runInitializeElastix(parameter)
pts = runCellCoordinateTransformation(parameter)
io.writePoints(os.path.join(basedirectory, 'cells_to_autofluo.csv'), pts)
## Visualize cfos to auto points
parameter.ImageProcessing.CellCoordinateFile = pts
parameter.ImageProcessing.CellTransformedCoordinateFile = None
pts2 = runCellCoordinateResampling(parameter)
ds = dataSize(os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif'))
voximg = vox.voxelizePixel(pts2, ds)
io.writeDataStack(
os.path.join(basedirectory, 'points_transformed_cfos_to_auto.tif'), voximg)
#pts0 = io.readPoints(os.path.join(basedirectory, 'cells.csv'));
##############################################################################
# Transform Points matched to Autofluorescence to Atlas Reference
##############################################################################
import os
from iDISCO.Parameter import *
from iDISCO.Run import runInitializeElastix, runCellCoordinateTransformationToReference
import iDISCO.Visualization.Plot as Plot
#Processes to use for Resampling
parameter.Resampling.Processes = 4;
resampledImage = runResampling(parameter);
print("Resampled image saved as %s" % resampledImage)
# voxelize result
voximg = vox.voxelizePixel(acenters, referencedata.shape);
io.writeDataStack(os.path.join(basedirectory, 'Synthetic/points_transformed_pixel.tif'), 5000* voximg)
if verbose:
transformdata = io.readData(os.path.join(transformdir, 'result.mhd'));
referencedata = io.readData(os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif'))
Plot.plotOverlayPoints(transformdata * 0.01, acenters);
Plot.plotOverlayPoints(referencedata * 0.01, acenters);
