def run():
srcDir = DirectoryChooser("Choose!").getDirectory()
if not srcDir:
# user canceled dialog
return
# Assumes all files have the same size
filepaths = []
pattern = re.compile('ch1(.*)_(.*)transformed.mha')
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-TIFF files
match = re.search(pattern, filename)
if (match == None) or (match.group(1) == None):
continue
print(filename)
path = os.path.join(root, filename)
filepaths.append(path)
# Upon finding the first image, initialize the VirtualStack
vs = None
sorted_filepaths = sorted(filepaths)
for f in sorted(filepaths):
IJ.openImage(f)
print(f.split('\\')[-1])
imp = IJ.getImage()
if vs is None:
vs = ImageStack(imp.width, imp.height)
# Add a slice, relative to the srcDir
vs.addSlice(f.split('\\')[-1],imp.getProcessor())
imp.hide()
ImagePlus("Stack from subdirectories", vs).show()
def reslice(image, pixelDepth):
w = image.getWidth()
h = image.getHeight()
cal = image.getCalibration()
stack = image.getStack()
numSlices = int(round(image.getStackSize() * cal.pixelDepth / pixelDepth))
newStack = ImageStack(w, h)
for z in range(numSlices):
currentPos = z * pixelDepth
ind_p = int(currentPos / cal.pixelDepth)
ind_n = ind_p + 1
d_p = currentPos - ind_p * cal.pixelDepth
d_n = ind_n * cal.pixelDepth - currentPos
if ind_n >= stack.getSize():
ind_n = stack.getSize() - 1
before = stack.getProcessor(ind_p + 1).duplicate()
after = stack.getProcessor(ind_n + 1).duplicate()
before.multiply(d_n / (d_n + d_p))
after.multiply(d_p / (d_n + d_p))
before.copyBits(after, 0, 0, Blitter.ADD)
newStack.addSlice("", before)
result = ImagePlus("Resliced", newStack)
cal = cal.copy()
cal.pixelDepth = pixelDepth
result.setCalibration(cal)
return result
def run():
sId = IJ.getString("Filenames contain:", "T0000");
srcDir = DirectoryChooser("Choose!").getDirectory()
if not srcDir:
# user canceled dialog
return
# Assumes all files have the same size
stack = None
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-TIFF files
if not (sId in filename):
continue
print(filename)
path = os.path.join(root, filename)
# Upon finding the first image, initialize the VirtualStack
imp = IJ.openImage(path)
if stack is None:
# stack = VirtualStack(imp.width, imp.height, None, srcDir)
stack = ImageStack(imp.width, imp.height)
# Add a slice to the virtual stack, relative to the srcDir
#
#stack.addSlice(path[len(srcDir):])
# Add a slice to the real stack
#
stack.addSlice(filename, imp.getProcessor())
# Make a ImagePlus from the stack
ImagePlus("Stack from subdirectories", stack).show()
def z_stack_opener(path, numberOfSlices="1", file_name_string="%s-Site_%s_%s_z%s.tif", file_name_variables=[]):
"""
Opens a series of tifs into a stack.
args:
path -- path to files
numberOfSlices -- the number of slices to open min 1
file_name_string -- string with %s formating spaces, z must be last
file_name_variables -- list of variables to fill in %s spaces
returns:
z_stack -- imageJ stack -- stack of processors
paths -- list of paths to the files that were opened
"""
paths = []
full_file_name_string = os.path.join(path, file_name_string)
## open the first slice
all_name_variables = tuple(file_name_variables + ["1"])
img = IJ.openImage(full_file_name_string % all_name_variables)
## open a stack
z_stack = ImageStack(img.width, img.height)
z_stack.addSlice(file_name_string % all_name_variables, img.getProcessor())
paths.append(full_file_name_string % all_name_variables)
## open the other slices
for i in range(2, numberOfSlices + 1):
sliceNameVariables = tuple(file_name_variables + [str(i)])
img = IJ.openImage(full_file_name_string % sliceNameVariables)
z_stack.addSlice(file_name_string % sliceNameVariables, img.getProcessor())
paths.append(full_file_name_string % sliceNameVariables)
return z_stack, paths
def getCroppedChannels(self, imp, cell):
splitter = ChannelSplitter()
imp.setRoi(None)
if cell.mode3D:
cropRoi = cell.getCropRoi()
else:
cropRoi = cell.roi
if cropRoi is None:
return None
crop = cropRoi.getBounds()
channels = []
for c in range(1, imp.getNChannels() + 1):
slices = ImageStack(crop.width, crop.height)
channel = splitter.getChannel(imp, c)
for z in range(1, channel.getSize() + 1):
zslice = channel.getProcessor(z)
zslice.setRoi(cropRoi)
nslice = zslice.crop()
if cell.mode3D:
oroi = cell.slices[z - 1].roi
else:
oroi = cell.roi
if oroi is not None:
roi = oroi.clone()
bounds = roi.getBounds()
roi.setLocation(bounds.x - crop.x, bounds.y - crop.y)
nslice.setColor(Color.black)
nslice.fillOutside(roi)
slices.addSlice(nslice)
channels.append(ImagePlus("Channel %i" % c, slices))
return channels
def outline(imp3, originalTitle):
#clij implementation
"""
src=clij2.push(imp3)
dst=clij2.create(src)
dst2=clij2.create(src)
clij2.detectLabelEdges(src,dst)
clij2.binaryNot(dst,dst2)
clij2.multiplyImages(src, dst2, dst)
imp4=clij2.pull(dst)
imp4.show()
clij2.clear()
"""
imp2 = imp3.duplicate()
stack1 = imp3.getStack()
width = imp3.getWidth()
height = imp3.getHeight()
stack2 = ImageStack(width, height)
pixlist = []
for i in range(imp3.getNSlices()):
pixlist = []
pixels1 = stack1.getPixels(i + 1)
#if pixel is different to the pixel to the left or above, set it to 0
pixels2 = map(
lambda j: pixels1[j] if pixels1[j] - pixels1[j - 1] == 0 and
pixels1[j] - pixels1[j - width] == 0 else 0, xrange(len(pixels1)))
processor = FloatProcessor(width, height, pixels2, None)
stack2.addSlice(processor)
imp2 = ImagePlus("Nearest point emission ratios of " + originalTitle,
stack2)
imp2.show()
return imp2
def run():
sId = IJ.getString("Filenames contain:", "T0000")
srcDir = DirectoryChooser("Choose!").getDirectory()
if not srcDir:
# user canceled dialog
return
# Assumes all files have the same size
stack = None
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-TIFF files
if not (sId in filename):
continue
print(filename)
path = os.path.join(root, filename)
# Upon finding the first image, initialize the VirtualStack
imp = IJ.openImage(path)
if stack is None:
# stack = VirtualStack(imp.width, imp.height, None, srcDir)
stack = ImageStack(imp.width, imp.height)
# Add a slice to the virtual stack, relative to the srcDir
#
#stack.addSlice(path[len(srcDir):])
# Add a slice to the real stack
#
stack.addSlice(filename, imp.getProcessor())
# Make a ImagePlus from the stack
ImagePlus("Stack from subdirectories", stack).show()
def images_to_frames_stack(imgdir, savestack=False):
'''
Method for preparing a stack of frames using images inside the input folder.
When savestack is true it saves the resulting stack to the images folder while opening the stack.
'''
title = "tracing_stack.tiff" # Title of the final image stack.
imgdir = imgdir.getPath()
imglist = buildList(imgdir, ext)
if not imglist:
raise IOError("No {0} were found in {0}.".format(ext, imgdir))
method = "max"
implist = []
for img in imglist:
imp = ImagePlus(img)
if imp.isStack():
imp = ZProjector.run(imp, method)
implist.append(imp)
stack = ImageStack(
implist[0].getWidth(),
implist[0].getHeight())
[stack.addSlice(img.getProcessor()) for img in implist]
stackimp = ImagePlus(title, stack)
IJ.run(stackimp, "Properties...", "slices=1 frames={0}".format(stackimp.getStackSize()))
if savestack:
IJ.log("# Saving tracing stack...")
save_string = os.path.join(imgdir, title)
fs = ThreadedFileSaver.ThreadedFileSaver(stackimp, save_string, "saveAsTiff")
fs.start()
stackimp.show()
def threshold(imPlus, edgeThreshold=2500):
mask = Duplicator().run(imPlus)
mask_stk = mask.getStack()
# First, we threshold based on edges
IJ.setThreshold(mask, edgeThreshold, 100000, "No Update")
for i in range(mask.getImageStackSize()):
mask_stk.getProcessor(i + 1).findEdges()
IJ.run(mask, "Make Binary", "method=Default background=Default black")
# Now, we need to clean up the binary images morphologically
IJ.run(mask, "Dilate", "stack")
IJ.run(mask, "Fill Holes", "stack")
IJ.run(mask, "Erode", "stack")
IJ.run(mask, "Erode", "stack")
# Finally, remove the small particles
stk = ImageStack(mask.getWidth(), mask.getHeight())
p = PA(PA.SHOW_MASKS, 0, None, 200, 100000)
p.setHideOutputImage(True)
for i in range(mask_stk.getSize()):
mask.setSliceWithoutUpdate(i + 1)
p.analyze(mask)
mmap = p.getOutputImage()
stk.addSlice(mmap.getProcessor())
mask.setStack(stk)
mask.setSliceWithoutUpdate(1)
mask.setTitle(mask_title(imPlus.getTitle()))
mask.show()
return mask
def segmentNuc(impc2):
impdup = Duplicator().run(impc2)
IJ.run(impdup, "8-bit", "")
IJ.run(impdup, "Gaussian Blur...", "sigma=1.5 stack")
# AutoThresholder().getThreshold(AutoThresholder.Method.valuOf('Otsu'), int[] histogram)
IJ.setAutoThreshold(impdup, "Otsu dark")
IJ.run(impdup, "Convert to Mask", "stack")
#IJ.setAutoThreshold(impdup, "Otsu dark")
#opt = PA.SHOW_MASKS + PA.SHOW_RESULTS + PA.EXCLUDE_EDGE_PARTICLES + PA.INCLUDE_HOLES # option for stack missing
opt = PA.SHOW_MASKS + PA.EXCLUDE_EDGE_PARTICLES + PA.INCLUDE_HOLES # option for stack missing
##area mean centroid bounding integrated stack redirect=None decimal=4
meas = Meas.AREA + Meas.MEAN + Meas.CENTROID + Meas.RECT + Meas.INTEGRATED_DENSITY + Meas.STACK_POSITION
rt = ResultsTable().getResultsTable()
pa = PA(opt, meas, rt, 10.0, 300000.0, 0, 1.0)
PA.processStack = True
pa.setHideOutputImage(True)
##run("Analyze Particles...", "size=800-Infinity circularity=0.00-1.00 pixel show=Masks display exclude include stack");
outstack = ImageStack(impdup.getWidth(), impdup.getHeight())
for i in range(1,impdup.getStackSize()+1):
impdup.setSlice(i)
pa.analyze(impdup)
impbin = pa.getOutputImage()
outstack.addSlice(impbin.getProcessor())
impbin = ImagePlus("out", outstack)
IJ.run(impbin, "Invert LUT", "")
#IJ.run(impbin, "Fill Holes", "stack")
return impbin, rt
def thresholdStackW(imp, low, high):
i = 1
stack = imp.getStack()
depth = imp.getNSlices()
print "thresholdStackW: depth", depth
width = stack.getProcessor(i).getWidth()
height = stack.getProcessor(i).getHeight()
winput = [None]
w = Weaver.inline(
"""
byte[] input = (byte[]) winput.get(0);
byte[] output = new byte[input.length];
for (int i=0; i<input.length; i++) {
if (input[i] < low || input[i] > high){
output[i] = (byte)0;
} else {
output[i] = (byte)255;
}
}
return output;
""",
{"winput":winput, "low":low, "high":high})
stackout = ImageStack(width, height)
for k in range(1, depth+1):
ip = stack.getProcessor(k)
winput[0] = ip.getPixels()
pixels = w.call()
ipout = ByteProcessor(width, height)
ipout.setPixels(pixels)
stackout.addSlice(ipout)
imp.setStack(stackout)
def GlidingSubtracter(imp):
name = imp.getTitle()
width, height, nChannels, nSlices, nFrames = imp.getDimensions()
IJ.log("nFrames: {}".format(nFrames))
# Catch wrong input dimensions.
if nChannels != 1:
IJ.log("GlidingSubtracter only takes single channel images.")
return None
if nFrames <= 1:
IJ.log("Stack has <= 1 frame. Perhaps switch Frames and Slices?")
return None
instack = imp.getImageStack()
outstack = ImageStack()
frame1 = instack.getProcessor(1)
frame1 = ImagePlus("frame1", frame1)
for i in range(1, nFrames):
frame2 = instack.getProcessor(i)
frame2 = ImagePlus("frame2", frame2)
subtracted = ImageCalculator().run("subtract create 32-bit", frame1,
frame2).getProcessor()
# ImagePlus("slice", subtracted).show()
outstack.addSlice(subtracted)
outname = "subtract-" + name
outstack = ImagePlus(outname, outstack)
return outstack
def extractChannel(imp, nChannel, nFrame):
""" Extract a stack for a specific color channel and time frame """
stack = imp.getImageStack()
ch = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
index = imp.getStackIndex(nChannel, i, nFrame)
ch.addSlice(str(i), stack.getProcessor(index))
return ImagePlus("Channel " + str(nChannel), ch)
def extractChannel(imp, nChannel, nChannels):
""" Extract a stack for a specific color channel """
stack = imp.getImageStack()
ch = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
index = (i - 1) * nChannels + nChannel
ch.addSlice(str(i), stack.getProcessor(index))
return ImagePlus("Channel " + str(nChannel), ch)
def stack_from_list_of_imp(list_of_imps):
''' Returns an ImageStack that contains the images of the given list.
:param list_of_imp: A list of ImagePlus objects.
'''
stack = ImageStack(list_of_imps[0].getWidth(), list_of_imps[0].getHeight())
for img in list_of_imps:
stack.addSlice(img.getTitle(), img.getProcessor())
return stack
def extractChannel(imp, nChannel, nFrame):
""" Extract a stack for a specific color channel and time frame """
stack = imp.getImageStack()
ch = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
index = imp.getStackIndex(nChannel, i, nFrame)
ch.addSlice(str(i), stack.getProcessor(index))
return ImagePlus("Channel " + str(nChannel), ch)
def extract_stack_under_arealist():
# Check that a Display is open
display = Display.getFront()
if display is None:
IJ.log("Open a TrakEM2 Display first!")
return
# Check that an AreaList is selected and active:
ali = display.getActive()
if ali is None or not isinstance(ali, AreaList):
IJ.log("Please select an AreaList first!")
return
# Get the range of layers to which ali paints:
ls = display.getLayerSet()
ifirst = ls.indexOf(ali.getFirstLayer())
ilast = ls.indexOf(ali.getLastLayer())
layers = display.getLayerSet().getLayers().subList(ifirst, ilast +1)
# Create a stack with the dimensions of ali
bounds = ali.getBoundingBox()
stack = ImageStack(bounds.width, bounds.height)
# Using 16-bit. To change to 8-bit, use GRAY8 and ByteProcessor in the two lines below:
type = ImagePlus.GRAY16
ref_ip = ShortProcessor(bounds.width, bounds.height)
for layer in layers:
area = ali.getArea(layer)
z = layer.getZ()
ip = ref_ip.createProcessor(bounds.width, bounds.height)
if area is None:
stack.addSlice(str(z), bp)
continue
# Create a ROI from the area of ali at layer:
aff = ali.getAffineTransformCopy()
aff.translate(-bounds.x, -bounds.y)
roi = ShapeRoi(area.createTransformedArea(aff))
# Create a cropped snapshot of the images at layer under ali:
flat = Patch.makeFlatImage(type, layer, bounds, 1.0, layer.getDisplayables(Patch), Color.black)
b = roi.getBounds()
flat.setRoi(roi)
ip.insert(flat.crop(), b.x, b.y)
# Clear the outside of ROI (ShapeRoi is a non-rectangular ROI type)
bimp = ImagePlus("", ip)
bimp.setRoi(roi)
ip.setValue(0)
ip.setBackgroundValue(0)
IJ.run(bimp, "Clear Outside", "")
# Accumulate slices
stack.addSlice(str(z), ip)
imp = ImagePlus("AreaList stack", stack)
imp.setCalibration(ls.getCalibrationCopy())
imp.show()
def extractFrames(imp, interval, offset, nFrames):
""" Extract a stack containing a subset of frames from a stack """
stack = imp.getImageStack()
man = ImageStack(imp.width, imp.height)
for i in range(0, nFrames):
index = imp.getStackIndex(0, 1, i * interval + offset)
man.addSlice(stack.getProcessor(index))
return ImagePlus("Manual_" + filename, man)
def analyzeParticles(imp, minsize, maxsize, mincirc, maxcirc,
filename='Test.czi',
addROIManager=True,
headless=True,
exclude=True):
if addROIManager is True:
if exclude is False:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_MANAGER \
+ PA.ADD_TO_OVERLAY \
if exclude is True:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_MANAGER \
+ PA.ADD_TO_OVERLAY \
+ PA.EXCLUDE_EDGE_PARTICLES
if addROIManager is False:
if exclude is False:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_OVERLAY \
if exclude is True:
options = PA.SHOW_ROI_MASKS \
+ PA.SHOW_RESULTS \
+ PA.DISPLAY_SUMMARY \
+ PA.ADD_TO_OVERLAY \
+ PA.EXCLUDE_EDGE_PARTICLES
measurements = PA.STACK_POSITION \
+ PA.LABELS \
+ PA.AREA \
+ PA.RECT \
results = ResultsTable()
p = PA(options, measurements, results, minsize, maxsize, mincirc, maxcirc)
p.setHideOutputImage(True)
particlestack = ImageStack(imp.getWidth(), imp.getHeight())
for i in range(imp.getStackSize()):
imp.setSliceWithoutUpdate(i + 1)
ip = imp.getProcessor()
#IJ.run(imp, "Convert to Mask", "")
p.analyze(imp, ip)
mmap = p.getOutputImage()
particlestack.addSlice(mmap.getProcessor())
return particlestack, results
def run(title):
gd = GenericDialog('Record Desktop')
gd.addNumericField('Max. frames:', 50, 0)
gd.addNumericField('Milisecond interval:', 300, 0)
gd.addSlider('Start in (seconds):', 0, 20, 5)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
delay = int(gd.getNextNumber())
snaps = []
try:
while delay > 0:
IJ.showStatus('Starting in ' + str(delay) + 's.')
time.sleep(1) # one second
delay -= 1
IJ.showStatus('')
System.out.println("Starting...")
# start capturing
robot = Robot()
box = Rectangle(IJ.getScreenSize())
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
# Initial shot
snaps.append(robot.createScreenCapture(box))
while len(snaps) < n_frames and last - start < n_frames * interval:
now = System.currentTimeMillis() / 1000.0 # in seconds
real_interval = now - last
if real_interval >= interval:
last = now
snaps.append(robot.createScreenCapture(box))
intervals.append(real_interval)
else:
time.sleep(interval / 5) # time in seconds
# Create stack
System.out.println("End")
awt = snaps[0]
stack = ImageStack(awt.getWidth(None), awt.getHeight(None), None)
t = 0
for snap, real_interval in zip(snaps, intervals):
stack.addSlice(str(IJ.d2s(t, 3)),
ImagePlus('', snap).getProcessor())
snap.flush()
t += real_interval
ImagePlus("Desktop recording", stack).show()
except Exception, e:
print "Some error ocurred:"
print e
for snap in snaps:
snap.flush()
def assembleChannelImagesInStacks(imageTitle, arrayOfImages, valeurSelectionDisplayMode, valeurSelectionTypeFichier):
maxNumberOfChannels = len(arrayOfImages)
maxNumberOfZDepth = 1;
maxNumberOfTimeStamps = 1;
print("assembleChannelImagesInStacks - arrayOfImages: "+str(arrayOfImages))
for channelNumber in range(len(arrayOfImages)):
if valeurSelectionTypeFichier == "1 fichier par canal (NOM_FICHIER_chXX.tif)":
numberOfZDepth = len(arrayOfImages[channelNumber])
if numberOfZDepth > maxNumberOfZDepth:
maxNumberOfZDepth = numberOfZDepth
if valeurSelectionTypeFichier == "1 fichier par canal + temps (NOM_FICHIER_tXX_chXX.tif)":
numberOfZDepth = len(arrayOfImages[channelNumber])
if numberOfZDepth > maxNumberOfZDepth:
maxNumberOfZDepth = numberOfZDepth
for zNumber in range(len(arrayOfImages[channelNumber])):
numberOfTime = len(arrayOfImages[channelNumber][zNumber])
if numberOfTime > maxNumberOfTimeStamps:
maxNumberOfTimeStamps = numberOfTime
if valeurSelectionTypeFichier == "1 fichier par canal et par profondeur (NOM_FICHIER_zXX_chXX.tif)":
numberOfZDepth = len(arrayOfImages[channelNumber])
if numberOfZDepth > maxNumberOfZDepth:
maxNumberOfZDepth = numberOfZDepth
if valeurSelectionTypeFichier == "1 fichier par canal et par profondeur + temps (NOM_FICHIER_tXX_zXX_chXX.tif)":
numberOfZDepth = len(arrayOfImages[channelNumber])
print(arrayOfImages[channelNumber])
if numberOfZDepth > maxNumberOfZDepth:
maxNumberOfZDepth = numberOfZDepth
for zNumber in range(len(arrayOfImages[channelNumber])):
print(arrayOfImages[channelNumber][zNumber])
numberOfTime = len(arrayOfImages[channelNumber][zNumber])
if numberOfTime > maxNumberOfTimeStamps:
maxNumberOfTimeStamps = numberOfTime
hyperStack = ImageStack()
#imageTitle = "HyperStack"
print("C: "+str(maxNumberOfChannels)+", Z: "+str(maxNumberOfZDepth)+", T: "+str(maxNumberOfTimeStamps))
for timeNumber in range(maxNumberOfTimeStamps):
for zDepthNumber in range(maxNumberOfZDepth):
for channelNumber in range(maxNumberOfChannels):
#print("Position: "+str(channelNumber)+", "+str(zDepthNumber)+", "+str(timeNumber))
currentImagePlus = arrayOfImages[channelNumber][zDepthNumber][timeNumber]
#print("ImagePlus: "+str(currentImagePlus))
currentImagePlus.setC(channelNumber)
currentImagePlus.setZ(zDepthNumber)
currentImagePlus.setT(timeNumber)
currentImageProcessor = currentImagePlus.getProcessor()
hyperStack.addSlice(currentImageProcessor)
hyperStackImagePlus = ImagePlus(imageTitle, hyperStack)
#hyperStackImagePlus.show()
if maxNumberOfChannels*maxNumberOfZDepth*maxNumberOfTimeStamps > 1:
converter = HyperStackConverter()
hyperStackImagePlus = converter.toHyperStack(hyperStackImagePlus, maxNumberOfChannels, maxNumberOfZDepth, maxNumberOfTimeStamps, valeurSelectionDisplayMode)
if valeurSelectionTypeFichier == "1 fichier par canal + temps (NOM_FICHIER_tXX_chXX.tif)":
hyperStackImagePlus = converter.toHyperStack(hyperStackImagePlus, maxNumberOfChannels, maxNumberOfTimeStamps, maxNumberOfZDepth, "xyctz", valeurSelectionDisplayMode);
return hyperStackImagePlus
def extract_frame(imp, frame, channel):
""" From a VirtualStack that is a hyperstack, contained in imp,
extract the timepoint frame as an ImageStack, and return it.
It will do so only for the given channel. """
stack = imp.getStack() # multi-time point virtual stack
vs = ImageStack(imp.width, imp.height, None)
for s in range(1, imp.getNSlices()+1):
i = imp.getStackIndex(channel, s, frame)
vs.addSlice(str(s), stack.getProcessor(i))
return vs
def SplitImage(ip, width, height): stack = ImageStack(width, height) for x in range(0,ip.width,width): for y in range(0,ip.height,height): roi = Roi(x,y,width,height) ip.setRoi(roi) ip2 = ip.crop() stack.addSlice(None, ip2) return stack
def get_substack(theImage,startSlice,endSlice):
retStack = ImageStack(theImage.getWidth(),theImage.getHeight())
for i in range(startSlice,endSlice+1):
theImage.setSliceWithoutUpdate(i)
ip = theImage.getProcessor()
newip = ip.duplicate()
retStack.addSlice(newip)
return(ImagePlus("dataimage",retStack))
def find_maxima_stack(imp, tolerance):
stack = imp.getImageStack()
stack_out = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
ip = stack.getProcessor(i)
# findMaxima(ImageProcessor ip, double tolerance, double threshold, int outputType, boolean excludeOnEdges, boolean isEDM)
ip_max = MaximumFinder().findMaxima(ip, tolerance, ImageProcessor.NO_THRESHOLD, MaximumFinder.IN_TOLERANCE, False, False)
stack_out.addSlice(str(i), ip_max)
#segip.invert()
return ImagePlus("Maxima", stack_out)
def SplitImage(ip, width, height):
stack = ImageStack(width, height)
for x in range(0, ip.width, width):
for y in range(0, ip.height, height):
roi = Roi(x, y, width, height)
ip.setRoi(roi)
ip2 = ip.crop()
stack.addSlice(None, ip2)
return stack
def find_maxima_stack(imp, tolerance):
stack = imp.getImageStack()
stack_out = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
ip = stack.getProcessor(i)
# findMaxima(ImageProcessor ip, double tolerance, double threshold, int outputType, boolean excludeOnEdges, boolean isEDM)
ip_max = MaximumFinder().findMaxima(ip, tolerance, ImageProcessor.NO_THRESHOLD, MaximumFinder.IN_TOLERANCE, False, False)
stack_out.addSlice(str(i), ip_max)
#segip.invert()
return ImagePlus("Maxima", stack_out)
def run(title):
gd = GenericDialog("Record Desktop")
gd.addNumericField("Max. frames:", 50, 0)
gd.addNumericField("Milisecond interval:", 300, 0)
gd.addSlider("Start in (seconds):", 0, 20, 5)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
delay = int(gd.getNextNumber())
snaps = []
try:
while delay > 0:
IJ.showStatus("Starting in " + str(delay) + "s.")
time.sleep(1) # one second
delay -= 1
IJ.showStatus("")
System.out.println("Starting...")
# start capturing
robot = Robot()
box = Rectangle(IJ.getScreenSize())
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
# Initial shot
snaps.append(robot.createScreenCapture(box))
while len(snaps) < n_frames and last - start < n_frames * interval:
now = System.currentTimeMillis() / 1000.0 # in seconds
real_interval = now - last
if real_interval >= interval:
last = now
snaps.append(robot.createScreenCapture(box))
intervals.append(real_interval)
else:
time.sleep(interval / 5) # time in seconds
# Create stack
System.out.println("End")
awt = snaps[0]
stack = ImageStack(awt.getWidth(None), awt.getHeight(None), None)
t = 0
for snap, real_interval in zip(snaps, intervals):
stack.addSlice(str(IJ.d2s(t, 3)), ImagePlus("", snap).getProcessor())
snap.flush()
t += real_interval
ImagePlus("Desktop recording", stack).show()
except Exception, e:
print "Some error ocurred:"
print e
for snap in snaps:
snap.flush()
def rot_around_x(input_stack): """do rotation around x axis""" output_slices = input_stack.getHeight(); output_width = input_stack.getWidth(); output_height = input_stack.getSize(); output_stack = ImageStack(output_width, output_height); for yidx in range(input_stack.getHeight()): IJ.showProgress(float(yidx)/output_slices); output_stack.addSlice(FloatProcessor(output_width, output_height, input_stack.getVoxels(0, yidx, 0, output_width, 1, output_height, []))); IJ.showProgress(1.0); return output_stack;
def make_tiled_imp(imp):
"""generate a ImageProcessor that is the input tiled 3 time horizontally"""
ip = imp.getProcessor()
stack = ImageStack(imp.getWidth(), imp.getHeight())
for idx in range(3):
stack.addSlice(ip)
temp_imp = ImagePlus("temp", stack)
tile_imp = MontageMaker().makeMontage2(temp_imp, 3, 1, 1, 1, 3, 1, 0,
False)
temp_imp.close()
return tile_imp
def multiply(imp, value):
# check: http://rsb.info.nih.gov/ij/plugins/stack-contrast/index.htm
stack = imp.getImageStack()
stack_out = ImageStack(imp.width, imp.height)
nz = stack.getSize()
for iz in range(1, nz + 1):
ip_out = stack.getProcessor(iz).duplicate()
#print iz, correction
ip_out.multiply(value)
stack_out.addSlice(str(iz), ip_out)
#segip.invert()
return ImagePlus("Multiplied", stack_out)
def stackFromPaths(paths):
firstIm = IJ.openImage(paths[0])
width = firstIm.getWidth()
height = firstIm.getHeight()
firstIm.close()
ims = ImageStack(width, height) # assemble the ImageStack of the channel
for path in paths:
ims.addSlice(IJ.openImage(path).getProcessor())
imp = ImagePlus('Title', ims)
imp.setDimensions(1, 1, len(paths)) # these have to be timeframes for trackmate
return imp
def generateRotations(imp, backgroundValue):
# Generate stack of rotations with noise
ip = imp.getProcessor()
rotations = ImageStack(ip.getWidth(), ip.getHeight())
for i in xrange(10): # up to 90 degrees
ipr = ip.duplicate()
ipr.setInterpolationMethod(ImageProcessor.BILINEAR)
ipr.setBackgroundValue(backgroundValue)
ipr.rotate(i * 10)
ipr.noise(25) # sd = 25
rotations.addSlice(ipr)
return rotations
def extractChannel(imp, nChannel, nFrame):
"""extract a channel from the image, at a given frame returning a new imagePlus labelled with the channel name"""
stack = imp.getImageStack()
ch = ImageStack(imp.width, imp.height)
for i in range(imp.getNSlices()):
index = imp.getStackIndex(nChannel, i, nFrame)
ch.addSlice(str(i), stack.getProcessor(index))
imp3 = ImagePlus("Channel " + str(nChannel), ch).duplicate()
stats = StackStatistics(imp3)
IJ.setMinAndMax(imp3, stats.min, stats.max)
return imp3
def extract_channel_frame(imp, nChannel, nFrame, title=""):
""" Extract a stack for a specific color channel and timeframe """
# todo: preserve spatial calibration
stack = imp.getImageStack()
ch = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
index = imp.getStackIndex(nChannel, i, nFrame)
ch.addSlice(str(i), stack.getProcessor(index))
if title:
imp_out = ImagePlus(title, ch)
else:
imp_out = ImagePlus("Channel " + str(nChannel), ch)
return imp_out
def createChannel(darray, h, w, z, nChannel):
""" Create a stack for a specific color channel """
ch = ImageStack(w, h)
# imp = ImagePlus("my new image", FloatProcessor(w, h))
# fp = imp.getProcessor()
# fparray = zeros(w,h,'f')
for i in range(0, z):
# fparray[:][:]=doutarray[:][:][nChannel][i]
# fp.setFloatArray(fparray)
ch.addSlice(
str(i),
FloatProcessor(w, h, [doutarray[:][:][nChannel][i].tolist()]))
return ImagePlus("Channel " + str(nChannel), ch)
def __end(self, event):
if len(self.__iplist)==0 :
IJ.showMessage("", "Stack is empty")
return
self.__iplist.sort(key = lambda ip : ip.width)
self.__ipw=[ ip.getWidth() for ip in self.__iplist ]
self.__iph=[ ip.getHeight() for ip in self.__iplist ]
maxw=max(self.__ipw)
maxh=max(self.__iph)
if self.__enlarge :
resizelist = [ ip.resize(maxw, maxh, True) for ip in self.__iplist ]
else :
resizelist = []
for ip in self.__iplist :
tempip = ShortProcessor(maxw, maxh)
xloc = int(math.floor((maxw/2.00) - (ip.width/2.00)))
yloc = int(math.floor((maxh/2.00) - (ip.height/2.00)))
tempip.copyBits(ip, xloc, yloc, Blitter.COPY)
resizelist.append(tempip)
ims = ImageStack(maxw, maxh)
#for ip in resizelist : ims.addSlice("", ip)
for i in range(len(resizelist)) :
ims.addSlice(self.__labels[i], resizelist[i])
self.__impRes = ImagePlus(self.__name, ims)
self.__impRes.show()
self.__sens = [1 for i in range(len(self.__iplist)) ]
if self.__appmedian : IJ.run(self.__impRes, "Median...", "radius=1 stack")
if self.__align : self.__falign()
if self.__avg : self.__favg()
if self.__mosa : self.__fmosa()
if self.__maxfinder : self.__fmaxfinder()
if self.__fire : IJ.run(self.__impRes, "Fire", "")
if self.__measures : self.__fmeasures()
self.__sens[:] = []
self.__listrois[:] = []
self.__iplist[:] = []
self.__cellsrois[:] = []
self.__ipw[:] = []
self.__iph[:] = []
self.__init = False
def extractFrame(imp, nFrame):
"""extract a frame from the image, returning a new 16 bit imagePlus labelled with the channel name"""
stack = imp.getImageStack()
fr = ImageStack(imp.width, imp.height)
for i in range(1, imp.getNSlices() + 1):
for nChannel in range(1, imp.getNChannels() + 1):
index = imp.getStackIndex(nChannel, i, nFrame)
fr.addSlice(str(i), stack.getProcessor(index))
imp3 = ImagePlus("Frame " + str(nFrame), fr).duplicate()
imp3.setDimensions(imp.getNChannels(), imp.getNSlices(), 1)
comp = CompositeImage(imp3, CompositeImage.COMPOSITE)
comp.show()
return comp
def openUnstitched(group):
print(group)
ipArr = []
frameNo = 1
frameNoLink = {}
nucIpArr = []
cmIpArr = []
for g in group:
checkKeys = {k:g[k] for k in g if k not in ["channel", "fileName"]}
existsNuc = False
existsCm = False
for gg in group:
checkKeys2 = {k:g[k] for k in g if k not in ["channel", "fileName"]}
if checkKeys2:
if gg['channel'] == nucChannel: existsNuc = True
elif gg['channel'] == cmChannel: existsCm = True
if not (existsCm and existsNuc): continue
fileName = g['fileName']
channel = g['channel']
checkKeys
if channel == nucChannel: nucIpArr.append(opener.openImage(folderPath + fileName))
elif channel == cmChannel: cmIpArr.append(opener.openImage(folderPath + fileName))
nucStack = ImageStack(nucIpArr[0].width, cmIpArr[0].height)
cmStack = ImageStack(nucIpArr[0].width, cmIpArr[0].height)
for nucIp, cmIp in nucIpArr, cmIpArr:
nucStack.addSlice(nucIp.getTitle(), nucIp.getProcessor())
cmStack.addSlice(cmIp.getTitle(), cmIp.getProcessor())
nucIp = ImagePlus("images{}".format(fileName), nucIpArr[0].getProcessor())
cmIp = ImagePlus("images{}".format(fileName), cmIpArr[0].getProcessor())
nucIp.setStack(nucStack)
cmIp.setStack(cmStack)
return nucIp, cmIp
def run_script(imp, close, far, cutoff):
stack = imp.getImageStack()
fin_stack = ImageStack(imp.width, imp.height)
# iterate each slice in the stack
for i in range(1, stack.getSize() + 1):
# get progress
IJ.showProgress(i, stack.getSize() + 1)
# image processor converted to float to avoid byte problems
ip = stack.getProcessor(i).convertToFloat()
# pixels points to the array of floats
pixels = ip.getPixels()
# initial subtraction
stddev = initial_subtract(pixels, imp.width, imp.height)
mask = [255] * (imp.width * imp.height)
# mask borders of image dependent on settings
if far:
fringe_mask(mask, imp.width, 2)
elif close:
fringe_mask(mask, imp.width, 1)
else:
pass
# update mask
if close:
init_mask(pixels, mask)
close_subtract(pixels, mask, imp.width, cutoff, stddev)
if far:
init_mask(pixels, mask)
far_subtract(pixels, mask, imp.width, cutoff, stddev)
if close or far:
apply_mask(pixels, mask)
fin_stack.addSlice(None,
FloatProcessor(imp.width, imp.height, pixels, None))
# create new image from final stack
imp_fin = ImagePlus(imp.title[:-4] + "_background-subtracted.tif",
fin_stack)
# keep the same image calibration
imp_fin.setCalibration(imp.getCalibration().copy())
imp_fin.show()
IJ.showProgress(1) # show progess bar
def attenuation_correction(imp, intensity_zmin, intensity_zmax):
# check: http://rsb.info.nih.gov/ij/plugins/stack-contrast/index.htm
stack = imp.getImageStack()
stack_out = ImageStack(imp.width, imp.height)
a = intensity_zmin
b = intensity_zmax
nz = imp.getNSlices()
for iz in range(1, nz + 1):
ip_out = stack.getProcessor(iz).duplicate()
correction = (a+b)/2 * (1/(a-(a-b)*(iz-1)/(nz-1)))
#print iz, correction
ip_out.multiply(correction)
stack_out.addSlice(str(iz), ip_out)
#segip.invert()
return ImagePlus("Attenuation_corrected", stack_out)
def attenuation_correction(imp, intensity_zmin, intensity_zmax):
# check: http://rsb.info.nih.gov/ij/plugins/stack-contrast/index.htm
stack = imp.getImageStack()
stack_out = ImageStack(imp.width, imp.height)
a = intensity_zmin
b = intensity_zmax
nz = imp.getNSlices()
for iz in range(1, nz + 1):
ip_out = stack.getProcessor(iz).duplicate()
correction = (a+b)/2 * (1/(a-(a-b)*(iz-1)/(nz-1)))
#print iz, correction
ip_out.multiply(correction)
stack_out.addSlice(str(iz), ip_out)
#segip.invert()
return ImagePlus("Attenuation_corrected", stack_out)
def retrieve_dapi(image, channel):
# get stack from current image
stack = image.getStack()
#print(image.getStackSize(), stack.getSize())
final_stack = ImageStack(image.width, image.height)
for i in range(1, image.getStackSize() + 1):
countchannel = i % totchannels
#print(i, countchannel, countchannel in channels)
if (countchannel == channel):
myslice = stack.getProcessor(i)
final_stack.addSlice(str(i), myslice)
return final_stack
def nearestZProject(imp1):
relicedImp = Slicer().reslice(imp1)
relicedStack = relicedImp.getStack()
width = imp1.getWidth()
height = imp1.getHeight()
depth = imp1.getNSlices()
topPixels = zeros('f', width * height)
stack2 = ImageStack(width, height)
for i in range(1, relicedImp.getNSlices()):
pixels = relicedStack.getPixels(i)
for x in xrange(width):
for pixel in xrange(x, x + width * (depth - 1), width):
#after finding the first pixel above the threshold value, add the value to the list
if pixels[pixel] != 0:
topPixels[i * width + x] = pixels[pixel]
#break from looping the y when 1st threshold pixel is found is met -> increases speed drastically! Otherwise need an if statement every loop...
break
ip2 = FloatProcessor(width, height, topPixels, None)
imp2 = ImagePlus("Nearest point proj", ip2)
imp3 = imp2.resize(imp2.getWidth() * 2, imp2.getHeight() * 2, 'none')
return imp3
def orthoStackFrom4D(imp):
stkA = ArrayList()
for i in range(1, imp.getNFrames()+1):
e4d = Extractfrom4D()
e4d.setGstarttimepoint(i)
IJ.log("current time point" + str(i))
aframe = e4d.coreheadless(imp, 3)
ortho = XYZMaxProject(aframe)
orthoimp = ortho.getXYZProject()
stkA.add(orthoimp)
#orthoimp.show()
stk = ImageStack(stkA.get(0).getWidth(), stkA.get(0).getHeight())
for item in stkA:
stk.addSlice("slcie", item.getProcessor())
out = ImagePlus("out", stk)
return out
def retrieve_dapi(image, channel): # get stack from current image stack = image.getStack() #print(image.getStackSize(), stack.getSize()) final_stack = ImageStack(image.width, image.height) for i in range(1, image.getStackSize()+1): countchannel = i % totchannels #print(i, countchannel, countchannel in channels) if (countchannel == channel): myslice = stack.getProcessor(i) final_stack.addSlice(str(i), myslice) return final_stack
def concatenateImagePlus(files, outfile):
"""concatenate images contained in files and save in outfile"""
'''
if len(files) == 1:
IJ.log(files[0] + " has only one time point! Nothing to concatenate!")
return
'''
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
options.setOpenAllSeries(1)
options.setQuiet(1)
images = BF.openImagePlus(options)
imageG = images[0]
nrPositions = len(images)
options.setOpenAllSeries(0)
for i in range(0, nrPositions):
concatImgPlus = IJ.createHyperStack("ConcatFile", imageG.getWidth(), imageG.getHeight(), imageG.getNChannels(), imageG.getNSlices(), len(files), imageG.getBitDepth())
concatStack = ImageStack(imageG.getWidth(), imageG.getHeight())
IJ.showStatus("Concatenating files")
for file in files:
try:
IJ.log(" Add file " + file)
options.setSeriesOn(i,1)
options.setId(file)
image = BF.openImagePlus(options)[0]
imageStack = image.getImageStack()
sliceNr = imageStack.getSize()
for j in range(1, sliceNr+1):
concatStack.addSlice(imageStack.getProcessor(j))
image.close()
options.setSeriesOn(i,0)
except:
traceback.print_exc()
IJ.log(file + " failed to concatenate!")
IJ.showProgress(files.index(file), len(files))
concatImgPlus.setStack(concatStack)
concatImgPlus.setCalibration(image.getCalibration())
if len(images) > 1:
outfileP = addPositionName(i+1,outfile)
IJ.saveAs(concatImgPlus, "Tiff", outfileP)
else:
IJ.saveAs(concatImgPlus, "Tiff", outfile)
concatImgPlus.close()
def getDICfocus(imp):
stack = imp.getStack()
focusStack = ImageStack(W,H)
for t in range(1,T+1):
sd = [0 for z in range(Z+1)]
for z in range(1,Z+1): #get best focussed C2 (DIC) slices
ip = stack.getProcessor(imp.getStackIndex(2,z,t)).convertToFloat()
ip.findEdges()
sd[z] = ImageStatistics.getStatistics(ip, Measurements.STD_DEV, cal).stdDev
focusZ = sd.index(max(sd))
focusSlice = stack.getProcessor(imp.getStackIndex(2,focusZ,t)).convertToFloatProcessor()
focusStack.addSlice("Z"+str(focusZ), focusSlice)
#ImagePlus("DIC focus", focusStack).show()
#exit(0)
return focusStack
def calculateThreshold(image, roi, method):
if roi != None:
bounds = roi.getBounds()
stack = image.getStack()
newstack = ImageStack(bounds.width, bounds.height)
for i in xrange(1, stack.getSize() + 1):
ip = stack.getProcessor(i).duplicate()
ip.fillOutside(roi)
ip.setRoi(roi)
c = ip.crop()
newstack.addSlice(str(i), c)
imp = ImagePlus("ThresholdImage", newstack)
else:
imp = image
thresholder = Auto_Threshold()
result = thresholder.exec(imp, method, False, False, True, False, False, True)
return result
def make_montage(self, xy="", montage_name=""):
if self.channels_to_montage == None:
channels_to_montage = self.channel_names
else:
channels_to_montage = self.channels_to_montage
w = self.cropped_imps[self.channel_names[0]].width
h = self.cropped_imps[self.channel_names[0]].height
new_stack = ImageStack(w, h)
# print self.cropped_imps.keys()
for channel in channels_to_montage:
img = self.cropped_imps[channel].getProcessor()
new_stack.addSlice(img)
tomontage = ImagePlus("to montage", new_stack)
montager = MontageMaker()
self.montage = montager.makeMontage2(
tomontage, len(channels_to_montage), 1, 1, 1, len(channels_to_montage), 1, 0, 0
)
directory = self.outdir
file_name = self.name
save_as = os.path.join(directory, "%s_%s_montage.tif" % (file_name, xy))
IJ.save(self.montage, save_as)
def Extract_Red_Channel(color):
imp = IJ.getImage()
stack = imp.getImageStack()
print "number of slices:", imp.getNSlices()
# A list of red slices
reds = []
# Iterate each slice in the stack
for i in xrange(1, imp.getNSlices()+1):
# Get the ColorProcessor slice at index i
cp = stack.getProcessor(i)
# Get its green channel as a FloatProcessor
fp = cp.toFloat(0, None)
# ... and store it in a list
reds.append(fp)
# Create a new stack with only the green channel
stack2 = ImageStack(imp.width, imp.height)
for fp in reds:
stack2.addSlice(None, fp)
# Create a new image with the stack of green channel slices
imp2 = ImagePlus("Red channel", stack2)
# Set a green look-up table:
IJ.run(imp2, "Red", "")
imp2.show()
def rotateStack(imp, axis, radian):
modelM = AffineModel3D()
modelM.rotate(axis, radian)
print 'model: ', modelM.toString()
ww = imp.getWidth()
hh = imp.getHeight()
dd = imp.getImageStackSize()
mapping = InverseTransformMapping( modelM );
minA = jarray.Array.newInstance(Float.TYPE, 3)
maxA = jarray.Array.newInstance(Float.TYPE, 3)
minA[0] = 0.0
minA[1] = 0.0
minA[2] = 0.0
maxA[0] = ww-1
maxA[1] = hh-1
maxA[2] = dd-1
minA, maxA, destsizeA = ReCalcStackSize(modelM, minA, maxA)
print destsizeA[0], destsizeA[1], destsizeA[2]
nww = int(destsizeA[0])
nhh = int(destsizeA[1])
ndd = int(destsizeA[2])
ReCalcOffset(modelM, minA)
print 'recalculated model: ', modelM.toString()
ip = imp.getStack().getProcessor( 1 ).createProcessor( 1, 1 )
target = ImageStack(nww, nhh)
for s in range(ndd):
ip = ip.createProcessor(nww, nhh)
mapping.setSlice( s + 1)
mapping.mapInterpolated( imp.getStack(), ip )
target.addSlice( "", ip )
impout = ImagePlus("out", target)
return impout
# extracting stack time frames and convert to ortho
imp = IJ.getImage()
stkA = ArrayList()
for i in range(1, 4):
#for i in range(1, imp.getNFrames()):
e4d = Extractfrom4D()
e4d.setGstarttimepoint(i)
IJ.log("current time point" + str(i))
aframe = e4d.coreheadless(imp, 3)
ortho = XYZMaxProject(aframe)
orthoimp = ortho.getXYZProject()
stkA.add(orthoimp)
#orthoimp.show()
stk = ImageStack(stkA.get(0).getWidth(), stkA.get(0).getHeight())
for item in stkA:
stk.addSlice("slcie", item.getProcessor())
out = ImagePlus("out", stk)
#out.setCalibration(imp.getCalibration().copy())
IJ.run(out, "Grays", "");
IJ.run(out, "RGB Color", "");
# load data from file
filepath = '/Users/miura/Dropbox/Mette/20_23h/20_23hrfull_corrected_1_6_6_netdispZ40.csv'
filename = os.path.basename(filepath)
newfilename = os.path.join(os.path.splitext(filename)[0], '_plotStack.tif')
out.setTitle(os.path.basename(filename)+'_OutStack.tif')
PLOT_ONLY_IN_FRAME1 = False
def scaleandfilter(infile,outfile,scalex,scaley,scalez,anisofilter,runtube):
print ("infile is: "+infile)
imp = Opener().openImage(infile)
print imp
print "scalex = %f; scaley = %f ; scalez = %f" % (scalex,scaley,scalez)
# Rescale
cal = imp.getCalibration()
iml = ImgLib.wrap(imp)
scaledimg = Scale3D(iml, scalex, scaley, scalez)
imp2=ImgLib.wrap(scaledimg)
# find range of pixel values for scaled image
from mpicbg.imglib.algorithm.math import ComputeMinMax
# (for imglib2 will be: net.imglib2.algorithm.stats)
minmax=ComputeMinMax(scaledimg)
minmax.process()
(min,max)=(minmax.getMin().get(),minmax.getMax().get())
# Make a copy of the stack (converting to 8 bit as we go)
stack = ImageStack(imp2.width, imp2.height)
print "min = %e, max =%e" % (min,max)
for i in xrange(1, imp2.getNSlices()+1):
imp2.setSliceWithoutUpdate(i)
ip=imp2.getProcessor()
# set range
ip.setMinAndMax(min,max)
stack.addSlice(str(i), ip.convertToByte(True))
# save copy of calibration info
cal=imp.getCalibration()
# close original image
imp.close()
# make an image plus with the copy
scaled = ImagePlus(imp2.title, stack)
# Deal with calibration info which didn't seem to come along for the ride
cal.pixelWidth/=scalex
cal.pixelHeight/=scaley
cal.pixelDepth/=scalez
scaled.setCalibration(cal)
print "dx = %f; dy=%f; dz=%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
intif=infile+".tif"
outtif=infile+"-filtered.tif"
if anisofilter.upper() != 'FALSE':
print("saving input file as "+intif)
f=FileSaver(scaled)
f.saveAsTiffStack(intif)
scaled.close()
# anisotropic filtering
anisopts="-scanrange:10 -tau:2 -nsteps:2 -lambda:0.1 -ipflag:0 -anicoeff1:1 -anicoeff2:0 -anicoeff3:0"
anisopts=anisopts+" -dx:%f -dy:%f -dz:%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
if sys.version_info > (2, 4):
#for testing
# subprocess.check_call(["cp",intif,outtif])
subprocess.check_call([anisofilter]+anisopts.split(' ')+[intif,outtif])
else:
os.system(" ".join([anisofilter]+anisopts.split(' ')+[intif,outtif]))
# Open anisofilter output back into Fiji
print("Opening output tif: "+outtif)
scaled = Opener().openImage(outtif)
scaled.setCalibration(cal)
# Hessian (tubeness)
print("Running tubeness")
if(runtube):
tp=TubenessProcessor(1.0,False)
result = tp.generateImage(scaled)
IJ.run(result, "8-bit","")
else:
result=scaled
# Save out file
fileName, fileExtension = os.path.splitext(outfile)
print("Saving as "+fileExtension+": "+outfile)
if fileExtension.lower()=='.nrrd':
nw=Nrrd_Writer()
nw.setNrrdEncoding("gzip")
nw.save(result,outfile)
else:
# Save to PIC
IJ.run(result,"Biorad ...", "biorad=["+outfile+"]")
scaled.close()
result.close()
def run():
""" Loads an image stack which contains both reference and target images for the registration
Scales the images to have their largest side equal to longSide
Registration is performed:
- translation (brute force optimization)
- rotation (brute force optimization)
- sift registration
- bunwarpj registration
Calculation of the errors by different methods """
# load the input stack as an ImagePlus
imp = IJ.openImage(filePath.getAbsolutePath())
stack = imp.getStack()
sizeZ = imp.getStackSize()
LAND_MARKS = 0
# Copy the reference and target slice
refId = 1
ref = stack.getProcessor(refId).duplicate()
if (Scale == 1):
[ref, s] = scaleLongSide(ref, longSide)
sizeZ = min(sizeZ, maxSlice)
stackReg = ImageStack(ref.getWidth(), ref.getHeight())
stackReg.addSlice(ref)
# = stack.duplicate()
for i in range(2, sizeZ+1):
targetId = i
target = stack.getProcessor(targetId).duplicate()
# Scale the slices: scale the reference slice using the longSide parameter, and use the same scale for the target slice.
if (Scale == 1):
target = scale(target, s)
#ImagePlus('Ref',ref).show()
#ImagePlus('Target',target).show()
if (Reg == 1):
if (translationReg == 1):
target = translation(ref, target)
if (rotationReg == 1):
[rot, target] = rotationSingle(ref,target,rotationStep)
if (siftReg == 1):
[roiRef, roiTarget] = siftSingle(ref, target)
impTarget = ImagePlus('Target',target)
impTarget.setRoi(roiTarget)
#impTarget.show()
impRef = ImagePlus('Ref',ref)
impRef.setRoi(roiRef)
#impRef.show()
LAND_MARKS = 1
if (bunwarpjReg == 1):
target = bunwarpjSingle(impRef, impTarget, LAND_MARKS, 'direct_transfo_' + str(i) + '.txt', 'inverse_transfo_' + str(i) + '.txt')
impTarget = ImagePlus('unwarpj_target', target)
#impTarget.show()
fileName = 'target_id' + str(targetId) + '.tif'
IJ.saveAs(impTarget, "Tiff", os.path.join(saveDir.getAbsolutePath(), fileName))
#stackReg.setProcessor(target.convertToShortProcessor(), i)
stackReg.addSlice(target)
if (calculateError == 1):
eCorrelation = zeros(sizeZ, 'f')
eMSE = zeros(sizeZ, 'f')
eMSE_ROI = zeros(sizeZ, 'f')
eRMSE = zeros(sizeZ, 'f')
eNRMSE = zeros(sizeZ, 'f')
eCVRMSE = zeros(sizeZ, 'f')
for i in range(1, sizeZ+1):
ip = stackReg.getProcessor(i).duplicate()
#ImagePlus('test',ip).show()
eCorrelation[i-1], eMSE[i-1], eMSE_ROI[i-1], eRMSE[i-1], eNRMSE[i-1], eCVRMSE[i-1] = measureError(ref,ip)
errorFileName = 'error.txt'
errorFilePath = os.path.join(saveDir.getAbsolutePath(), errorFileName)
writeCSV( errorFilePath, [eCorrelation,eMSE, eMSE_ROI, eRMSE,eNRMSE,eCVRMSE], ["Correlation","MSE","MSE_ROI","RMSE","N_RMSE","CV_RMSE"] )
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())
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)
from java.io import File from ij import IJ,WindowManager,ImagePlus,ImageStack from ij.process import FloatProcessor path = "/home/ab/Dropbox/arabido/test/" imp = WindowManager.getCurrentImage() stack = imp.getStack() N_larg = 4 N_lon = 4 # 2 - Create a new stack to store the result new_stack = ImageStack(imp.width, imp.height) for i in range(1, imp.getNSlices()+1): slice = stack.getProcessor(i) red = slice.toFloat(0, None) green = slice.toFloat(1, None) blue = slice.toFloat(2, None) pix_red = red.getPixels() pix_green = green.getPixels() pix_blue = blue.getPixels() new_red = FloatProcessor(imp.width, imp.height) pix_new_red = new_red.getPixels() new_green = FloatProcessor(imp.width, imp.height) pix_new_green = new_green.getPixels()