Python ImagePlus.getNSlices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 getNSlices [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 getNSlices [as 别名]
def create_registered_hyperstack(imp, channel, 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."""
  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
  # 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())
#.........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 getNSlices [as 别名]
def CreateCover(ip, width, height, dbpath):
	# split input image into appropriate tiles
	stackt = SplitImage(ip, width, height)
	impt = ImagePlus("template", stackt)
	nSlicestmp = impt.getNSlices()

	# open the preprocessed database
	print dbpath
	impd = IJ.openImage(dbpath)
	stackd = impd.getImageStack()
	nSlicesdb = impd.getNSlices()

	#associate index with image names
	imageNames = impd.getProperty('Info')
	imageList = imageNames.split(';')

	# set up preview output
	outputip = ColorProcessor(ip.width, ip.height)
	outputimp = ImagePlus("output", outputip)
	outputimp.show()

	cols = ip.width/width
	rows = ip.height/height

	print str(cols) + "," + str(rows)

	x = 0
	y = 0

	arrays = [None, None] # a list of two elements
	cruncher = Inline(arrays)
	tileNames = {}
	tileIndex = {}
	placed = {}
	used = {}

	while len(placed) < nSlicestmp:
		randomTileIndex = random.randint(1, nSlicestmp)
		if randomTileIndex in placed:
			continue
		# transform to row adn column coordinate
		if randomTileIndex%rows == 0:
			y = rows-1
			x = (randomTileIndex/rows)-1
		else:
			y = (randomTileIndex%rows)-1
			x = int(randomTileIndex/rows)

		pixelst = stackt.getPixels(randomTileIndex)
		minimum = Float.MAX_VALUE
		#iterate through database images
		j = 1
		indexOfBestMatch = 0
		arrays[0] = pixelst
		while j < nSlicesdb:
			if j in used:
				j +=1
				continue
			arrays[1] = stackd.getPixels(j)
			diff = cruncher.call()
			if diff < minimum:
				minimum = diff
				indexOfBestMatch = j
			j += 1
		ip = stackd.getProcessor(indexOfBestMatch)
		outputip.copyBits(ip, x*width, y*height, 0)
		used[indexOfBestMatch] = 1
		tileNames[randomTileIndex] = imageList[indexOfBestMatch-1]
		tileIndex[randomTileIndex] = indexOfBestMatch-1
		outputimp.draw()
		placed[randomTileIndex] = 1

	return tileNames, tileIndex, cols, rows