def main(argv=None):
parser = argparse.ArgumentParser(description='microscope server control')
parser.add_argument('--debug', action='store_true', help='show full stack traces on error')
subparsers = parser.add_subparsers(help='sub-command help', dest='command')
subparsers.required = True
parser_start = subparsers.add_parser('start', help='start the microscope server, if not running')
parser_start.add_argument('--local', action='store_false', dest='public', help='Allow only local connections to the server [default: allow network connections]')
parser_start.add_argument('--verbose', action='store_true', help='Log all RPC calls and property state changes.')
parser_stop = subparsers.add_parser('stop', help='stop the microscope server, if running')
parser_stop.add_argument('-f', '--force', action='store_true', help='forcibly kill the server process')
parser_restart = subparsers.add_parser('restart', help='restart the microscope server, if running')
parser_restart.add_argument('-f', '--force', action='store_true', help='forcibly kill the server process')
parser_status = subparsers.add_parser('status', help='report whether the microscope server is running')
args = parser.parse_args(argv)
try:
server = scope_server.ScopeServer()
if args.command == 'status':
server.status()
if args.command in {'stop', 'restart'}:
server.stop(args.force)
if args.command == 'start':
with server.arg_file.open('w') as f:
datafile.json_encode_legible_to_file(dict(public=args.public, verbose=args.verbose), f)
if args.command in {'start', 'restart'}:
server.start()
except Exception as e:
if args.debug:
traceback.print_exc(file=sys.stderr)
else:
sys.stderr.write(str(e)+'\n')
return 1
def take_sequential_images(scope, out_dir, tl_intensity=255, exposure_time=2):
'''
Take sequential images as one specifies positions on a stage
'''
out_dir = pathlib.Path(out_dir)
scope.camera.acquisition_sequencer.new_sequence()
scope.camera.acquisition_sequencer.add_step(exposure_time,
'TL',
tl_intensity=tl_intensity)
out_dir.mkdir(exist_ok=True)
pos_num = 0
print(
'Press enter after each position has been found; press control-c to end'
)
while True:
try:
input()
except KeyboardInterrupt:
break
bf_image = scope.camera.acquisition_sequencer.run()[0]
freeimage.write(bf_image, out_dir / f'_{pos_num:03d}.png')
pos_num += 1
if pos_num > 0:
imaging_parameters = {
'lamp': 'TL',
'exposure': exposure_time,
'intensity': tl_intensity
}
with (out_dir / 'imaging_parameters.json').open('w') as param_file:
datafile.json_encode_legible_to_file(imaging_parameters,
param_file)
def reset_positions_with_offset(experiment_dir, offset):
''' Modify position coordinates based on a fixed x-y offset
Parameters:
experiment_dir - str/pathlib.Path to experiment root
offset - list giving the x-y offset
'''
experiment_dir = pathlib.Path(experiment_dir)
print(f'Modifying positions for {experiment_dir.name}')
metadata = load_data.read_metadata(experiment_dir)
new_metadata = metadata.copy()
if len(offset) == 2:
offset.extend([0])
try:
time_label = time.strftime('%Y%m%d-%H%M-%S')
for position in metadata['positions']:
position_coords = metadata['positions'][position]
new_metadata['positions'][position] = [
position_coords[0] + offset[0], position_coords[1] + offset[1],
position_coords[2] + offset[2]
]
with (experiment_dir /
f'experiment_metadata_beforechangingpositions_{time_label}.json'
).open('w') as mdata_file:
datafile.json_encode_legible_to_file(metadata, mdata_file)
load_data.write_metadata(new_metadata, experiment_dir)
except KeyboardInterrupt:
pass
def main(argv=None):
parser = argparse.ArgumentParser(description='microscope server control')
parser.add_argument('--debug',
action='store_true',
help='show full stack traces on error')
subparsers = parser.add_subparsers(help='sub-command help', dest='command')
subparsers.required = True
parser_start = subparsers.add_parser(
'start', help='start the microscope server, if not running')
parser_start.add_argument(
'--local',
action='store_false',
dest='public',
help=
'Allow only local connections to the server [default: allow network connections]'
)
parser_start.add_argument(
'--verbose',
action='store_true',
help='Log all RPC calls and property state changes.')
parser_stop = subparsers.add_parser(
'stop', help='stop the microscope server, if running')
parser_stop.add_argument('-f',
'--force',
action='store_true',
help='forcibly kill the server process')
parser_restart = subparsers.add_parser(
'restart', help='restart the microscope server, if running')
parser_restart.add_argument('-f',
'--force',
action='store_true',
help='forcibly kill the server process')
parser_status = subparsers.add_parser(
'status', help='report whether the microscope server is running')
args = parser.parse_args(argv)
try:
server = scope_server.ScopeServer()
if args.command == 'status':
server.status()
if args.command in {'stop', 'restart'}:
server.stop(args.force)
if args.command == 'start':
with server.arg_file.open('w') as f:
datafile.json_encode_legible_to_file(
dict(public=args.public, verbose=args.verbose), f)
if args.command in {'start', 'restart'}:
server.start()
except Exception as e:
if args.debug:
traceback.print_exc(file=sys.stderr)
else:
sys.stderr.write(str(e) + '\n')
return 1
def create_metadata_file(data_dir, positions, z_max, reference_positions,
nominal_temperature, objective, optocoupler, filter_cube,
fluorescence_flatfield_lamp, save_focus_stacks=None, **other_metadata):
""" Create the experiment_metadata.json file for timecourse acquisitions.
Parameters:
data_dir: directory to write metadata file into
positions: list of (x,y,z) positions, OR dict mapping different category
names to lists of (x,y,z) positions.
z_max: maximum z-value allowed during autofocus
reference_positions: list of (x,y,z) positions to be used to generate
brightfield and optionally fluorescence flat-field images.
nominal_temperature: intended temperature for experiment
objective, optocoupler: objective and optocoupler to be used.
filter_cube: name of the filter cube to use
fluorescence_flatfield_lamp: if fluorescent flatfield images are
desired, provide the name of an appropriate spectra x lamp that is
compatible with the specified filter cube. Use None to disable
fluorescence flatfielding.
save_focus_stacks: if None, don't save any focus stacks. If a list of position
names, save focus stacks for those positions. If a number, save
focus stacks for that number of positions.
**other_metadata: key-values that will be saved directly in metadata json.
"""
data_dir = pathlib.Path(data_dir)
data_dir.mkdir(parents=True, exist_ok=True)
try:
items = positions.items()
except AttributeError:
items = [('', positions)]
named_positions = {}
for name_prefix, positions in items:
names = _name_positions(len(positions), name_prefix)
named_positions.update(zip(names, positions))
bf_meter_position_name = _choose_bf_metering_pos(named_positions)
metadata = dict(z_max=z_max, reference_positions=reference_positions,
positions=named_positions, bf_meter_position_name=bf_meter_position_name,
objective=int(objective), optocoupler=float(optocoupler),
nominal_temperature=float(nominal_temperature), filter_cube=str(filter_cube),
fluorescence_flatfield_lamp=fluorescence_flatfield_lamp, **other_metadata)
if save_focus_stacks:
try:
# check if it's iterable
for pos in save_focus_stacks:
assert pos in named_positions
except TypeError:
num_to_save = int(save_focus_stacks)
save_indices = numpy.random.permutation(len(named_positions))[:num_to_save]
names = list(named_positions.keys())
save_focus_stacks = [names[i] for i in save_indices]
metadata['save_focus_stacks'] = save_focus_stacks
with (data_dir / 'experiment_metadata.json').open('w') as f:
datafile.json_encode_legible_to_file(metadata, f)
def create_metadata_file(data_dir, positions, z_max, reference_positions,
nominal_temperature, objective, optocoupler, filter_cube,
fluorescence_flatfield_lamp, save_focus_stacks=None, **other_metadata):
""" Create the experiment_metadata.json file for timecourse acquisitions.
Parameters:
data_dir: directory to write metadata file into
positions: list of (x,y,z) positions, OR dict mapping different category
names to lists of (x,y,z) positions.
z_max: maximum z-value allowed during autofocus
reference_positions: list of (x,y,z) positions to be used to generate
brightfield and optionally fluorescence flat-field images.
nominal_temperature: intended temperature for experiment
objective, optocoupler: objective and optocoupler to be used.
filter_cube: name of the filter cube to use
fluorescence_flatfield_lamp: if fluorescent flatfield images are
desired, provide the name of an appropriate spectra x lamp that is
compatible with the specified filter cube. Use None to disable
fluorescence flatfielding.
save_focus_stacks: if None, don't save any focus stacks. If a list of position
names, save focus stacks for those positions. If a number, save
focus stacks for that number of positions.
**other_metadata: key-values that will be saved directly in metadata json.
"""
data_dir = pathlib.Path(data_dir)
data_dir.mkdir(parents=True, exist_ok=True)
try:
items = positions.items()
except AttributeError:
items = [('', positions)]
named_positions = {}
for name_prefix, positions in items:
names = _name_positions(len(positions), name_prefix)
named_positions.update(zip(names, positions))
bf_meter_position_name = _choose_bf_metering_pos(named_positions)
metadata = dict(z_max=z_max, reference_positions=reference_positions,
positions=named_positions, bf_meter_position_name=bf_meter_position_name,
objective=int(objective), optocoupler=float(optocoupler),
nominal_temperature=float(nominal_temperature), filter_cube=str(filter_cube),
fluorescence_flatfield_lamp=fluorescence_flatfield_lamp, **other_metadata)
if save_focus_stacks:
try:
# check if it's iterable
for pos in save_focus_stacks:
assert pos in named_positions
except TypeError:
num_to_save = int(save_focus_stacks)
save_indices = numpy.random.permutation(len(named_positions))[:num_to_save]
names = list(named_positions.keys())
save_focus_stacks = [names[i] for i in save_indices]
metadata['save_focus_stacks'] = save_focus_stacks
with (data_dir / 'experiment_metadata.json').open('w') as f:
datafile.json_encode_legible_to_file(metadata, f)
def take_automated_plate_images(scope, out_dir):
out_dir = pathlib.Path(out_dir)
scope.camera.acquisition_sequencer.new_sequence()
scope.camera.acquisition_sequencer.add_step(2, 'TL', tl_intensity=255)
out_dir.mkdir(exist_ok=True)
field_spacing = 2160 * 0.0065 * 1 / 2.5 # FILL ME IN WITH APPROPRIATE FIELD SIZE BASED ON 2.5X OBJECTIVE
try:
input('Specify center of plate')
center_position = scope.stage.position
input('Specify outer extent of plate')
outer_position = scope.stage.position
roi_radius = ((center_position[0] - outer_position[0])**2 +
(center_position[1] - outer_position[1])**2)**0.5
# Define function to interpolate z - assume the plate surface is a parabola with radial symmetry about its center w.r.t. both x & y
scale_param = (outer_position[2] - center_position[2]) / (roi_radius**
2)
interpolate_z = lambda x, y: scale_param * (
(x - center_position[0])**2 +
(y - center_position[1])**2) + center_position[2]
grid_x = np.arange(center_position[0] - roi_radius / np.sqrt(2),
center_position[0] + roi_radius / np.sqrt(2),
field_spacing)
grid_y = np.arange(center_position[1] - roi_radius / np.sqrt(2),
center_position[1] + roi_radius / np.sqrt(2),
field_spacing)
xcoor, ycoor = np.meshgrid(grid_x, grid_y)
xcoor = np.array(
[pts if num % 2 else pts[::-1] for num, pts in enumerate(xcoor)]
) # invert the x-coordinates appropriately so that we make take min time to traverse the slide
#raise Exception()
pos_num = 0
for x, y in zip(xcoor.flatten(), ycoor.flatten()):
scope.stage.position = [x, y, interpolate_z(x, y)]
bf_image = scope.camera.acquisition_sequencer.run()[0]
freeimage.write(bf_image, out_dir / f'_{pos_num:03d}.png')
pos_num += 1
imaging_parameters = {'lamp': 'TL', 'exposure': 2, 'intensity': 255}
with (out_dir / 'imaging_parameters.json').open('w') as param_file:
datafile.json_encode_legible_to_file(imaging_parameters,
param_file)
scope.stage.position = center_position
except KeyboardInterrupt:
return
def reset_positions_manual(scope,
experiment_dir,
*annotation_filters,
revert_z=False):
'''Reset positions manually for an experiment (i.e. with a separate ris_widget window open)
Parameters:
scope - ScopeClient object as defined by scope.scope_client
experiment_dir - str/pathlib.Path to experiment
annotation_filters - Optional variable filters to use to isolate specific positions of interest
Call with annotation filters like so:
reset_position.reset_positions(scope, experiment_dir, elegant_filters.filter_excluded, elegant_filters.filter_live_animals)
'''
experiment_dir = pathlib.Path(experiment_dir)
print(f'Traversing {experiment_dir.name}')
metadata = load_data.read_metadata(experiment_dir)
if annotation_filters:
experiment_annotations = load_data.read_annotations(experiment_dir)
for filter in annotation_filters:
experiment_annotations = load_data.filter_annotations(
experiment_annotations, filter)
positions = experiment_annotations.keys()
else:
positions = metadata['positions'].keys()
new_positions = poll_positions(scope,
metadata,
positions,
revert_z=revert_z)
if new_positions:
try:
input(f'\nPress any key to save positions; ctrl-c to abort')
time_label = time.strftime('%Y%m%d-%H%M-%S')
with (experiment_dir /
f'experiment_metadata_beforechangingpositions_{time_label}.json'
).open('w') as mdata_file:
datafile.json_encode_legible_to_file(metadata, mdata_file)
metadata['positions'].update(new_positions)
load_data.write_metadata(metadata, experiment_dir)
except KeyboardInterrupt:
pass
else:
print('No positions found to reset')
def well_plate_acquisition(scope,
out_dir,
tl_intensity,
grid_size=[4, 6],
well_spacing_cc=12.92):
'''
grid_size, well_spacing_cc for nominal Falcon 48-well plate (latter in mm)
'''
out_dir = pathlib.Path(out_dir)
scope.camera.acquisition_sequencer.new_sequence()
scope.camera.acquisition_sequencer.add_step(2,
'TL',
tl_intensity=tl_intensity)
out_dir.mkdir()
try:
print('Specify xy-position for top-left well; press ctrl-c to abort.')
input()
topleft_position = scope.stage.position
pos_num = 0
for row_num in range(grid_size[0]):
for column_num in range(grid_size[1]):
scope.stage.position = [
topleft_position[0] + column_num * well_spacing_cc,
topleft_position[1] + row_num * well_spacing_cc,
topleft_position[2],
]
print('Adjust to desired z-position; press ctrl-c to abort.')
input()
bf_image = scope.camera.acquisition_sequencer.run()[0]
freeimage.write(bf_image, out_dir / f'_{pos_num:03d}.png')
pos_num += 1
imaging_parameters = {
'lamp': 'TL',
'exposure': 2,
'intensity': tl_intensity
}
with (out_dir / 'imaging_parameters.json').open('w') as param_file:
datafile.json_encode_legible_to_file(imaging_parameters,
param_file)
except KeyboardInterrupt:
return
def make_align_img(scope, expt_dir):
expt_dir = pathlib.Path(expt_dir)
try:
scope_pos, my_image = take_img(scope, expt_dir)
except KeyboardInterrupt:
return
time_label = time.strftime('%Y%m%d-%H%M-%S')
with (expt_dir / 'experiment_metadata.json').open('r') as mdata_file:
metadata = json.load(mdata_file)
with (expt_dir / f'experiment_metadata_noalign_{time_label}.json'
).open('w') as mdata_file:
datafile.json_encode_legible_to_file(metadata, mdata_file)
metadata['align_position'] = scope_pos
with (expt_dir / 'experiment_metadata.json').open('w') as mdata_file:
datafile.json_encode_legible_to_file(metadata, mdata_file)
(expt_dir / 'calibrations').mkdir(exist_ok=True)
freeimage.write(my_image, expt_dir / 'calibrations' / 'align_image.png')
def _write(self, jobs):
"""Write Job tuples as json to self.backing_file."""
job_list = [[str(exec_file)] + rest
for exec_file, *rest in jobs.values()]
with self.jobs_lock, self.backing_file.open('w') as bf:
datafile.json_encode_legible_to_file(job_list, bf)
def _write(self, jobs):
"""Write Job tuples as json to self.backing_file."""
job_list = [[str(exec_file)] + rest for exec_file, *rest in jobs.values()]
with self.jobs_lock, self.backing_file.open('w') as bf:
datafile.json_encode_legible_to_file(job_list, bf)
def perform_alignment(scope, expt_dir, rw):
px_conversion = 1.304 / 1000 #mm/px
expt_dir = pathlib.Path(expt_dir)
before_img = freeimage.read(
str(expt_dir / 'calibrations' / 'align_image.png'))
with (expt_dir / 'experiment_metadata.json').open('r') as mdata_file:
metadata = json.load(mdata_file)
before_scope_pos = np.array(metadata['align_position'])
if scope is not None:
scope.stage.position = before_scope_pos # Set z to same position
after_scope_pos, after_img = take_img(scope, expt_dir)
else: # old debugging not on scope
after_scope_pos = np.array([163.6972, 3.085, 23.739])
#~ after_img = freeimage.read('/mnt/scopearray/Sinha_Drew/testing/align_pics/after_img.png')
#after_img = freeimage.read('/media/Data/Documents/Dropbox/align_pics/after_img.png')
#after_img = freeimage.read('/home/zplab/Desktop/align_pics/after_img.png')
if len(rw.flipbook.pages) > 0: rw.flipbook.pages.clear()
rw.flipbook.pages.append(ImageList([Image(before_img), Image(after_img)]))
#rw.layers[0].tint=[255,232,185,0.5]
#rw.layers[1].tint = [270,70,255,0.5]
# my_ptpicker = PointListPicker(rw.main_view,rw.main_scene.layer_stack_item)
# my_ptpicker = SimplePointPicker(rw.main_view,rw.main_scene.layer_stack_item)
my_ptpicker = point_set.PointSet(rw)
#ip_input('Click on first landmark in old and new images; press Enter when done.')
input(
'Click on first landmark in old and new images; press Enter when done.'
)
before_first_pos, after_first_pos = [
np.array(point) for point in my_ptpicker.points
] # IN PIXELS
print('Acquired first landmark')
# my_ptpicker.points = []
for point in my_ptpicker.points:
point.remove()
ip_input(
'Click on second landmark in old and new images; press Enter when done.'
)
before_next_pos, after_next_pos = [
np.array(point) for point in my_ptpicker.points
]
print('Acquired second landmark')
# my_ptpicker.points = []
for point in my_ptpicker.points:
point.remove()
xy_offset = after_scope_pos[:2] + after_first_pos * px_conversion - (
before_scope_pos[:2] + before_first_pos * px_conversion)
xy_offset = xy_offset * [
-1, 1
] #Correct for directionality of stage on ISCOPE CHECK THIS ON SCOPE!!!!!!!!!!!
print(xy_offset)
before_next_adj = before_next_pos - before_first_pos
after_next_adj = after_next_pos - after_first_pos
before_incline = np.arctan(before_next_adj[1] / before_next_adj[0])
after_incline = np.arctan(after_next_adj[1] / after_next_adj[0])
incline_offset = after_incline - before_incline
print('Before incline:{:.2f}\nAfter incline:{:.2f}\nOffset:{:.2f}'.format(
before_incline, after_incline, incline_offset)) # GOOD UP TO HERE.
#raise Exception("xy:{} (px), incline:{} (deg)".format(xy_offset,incline_offset*360/2*np.pi))
old_metadata = metadata.copy()
metadata['align_position'].append(after_scope_pos) # Save the old!
for well in metadata['positions']:
# Do rotation first
rotated_point = np.dot(
np.array([[np.cos(incline_offset), -np.sin(incline_offset)],
[np.sin(incline_offset),
np.cos(incline_offset)]]),
np.array(metadata['positions'][well][:2] -
np.array(before_scope_pos[:2] +
before_first_pos * px_conversion))
) + np.array(before_scope_pos[:2] + before_first_pos * px_conversion)
metadata['positions'][well][:2] = list(rotated_point + xy_offset)
wells = [
well_dir.parts[-1] for well_dir in expt_dir.iterdir()
if str(well_dir.parts[-1]).isnumeric()
]
metadata['realignment_time'] = metadata.get('realignment_time', []).append(
time.strftime("%Y-%m-%dt%H%M"))
# Compare before and after positions (offset only)
scope.stage.position = list(
np.append(before_scope_pos[:2] + xy_offset, before_scope_pos[2]))
trash, final_landmark_img = take_img(scope, expt_dir, poll=False)
rw.flipbook.pages.append(
ImageList([Image(before_img),
Image(final_landmark_img)]))
ip_input(
'Press anything if landmarks looks aligned (xy-offset); ctrl-c to abort'
)
# Compare first and last wells
rw.flipbook.pages.clear()
before_first_img = freeimage.read([
bf_file for bf_file in (expt_dir / wells[0]).iterdir()
if 'bf.png' in bf_file.parts[-1]
][0])
scope.stage.position = list(
np.append(
np.array(old_metadata['positions'][wells[0]][:2]) + xy_offset,
old_metadata['positions'][
wells[0]][2])) # Do one with the offset for debugging
trash, after_first_offset_img = take_img(scope, expt_dir, poll=False)
rw.flipbook.pages.append(
ImageList([Image(before_first_img),
Image(after_first_offset_img)
])) #,name='Before After Well'+str(wells[0]))
scope.stage.position = metadata['positions'][wells[0]]
trash, after_first_img = take_img(scope, expt_dir, poll=False)
rw.flipbook.pages.append(
ImageList([Image(before_first_img),
Image(after_first_img)
])) #,name='Before After Well'+str(wells[0]))
ip_input('Press anything if first well looks aligned; ctrl-c to abort')
before_last_img = freeimage.read([
bf_file for bf_file in (expt_dir / wells[-1]).iterdir()
if 'bf.png' in bf_file.parts[-1]
][0])
scope.stage.position = metadata['positions'][wells[-1]]
trash, after_last_img = take_img(scope, expt_dir, poll=False)
rw.flipbook.pages.clear()
rw.flipbook.pages.append(
ImageList([Image(before_last_img),
Image(after_last_img)
])) # ,name='Before After Well'+str(wells[-1]))
ip_input('Press anything if last well looks aligned; ctrl-c to abort')
with (expt_dir /
'experiment_metadata_oldprealignment.json').open('w') as mdata_file:
datafile.json_encode_legible_to_file(old_metadata, mdata_file)
with (expt_dir / 'experiment_metadata.json').open('w') as mdata_file:
datafile.json_encode_legible_to_file(metadata, mdata_file)
freeimage.write(before_img,
str(expt_dir / 'calibrations' / 'old_align_image.png'))
freeimage.write(after_img,
str(expt_dir / 'calibrations' / 'align_image.png'))