io.writeData(os.path.join(resultDir, fName + '_CellShapes.tif'),
255 * dataShape.astype('int32') / dataShape.max())
#cintensity = findIntensity(imgD, points);
#points, intensities = thresholdPoints(points,cintensity, threshold = (5,20), row = (1,1));
points, cellSizesPost = thresholdPoints(points,
cellSizesPre,
threshold=pointsThresh,
row=threshType)
#pdb.set_trace()
#io.writeData(os.path.join(homeDir, 'Results/OverlayWatershed.tif'), overlay_Img);
overlay_Img = plt.fredOverlayPoints(cfos_fn,
points,
pointColor=[200, 0, 0])
io.writeData(os.path.join(resultDir, fName + '_PointsOriginalImg.tif'),
overlay_Img)
overlay_Img = plt.overlayPoints(imgD, points, pointColor=[200, 0, 0])
io.writeData(os.path.join(resultDir, fName + '_PointsFilterDoG.tif'),
overlay_Img)
#Convert points from 3d to 2d
points = numpy.delete(points, 2, axis=1)
io.writePoints(points_fn, points)
##############################################################333
imgR = io.readData(auto_fn)
cellSizesPre = findCellSize(dataShape, maxlabel=points.shape[0])
io.writeData(os.path.join(homeDir, 'Results/CellShapes.tif'),
20 * dataShape.astype('int32'))
#cintensity = findIntensity(imgD, points);
#points, intensities = thresholdPoints(points,cintensity, threshold = (5,20), row = (1,1));
points, cellSizesPost = thresholdPoints(points,
cellSizesPre,
threshold=(5, 100),
row=(3, 3))
#pdb.set_trace()
#io.writeData(os.path.join(homeDir, 'Results/OverlayWatershed.tif'), overlay_Img);
overlay_Img = plt.fredOverlayPoints(input_fn, points, pointColor=[200, 0, 0])
io.writeData(os.path.join(homeDir, 'Results/PointsOriginalImg.tif'),
overlay_Img)
overlay_Img = plt.fredOverlayPoints(os.path.join(homeDir,
'Results/FilterDoG.tif'),
points,
pointColor=[200, 0, 0])
io.writeData(os.path.join(homeDir, 'Results/PointsFilterDoG.tif'), overlay_Img)
#################################################################################################
#Convert points from 3d to 2d
points = numpy.delete(points, 2, axis=1)
io.writePoints(points_fn, points)
#Resampled Img
imgR = io.readData(auto_fn)
