Python ImageJFunctions.wrapUnsignedByte Examples

Example #1

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    

Example #2

File: Correct_3D_Drift_Plus--ImgLib2.py Project: tischi/fiji-correct-3d-drift

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    

Example #3

File: 2016-01-21--Tischi--Correct_3D_Drift_Plus.py Project: rmd13/fiji-correct-3d-drift

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    

Example #4

File: Particle_Orientation_Analysis.py Project: bic-kn/ParticleOrientationAnalysis

# 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)));