############################################################################## # 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 basedirectory = os.path.join(iDISCOPath(), 'Test'); verbose = True; resultdir = os.path.join(basedirectory, 'Synthetic/elastix'); transformfile = elx.getTransformParameterFile(resultdir) # tranform points according to alignment of data and reference resamplefile = os.path.join(basedirectory, 'Synthetic/test_iDISCO_reference.tif'); transformdir = os.path.join(basedirectory, 'Synthetic/transformix') elx.initializeElastix('/home/ckirst/programs/elastix') elx.ElastixSettings.printInfo() #elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname) elx.transformData(resamplefile, transformparameterfile = os.path.join(basedirectory, 'Synthetic/elastix/TransformParameters.0.txt'), outdirectory = transformdir) ############################################################################## # Transform Points from Raw Data to Reference
import os import iDISCO.Settings as settings import iDISCO.IO.IO as io import iDISCO.Alignment.Elastix as elx import iDISCO.Visualization.Plot as plot baseDirectory = os.path.join(settings.IDISCOPath, 'Test'); verbose = True; transformDirectory = os.path.join(baseDirectory, 'Synthetic/elastix'); transformFile = elx.getTransformParameterFile(transformDirectory) # tranform points according to alignment of data and reference resampleFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_resample.tif'); referenceFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'); resultDirectory = os.path.join(baseDirectory, 'Synthetic/transformix') #elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname) resultFile = elx.transformData(referenceFile, transformDirectory = transformDirectory, resultDirectory = resultDirectory) if verbose: resampledata = io.readData(resampleFile); referencedata = io.readData(referenceFile); transformdata = io.readData(resultFile);
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
import os import iDISCO.Settings as settings import iDISCO.IO.IO as io import iDISCO.Alignment.Elastix as elx import iDISCO.Visualization.Plot as plot baseDirectory = os.path.join(settings.IDISCOPath, 'Test'); verbose = True; transformDirectory = os.path.join(baseDirectory, 'Synthetic/elastix'); transformFile = elx.getTransformParameterFile(transformDirectory) # tranform points according to alignment of data and reference resampleFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_resample.tif'); referenceFile = os.path.join(baseDirectory, 'Synthetic/test_iDISCO_reference.tif'); resultDirectory = os.path.join(baseDirectory, 'Synthetic/transformix') #elx.transformData(dataresname, alignmentdirectory = resultdir, outdirectory = dataalgname) resultFile = elx.transformData(referenceFile, transformDirectory = transformDirectory, resultDirectory = resultDirectory) if verbose: resampledata = io.readData(resampleFile); referencedata = io.readData(referenceFile); transformdata = io.readData(resultFile);