def execute(self):
corgie_logger.debug(f"ComputeFieldTask")
src_bcube = self.bcube.uncrop(self.pad, self.mip)
tgt_bcube = src_bcube.translate(z_offset=self.tgt_z_offset)
processor = procspec.parse_proc(spec_str=self.processor_spec)
corgie_logger.debug(f"Read target")
tgt_translation, tgt_data_dict = self.tgt_stack.read_data_dict(
tgt_bcube, mip=self.mip, stack_name="tgt")
# Compensate if target was moved to one side a lot
# tgt_drift = helpers.percentile_trans_adjuster(
# tgt_data_dict["tgt_agg_field"], unaligned_img=tgt_data_dict["tgt_img"]
# )
tgt_drift = helpers.Translation(0, 0)
corgie_logger.debug(f"Read source")
src_translation, src_data_dict = self.src_stack.read_data_dict(
src_bcube, mip=self.mip, stack_name="src", translation=tgt_drift)
# translation_adjuster=helpers.percentile_trans_adjuster)
# )
processor_input = {**src_data_dict, **tgt_data_dict}
corgie_logger.debug(f"Compute field")
predicted_field = processor(processor_input, output_key="src_cf_field")
predicted_field.x += tgt_drift.x
predicted_field.y += tgt_drift.y
cropped_field = helpers.crop(predicted_field, self.crop)
corgie_logger.debug(f"Write field")
self.dst_layer.write(cropped_field, bcube=self.bcube, mip=self.mip)
def read_data_dict(self,
bcube,
mip,
translation_adjuster=None,
stack_name=None,
add_prefix=True,
translation=None):
data_dict = {}
if translation is None:
translation = helpers.Translation(0, 0)
if stack_name is None:
stack_name == self.name
if stack_name is None or not add_prefix:
name_prefix = ""
else:
name_prefix = f"{stack_name}_"
agg_field = None
field_layers = self.get_layers_of_type("field")
# Assume that the last field is the final one
if len(field_layers) > 0:
l = field_layers[-1]
global_name = "{}{}".format(name_prefix, l.name)
this_field = l.read(bcube=bcube, mip=mip)
data_dict[global_name] = this_field
agg_field = this_field
'''for l in field_layers:
global_name = "{}{}".format(name_prefix, l.name)
this_field = l.read(bcube=bcube, mip=mip)
data_dict[global_name] = this_field
agg_field = this_field
if agg_field is None:
agg_field = this_field
else:
agg_field = this_field.field().from_pixels()(agg_field.field().from_pixels()).pixels()'''
assert (f"{name_prefix}agg_field" not in data_dict)
data_dict[f"{name_prefix}agg_field"] = agg_field
if translation_adjuster is not None:
src_field_trans = translation_adjuster(agg_field)
translation.x += src_field_trans.x
translation.y += src_field_trans.y
#if translation.x != 0 or translation.y != 0:
#import pdb; pdb.set_trace()
final_bcube = copy.deepcopy(bcube)
final_bcube = final_bcube.translate(x_offset=translation.y,
y_offset=translation.x,
mip=mip)
for l in self.get_layers_of_type(["mask", "img"]):
global_name = f"{name_prefix}{l.name}"
data_dict[global_name] = l.read(bcube=final_bcube, mip=mip)
return translation, data_dict
def read_data_dict(self,
bcube,
mip,
translation_adjuster=None,
stack_name=None):
data_dict = {}
field_layers = self.get_layers_of_type("field")
agg_field = None
if stack_name is None:
stack_name == self.name
if stack_name is None:
name_prefix = ""
else:
name_prefix = f"{stack_name}_"
for l in field_layers:
this_field = l.read(bcube=bcube, mip=mip)
global_name = "{}{}".format(name_prefix, l.name)
data_dict[global_name] = this_field
if agg_field is not None:
agg_field = compose_fields(agg_field,
this_field,
is_pix_res=True)
else:
agg_field = this_field
assert (f"{name_prefix}_agg_field" not in data_dict)
data_dict[f"{name_prefix}agg_field"] = agg_field
if translation_adjuster is not None:
translaiton = translation_adjuster(agg_field)
else:
translation = helpers.Translation(0, 0)
final_bcube = copy.deepcopy(bcube)
final_bcube = final_bcube.translate(x=translation.x, y=translation.y)
for l in self.get_layers_of_type(["mask", "img"]):
global_name = f"{name_prefix}{l.name}"
data_dict[global_name] = l.read(bcube=bcube, mip=mip)
return translation, data_dict