"""
Utilities for multiprocessing of stacks of images.
"""
import sys
import multiprocessing
from typing import Callable, List, Optional
import numpy as np
from typeguard import typechecked
from pynpoint.core.dataio import InputPort, OutputPort
from pynpoint.util.module import update_arguments
from pynpoint.util.multiproc import TaskInput, TaskResult, TaskCreator, TaskProcessor, \
MultiprocessingCapsule, apply_function
[docs]class StackReader(TaskCreator):
"""
Reader of task inputs for :class:`~pynpoint.util.multistack.StackProcessingCapsule`.
Reads continuously stacks of images of a dataset and puts them into a task queue.
"""
@typechecked
def __init__(self,
data_port_in: InputPort,
tasks_queue_in: multiprocessing.JoinableQueue,
data_mutex_in: multiprocessing.Lock,
num_proc: int,
stack_size: int,
result_shape: tuple) -> None:
"""
Parameters
----------
data_port_in : pynpoint.core.dataio.InputPort
Input port.
tasks_queue_in : multiprocessing.queues.JoinableQueue
Tasks queue.
data_mutex_in : multiprocessing.synchronize.Lock
A mutex shared with the writer to ensure that no read and write operations happen at
the same time.
num_proc : int
Number of processors.
stack_size: int
Number of images per stack.
result_shape : tuple(int, )
Shape of the array with the output results (usually a stack of images).
Returns
-------
NoneType
None
"""
super(StackReader, self).__init__(data_port_in, tasks_queue_in, data_mutex_in, num_proc)
self.m_stack_size = stack_size
self.m_result_shape = result_shape
[docs] @typechecked
def run(self) -> None:
"""
Returns
-------
NoneType
None
"""
with self.m_data_mutex:
self.m_data_in_port._check_status_and_activate()
nimages = self.m_data_in_port.get_shape()[0]
self.m_data_in_port.close_port()
i = 0
while i < nimages:
j = min((i + self.m_stack_size), nimages)
# lock mutex and read data
with self.m_data_mutex:
self.m_data_in_port._check_status_and_activate()
tmp_data = self.m_data_in_port[i:j, ] # read images from i to j
self.m_data_in_port.close_port()
# first dimension (start, stop, step)
stack_slice = [(i, j, None)]
# additional dimensions
for _ in self.m_result_shape:
stack_slice.append((None, None, None))
param = (self.m_result_shape, tuple(stack_slice))
self.m_task_queue.put(TaskInput(tmp_data, param))
i = j
self.create_poison_pills()
[docs]class StackTaskProcessor(TaskProcessor):
"""
Processor of task inputs for :class:`~pynpoint.util.multistack.StackProcessingCapsule`. A
processor applies a function on a stack of images.
"""
@typechecked
def __init__(self,
tasks_queue_in: multiprocessing.JoinableQueue,
result_queue_in: multiprocessing.JoinableQueue,
function: Callable,
function_args: Optional[tuple],
nimages: int) -> None:
"""
Parameters
----------
tasks_queue_in : multiprocessing.queues.JoinableQueue
Tasks queue.
result_queue_in : multiprocessing.queues.JoinableQueue
Results queue.
function : function
Input function that is applied to the images.
function_args : tuple, None
Function arguments.
nimages : int
Total number of images.
Returns
-------
NoneType
None
"""
super(StackTaskProcessor, self).__init__(tasks_queue_in, result_queue_in)
self.m_function = function
self.m_function_args = function_args
self.m_nimages = nimages
[docs] @typechecked
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_task.m_input_data[i, ], i, self.m_function, args)
sys.stdout.write('.')
sys.stdout.flush()
return TaskResult(result_arr, tmp_task.m_job_parameter[1])
[docs]class StackProcessingCapsule(MultiprocessingCapsule):
"""
Capsule for parallel processing of stacks of images with the poison pill pattern. A function
is applied in parallel to each stack of images.
"""
@typechecked
def __init__(self,
image_in_port: InputPort,
image_out_port: OutputPort,
num_proc: int,
function: Callable,
function_args: Optional[tuple],
stack_size: int,
result_shape: tuple,
nimages: int) -> None:
"""
Parameters
----------
image_in_port : pynpoint.core.dataio.InputPort
Input port.
image_out_port : pynpoint.core.dataio.OutputPort
Output port.
num_proc : int
Number of processors.
function : function
Input function.
function_args : tuple, None
Function arguments.
stack_size: int
Number of images per stack.
result_shape : tuple(int, )
Shape of the array with output results (usually a stack of images).
nimages : int
Total number of images.
Returns
-------
NoneType
None
"""
self.m_function = function
self.m_function_args = function_args
self.m_stack_size = stack_size
self.m_result_shape = result_shape
self.m_nimages = nimages
super(StackProcessingCapsule, self).__init__(image_in_port, image_out_port, num_proc)
[docs] @typechecked
def create_processors(self) -> List[StackTaskProcessor]:
"""
Returns
-------
list(pynpoint.util.multiproc.StackTaskProcessor, )
List with instances of :class:`~pynpoint.util.multiproc.StackTaskProcessor`.
"""
processors = []
for _ in range(self.m_num_proc):
processors.append(StackTaskProcessor(tasks_queue_in=self.m_tasks_queue,
result_queue_in=self.m_result_queue,
function=self.m_function,
function_args=self.m_function_args,
nimages=self.m_nimages))
return processors
[docs] @typechecked
def init_creator(self,
image_in_port: InputPort) -> StackReader:
"""
Parameters
----------
image_in_port : pynpoint.core.dataio.InputPort
Input port from where the subsets of images are read.
Returns
-------
pynpoint.util.multistack.StackReader
Reader of stacks of images.
"""
return StackReader(data_port_in=image_in_port,
tasks_queue_in=self.m_tasks_queue,
data_mutex_in=self.m_data_mutex,
num_proc=self.m_num_proc,
stack_size=self.m_stack_size,
result_shape=self.m_result_shape)
