"""
Capsule for multiprocessing of the PSF subtraction with PCA. Residuals are created in parallel for
a range of principal components for which the PCA basis is required as input.
"""
import sys
import multiprocessing
from typing import List, Optional, Tuple, Union
import numpy as np
from typeguard import typechecked
from sklearn.decomposition import PCA
from pynpoint.core.dataio import OutputPort
from pynpoint.util.multiproc import TaskProcessor, TaskCreator, TaskWriter, TaskResult, \
TaskInput, MultiprocessingCapsule, to_slice
from pynpoint.util.postproc import postprocessor
from pynpoint.util.residuals import combine_residuals
[docs]class PcaTaskCreator(TaskCreator):
"""
The TaskCreator of the PCA multiprocessing. Creates one task for each principal component
number. Does not require an input port since the data is directly given to the task processors.
"""
@typechecked
def __init__(self,
tasks_queue_in: multiprocessing.JoinableQueue,
num_proc: int,
pca_numbers: Union[np.ndarray, tuple]) -> None:
"""
Parameters
----------
tasks_queue_in : multiprocessing.queues.JoinableQueue
Input task queue.
num_proc : int
Number of processors.
pca_numbers : np.ndarray, tuple
Principal components for which the residuals are computed.
Returns
-------
NoneType
None
"""
super(PcaTaskCreator, self).__init__(None, tasks_queue_in, None, num_proc)
self.m_pca_numbers = pca_numbers
[docs] @typechecked
def run(self) -> None:
"""
Run method of PcaTaskCreator.
Returns
-------
NoneType
None
"""
if isinstance(self.m_pca_numbers, tuple):
for i, pca_first in enumerate(self.m_pca_numbers[0]):
for j, pca_secon in enumerate(self.m_pca_numbers[1]):
parameters = (((i, i+1, None), (j, j+1, None), (None, None, None)), )
self.m_task_queue.put(TaskInput(tuple((pca_first, pca_secon)), parameters))
self.create_poison_pills()
else:
for i, pca_number in enumerate(self.m_pca_numbers):
parameters = (((i, i+1, None), (None, None, None), (None, None, None)), )
self.m_task_queue.put(TaskInput(pca_number, parameters))
self.create_poison_pills()
[docs]class PcaTaskProcessor(TaskProcessor):
"""
The TaskProcessor of the PCA multiprocessing is the core of the parallelization. An instance
of this class will calculate one forward and backward PCA transformation given the pre-trained
scikit-learn PCA model. It does not get data from the TaskCreator but uses its own copy of the
input data, which are the same and independent for each task. The following residuals can be
created:
* Mean residuals -- requirements[0] = True
* Median residuals -- requirements[1] = True
* Noise-weighted residuals -- requirements[2] = True
* Clipped mean of the residuals -- requirements[3] = True
"""
@typechecked
def __init__(self,
tasks_queue_in: multiprocessing.JoinableQueue,
result_queue_in: multiprocessing.JoinableQueue,
star_reshape: np.ndarray,
angles: np.ndarray,
scales: Optional[np.ndarray],
pca_model: Optional[PCA],
im_shape: tuple,
indices: Optional[np.ndarray],
requirements: Tuple[bool, bool, bool, bool],
processing_type: str) -> None:
"""
Parameters
----------
tasks_queue_in : multiprocessing.queues.JoinableQueue
Input task queue.
result_queue_in : multiprocessing.queues.JoinableQueue
Input result queue.
star_reshape : np.ndarray
Reshaped (2D) stack of images.
angles : np.ndarray
Derotation angles (deg).
scales : np.ndarray
scaling factors
pca_model : sklearn.decomposition.pca.PCA
PCA object with the basis.
im_shape : tuple(int, int, int)
Original shape of the stack of images.
indices : np.ndarray
Non-masked image indices.
requirements : tuple(bool, bool, bool, bool)
Required output residuals.
processing_type : str
selected processing type.
Returns
-------
NoneType
None
"""
super(PcaTaskProcessor, self).__init__(tasks_queue_in, result_queue_in)
self.m_star_reshape = star_reshape
self.m_pca_model = pca_model
self.m_angles = angles
self.m_scales = scales
self.m_im_shape = im_shape
self.m_indices = indices
self.m_requirements = requirements
self.m_processing_type = processing_type
[docs] @typechecked
def run_job(self,
tmp_task: TaskInput) -> TaskResult:
"""
Run method of PcaTaskProcessor.
Parameters
----------
tmp_task : pynpoint.util.multiproc.TaskInput
Input task.
Returns
-------
pynpoint.util.multiproc.TaskResult
Output residuals.
"""
# correct data type of pca_number if necessary
if isinstance(tmp_task.m_input_data, tuple):
pca_number = tmp_task.m_input_data
else:
pca_number = int(tmp_task.m_input_data)
residuals, res_rot = postprocessor(images=self.m_star_reshape,
angles=self.m_angles,
scales=self.m_scales,
pca_number=pca_number,
pca_sklearn=self.m_pca_model,
im_shape=self.m_im_shape,
indices=self.m_indices,
processing_type=self.m_processing_type)
# differentiate between IFS data or Mono-Wavelength data
if res_rot.ndim == 3:
res_output = np.zeros((4, res_rot.shape[-2], res_rot.shape[-1]))
else:
res_output = np.zeros((4, len(self.m_star_reshape),
res_rot.shape[-2], res_rot.shape[-1]))
if self.m_requirements[0]:
res_output[0, ] = combine_residuals(method='mean',
res_rot=res_rot)
if self.m_requirements[1]:
res_output[1, ] = combine_residuals(method='median',
res_rot=res_rot)
if self.m_requirements[2]:
res_output[2, ] = combine_residuals(method='weighted',
res_rot=res_rot,
residuals=residuals,
angles=self.m_angles)
if self.m_requirements[3]:
res_output[3, ] = combine_residuals(method='clipped',
res_rot=res_rot)
sys.stdout.write('.')
sys.stdout.flush()
return TaskResult(res_output, tmp_task.m_job_parameter[0])
[docs]class PcaTaskWriter(TaskWriter):
"""
The TaskWriter of the PCA parallelization. Four different ports are used to save the
results of the task processors (mean, median, weighted, and clipped).
"""
@typechecked
def __init__(self,
result_queue_in: multiprocessing.JoinableQueue,
mean_out_port: Optional[OutputPort],
median_out_port: Optional[OutputPort],
weighted_out_port: Optional[OutputPort],
clip_out_port: Optional[OutputPort],
data_mutex_in: multiprocessing.Lock,
requirements: Tuple[bool, bool, bool, bool]) -> None:
"""
Constructor of PcaTaskWriter.
Parameters
----------
result_queue_in : multiprocessing.queues.JoinableQueue
Input result queue.
mean_out_port : pynpoint.core.dataio.OutputPort
Output port with the mean residuals. Not used if set to None.
median_out_port : pynpoint.core.dataio.OutputPort
Output port with the median residuals. Not used if set to None.
weighted_out_port : pynpoint.core.dataio.OutputPort
Output port with the noise-weighted residuals. Not used if set to None.
clip_out_port : pynpoint.core.dataio.OutputPort
Output port with the clipped mean residuals. Not used if set to None.
data_mutex_in : multiprocessing.synchronize.Lock
A mutual exclusion variable which ensure that no read and write simultaneously occur.
requirements : tuple(bool, bool, bool, bool)
Required output residuals.
Returns
-------
NoneType
None
"""
super(PcaTaskWriter, self).__init__(result_queue_in, None, data_mutex_in)
self.m_mean_out_port = mean_out_port
self.m_median_out_port = median_out_port
self.m_weighted_out_port = weighted_out_port
self.m_clip_out_port = clip_out_port
self.m_requirements = requirements
[docs] @typechecked
def run(self) -> None:
"""
Run method of PcaTaskWriter. Writes the residuals to the output ports.
Returns
-------
NoneType
None
"""
while True:
next_result = self.m_result_queue.get()
poison_pill_case = self.check_poison_pill(next_result)
if poison_pill_case == 1:
break
if poison_pill_case == 2:
continue
with self.m_data_mutex:
res_slice = to_slice(next_result.m_position)
if next_result.m_position[1][0] is None:
res_slice = (next_result.m_position[0][0])
else:
res_slice = (next_result.m_position[0][0], next_result.m_position[1][0])
if self.m_requirements[0]:
self.m_mean_out_port._check_status_and_activate()
self.m_mean_out_port[res_slice] = next_result.m_data_array[0]
self.m_mean_out_port.close_port()
if self.m_requirements[1]:
self.m_median_out_port._check_status_and_activate()
self.m_median_out_port[res_slice] = next_result.m_data_array[1]
self.m_median_out_port.close_port()
if self.m_requirements[2]:
self.m_weighted_out_port._check_status_and_activate()
self.m_weighted_out_port[res_slice] = next_result.m_data_array[2]
self.m_weighted_out_port.close_port()
if self.m_requirements[3]:
self.m_clip_out_port._check_status_and_activate()
self.m_clip_out_port[res_slice] = next_result.m_data_array[3]
self.m_clip_out_port.close_port()
self.m_result_queue.task_done()
[docs]class PcaMultiprocessingCapsule(MultiprocessingCapsule):
"""
Capsule for PCA multiprocessing with the poison pill pattern.
"""
@typechecked
def __init__(self,
mean_out_port: Optional[OutputPort],
median_out_port: Optional[OutputPort],
weighted_out_port: Optional[OutputPort],
clip_out_port: Optional[OutputPort],
num_proc: int,
pca_numbers: Union[tuple, np.ndarray],
pca_model: Optional[PCA],
star_reshape: np.ndarray,
angles: np.ndarray,
scales: Optional[np.ndarray],
im_shape: tuple,
indices: Optional[np.ndarray],
processing_type: str) -> None:
"""
Constructor of PcaMultiprocessingCapsule.
Parameters
----------
mean_out_port : pynpoint.core.dataio.OutputPort
Output port for the mean residuals.
median_out_port : pynpoint.core.dataio.OutputPort
Output port for the median residuals.
weighted_out_port : pynpoint.core.dataio.OutputPort
Output port for the noise-weighted residuals.
clip_out_port : pynpoint.core.dataio.OutputPort
Output port for the mean clipped residuals.
num_proc : int
Number of processors.
pca_numbers : np.ndarray
Number of principal components.
pca_model : sklearn.decomposition.pca.PCA
PCA object with the basis.
star_reshape : np.ndarray
Reshaped (2D) input images.
angles : np.ndarray
Derotation angles (deg).
scales : np.ndarray
scaling factors.
im_shape : tuple(int, int, int)
Original shape of the input images.
indices : np.ndarray
Non-masked pixel indices.
processing_type : str
selection of processing type
Returns
-------
NoneType
None
"""
self.m_mean_out_port = mean_out_port
self.m_median_out_port = median_out_port
self.m_weighted_out_port = weighted_out_port
self.m_clip_out_port = clip_out_port
self.m_pca_numbers = pca_numbers
self.m_pca_model = pca_model
self.m_star_reshape = star_reshape
self.m_angles = angles
self.m_scales = scales
self.m_im_shape = im_shape
self.m_indices = indices
self.m_processing_type = processing_type
self.m_requirements = [False, False, False, False]
if self.m_mean_out_port is not None:
self.m_requirements[0] = True
if self.m_median_out_port is not None:
self.m_requirements[1] = True
if self.m_weighted_out_port is not None:
self.m_requirements[2] = True
if self.m_clip_out_port is not None:
self.m_requirements[3] = True
self.m_requirements = tuple(self.m_requirements)
super(PcaMultiprocessingCapsule, self).__init__(None, None, num_proc)
[docs] @typechecked
def create_writer(self,
image_out_port: None) -> PcaTaskWriter:
"""
Method to create an instance of PcaTaskWriter.
Parameters
----------
image_out_port : None
Output port, not used.
Returns
-------
pynpoint.util.multipca.PcaTaskWriter
PCA task writer.
"""
return PcaTaskWriter(self.m_result_queue,
self.m_mean_out_port,
self.m_median_out_port,
self.m_weighted_out_port,
self.m_clip_out_port,
self.m_data_mutex,
self.m_requirements)
[docs] @typechecked
def init_creator(self,
image_in_port: None) -> PcaTaskCreator:
"""
Method to create an instance of PcaTaskCreator.
Parameters
----------
image_in_port : None
Input port, not used.
Returns
-------
pynpoint.util.multipca.PcaTaskCreator
PCA task creator.
"""
return PcaTaskCreator(self.m_tasks_queue,
self.m_num_proc,
self.m_pca_numbers)
[docs] @typechecked
def create_processors(self) -> List[PcaTaskProcessor]:
"""
Method to create a list of instances of PcaTaskProcessor.
Returns
-------
list(pynpoint.util.multipca.PcaTaskProcessor, )
PCA task processors.
"""
processors = []
for _ in range(self.m_num_proc):
processors.append(PcaTaskProcessor(self.m_tasks_queue,
self.m_result_queue,
self.m_star_reshape,
self.m_angles,
self.m_scales,
self.m_pca_model,
self.m_im_shape,
self.m_indices,
self.m_requirements,
self.m_processing_type))
return processors
