def run_job(self, tmp_task: TaskInput) -> TaskResult:
"""
Parameters
----------
tmp_task : pynpoint.util.multiproc.TaskInput
Task input with the subsets of images and the job parameters.
Returns
-------
pynpoint.util.multiproc.TaskResult
Task result.
"""
result_nimages = tmp_task.m_input_data.shape[0]
result_shape = tmp_task.m_job_parameter[0]
# first dimension
full_shape = [result_nimages]
# additional dimensions
for item in result_shape:
full_shape.append(item)
result_arr = np.zeros(full_shape)
for i in range(result_nimages):
# job parameter contains (result_shape, tuple(stack_slice))
index = tmp_task.m_job_parameter[1][0][0] + i
args = update_arguments(index, self.m_nimages,
self.m_function_args)
result_arr[i, ] = apply_function(
tmp_data=tmp_task.m_input_data[i, ],
func=self.m_function,
func_args=args)
sys.stdout.write('.')
sys.stdout.flush()
return TaskResult(result_arr, tmp_task.m_job_parameter[1])
def apply_function_to_images(self,
func,
image_in_port,
image_out_port,
message,
func_args=None):
"""
Function which applies a function to all images of an input port. Stacks of images are
processed in parallel if the CPU and MEMORY attribute are set in the central configuration.
The number of images per process is equal to the value of MEMORY divided by the value of
CPU. Note that the function *func* is not allowed to change the shape of the images if the
input and output port have the same tag and ``MEMORY`` is not set to None.
Parameters
----------
func : function
The function which is applied to all images. Its definitions should be similar to::
def function(image_in,
parameter1,
parameter2,
parameter3)
image_in_port : pynpoint.core.dataio.InputPort
Input port which is linked to the input data.
image_out_port : pynpoint.core.dataio.OutputPort
Output port which is linked to the results.
message : str
Progress message.
func_args : tuple
Additional arguments that are required by the input function.
Returns
-------
NoneType
None
"""
memory = self._m_config_port.get_attribute('MEMORY')
cpu = self._m_config_port.get_attribute('CPU')
nimages = image_in_port.get_shape()[0]
if memory == 0 or image_out_port.tag == image_in_port.tag:
# load all images in the memory at once if the input and output tag are the
# same or if the MEMORY attribute is set to None in the configuration file
images = image_in_port.get_all()
result = []
start_time = time.time()
for i in range(nimages):
progress(i, nimages, message+'...', start_time)
args = update_arguments(i, nimages, func_args)
if args is None:
result.append(func(images[i, ]))
else:
result.append(func(images[i, ], *args))
image_out_port.set_all(np.asarray(result), keep_attributes=True)
elif cpu == 1:
# process images one-by-one with a single process if CPU is set to 1
image_out_port.del_all_attributes()
image_out_port.del_all_data()
start_time = time.time()
for i in range(nimages):
progress(i, nimages, message+'...', start_time)
args = update_arguments(i, nimages, func_args)
if args is None:
result = func(image_in_port[i, ])
else:
result = func(image_in_port[i, ], *args)
if result.ndim == 1:
image_out_port.append(result, data_dim=2)
elif result.ndim == 2:
image_out_port.append(result, data_dim=3)
else:
print(message, end='')
# process images in parallel in stacks of MEMORY/CPU images
image_out_port.del_all_attributes()
image_out_port.del_all_data()
result = apply_function(tmp_data=image_in_port[0, :, :],
func=func,
func_args=update_arguments(0, nimages, func_args))
result_shape = result.shape
out_shape = [nimages]
for item in result_shape:
out_shape.append(item)
image_out_port.set_all(data=np.zeros(out_shape),
data_dim=len(result_shape)+1,
keep_attributes=False)
image_in_port.close_port()
image_out_port.close_port()
capsule = StackProcessingCapsule(image_in_port=image_in_port,
image_out_port=image_out_port,
num_proc=cpu,
function=func,
function_args=func_args,
stack_size=int(memory/cpu),
result_shape=result_shape,
nimages=nimages)
capsule.run()
print(' [DONE]')
def apply_function_to_images(self,
func,
image_in_port,
image_out_port,
message,
func_args=None):
"""
Function which applies a function to all images of an input port. Stacks of images are
processed in parallel if the CPU and MEMORY attribute are set in the central configuration.
The number of images per process is equal to the value of MEMORY divided by the value of
CPU. Note that the function *func* is not allowed to change the shape of the images if the
input and output port have the same tag and ``MEMORY`` is not set to None.
Parameters
----------
func : function
The function which is applied to all images. Its definitions should be similar to::
def function(image_in,
parameter1,
parameter2,
parameter3)
image_in_port : pynpoint.core.dataio.InputPort
Input port which is linked to the input data.
image_out_port : pynpoint.core.dataio.OutputPort
Output port which is linked to the results.
message : str
Progress message that is printed.
func_args : tuple
Additional arguments that are required by the input function.
Returns
-------
NoneType
None
"""
memory = self._m_config_port.get_attribute('MEMORY')
cpu = self._m_config_port.get_attribute('CPU')
nimages = image_in_port.get_shape()[0]
if memory == 0 or image_out_port.tag == image_in_port.tag:
# load all images in the memory at once if the input and output tag are the
# same or if the MEMORY attribute is set to None in the configuration file
images = image_in_port.get_all()
result = []
start_time = time.time()
for i in range(nimages):
progress(i, nimages, message + '...', start_time)
args = update_arguments(i, nimages, func_args)
if args is None:
result.append(func(images[i, ]))
else:
result.append(func(images[i, ], *args))
result = np.asarray(result)
if image_out_port.tag == image_in_port.tag:
if images.shape[-2] != result.shape[-2] or images.shape[
-1] != result.shape[-1]:
raise ValueError(
'Input and output port have the same tag while the input '
'function is changing the image shape. This is only possible '
'with MEMORY=None.')
image_out_port.set_all(result, keep_attributes=True)
sys.stdout.write(message + ' [DONE]\n')
sys.stdout.flush()
elif cpu == 1 or cpu > 1:
# process images one-by-one with a single process if CPU is set to 1
image_out_port.del_all_attributes()
image_out_port.del_all_data()
start_time = time.time()
for i in range(nimages):
progress(i, nimages, message + '...', start_time)
args = update_arguments(i, nimages, func_args)
if args is None:
result = func(image_in_port[i, ])
else:
result = func(image_in_port[i, ], *args)
if result.ndim == 1:
image_out_port.append(result, data_dim=2)
elif result.ndim == 2:
image_out_port.append(result, data_dim=3)
sys.stdout.write(message + ' [DONE]\n')
sys.stdout.flush()