Python ImagePlus.setOpenAsHyperStack方法代码示例

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import setOpenAsHyperStack [as 别名]

#.........这里部分代码省略.........
  for s in shifts:
    print s.x, s.y, s.z
  # new canvas dimensions:
  width = imp.width + maxx - minx
  height = maxy - miny + imp.height
  slices = maxz - minz + imp.getNSlices()

  print "New dimensions:", width, height, slices
  # Prepare empty slice to pad in Z when necessary
  empty = imp.getProcessor().createProcessor(width, height)

  # if it's RGB, fill the empty slice with blackness
  if isinstance(empty, ColorProcessor):
    empty.setValue(0)
    empty.fill()
  # Write all slices to files:
  stack = imp.getStack()

  if virtual is False:
  	registeredstack = ImageStack(width, height, imp.getProcessor().getColorModel())
  names = []
  for frame in range(1, imp.getNFrames()+1):
    shift = shifts[frame-1]
    fr = "t" + zero_pad(frame, len(str(imp.getNFrames())))
    # Pad with empty slices before reaching the first slice
    for s in range(shift.z):
      ss = "_z" + zero_pad(s + 1, len(str(slices))) # slices start at 1
      for ch in range(1, imp.getNChannels()+1):
        name = fr + ss + "_c" + zero_pad(ch, len(str(imp.getNChannels()))) +".tif"
        names.append(name)

        if virtual is True:
          currentslice = ImagePlus("", empty)
          currentslice.setCalibration(imp.getCalibration().copy())
          currentslice.setProperty("Info", imp.getProperty("Info"))
          FileSaver(currentslice).saveAsTiff(target_folder + "/" + name)
        else:
          empty = imp.getProcessor().createProcessor(width, height)
          registeredstack.addSlice(str(name), empty)
    # Add all proper slices
    stack = imp.getStack()
    for s in range(1, imp.getNSlices()+1):
      ss = "_z" + zero_pad(s + shift.z, len(str(slices)))
      for ch in range(1, imp.getNChannels()+1):
         ip = stack.getProcessor(imp.getStackIndex(ch, s, frame))
         ip2 = ip.createProcessor(width, height) # potentially larger
         ip2.insert(ip, shift.x, shift.y)
         name = fr + ss + "_c" + zero_pad(ch, len(str(imp.getNChannels()))) +".tif"
         names.append(name)

         if virtual is True:
           currentslice = ImagePlus("", ip2)
           currentslice.setCalibration(imp.getCalibration().copy())
           currentslice.setProperty("Info", imp.getProperty("Info"));
           FileSaver(currentslice).saveAsTiff(target_folder + "/" + name)
         else:
           registeredstack.addSlice(str(name), ip2)

    # Pad the end
    for s in range(shift.z + imp.getNSlices(), slices):
      ss = "_z" + zero_pad(s + 1, len(str(slices)))
      for ch in range(1, imp.getNChannels()+1):
        name = fr + ss + "_c" + zero_pad(ch, len(str(imp.getNChannels()))) +".tif"
        names.append(name)

        if virtual is True:
          currentslice = ImagePlus("", empty)
          currentslice.setCalibration(imp.getCalibration().copy())
          currentslice.setProperty("Info", imp.getProperty("Info"))
          FileSaver(currentslice).saveAsTiff(target_folder + "/" + name)
        else:
          registeredstack.addSlice(str(name), empty)

  if virtual is True:
      # Create virtual hyper stack with the result
      registeredstack = VirtualStack(width, height, None, target_folder)
      for name in names:
        registeredstack.addSlice(name)
      registeredstack_imp = ImagePlus("registered time points", registeredstack)
      registeredstack_imp.setDimensions(imp.getNChannels(), len(names) / (imp.getNChannels() * imp.getNFrames()), imp.getNFrames())
      registeredstack_imp.setCalibration(imp.getCalibration().copy())
      registeredstack_imp.setOpenAsHyperStack(True)

  else:
    registeredstack_imp = ImagePlus("registered time points", registeredstack)
    registeredstack_imp.setCalibration(imp.getCalibration().copy())
    registeredstack_imp.setProperty("Info", imp.getProperty("Info"))
    registeredstack_imp.setDimensions(imp.getNChannels(), len(names) / (imp.getNChannels() * imp.getNFrames()), imp.getNFrames())
    registeredstack_imp.setOpenAsHyperStack(True)
    if 1 == registeredstack_imp.getNChannels():
      return registeredstack_imp
  IJ.log("\nHyperstack dimensions: time frames:" + str(registeredstack_imp.getNFrames()) + ", slices: " + str(registeredstack_imp.getNSlices()) + ", channels: " + str(registeredstack_imp.getNChannels()))

  # Else, as composite
  mode = CompositeImage.COLOR;
  if isinstance(imp, CompositeImage):
    mode = imp.getMode()
  else:
    return registeredstack_imp
  return CompositeImage(registeredstack_imp, mode)

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import setOpenAsHyperStack [as 别名]
def create_registered_hyperstack(imp, target_folder, channel):
  """ Takes the imp, which contains a virtual hyper stack,
  and determines the x,y,z drift for each pair of time points,
  using the preferred given channel,
  and output one image for each slide into the target folder."""
  print "starting to calculate translations..."
  shifts = compute_frame_translations(imp, channel)
  # Make shifts relative to 0,0,0 of the original imp:
  shifts = concatenate_shifts(shifts)
  print "shifts concatenated:"
  for s in shifts:
    print s.x, s.y, s.z
  # Compute bounds of the new volume,
  # which accounts for all translations:
  minx, miny, minz, maxx, maxy, maxz = compute_min_max(shifts)
  # Make shifts relative to new canvas dimensions
  # so that the min values become 0,0,0
  for shift in shifts:
    shift.x -= minx
    shift.y -= miny
    shift.z -= minz
  print "shifts relative to new dimensions:"
  for s in shifts:
    print s.x, s.y, s.z
  writer = CSVWriter(FileWriter(target_folder+"/shifts.csv"), ',')
  data = Array.newInstance(Class.forName("java.lang.String"), 3)  
  for s in shifts:
     data[0] = str(s.x)
     data[1] = str(s.y)
     data[2] = str(s.z)
     writer.writeNext(data)
  writer.close()
  # new canvas dimensions:
  width = imp.width + maxx - minx
  height = maxy - miny + imp.height
  slices = maxz - minz + imp.getNSlices()

  print "New dimensions:", width, height, slices
  # Count number of digits of each dimension, to output zero-padded numbers:
  slice_digits = len(str(slices))
  frame_digits = len(str(imp.getNFrames()))
  channel_digits = len(str(imp.getNChannels()))
  # List to accumulate all created names:
  names = []
  # Prepare empty slice to pad in Z when necessary
  empty = imp.getProcessor().createProcessor(width, height)
  # if it's RGB, fill the empty slice with blackness
  if isinstance(empty, ColorProcessor):
    empty.setValue(0)
    empty.fill()
  # Write all slices to files:
  stack = imp.getStack()
  for frame in range(1, imp.getNFrames()+1):
    shift = shifts[frame-1]
    fr = "t" + zero_pad(frame, frame_digits)
    # Pad with mpty slices before reaching the first slice
    for s in range(shift.z):
      ss = "_z" + zero_pad(s + 1, slice_digits) # slices start at 1
      for ch in range(1, imp.getNChannels()+1):
        name = fr + ss + "_c" + zero_pad(ch, channel_digits) +".tif"
        names.append(name)
        FileSaver(ImagePlus("", empty)).saveAsTiff(target_folder + "/" + name)
    # Add all proper slices
    for s in range(1, imp.getNSlices()+1):
      ss = "_z" + zero_pad(s + shift.z, slice_digits)
      for ch in range(1, imp.getNChannels()+1):
         ip = stack.getProcessor(imp.getStackIndex(ch, s, frame))
         ip2 = ip.createProcessor(width, height) # potentially larger
         ip2.insert(ip, shift.x, shift.y)
         name = fr + ss + "_c" + zero_pad(ch, channel_digits) +".tif"
         names.append(name)
         FileSaver(ImagePlus("", ip2)).saveAsTiff(target_folder + "/" + name)
    # Pad the end
    for s in range(shift.z + imp.getNSlices(), slices):
      ss = "_z" + zero_pad(s + 1, slice_digits)
      for ch in range(1, imp.getNChannels()+1):
        name = fr + ss + "_c" + zero_pad(ch, channel_digits) +".tif"
        names.append(name)
        FileSaver(ImagePlus("", empty)).saveAsTiff(target_folder + "/" + name)
  
  # Create virtual hyper stack with the result
  vs = VirtualStack(width, height, None, target_folder)
  for name in names:
    vs.addSlice(name)
  vs_imp = ImagePlus("registered time points", vs)
  vs_imp.setDimensions(imp.getNChannels(), len(names) / (imp.getNChannels() * imp.getNFrames()), imp.getNFrames())
  vs_imp.setOpenAsHyperStack(True)
  IJ.log("\nHyperstack dimensions: time frames:" + str(vs_imp.getNFrames()) + ", slices: " + str(vs_imp.getNSlices()) + ", channels: " + str(vs_imp.getNChannels()))
  if 1 == vs_imp.getNSlices():
    return vs_imp
  # Else, as composite
  mode = CompositeImage.COLOR;
  if isinstance(imp, CompositeImage):
    mode = imp.getMode()
  else:
    return vs_imp
  return CompositeImage(vs_imp, mode)

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import setOpenAsHyperStack [as 别名]
def register_hyperstack_subpixel(imp, channel, shifts, target_folder, virtual):
  """ Takes the imp, determines the x,y,z drift for each pair of time points, using the preferred given channel,
  and outputs as a hyperstack.
  The shifted image is computed using TransformJ allowing for sub-pixel shifts using interpolation.
  This is quite a bit slower than just shifting the image by full pixels as done in above function register_hyperstack().
  However it significantly improves the result by removing pixel jitter.
  """
  # Compute bounds of the new volume,
  # which accounts for all translations:
  minx, miny, minz, maxx, maxy, maxz = compute_min_max(shifts)
  # Make shifts relative to new canvas dimensions
  # so that the min values become 0,0,0
  for shift in shifts:
    shift.x -= minx
    shift.y -= miny
    shift.z -= minz
  # new canvas dimensions:
  width = int(imp.width + maxx - minx)
  height = int(maxy - miny + imp.height)
  slices = int(maxz - minz + imp.getNSlices())

  print "New dimensions:", width, height, slices

  # prepare stack for final results
  stack = imp.getStack()
  if virtual is True:
    names = []
  else:
    registeredstack = ImageStack(width, height, imp.getProcessor().getColorModel())

  # prepare empty slice for padding
  empty = imp.getProcessor().createProcessor(width, height)

  IJ.showProgress(0)

  # get raw data as stack
  stack = imp.getStack()

  # loop across frames
  for frame in range(1, imp.getNFrames()+1):

    IJ.showProgress(frame / float(imp.getNFrames()+1))
    fr = "t" + zero_pad(frame, len(str(imp.getNFrames()))) # for saving files in a virtual stack

    # get and report current shift
    shift = shifts[frame-1]
    print "frame",frame,"correcting drift",-shift.x-minx,-shift.y-miny,-shift.z-minz
    IJ.log("    frame "+str(frame)+" correcting drift "+str(round(-shift.x-minx,2))+","+str(round(-shift.y-miny,2))+","+str(round(-shift.z-minz,2)))

    # loop across channels
    for ch in range(1, imp.getNChannels()+1):

      tmpstack = ImageStack(width, height, imp.getProcessor().getColorModel())

      # get all slices of this channel and frame
      for s in range(1, imp.getNSlices()+1):
        ip = stack.getProcessor(imp.getStackIndex(ch, s, frame))
        ip2 = ip.createProcessor(width, height) # potentially larger
        ip2.insert(ip, 0, 0)
        tmpstack.addSlice("", ip2)

      # Pad the end (in z) of this channel and frame
      for s in range(imp.getNSlices(), slices):
        tmpstack.addSlice("", empty)

      # subpixel translation
      imp_tmpstack = ImagePlus("", tmpstack)
      imp_translated = translate_single_stack_using_imglib2(imp_tmpstack, shift.x, shift.y, shift.z)

      # Add translated frame to final time-series
      translated_stack = imp_translated.getStack()
      for s in range(1, translated_stack.getSize()+1):
        ss = "_z" + zero_pad(s, len(str(slices)))
        ip = translated_stack.getProcessor(s).duplicate() # duplicate is important as otherwise it will only be a reference that can change its content
        if virtual is True:
          name = fr + ss + "_c" + zero_pad(ch, len(str(imp.getNChannels()))) +".tif"
          names.append(name)
          currentslice = ImagePlus("", ip)
          currentslice.setCalibration(imp.getCalibration().copy())
          currentslice.setProperty("Info", imp.getProperty("Info"));
          FileSaver(currentslice).saveAsTiff(target_folder + "/" + name)
        else:
          registeredstack.addSlice("", ip)

  IJ.showProgress(1)

  if virtual is True:
    # Create virtual hyper stack with the result
    registeredstack = VirtualStack(width, height, None, target_folder)
    for name in names:
      registeredstack.addSlice(name)
    registeredstack_imp = ImagePlus("registered time points", registeredstack)
    registeredstack_imp.setDimensions(imp.getNChannels(), slices, imp.getNFrames())
    registeredstack_imp.setCalibration(imp.getCalibration().copy())
    registeredstack_imp.setOpenAsHyperStack(True)
  else:
    registeredstack_imp = ImagePlus("registered time points", registeredstack)
    registeredstack_imp.setCalibration(imp.getCalibration().copy())
    registeredstack_imp.setProperty("Info", imp.getProperty("Info"))
    registeredstack_imp.setDimensions(imp.getNChannels(), slices, imp.getNFrames())
#.........这里部分代码省略.........

# 需要导入模块: from ij import ImagePlus [as 别名]
# 或者: from ij.ImagePlus import setOpenAsHyperStack [as 别名]
		rest = ResultsTable.open(directory+"/"+filename+"_results.csv")
		
		#print(rest.getColumnHeadings())
		remove_outside_cell(rest,mask)
		rest.save(directory+"/"+filename+"_results.csv" )
	else:
		rest = rt

	
	
	
	
	
	
	image.setDimensions(2, z_slices, 1)
	image.setOpenAsHyperStack(True)
	print(image.isHyperStack(), image.getNChannels(), image.getOverlay())
	#image.flattenStack()
	image.show()
	fs = FileSaver(image)
	filepath = directory + "/" + filename + "_coloc.tiff" 
	
	fs.saveAsTiff(filepath) 
	image.close()

	image = IJ.getImage()
	IJ.run(image_dapi,"Convert to Mask", "method=Otsu background=Default calculate")
	fs = FileSaver(image_dapi)
	filepath = directory + "/" + filename + "_dapi.tiff" 
	
	fs.saveAsTiff(filepath)