Python voxelize示例

示例#1

文件： Run.py 项目： ChristophKirst/ClearMap

def runVoxelization(parameter):
    """Voxelize a set of points"""
    
    cf = parameter.ImageProcessing.CellTransformedCoordinateFile;
    if cf is None:
        cf =  parameter.ImageProcessing.CellCoordinateFile;
    
    points = io.readPoints(cf);
    
    pv = parameter.Voxelization;

    si = pv.Size;
    if si is None:
        si = parameter.Alignment.MovingImage;
        if si is None:    
            si = parameter.Resampling.ResampledFile;
            
    if isinstance(si, basestring):
        si = dataSize(si);
        
    print si

    vox = voxelize(points, si, average = pv.AveragingDiameter, mode = pv.Mode);
    
    vf = pv.File;
    if vf is None:
        return vox;
    else:
        io.writeDataStack(vf, vox.astype('int32'));
        return vf;

示例#2

文件： Run.py 项目： MoritzNegwer/FriendlyClearmap

def runVoxelization(parameter):
    """Voxelize a set of points"""

    cf = parameter.ImageProcessing.CellTransformedCoordinateFile
    if cf is None:
        cf = parameter.ImageProcessing.CellCoordinateFile

    points = io.readPoints(cf)

    pv = parameter.Voxelization

    si = pv.Size
    if si is None:
        si = parameter.Alignment.MovingImage
        if si is None:
            si = parameter.Resampling.ResampledFile

    if isinstance(si, str):
        si = dataSize(si)

    print(si)

    vox = voxelize(points, si, average=pv.AveragingDiameter, mode=pv.Mode)

    vf = pv.File
    if vf is None:
        return vox
    else:
        io.writeDataStack(vf, vox.astype('int32'))
        return vf

示例#3

文件： test_chain_synthetic.py 项目： MoritzNegwer/FriendlyClearmap

    # Voxelization weigths (e/g intensities)
    "voxelizationWeights" : None
    };


#Points
transformedPointsFile = os.path.join(baseDirectory, 'Synthetic/cells_transformed_to_reference.csv')

#Reference file
referenceFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif');

#voxelization file 
voxelizationFile = None;

voxdata = voxelize(transformedPointsFile, dataSize = referenceFile, sink = voxelizationFile, **voxelizationParameter)

if verbose:
    #voxdata = io.readData(parameter.Alignment.FixedImage);
    voxdata = io.readData(voxdata);
    points  = io.readPoints(transformedPointsFile)
    plot.plotOverlayPoints(voxdata.astype('float') / voxdata.max(), points)



## with weights
import numpy

points  = io.readPoints(transformedPointsFile)

voxelizationParameter["voxelizationSize"]    = (9,9,9);

示例#4

文件： test_chain_synthetic.py 项目： ChristophKirst/ClearMap

    # Voxelization weigths (e/g intensities)
    "voxelizationWeights" : None
    };


#Points
transformedPointsFile = os.path.join(baseDirectory, 'Synthetic/cells_transformed_to_reference.csv')

#Reference file
referenceFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif');

#voxelization file 
voxelizationFile = None;

voxdata = voxelize(transformedPointsFile, dataSize = referenceFile, sink = voxelizationFile, **voxelizationParameter)

if verbose:
    #voxdata = io.readData(parameter.Alignment.FixedImage);
    voxdata = io.readData(voxdata);
    points  = io.readPoints(transformedPointsFile)
    plot.plotOverlayPoints(voxdata.astype('float') / voxdata.max(), points)



## with weights
import numpy

points  = io.readPoints(transformedPointsFile)

voxelizationParameter["voxelizationSize"]    = (9,9,9);