def long_func2():
for i in trange(4):
for x in trange(4):
pass
for x in trange(4):
pass
def test_tqdm_outside_of_functiongui():
"""Test that we can make a tqdm wrapper with ProgressBar outside of @magicgui."""
with trange(10) as pbar:
assert pbar.n == 0
assert pbar.total == 10
assert not pbar._mgui
assert tuple(trange(5)) == tuple(range(5))
def long_function(steps=10,
repeats=4,
choices="ABCDEFGHIJKLMNOP12345679",
char="",
delay=0.05):
"""Long running computation with nested iterators."""
# trange and tqdm accept all the kwargs from tqdm itself, as well as any
# valid kwargs for magicgui.widgets.ProgressBar, (such as "label")
for r in trange(repeats, label="repeats"):
letters = [random.choice(choices) for _ in range(steps)]
# `tqdm`, like `tqdm`, accepts any iterable
# this progress bar is nested and will be run & reset multiple times
for letter in tqdm(letters, label="steps"):
long_function.char.value = letter
sleep(delay)
def long_running(steps=10, delay=0.1):
"""Long running computation with range iterator."""
# trange(steps) is a shortcut for `tqdm(range(steps))`
for i in trange(steps):
sleep(delay)
def _process_data(self):
# create parameter array from scan parameters saved by acquisition code
df_metadata = read_metadata(self.data_path / Path('scan_metadata.csv'))
root_name = df_metadata['root_name']
scan_type = df_metadata['scan_type']
theta = df_metadata['theta']
scan_step = df_metadata['scan_step']
pixel_size = df_metadata['pixel_size']
num_t = df_metadata['num_t']
num_y = df_metadata['num_y']
num_z = df_metadata['num_z']
num_ch = df_metadata['num_ch']
num_images = df_metadata['scan_axis_positions']
y_pixels = df_metadata['y_pixels']
x_pixels = df_metadata['x_pixels']
chan_405_active = df_metadata['405_active']
chan_488_active = df_metadata['488_active']
chan_561_active = df_metadata['561_active']
chan_635_active = df_metadata['635_active']
chan_730_active = df_metadata['730_active']
active_channels = [chan_405_active,chan_488_active,chan_561_active,chan_635_active,chan_730_active]
channel_idxs = [0,1,2,3,4]
channels_in_data = list(compress(channel_idxs, active_channels))
n_active_channels = len(channels_in_data)
self.active_channels = active_channels
self.channels_in_data = channels_in_data
# calculate pixel sizes of deskewed image in microns
deskewed_x_pixel = pixel_size
deskewed_y_pixel = pixel_size
deskewed_z_pixel = pixel_size
if self.debug:
print('Deskewed pixel sizes before downsampling (um). x='+str(deskewed_x_pixel)+', y='+str(deskewed_y_pixel)+', z='+str(deskewed_z_pixel)+'.')
# deskew parameters
deskew_parameters = np.empty([3])
deskew_parameters[0] = theta # (degrees)
deskew_parameters[1] = scan_step*100 # (nm)
deskew_parameters[2] = pixel_size*100 # (nm)
# amount of down sampling in z
z_down_sample = 1
# load dataset
dataset_zarr = zarr.open(self.data_path / Path(root_name+'.zarr'),mode='r')
# create output directory
if self.decon == 0 and self.flatfield == 0:
output_dir_path = self.data_path / 'deskew_output'
elif self.decon == 0 and self.flatfield == 1:
output_dir_path = self.data_path / 'deskew_flatfield_output'
elif self.decon == 1 and self.flatfield == 0:
output_dir_path = self.data_path / 'deskew_decon_output'
elif self.decon == 1 and self.flatfield == 1:
output_dir_path = self.data_path / 'deskew_flatfield_decon_output'
output_dir_path.mkdir(parents=True, exist_ok=True)
# create name for zarr directory
zarr_output_path = output_dir_path / Path('OPM_processed.zarr')
# calculate size of one volume
# change step size from physical space (nm) to camera space (pixels)
pixel_step = scan_step/pixel_size # (pixels)
# calculate the number of pixels scanned during stage scan
scan_end = num_images * pixel_step # (pixels)
# calculate properties for final image
ny = np.int64(np.ceil(scan_end+y_pixels*np.cos(theta*np.pi/180))) # (pixels)
nz = np.int64(np.ceil(y_pixels*np.sin(theta*np.pi/180))) # (pixels)
nx = np.int64(x_pixels) # (pixels)
# create and open zarr file
opm_data = zarr.open(str(zarr_output_path), mode="w", shape=(num_t, num_ch, nz, ny, nx), chunks=(1, 1, int(nz), int(ny), int(nx)), dtype=np.uint16)
# if retrospective flatfield is requested, try to import CuPY based flat-fielding
if self.flatfield:
pass
# if decon is requested, try to import microvolution wrapper or dexp library
if self.decon:
from src.utils.opm_psf import generate_skewed_psf
from src.utils.image_post_processing import lr_deconvolution_cupy
ex_wavelengths = [.405,.488,.561,.635,.730]
em_wavelengths = [.420,.520,.605,.680,.760]
skewed_psf = []
for ch_idx in active_channels:
skewed_psf.append(generate_skewed_psf(0.1,ex_wavelengths[ch_idx],em_wavelengths[ch_idx]))
# loop over all timepoints and channels
for t_idx in trange(num_t,desc='t',position=0):
for ch_idx in trange(n_active_channels,desc='c',position=1, leave=False):
# pull data stack into memory
if self.debug:
print('Process timepoint '+str(t_idx)+'; channel '+str(ch_idx) +'.')
raw_data = return_data_from_zarr_to_numpy(dataset_zarr, t_idx, ch_idx, num_images, y_pixels,x_pixels)
# run deconvolution on deskewed image
if self.decon:
if self.debug:
print('Deconvolve.')
decon = lr_deconvolution_cupy(raw_data,skewed_psf[ch_idx])
else:
decon = raw_data
pass
del raw_data
# perform flat-fielding
if self.flatfield:
corrected=decon
else:
if self.debug:
print('Flatfield.')
corrected=decon
del decon
# deskew
if self.debug:
print('Deskew.')
deskewed = deskew(np.flipud(corrected),*deskew_parameters)
del corrected
# downsample in z due to oversampling when going from OPM to coverslip geometry
if z_down_sample==1:
deskewed_downsample = deskewed
else:
if self.debug:
print('Downsample.')
deskewed_downsample = block_reduce(deskewed, block_size=(z_down_sample,1,1), func=np.mean)
del deskewed
if self.debug:
print('Write data into Zarr container')
opm_data[t_idx, ch_idx, :, :, :] = deskewed_downsample
# free up memory
del deskewed_downsample
gc.collect()
# exit
self.dataset_zarr = zarr_output_path
self.scale = [1,deskewed_z_pixel,deskewed_y_pixel,deskewed_x_pixel]
def _on_click(self):
for i in trange(10):
sleep(0.1)
def f2():
with trange(10, leave=False) as pbar2:
pass
assert pbar2.progressbar.visible is False
def f():
with trange(10, leave=True) as pbar1:
pass
assert pbar1.progressbar.visible is True
def f():
with trange(10, disable=True) as pbar:
assert not hasattr(pbar, "progressbar")
assert not pbar._mgui
def _indirectly_decorated(steps=2):
for i in trange(4):
pass
def long_func(steps=2):
for i in trange(4):
pass
def _acquire_3d_t_data(self):
with RemoteMMCore() as mmc_3d_time:
#------------------------------------------------------------------------------------------------------------------------------------
#----------------------------------------------Begin setup of scan parameters--------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
# parse which channels are active
active_channel_indices = [ind for ind, st in zip(self.do_ind, self.channel_states) if st]
self.n_active_channels = len(active_channel_indices)
if self.debug:
print("%d active channels: " % self.n_active_channels, end="")
for ind in active_channel_indices:
print("%s " % self.channel_labels[ind], end="")
print("")
if self.ROI_changed:
self._crop_camera()
self.ROI_changed = False
# set exposure time
if self.exposure_changed:
mmc_3d_time.setExposure(self.exposure_ms)
self.exposure_changed = False
if self.powers_changed:
self._set_mmc_laser_power()
self.powers_changed = False
if self.channels_changed or self.footprint_changed or not(self.DAQ_running):
if self.DAQ_running:
self.opmdaq.stop_waveform_playback()
self.DAQ_running = False
self.opmdaq.set_scan_type('mirror')
self.opmdaq.set_channels_to_use(self.channel_states)
self.opmdaq.set_interleave_mode(True)
self.scan_steps = self.opmdaq.set_scan_mirror_range(self.scan_axis_step_um,self.scan_mirror_footprint_um)
self.opmdaq.generate_waveforms()
self.channels_changed = False
self.footprint_changed = False
# create directory for timelapse
time_string = datetime.now().strftime("%Y_%m_%d-%I_%M_%S")
self.output_dir_path = self.save_path / Path('timelapse_'+time_string)
self.output_dir_path.mkdir(parents=True, exist_ok=True)
# create name for zarr directory
zarr_output_path = self.output_dir_path / Path('OPM_data.zarr')
# create and open zarr file
opm_data = zarr.open(str(zarr_output_path), mode="w", shape=(self.n_timepoints, self.n_active_channels, self.scan_steps, self.ROI_width_y, self.ROI_width_x), chunks=(1, 1, 1, self.ROI_width_y, self.ROI_width_x),compressor=None, dtype=np.uint16)
#------------------------------------------------------------------------------------------------------------------------------------
#----------------------------------------------End setup of scan parameters----------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
#----------------------------------------------------Start acquisition---------------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
# set circular buffer to be large
mmc_3d_time.clearCircularBuffer()
circ_buffer_mb = 96000
mmc_3d_time.setCircularBufferMemoryFootprint(int(circ_buffer_mb))
# run hardware triggered acquisition
if self.wait_time == 0:
self.opmdaq.start_waveform_playback()
self.DAQ_running = True
mmc_3d_time.startSequenceAcquisition(int(self.n_timepoints*self.n_active_channels*self.scan_steps),0,True)
for t in trange(self.n_timepoints,desc="t", position=0):
for z in trange(self.scan_steps,desc="z", position=1, leave=False):
for c in range(self.n_active_channels):
while mmc_3d_time.getRemainingImageCount()==0:
pass
opm_data[t, c, z, :, :] = mmc_3d_time.popNextImage()
mmc_3d_time.stopSequenceAcquisition()
self.opmdaq.stop_waveform_playback()
self.DAQ_running = False
else:
for t in trange(self.n_timepoints,desc="t", position=0):
self.opmdaq.start_waveform_playback()
self.DAQ_running = True
mmc_3d_time.startSequenceAcquisition(int(self.n_active_channels*self.scan_steps),0,True)
for z in trange(self.scan_steps,desc="z", position=1, leave=False):
for c in range(self.n_active_channels):
while mmc_3d_time.getRemainingImageCount()==0:
pass
opm_data[t, c, z, :, :] = mmc_3d_time.popNextImage()
mmc_3d_time.stopSequenceAcquisition()
self.opmdaq.stop_waveform_playback()
self.DAQ_running = False
time.sleep(self.wait_time)
# construct metadata and save
self._save_metadata()
#------------------------------------------------------------------------------------------------------------------------------------
#--------------------------------------------------------End acquisition-------------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------------------------
# set circular buffer to be small
mmc_3d_time.clearCircularBuffer()
circ_buffer_mb = 4000
mmc_3d_time.setCircularBufferMemoryFootprint(int(circ_buffer_mb))
