Ejemplos de IO.readPoints en Python

Ejemplo n.º 1

Archivo: Run.py Proyecto: 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;

Ejemplo n.º 2

Archivo: Run.py Proyecto: 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

Ejemplo n.º 3

Archivo: test_elastix_transform.py Proyecto: ChristophKirst/ClearMap

parameter.Alignment.MovingImage = os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif');
parameter.Alignment.FixedImage  = os.path.join(basedirectory, 'Synthetic/test_iDISCO_reference.tif');
parameter.Alignment.FixedImageMask = None;
  
#elastix parameter files for alignment
parameter.Alignment.AffineParameterFile  = os.path.join(parameter.Alignment.AlignmentDirectory, 'ElastixParameterAffine.txt');
#parameter.Alignment.BSplineParameterFile = os.path.join(parameter.Alignment.AlignmentDirectory, 'ElastixParameterBSpline.txt');
parameter.Alignment.BSplineParameterFile = None;

runInitializeElastix(parameter)

runCellCoordinateTransformationToReference(parameter)

if verbose:
    refdata = io.readData(parameter.Alignment.FixedImage);
    pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
    Plot.plotOverlayPoints(0.01 * refdata, pts)




##############################################################################
# Test Voxelization
##############################################################################

import os

from iDISCO.Parameter import *
from iDISCO.Run import runVoxelization

import iDISCO.Visualization.Plot as Plot

Ejemplo n.º 4

Archivo: test_chain_data.py Proyecto: MoritzNegwer/FriendlyClearmap

#pts[0,:] = [0,0,0];
#pts = pts[:, [1,0,2]];

runCellCoordinateTransformationToReference(parameter)

#pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
#pts2 = pts2[:,[1,0,2]];

if verbose:
    refdata = io.readData(parameter.Alignment.FixedImage)
    #pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
    Plot.plotOverlayPoints(0.1 * refdata, pts2)

refdata.shape

pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile)
#pts2 = pts2[:,[1,0,2]];
voximg = vox.voxelizePixel(pts2, refdata.shape)
io.writeDataStack(os.path.join(basedirectory, 'points_transformed_pixel.tif'),
                  voximg)

##############################################################################
# Test Resample Points
##############################################################################

import os
import numpy

from iDISCO.Parameter import *
from iDISCO.Run import runResampling
import iDISCO.IO.IO as io

Ejemplo n.º 5

Archivo: test_chain_data.py Proyecto: ChristophKirst/ClearMap

runCellCoordinateTransformationToReference(parameter)

#pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
#pts2 = pts2[:,[1,0,2]];


if verbose:
    refdata = io.readData(parameter.Alignment.FixedImage);
    #pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
    Plot.plotOverlayPoints(0.1 * refdata, pts2)


refdata.shape

pts2 = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
#pts2 = pts2[:,[1,0,2]];
voximg = vox.voxelizePixel(pts2, refdata.shape);
io.writeDataStack(os.path.join(basedirectory, 'points_transformed_pixel.tif'), voximg)






##############################################################################
# Test Resample Points
############################################################################## 

import os
import numpy;

Ejemplo n.º 6

Archivo: test_chain_synthetic.py Proyecto: MoritzNegwer/FriendlyClearmap

allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : (100,160), 'y' : (10,140), 'z' : (2,38)})
#allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : all, 'y' : all, 'z' : all})

result = detectCells(**allParameter);
print(result)

verbose = True;
if verbose:
    import iDISCO.IO.IO as io
    import iDISCO.Visualization.Plot as plot   
    
    dataraw = io.readData(spotDetectionParameter["source"]);
    dataraw[dataraw > 50] = 50;
    dataraw = dataraw.astype('float') / dataraw.max();
    points  = io.readPoints(spotDetectionParameter["sink"][0]);
    plot.plotOverlayPoints(dataraw, points, pointColor = [1,0,0]);


dataraw = io.readData(spotDetectionParameter["source"], x = (100,160), y = (10,140), z =  (2,38));
io.writeData( os.path.join(baseDirectory, 'Synthetic/raw.tif'), dataraw)

##############################################################################
# Test Resample Points
############################################################################## 

import os

import iDISCO.Settings as settings
import iDISCO.IO.IO as io
import iDISCO.Visualization.Plot as plot

Ejemplo n.º 7

parameter.Alignment.MovingImage = os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif');
parameter.Alignment.FixedImage  = os.path.join(basedirectory, 'Synthetic/test_iDISCO_reference.tif');
parameter.Alignment.FixedImageMask = None;
  
#elastix parameter files for alignment
parameter.Alignment.AffineParameterFile  = os.path.join(parameter.Alignment.AlignmentDirectory, 'ElastixParameterAffine.txt');
#parameter.Alignment.BSplineParameterFile = os.path.join(parameter.Alignment.AlignmentDirectory, 'ElastixParameterBSpline.txt');
parameter.Alignment.BSplineParameterFile = None;

runInitializeElastix(parameter)

runCellCoordinateTransformationToReference(parameter)

if verbose:
    refdata = io.readData(parameter.Alignment.FixedImage);
    pts = io.readPoints(parameter.ImageProcessing.CellTransformedCoordinateFile);
    Plot.plotOverlayPoints(0.01 * refdata, pts)




##############################################################################
# Test Voxelization
##############################################################################

import os

from iDISCO.Parameter import *
from iDISCO.Run import runVoxelization

import iDISCO.Visualization.Plot as Plot

Ejemplo n.º 8

Archivo: test_chain_synthetic.py Proyecto: ChristophKirst/ClearMap

allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : (100,160), 'y' : (10,140), 'z' : (2,38)})
#allParameter = joinParameter(stackProcessingParameter, spotDetectionParameter, {'x' : all, 'y' : all, 'z' : all})

result = detectCells(**allParameter);
print result

verbose = True;
if verbose:
    import iDISCO.IO.IO as io
    import iDISCO.Visualization.Plot as plot   
    
    dataraw = io.readData(spotDetectionParameter["source"]);
    dataraw[dataraw > 50] = 50;
    dataraw = dataraw.astype('float') / dataraw.max();
    points  = io.readPoints(spotDetectionParameter["sink"][0]);
    plot.plotOverlayPoints(dataraw, points, pointColor = [1,0,0]);


dataraw = io.readData(spotDetectionParameter["source"], x = (100,160), y = (10,140), z =  (2,38));
io.writeData( os.path.join(baseDirectory, 'Synthetic/raw.tif'), dataraw)

##############################################################################
# Test Resample Points
############################################################################## 

import os

import iDISCO.Settings as settings
import iDISCO.IO.IO as io
import iDISCO.Visualization.Plot as plot