# -*- coding: utf-8 -*-
"""
MeasurePointList
================
Measurements on a subset of points in large arrays.
Paralllel measuremnts at specified points of the data only.
Useful to speed up processing in large arrays and only a smaller number
of measurement points.
See also
--------
:mod:`ClearMap.Analysis.Measurements`.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = 'http://idisco.info'
__download__ = 'http://www.github.com/ChristophKirst/ClearMap2'
import numpy as np;
import pyximport;
pyximport.install(setup_args={"include_dirs": [np.get_include()]}, reload_support=True)
import ClearMap.ParallelProcessing.DataProcessing.ArrayProcessing as ap
import ClearMap.ParallelProcessing.DataProcessing.MeasurePointListCode as code
###############################################################################
### Measure extrema
###############################################################################
[docs]def measure_max(source, points, search, max_search_indices, sink = None, processes = None, verbose = False):
"""Find local maximum in a large array for a list of center points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
max_search_indices : array
The maximal index in the search array for each point to use.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the local maxima.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='measure_max');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape[0], dtype=source.dtype);
if sink_buffer.shape[0] != points.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points.shape));
points, points_buffer = ap.initialize_source(points);
if points_buffer.ndim == 1:
points_buffer = points_buffer[:,None];
#print(source1d.shape, shape, strides, points.shape, search.shape, max_search_indices.shape, sink.shape)
code.measure_max(source_buffer, source_shape, source_strides, points_buffer, search, max_search_indices, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='measure_max', timer=timer);
return sink;
[docs]def measure_min(source, points, search, max_search_indices, sink = None, processes = None, verbose = False):
"""Find local minimum in a large array for a list of center points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
max_search_indices : array
The maximal index in the search array for each point to use.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the local minima.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='measure_max');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape[0], dtype=source.dtype);
if sink.shape[0] != points.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points.shape));
points, points_buffer = ap.initialize_source(points);
if points_buffer.ndim == 1:
points_buffer = points_buffer[:,None];
code.measure_min(source_buffer, source_shape, source_strides, points_buffer, search, max_search_indices, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='measure_max', timer=timer);
return sink;
[docs]def measure_mean(source, points, search, max_search_indices, sink = None, processes = None, verbose = False):
"""Find local mean in a large array for a list of center points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
max_search_indices : array
The maximal index in the search array for each point to use.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the local mean.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='measure_mean');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape[0], dtype=float);
points_buffer = ap.initialize_source(points);
if points_buffer.ndim == 1:
points_buffer = points_buffer[:,None];
if sink.shape[0] != points_buffer.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points_buffer.shape));
code.measure_mean(source_buffer, source_shape, source_strides, points_buffer, search, max_search_indices, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='measure_mean', timer=timer);
return sink;
[docs]def measure_sum(source, points, search, max_search_indices, sink = None, processes = None, verbose = False):
"""Find local mean in a large array for a list of center points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
max_search_indices : array
The maximal index in the search array for each point to use.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the local mean.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='measure_mean');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape[0], dtype=float);
points_buffer = ap.initialize_source(points);
if points_buffer.ndim == 1:
points_buffer = points_buffer[:,None];
if sink.shape[0] != points_buffer.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points_buffer.shape));
code.measure_sum(source_buffer, source_shape, source_strides, points_buffer, search, max_search_indices, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='measure_mean', timer=timer);
return sink;
###############################################################################
### Find in local neighbourhood
###############################################################################
[docs]def find_smaller_than_value(source, points, search, value, sink = None, processes = None, verbose = False):
"""Find index in local search indices with a voxel with value smaller than a specified value for a list of points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
value : float
Search for first voxel in local area with value smaller than this value.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the first search index with voxel below value.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='find_smaller_than_value');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape[0], dtype=int);
if sink.shape[0] != points.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points.shape));
points, points_buffer = ap.initialize_source(points);
if points_buffer.ndim == 1:
points_buffer = points_buffer[:,None];
code.find_smaller_than_value(source_buffer, source_shape, source_strides, points_buffer, search, value, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='find_smaller_than_value', timer=timer);
return sink;
[docs]def find_smaller_than_fraction(source, points, search, fraction, sink = None, processes = None, verbose = False):
"""Find index in local search indices with a voxel with value smaller than a fraction of the value of the center voxel for a list of points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
fraction : float
Search for first voxel in local area with value smaller than this fraction of the center value.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the first search index with voxel below the fraction of the center value.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='find_smaller_than_fraction');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape[0], dtype=int);
if sink.shape[0] != points.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points.shape));
points, points_buffer = ap.initialize_source(points);
if points.ndim == 1:
points = points[:,None];
code.find_smaller_than_fraction(source_buffer, source_shape, source_strides, points_buffer, search, fraction, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='find_smaller_than_fraction', timer=timer);
return sink;
[docs]def find_smaller_than_values(source, points, search, values, sink = None, processes = None, verbose = False):
"""Find index in local search indices with a voxel with value smaller than a fraction of the value of the center voxel for a list of points.
Arguments
---------
source : array
Data source.
points : array
List of linear indices of center points.
search : array
List of linear indices to add to the center index defining the local search area.
fraction : float
Search for first voxel in local area with value smaller than this fraction of the center value.
sink : array or None
Optional sink for result indices.
processes : int or None
Number of processes to use.
verbose : bool
If True, print progress info.
Returns
-------
sink : array
Linear array with length of points containing the first search index with voxel below the fraction of the center value.
"""
processes, timer = ap.initialize_processing(processes=processes, verbose=verbose, function='find_smaller_than_values');
source, source_buffer, source_shape, source_strides = ap.initialize_source(source, as_1d=True, return_shape=True, return_strides=True);
sink, sink_buffer = ap.initialize_sink(sink=sink, shape=points.shape, dtype=int);
if sink.shape[0] != points.shape[0]:
raise RuntimeError('Sink has invalid size %r not %r' % (sink.shape, points.shape));
points, points_buffer = ap.initialize_source(points);
if points_buffer.ndim == 1:
points_buffer = points_buffer[:,None];
code.find_smaller_than_fraction(source_buffer, source_shape, source_strides, points_buffer, search, values, sink_buffer, processes);
ap.finalize_processing(verbose=verbose, function='find_smaller_than_values', timer=timer);
return sink;
###############################################################################
### Tests
###############################################################################
[docs]def test():
import numpy as np
import ClearMap.Analysis.Measurements.MeasureRadius as mr;
import ClearMap.ParallelProcessing.DataProcessing.MeasurePointList as mpl
from importlib import reload
reload(mpl);
reload(mpl.code);
# find_smaller_than_value
goal = (50,55,42);
d = np.ones((100,100,100));
d[goal] = 0.3;
strides = np.array(d.strides) / np.array(d.itemsize);
search, dist = mr.indices_from_center(radius = 15, strides = strides);
indices = np.array([np.ravel_multi_index((50,50,50), d.shape)]);
result = mpl.find_smaller_than_value(d, indices, search, max_value = 0.5, out = None, processes = None);
coords = np.unravel_index(indices + search[result], d.shape)
coords = np.array(coords).reshape(-1);
assert np.all(coords == goal)
# find_smaller_than_fraction
result = mpl.find_smaller_than_fraction(d, indices, search, fraction = 0.5, out = None, processes = None);
coords = np.unravel_index(indices + search[result], d.shape)
coords = np.array(coords).reshape(-1);
assert np.all(coords == goal)
Source
