Imaging data following bar stimulation',
'intrinsic',
datetime.datetime.utcnow(),
file_create_date=datetime.datetime.utcnow())
# Create our time series
angles = pynwb.TimeSeries(
name='angle_timeseries',
data=self.STIM[self.STIM['label'][self.iEp %
len(self.STIM['label'])] +
'-angle'],
unit='Rd',
timestamps=self.STIM[self.STIM['label'][self.iEp %
len(self.STIM['label'])] +
'-times'])
nwbfile.add_acquisition(angles)
images = pynwb.image.ImageSeries(
name='image_timeseries',
data=np.array(self.FRAMES, dtype=np.float64),
unit='a.u.',
timestamps=self.STIM[self.STIM['label'][self.iEp %
len(self.STIM['label'])] +
'-times'])
nwbfile.add_acquisition(images)
# Write the data to file
io = pynwb.NWBHDF5IO(os.path.join(self.datafolder, filename), 'w')
print('writing:', filename)
io.write(nwbfile)
io.close()
print(filename, ' saved !')
def save_metadata(self):
filename = generate_filename_path(FOLDERS[self.folderB.currentText()],
filename='metadata',
extension='.npy')
metadata = {
'subject': str(self.subjectBox.currentText()),
'exposure': self.exposure,
'bar-size': float(self.barBox.text()),
'acq-freq': float(self.freqBox.text()),
'period': float(self.periodBox.text()),
'Nrepeat': int(self.repeatBox.text()),
'imgsize': self.imgsize,
'STIM': self.STIM
}
np.save(filename, metadata)
if self.vasculature_img is not None:
np.save(filename.replace('metadata', 'vasculature'),
self.vasculature_img)
self.datafolder = os.path.dirname(filename)
def launch_protocol(self):
if not self.running:
self.running = True
# initialization of data
self.FRAMES = []
self.img = self.get_frame()
self.imgsize = self.img.shape
self.pimg.setImage(self.img)
self.view.autoRange(padding=0.001)
self.run()
else:
print(
' /!\ --> pb in launching acquisition (either already running or missing camera)'
)
def live_view(self):
self.running, self.t0 = True, time.time()
self.update_Image()
def stop_protocol(self):
if self.running:
self.running = False
if self.stim is not None:
self.stim.close()
else:
print('acquisition not launched')
def get_frame(self, force_HQ=False):
if self.exposure > 0:
self.core.snap_image()
tagged_image = self.core.get_tagged_image()
#pixels by default come out as a 1D array. We can reshape them into an image
img = np.reshape(tagged_image.pix,
newshape=[
tagged_image.tags['Height'],
tagged_image.tags['Width']
])
elif (self.stim is not None) and (self.STIM is not None):
it = int((time.time() - self.t0_episode) / self.dt_save) % int(
self.period / self.dt_save)
protocol = self.STIM['label'][self.iEp % len(self.STIM['label'])]
if protocol == 'left':
img = np.random.randn(*self.stim.x.shape)+\
np.exp(-(self.stim.x-(40*it/self.Npoints-20))**2/2./10**2)*\
np.exp(-self.stim.z**2/2./15**2)
elif protocol == 'right':
img = np.random.randn(*self.stim.x.shape)+\
np.exp(-(self.stim.x+(40*it/self.Npoints-20))**2/2./10**2)*\
np.exp(-self.stim.z**2/2./15**2)
elif protocol == 'up':
img = np.random.randn(*self.stim.x.shape)+\
np.exp(-(self.stim.z-(40*it/self.Npoints-20))**2/2./10**2)*\
np.exp(-self.stim.x**2/2./15**2)
else: # down
img = np.random.randn(*self.stim.x.shape)+\
np.exp(-(self.stim.z+(40*it/self.Npoints-20))**2/2./10**2)*\
np.exp(-self.stim.x**2/2./15**2)
else:
img = np.random.randn(720, 1280)
if (int(self.spatialBox.text()) > 1) and not force_HQ:
return 1.0 * analysis.resample_img(img, int(
self.spatialBox.text()))
else:
return 1.0 * img
def update_Image(self):
# plot it
self.pimg.setImage(self.get_frame())
new_t0 = time.time()
print('dt=%.1f ms' % (1e3 * (new_t0 - self.t0)))
self.t0 = new_t0
if self.running:
QtCore.QTimer.singleShot(1, self.update_Image)
def hitting_space(self):
if not self.running:
self.launch_protocol()
else:
self.stop_protocol()
def process(self):
self.launch_analysis()
def quit(self):
if self.exposure > 0:
self.bridge.close()
sys.exit()
