print "Aligned images: result directory: %s" % resultDirectory ############################################################################## # Test Transform Points ############################################################################## import iDISCO.Visualization.Plot as Plot; 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
print("Aligned cfos with autofluo: result directory: %s" % resultDirectory) ############################################################################## # Test Transform data auto to cfos ############################################################################## from iDISCO.Parameter import * import iDISCO.Alignment.Elastix as elx import iDISCO.Visualization.Plot as Plot import iDISCO.IO.IO as io basedirectory = '/home/mtllab/Documents/whiskers/2ndgroup/C' resultdir = os.path.join(basedirectory, 'elastix_cfos_auto') transformfile = elx.getTransformParameterFile(resultdir) # tranform points according to alignment of data and reference resamplefile = os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif') transformdir = os.path.join(basedirectory, 'transform_data_cfos_auto') elx.initializeElastix('/usr/local/elastix') elx.ElastixSettings.printInfo() #elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname) elx.transformData(resamplefile, transformparameterfile=transformfile, outdirectory=transformdir) ############################################################################## # Transform Points from Cfos to Autofluo
############################################################################## # Test Transform data auto to cfos ############################################################################## from iDISCO.Parameter import * import iDISCO.Alignment.Elastix as elx import iDISCO.Visualization.Plot as Plot import iDISCO.IO.IO as io basedirectory = '/home/mtllab/Documents/whiskers/2ndgroup/C'; resultdir = os.path.join(basedirectory, 'elastix_cfos_auto'); transformfile = elx.getTransformParameterFile(resultdir) # tranform points according to alignment of data and reference resamplefile = os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif'); transformdir = os.path.join(basedirectory, 'transform_data_cfos_auto') elx.initializeElastix('/usr/local/elastix') elx.ElastixSettings.printInfo() #elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname) elx.transformData(resamplefile, transformparameterfile = transformfile, outdirectory = transformdir)
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
print("Aligned images: result directory: %s" % resultDirectory) ############################################################################## # Test Transform Points ############################################################################## import iDISCO.Visualization.Plot as Plot; 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)
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