def test():
"""Test voxelization module"""
import iDISCO.Analysis.Voxelization as self
reload(self)
import iDISCO.Analysis.VoxelizationCode as vox
import numpy
points = numpy.random.rand(200,3) * 10;
#use cython code
vi = vox.voxelizeSphere(points, 20,20,20, 5,5,5);
import iDISCO.Visualization.Plot as Plot
Plot.plotTiling(vi)
#use voxelize
vi = self.voxelize(points, dataSize = (20,20,20), average = (5,5,5));
Plot.plotTiling(vi)
#weighted voxelization
points = numpy.random.rand(10,3) * 10;
weights = numpy.random.rand(10);
#use voxelize
vi = self.voxelize(points, dataSize = (20,20,20), average = (5,5,5));
viw = self.voxelize(points, dataSize = (20,20,20), average = (5,5,5), weights = weights);
Plot.plotTiling(vi)
Plot.plotTiling(viw)
def test():
"""Test voxelization module"""
import ClearMap.Analysis.Voxelization as self
reload(self)
import ClearMap.Analysis.VoxelizationCode as vox
import numpy
points = numpy.random.rand(200,3) * 10;
#use cython code
vi = vox.voxelizeSphere(points, 20,20,20, 5,5,5);
import ClearMap.Visualization.Plot as Plot
Plot.plotTiling(vi)
#use voxelize
vi = self.voxelize(points, dataSize = (20,20,20), size = (5,5,5));
Plot.plotTiling(vi)
#weighted voxelization
points = numpy.random.rand(10,3) * 10;
weights = numpy.random.rand(10);
#use voxelize
vi = self.voxelize(points, dataSize = (20,20,20), size = (5,5,5));
viw = self.voxelize(points, dataSize = (20,20,20), size = (5,5,5), weights = weights);
Plot.plotTiling(vi)
Plot.plotTiling(viw)
def voxelize(points, dataSize = None, sink = None, voxelizeParameter = None, method = 'Spherical', size = (5,5,5), weights = None):
"""Converts a list of points into an volumetric image array
Arguments:
points (array): point data array
dataSize (tuple): size of final image
sink (str, array or None): the location to write or return the resulting voxelization image, if None return array
voxelizeParameter (dict):
========== ==================== ===========================================================
Name Type Descritption
========== ==================== ===========================================================
*method* (str or None) method for voxelization: 'Spherical', 'Rectangular' or 'Pixel'
*size* (tuple) size parameter for the voxelization
*weights* (array or None) weights for each point, None is uniform weights
========== ==================== ===========================================================
Returns:
(array): volumetric data of smeared out points
"""
if dataSize is None:
dataSize = tuple(int(math.ceil(points[:,i].max())) for i in range(points.shape[1]));
elif isinstance(dataSize, basestring):
dataSize = io.dataSize(dataSize);
points = io.readPoints(points);
if method.lower() == 'spherical':
if weights is None:
data = vox.voxelizeSphere(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2]);
else:
data = vox.voxelizeSphereWithWeights(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2], weights);
elif method.lower() == 'rectangular':
if weights is None:
data = vox.voxelizeRectangle(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2]);
else:
data = vox.voxelizeRectangleWithWeights(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2], weights);
elif method.lower() == 'pixel':
data = voxelizePixel(points, dataSize, weights);
else:
raise RuntimeError('voxelize: mode: %s not supported!' % method);
return io.writeData(sink, data);
def voxelize(points, dataSize = None, sink = None, voxelizeParameter = None, method = 'Spherical', size = (5,5,5), weights = None):
"""Converts a list of points into an volumetric image array
Arguments:
points (array): point data array
dataSize (tuple): size of final image
sink (str, array or None): the location to write or return the resulting voxelization image, if None return array
voxelizeParameter (dict):
========== ==================== ===========================================================
Name Type Descritption
========== ==================== ===========================================================
*method* (str or None) method for voxelization: 'Spherical', 'Rectangular' or 'Pixel'
*size* (tuple) size parameter for the voxelization
*weights* (array or None) weights for each point, None is uniform weights
========== ==================== ===========================================================
Returns:
(array): volumetric data of smeared out points
"""
if dataSize is None:
dataSize = tuple(int(math.ceil(points[:,i].max())) for i in range(points.shape[1]));
elif isinstance(dataSize, basestring):
dataSize = io.dataSize(dataSize);
points = io.readPoints(points);
if method.lower() == 'spherical':
if weights is None:
data = vox.voxelizeSphere(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2]);
else:
data = vox.voxelizeSphereWithWeights(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2], weights);
elif method.lower() == 'rectangular':
if weights is None:
data = vox.voxelizeRectangle(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2]);
else:
data = vox.voxelizeRectangleWithWeights(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2], weights);
elif method.lower() == 'pixel':
data = voxelizePixel(points, dataSize, weights);
else:
raise RuntimeError('voxelize: mode: %s not supported!' % method);
return io.writeData(sink, data);