def translate_single_stack_using_imglib2(imp, dx, dy, dz): # wrap into a float imglib2 and translate # conversion into float is necessary due to "overflow of n-linear interpolation due to accuracy limits of unsigned bytes" # see: https://github.com/fiji/fiji/issues/136#issuecomment-173831951 img = ImagePlusImgs.from(imp.duplicate()) extended = Views.extendZero(img) converted = Converters.convert(extended, RealFloatSamplerConverter()) interpolant = Views.interpolate(converted, NLinearInterpolatorFactory()) # translate if imp.getNDimensions()==3: transformed = RealViews.affine(interpolant, Translation3D(dx, dy, dz)) elif imp.getNDimensions()==2: transformed = RealViews.affine(interpolant, Translation2D(dx, dy)) else: IJ.log("Can only work on 2D or 3D stacks") return None cropped = Views.interval(transformed, img) # wrap back into bit depth of input image and return bd = imp.getBitDepth() if bd==8: return(ImageJFunctions.wrapUnsignedByte(cropped,"imglib2")) elif bd == 16: return(ImageJFunctions.wrapUnsignedShort(cropped,"imglib2")) elif bd == 32: return(ImageJFunctions.wrapFloat(cropped,"imglib2")) else: return None
def translate_single_stack_using_imglib2(imp, dx, dy, dz): # wrap into a float imglib2 and translate # conversion into float is necessary due to "overflow of n-linear interpolation due to accuracy limits of unsigned bytes" # see: https://github.com/fiji/fiji/issues/136#issuecomment-173831951 img = ImagePlusImgs.from(imp.duplicate()) extended = Views.extendBorder(img) converted = Converters.convert(extended, RealFloatSamplerConverter()) interpolant = Views.interpolate(converted, NLinearInterpolatorFactory()) # translate if imp.getNDimensions()==3: transformed = RealViews.affine(interpolant, Translation3D(dx, dy, dz)) elif imp.getNDimensions()==2: transformed = RealViews.affine(interpolant, Translation2D(dx, dy)) else: IJ.log("Can only work on 2D or 3D stacks") return None cropped = Views.interval(transformed, img) # wrap back into bit depth of input image and return bd = imp.getBitDepth() if bd==8: return(ImageJFunctions.wrapUnsignedByte(cropped,"imglib2")) elif bd == 16: return(ImageJFunctions.wrapUnsignedShort(cropped,"imglib2")) elif bd == 32: return(ImageJFunctions.wrapFloat(cropped,"imglib2")) else: return None
def translate_using_imglib2(imp, dx, dy, dz): print "imp channels",imp.getNChannels() # todo: # if multiple channels use Duplicator to translate each channel individually ## wrap # http://javadoc.imagej.net/ImgLib2/net/imglib2/img/imageplus/ImagePlusImg.html img = ImagePlusImgs.from(imp.duplicate()) print "dimensions:",img.numDimensions() print img.getChannels() ## prepare image print "img",img ddd extended = Views.extendBorder(img) #print "extended",extended #print "extended",extended.dimension(1) dims = zeros(4, 'l') img.dimensions(dims) print "dims",dims converted = Converters.convert(extended, RealFloatSamplerConverter()) composite = Views.collapseReal(converted, imp.getNChannels()) print "composite",composite interpolant = Views.interpolate(composite, NLinearInterpolatorFactory()) #print "interpolant",interpolant transformed = RealViews.affine(interpolant, Translation3D(dx, dy, dz)) print "transformed", transformed cropped = Views.interval(transformed, img) print "cropped.numDimensions()", cropped.numDimensions() print "cropped",cropped ## wrap back and return bd = imp.getBitDepth() # maybe simply wrap works? if bd==8: return(ImageJFunctions.wrapUnsignedByte(cropped,"imglib2")) elif bd == 16: return(ImageJFunctions.wrapUnsignedShort(cropped,"imglib2")) elif bd == 32: return(ImageJFunctions.wrapFloat(cropped,"imglib2")) else: return None
# Map with and Ops.Math.And andOp = ops.op(Ops.Math.And, BitType(), BitType(), BitType()); if useEnergy: overallSelectionMask = ops.map(overallSelectionMask, energyMask, invertedManualMask, andOp); else: overallSelectionMask = manualMask.copy(); newMask = ops.map(newMask, overallSelectionMask, coherencyMask, andOp); if IJ.debugMode: displays.createDisplay("oriented-mask", ImgPlus(newMask)); displays.createDisplay("overall-mask", ImgPlus(overallSelectionMask)); ### Compute area fraction of oriented regions ### # Compute area of oriented mask newMaskImp = ImageJFunctions.wrapUnsignedByte(newMask, "New mask"); newMaskImp.getProcessor().setThreshold(1.0, 1.5, False); # [0.5, 1.0] does not work due to rounding problems rt = ResultsTable(); analyzer = Analyzer(newMaskImp, Measurements.AREA | Measurements.LIMIT, rt); analyzer.measure(); # Compute area of overall selection mask energyMaskImp = ImageJFunctions.wrapUnsignedByte(overallSelectionMask, "Energy mask"); energyMaskImp.getProcessor().setThreshold(1.0, 1.5, False); # [0.5, 1.0] does not work due to rounding problems rtEnergy = ResultsTable(); analyzerEnergy = Analyzer(energyMaskImp, Measurements.AREA | Measurements.LIMIT, rtEnergy); analyzerEnergy.measure(); # Print Area% (through SciJava OUTPUT, see L5) if IJ.debugMode: print("Coherency area: "+str(rt.getValueAsDouble(rt.getColumnIndex("Area"), rt.size()-1)));