import iDISCO.Alignment.Elastix as elx; import iDISCO.Analysis.Voxelization as vox import iDISCO.IO.IO as io elx.initializeElastix('/home/ckirst/programs/elastix') elx.ElastixSettings.printInfo() verbose = True; parameter.Alignment.AlignmentDirectory = os.path.join(basedirectory, 'Synthetic/elastix'); rcenters = numpy.array([[0,0,0],[0,52,0], [0,0,23], [74,0,0],[74,52,0]]); #acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir); acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory); print acenters ############################################################################## # Test Transform data ############################################################################## from iDISCO.Parameter import * import iDISCO.Alignment.Elastix as elx import iDISCO.Visualization.Plot as Plot import iDISCO.IO.IO as io
import iDISCO.Alignment.Elastix as elx; verbose = True; # directory in with elastix alignment result transformDirectory = os.path.join(baseDirectory, 'Synthetic/elastix'); #result diectory to write transformed points to (None = read back as array) resultDirectory = os.path.join(baseDirectory, 'Synthetic/transformix') #define (y,x,z) coordinates for testing points = numpy.array([[0,0,0],[74,0,0],[0,52,0],[0,0,23],[74,52,0]]); #acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir); pointsa = elx.transformPoints(points, resultDirectory = resultDirectory, transformDirectory = transformDirectory); print(pointsa) ############################################################################## # Test Transform Reference to Resampled Data ############################################################################## import os import iDISCO.Settings as settings import iDISCO.IO.IO as io import iDISCO.Alignment.Elastix as elx
elx.ElastixSettings.printInfo() verbose = True parameter.Alignment.AlignmentDirectory = os.path.join(basedirectory, 'elastix') #rcenters = numpy.array([[0,0,0],[0,52,0], [0,0,23], [74,0,0],[74,52,0]]); #acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir); #rcenters = io.readPoints(os.path.join(basedirectory, 'cells_resampled.csv')); rcenters2 = rcenters.copy() rcenters2 = rcenters2[:, [1, 0, 2]] print(rcenters2.shape) acenters = elx.transformPoints( rcenters2, alignmentdirectory=parameter.Alignment.AlignmentDirectory) acenters2 = acenters.copy() acenters2 = acenters2[:, [1, 0, 2]] #print acenters #rdata = io.readData(os.path.join(basedirectory, 'autofluo_resample.tif')); rdata = io.readData(os.path.join(basedirectory, 'half_template_25_right.tif')) voximg = vox.voxelizePixel(acenters2, rdata.shape) * 5000 io.writeDataStack(os.path.join(basedirectory, 'cells_transformed.tif'), voximg.astype('int16'))
import iDISCO.Alignment.Elastix as elx; verbose = True; # directory in with elastix alignment result transformDirectory = os.path.join(baseDirectory, 'Synthetic/elastix'); #result diectory to write transformed points to (None = read back as array) resultDirectory = os.path.join(baseDirectory, 'Synthetic/transformix') #define (y,x,z) coordinates for testing points = numpy.array([[0,0,0],[74,0,0],[0,52,0],[0,0,23],[74,52,0]]); #acenters = elx.transformPoints(rcenters, alignmentdirectory = parameter.Alignment.AlignmentDirectory, outdirectory = pointsdir); pointsa = elx.transformPoints(points, resultDirectory = resultDirectory, transformDirectory = transformDirectory); print pointsa ############################################################################## # Test Transform Reference to Resampled Data ############################################################################## import os import iDISCO.Settings as settings import iDISCO.IO.IO as io import iDISCO.Alignment.Elastix as elx