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
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
from iDISCO.Parameter import *
from iDISCO.Run import runInitializeElastix, runCellCoordinateTransformationToReference
