def main(args):
"""Main function of cellanneal."""
if (args.start_temp is not None
or args.end_temp is not None) and args.auto_temp == 1:
raise Exception(
"when auto_temp is set to 1(default value), starting temperature or ending temperature should not be set manually"
)
if not args.no_parallel:
import dask
from dask.distributed import Client, LocalCluster
if not args.cluster:
cluster = LocalCluster(
n_workers=args.workers,
local_dir="/tmp/CellUniverse/dask-worker-space")
else:
cluster = args.cluster
client = Client(cluster)
else:
client = None
lineagefile = None
start = time.time()
try:
if args.debug:
debugmode = True
config = load_config(args.config)
celltype = config['global.cellType'].lower()
# setup the colony from a file with the initial properties
lineageframes = LineageFrames()
colony = lineageframes.forward()
load_colony(colony, args.initial, config)
# open the lineage file for writing
lineagefile = open(args.output / 'lineage.csv', 'w')
header = ['file', 'name']
if celltype == 'bacilli':
header.extend(['x', 'y', 'width', 'length', 'rotation'])
print(','.join(header), file=lineagefile)
if args.global_optimization:
import global_optimization
global_optimization.optimize(get_inputfiles(args), lineageframes,
lineagefile, args, config)
return 0
if args.auto_temp == 1:
temperature, end_temperature = auto_temp_schedule(
get_inputfiles(args)[0], lineageframes.forward(), args, config)
setattr(args, 'start_temp', temperature)
setattr(args, 'end_temp', end_temperature)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
for imagefile in get_inputfiles(args):
colony = optimize(imagefile, lineageframes, args, config, client)
# flatten modifications and save cell properties
colony.flatten()
for cellnode in colony:
properties = [imagefile.name, cellnode.cell.name]
if celltype == 'bacilli':
properties.extend([
str(cellnode.cell.x),
str(cellnode.cell.y),
str(cellnode.cell.width),
str(cellnode.cell.length),
str(cellnode.cell.rotation)
])
print(','.join(properties), file=lineagefile)
except KeyboardInterrupt as error:
raise error
finally:
if lineagefile:
lineagefile.close()
print(f'{time.time() - start} seconds')
return 0
def main(args):
"""Main function of cellanneal."""
if (args.start_temp is not None or args.end_temp is not None) and args.auto_temp == 1:
raise Exception("when auto_temp is set to 1(default value), starting temperature or ending temperature should not be set manually")
# if not args.no_parallel:
# import dask
# from dask.distributed import Client, LocalCluster
# if not args.cluster:
# cluster = LocalCluster(
# n_workers=args.workers,local_dir="/tmp/CellUniverse/dask-worker-space"
# )
# else:
# cluster = args.cluster
#
# client = Client(cluster)
# else:
client = None
lineagefile = None
start = time.time()
try:
config = load_config(args.config)
simulation_config = config["simulation"]
#Maybe better to store the image type in the config file in the first place, instead of using cmd?
if args.graySynthetic == True:
simulation_config["image.type"] = "graySynthetic"
elif args.phaseContrast == True:
simulation_config["image.type"] = "phaseContrastImage"
elif args.binary == True:
simulation_config["image.type"] = "binary"
else:
raise ValueError("Invalid Command: Synthetic image type must be specified")
if not args.output.is_dir():
args.output.mkdir()
if not args.bestfit.is_dir():
args.bestfit.mkdir()
if args.residual and not args.residual.is_dir():
args.residual.mkdir()
seed = int(start * 1000) % (2**32)
if args.seed != None:
seed = args.seed
np.random.seed(seed)
print("Seed: {}".format(seed))
celltype = config['global.cellType'].lower()
# setup the colony from a file with the initial properties
lineageframes = LineageFrames()
colony = lineageframes.forward()
imagefiles = get_inputfiles(args)
if args.lineage_file:
load_colony(colony, args.lineage_file, config, initial_frame = imagefiles[0].name)
else:
load_colony(colony, args.initial, config)
cost_diff = (-1, -1)
# open the lineage file for writing
lineagefile = open(args.output/'lineage.csv', 'w')
header = ['file', 'name']
if celltype == 'bacilli':
header.extend(['x', 'y', 'width', 'length', 'rotation', "split_alpha", "opacity"])
print(','.join(header), file=lineagefile)
if args.debug:
with open(args.debug/'debug.csv', 'w') as debugfile:
print(','.join(['window_start', 'window_end', 'pbad_total', 'bad_count', 'temperature', 'total_cost_diff', 'current_iteration', 'total_iterations']), file=debugfile)
if args.global_optimization:
global useDistanceObjective
useDistanceObjective = args.dist
realimages = [optimization.load_image(imagefile) for imagefile in imagefiles]
window = config["global_optimizer.window_size"]
if args.lineage_file:
lineage = global_optimization.build_initial_lineage(imagefiles, args.lineage_file, args.continue_from, config["simulation"])
else:
lineage = global_optimization.build_initial_lineage(imagefiles, args.initial, args.continue_from, config["simulation"])
lineage = global_optimization.find_optimal_simulation_confs(imagefiles, lineage, realimages, args.continue_from)
sim_start = args.continue_from - args.frame_first
print(sim_start)
shape = realimages[0].shape
synthimages = []
cellmaps = []
distmaps = []
iteration_per_cell = config["iteration_per_cell"]
if not useDistanceObjective:
distmaps = [None] * len(realimages)
for window_start in range(1 - window, len(realimages)):
window_end = window_start + window
print(window_start, window_end)
if window_end <= len(realimages):
# get initial estimate
if window_start >= sim_start:
if window_end > 1:
lineage.copy_forward()
realimage = realimages[window_end - 1]
synthimage, cellmap = optimization.generate_synthetic_image(lineage.frames[window_end - 1].nodes, shape, lineage.frames[window_end - 1].simulation_config)
synthimages.append(synthimage)
cellmaps.append(cellmap)
if useDistanceObjective:
distmap = distance_transform_edt(realimage < .5)
distmap /= config[f'{config["global.cellType"].lower()}.distanceCostDivisor'] * config[
'global.pixelsPerMicron']
distmap += 1
distmaps.append(distmap)
if args.auto_temp == 1 and window_end == 1:
print("auto temperature schedule started")
args.start_temp, args.end_temp = \
global_optimization.auto_temp_schedule(imagefiles, lineage, realimages, synthimages, cellmaps, distmaps, 0, 1, lineagefile, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
if args.auto_meth == "frame" and optimization.auto_temp_schedule_frame(window_end, 3):
print("auto temperature schedule restarted")
args.start_temp, args.end_temp = \
global_optimization.auto_temp_schedule(imagefiles, lineage, realimages, synthimages, cellmaps, distmaps, window_start, window_end, lineagefile, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
if window_start >= sim_start:
if useDistanceObjective:
global_optimization.totalCostDiff = optimization.dist_objective(realimage, synthimage, distmap, cellmap, config["overlap.cost"])
else:
global_optimization.totalCostDiff = optimization.objective(realimage, synthimage, cellmap, config["overlap.cost"], config["cell.importance"])
global_optimization.optimize(imagefiles, lineage, realimages, synthimages, cellmaps, distmaps, window_start, window_end, lineagefile, args, config, iteration_per_cell)
if window_start >= 0:
global_optimization.save_lineage(imagefiles[window_start].name, lineage.frames[window_start].nodes, lineagefile)
global_optimization.save_output(imagefiles[window_start].name, synthimages[window_start], realimages[window_start], lineage.frames[window_start].nodes, args, config)
return 0
config["simulation"] = optimization.find_optimal_simulation_conf(config["simulation"], optimization.load_image(imagefiles[0]), list(colony))
if args.auto_temp == 1:
print("auto temperature schedule started")
args.start_temp, args.end_temp = optimization.auto_temp_schedule(imagefiles[0], lineageframes.forward(), args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
frame_num = 0
prev_cell_num = len(colony)
for imagefile in imagefiles: # Recomputing temperature when needed
frame_num += 1
if args.auto_meth == "frame":
if optimization.auto_temp_schedule_frame(frame_num, 8):
print("auto temperature schedule started (recomputed)")
args.start_temp, args.end_temp = optimization.auto_temp_schedule(imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
elif args.auto_meth == "factor":
if optimization.auto_temp_schedule_factor(len(colony), prev_cell_num, 1.1):
print("auto temperature schedule started (recomputed)")
args.start_temp, args.end_temp = optimization.auto_temp_schedule(imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
prev_cell_num = len(colony)
elif args.auto_meth == "const":
if optimization.auto_temp_schedule_const(len(colony), prev_cell_num, 10):
print("auto temperature schedule started (recomputed)")
args.start_temp, args.end_temp = optimization.auto_temp_schedule(imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
prev_cell_num = len(colony)
elif args.auto_meth == "cost":
print(cost_diff, frame_num, optimization.auto_temp_shcedule_cost(cost_diff))
if frame_num >= 2 and optimization.auto_temp_shcedule_cost(cost_diff):
print("auto temperature schedule started cost_diff (recomputed)")
args.start_temp, args.end_temp = optimization.auto_temp_schedule(imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp, "ending temperature is ", args.end_temp)
colony = optimize(imagefile, lineageframes, args, config, client)
cost_diff = optimization.update_cost_diff(colony, cost_diff)
# flatten modifications and save cell properties
colony.flatten()
for cellnode in colony:
properties = [imagefile.name, cellnode.cell.name]
if celltype == 'bacilli':
properties.extend([
str(cellnode.cell.x),
str(cellnode.cell.y),
str(cellnode.cell.width),
str(cellnode.cell.length),
str(cellnode.cell.rotation)])
print(','.join(properties), file=lineagefile)
except KeyboardInterrupt as error:
raise error
finally:
if lineagefile:
lineagefile.close()
print(f'{time.time() - start} seconds')
return 0
def main(args):
"""Main function of cellanneal."""
if (args.start_temp is not None
or args.end_temp is not None) and args.auto_temp == 1:
raise Exception(
"when auto_temp is set to 1(default value), starting temperature or ending temperature should not be set manually"
)
# if not args.no_parallel:
# import dask
# from dask.distributed import Client, LocalCluster
# if not args.cluster:
# cluster = LocalCluster(
# n_workers=args.workers,local_dir="/tmp/CellUniverse/dask-worker-space"
# )
# else:
# cluster = args.cluster
#
# client = Client(cluster)
# else:
client = None
lineagefile = None
start = time.time()
try:
config = load_config(args.config)
simulation_config = config["simulation"]
#Maybe better to store the image type in the config file in the first place, instead of using cmd?
if args.graySynthetic == True:
simulation_config["image.type"] = "graySynthetic"
elif args.phaseContrast == True:
simulation_config["image.type"] = "phaseContrastImage"
elif args.binary == True:
simulation_config["image.type"] = "binary"
else:
raise ValueError(
"Invalid Command: Synthetic image type must be specified")
if args.debug:
debugmode = True
celltype = config['global.cellType'].lower()
# setup the colony from a file with the initial properties
lineageframes = LineageFrames()
colony = lineageframes.forward()
load_colony(colony, args.initial, config)
cost_diff = (-1, -1)
# open the lineage file for writing
lineagefile = open(args.output / 'lineage.csv', 'w')
header = ['file', 'name']
if celltype == 'bacilli':
header.extend(['x', 'y', 'width', 'length', 'rotation'])
print(','.join(header), file=lineagefile)
#optimze configuration
config["simulation"] = find_optimal_simulation_conf(
config["simulation"], load_image(get_inputfiles(args)[0]),
list(colony))
if args.global_optimization:
import global_optimization
if args.auto_temp == 1:
print("auto temperature schedule started")
args.start_temp, args.end_temp = \
global_optimization.auto_temp_schedule(get_inputfiles(args), lineageframes, lineagefile, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
global_optimization.optimize(get_inputfiles(args), lineageframes,
lineagefile, args, config)
return 0
if args.auto_temp == 1:
print("auto temperature schedule started")
args.start_temp, args.end_temp = auto_temp_schedule(
get_inputfiles(args)[0], lineageframes.forward(), args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
frame_num = 0
prev_cell_num = len(colony)
for imagefile in get_inputfiles(
args): # Recomputing temperature when needed
frame_num += 1
if args.auto_meth == "frame":
if auto_temp_schedule_frame(frame_num, 8):
print("auto temperature schedule started (recomputed)")
args.start_temp, args.end_temp = auto_temp_schedule(
imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
elif args.auto_meth == "factor":
if auto_temp_schedule_factor(len(colony), prev_cell_num, 1.1):
print("auto temperature schedule started (recomputed)")
args.start_temp, args.end_temp = auto_temp_schedule(
imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
prev_cell_num = len(colony)
elif args.auto_meth == "const":
if auto_temp_schedule_const(len(colony), prev_cell_num, 10):
print("auto temperature schedule started (recomputed)")
args.start_temp, args.end_temp = auto_temp_schedule(
imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
prev_cell_num = len(colony)
elif args.auto_meth == "cost":
print(cost_diff, frame_num, auto_temp_shcedule_cost(cost_diff))
if frame_num >= 2 and auto_temp_shcedule_cost(cost_diff):
print(
"auto temperature schedule started cost_diff (recomputed)"
)
args.start_temp, args.end_temp = auto_temp_schedule(
imagefile, colony, args, config)
print("auto temperature schedule finished")
print("starting temperature is ", args.start_temp,
"ending temperature is ", args.end_temp)
colony = optimize(imagefile, lineageframes, args, config, client)
cost_diff = update_cost_diff(colony, cost_diff)
# flatten modifications and save cell properties
colony.flatten()
for cellnode in colony:
properties = [imagefile.name, cellnode.cell.name]
if celltype == 'bacilli':
properties.extend([
str(cellnode.cell.x),
str(cellnode.cell.y),
str(cellnode.cell.width),
str(cellnode.cell.length),
str(cellnode.cell.rotation)
])
print(','.join(properties), file=lineagefile)
except KeyboardInterrupt as error:
raise error
finally:
if lineagefile:
lineagefile.close()
print(f'{time.time() - start} seconds')
return 0
def main(args):
"""Main function of cellanneal."""
import dask
from dask.distributed import Client, LocalCluster
if not args.cluster:
cluster = LocalCluster(n_workers=args.workers, )
else:
cluster = args.cluster
client = Client(cluster)
lineagefile = None
start = time.time()
try:
if args.debug:
debugmode = True
config = load_config(args.config)
celltype = config['global.cellType'].lower()
# setup the colony from a file with the initial properties
lineageframes = LineageFrames()
colony = lineageframes.forward()
load_colony(colony, args.initial, config)
# open the lineage file for writing
lineagefile = open(args.output / 'lineage.csv', 'w')
header = ['file', 'name']
if celltype == 'bacilli':
header.extend(['x', 'y', 'width', 'length', 'rotation'])
print(','.join(header), file=lineagefile)
for imagefile in get_inputfiles(args):
colony = optimize(imagefile, lineageframes, args, config, client)
# flatten modifications and save cell properties
colony.flatten()
for cellnode in colony:
properties = [imagefile.name, cellnode.cell.name]
if celltype == 'bacilli':
properties.extend([
str(cellnode.cell.x),
str(cellnode.cell.y),
str(cellnode.cell.width),
str(cellnode.cell.length),
str(cellnode.cell.rotation)
])
print(','.join(properties), file=lineagefile)
except KeyboardInterrupt as error:
raise error
finally:
if lineagefile:
lineagefile.close()
print(f'{time.time() - start} seconds')
return 0