def execute(self):
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)
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'])
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}
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)
self.dst_layer.write(cropped_field, bcube=self.bcube, mip=self.mip)
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 execute(self):
src_bcube = self.bcube.uncrop(self.pad, self.mip)
processor = procspec.parse_proc(spec_str=self.processor_spec)
src_translation, src_data_dict = self.src_stack.read_data_dict(
src_bcube, mip=self.mip, stack_name='src')
processor_input = {**src_data_dict}
result = processor(processor_input, output_key='output')
cropped_result = helpers.crop(result, self.crop)
self.dst_layer.write(cropped_result, bcube=self.bcube, mip=self.mip)
def execute(self):
src_bcube = self.bcube.uncrop(self.pad, self.mip)
tgt_bcube = src_bcube.translate(z=self.tgt_z_offset)
processor = procspec.parse_proc(spec_str=self.processor_spec, default_output='src_cf_field')
src_translation, src_data_dict = self.src_stack.read_data_dict(src_bcube,
mip=self.mip, stack_name='src')
tgt_translation, tgt_data_dict = self.tgt_stack.read_data_dict(tgt_bcube,
mip=self.mip, stack_name='tgt')
processor_input = {**src_data_dict, **tgt_data_dict}
predicted_field = processor(processor_input)
cropped_field = helpers.crop(predicted_field, self.crop)
self.dst_layer.write(cropped_field, bcube=self.bcube, mip=self.mip)
def execute(self):
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)
_, tgt_data_dict = self.tgt_stack.read_data_dict(tgt_bcube,
mip=self.mip,
stack_name='tgt')
_, src_data_dict = self.src_stack.read_data_dict(src_bcube,
mip=self.mip,
stack_name='src')
processor_input = {**src_data_dict, **tgt_data_dict}
result = processor(processor_input, output_key='result')
cropped_result = helpers.crop(result, self.crop)
self.dst_layer.write(cropped_result, bcube=self.bcube, mip=self.mip)
def execute(self):
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)
_, tgt_data_dict = self.tgt_stack.read_data_dict(tgt_bcube,
mip=self.mip,
stack_name="tgt")
_, src_data_dict = self.src_stack.read_data_dict(src_bcube,
mip=self.mip,
stack_name="src")
processor_input = {**src_data_dict, **tgt_data_dict}
result = processor(processor_input, output_key="result")
tgt_pixel_data = self.pixel_offset_layer.read(
bcube=self.bcube.translate(z_offset=self.tgt_z_offset),
mip=self.mip)
written_pixel_data = self.pixel_offset_layer.read(bcube=self.bcube,
mip=self.mip)
written_mask_data = self.dst_layer.read(bcube=self.bcube, mip=self.mip)
result = result.to(device=written_mask_data.device)
cropped_result = helpers.crop(result, self.crop)
if self.seethrough_limit > 0:
seethrough_mask = (cropped_result > 0) & (tgt_pixel_data <
self.seethrough_limit)
else:
seethrough_mask = cropped_result > 0
written_mask_data[seethrough_mask] = True
written_pixel_data[seethrough_mask] = (torch.minimum(
tgt_pixel_data[seethrough_mask],
torch.ones_like(tgt_pixel_data[seethrough_mask]) * 254,
) + 1)
self.dst_layer.write(written_mask_data, bcube=self.bcube, mip=self.mip)
self.pixel_offset_layer.write(written_pixel_data,
bcube=self.bcube,
mip=self.mip)
def execute(self):
tgt_bcube = self.bcube.uncrop(self.pad, self.mip)
_, tgt_data_dict = self.tgt_stack.read_data_dict(tgt_bcube,
mip=self.mip,
stack_name="tgt")
dst_layers = self.dst_stack.get_layers_of_type("img")
for dst_layer in dst_layers:
z_offset = int(dst_layer.name)
src_bcube = tgt_bcube.translate(z_offset=z_offset)
processor = procspec.parse_proc(spec_str=self.processor_spec)
_, src_data_dict = self.src_stack.read_data_dict(src_bcube,
mip=self.mip,
stack_name="src")
processor_input = {**src_data_dict, **tgt_data_dict}
result = processor(processor_input, output_key="result")
crop = self.pad // 2**(self.dst_mip - self.mip)
cropped_result = helpers.crop(result, crop)
dst_layer.write(cropped_result, bcube=self.bcube, mip=self.dst_mip)
import procspec yaml_path = './specs/very_complex_processor.yaml' proc = procspec.parse_proc(yaml_path=yaml_path, default_output='src_field') import pdb pdb.set_trace()
