def segCentrosome(imp):
IJ.run(imp, "Unsharp Mask...", "radius=20 mask=0.60");
#IJ.run(imp, "FeatureJ Laplacian", "compute smoothing=1.0");
fjimg = FJimage.wrap(imp)
fjimglap = Laplacian().run(fjimg, 1.0)
imp2 = fjimglap.imageplus()
IJ.run(imp2, "Invert", "")
IJ.run(imp2, "Unsharp Mask...", "radius=1 mask=0.60")
if TESTMODE == True:
imp2.show()
segip = MaximumFinder().findMaxima( imp2.getProcessor(), MAXFIND_TOLERANCE, ImageProcessor.NO_THRESHOLD, MaximumFinder.SINGLE_POINTS , False, False)
#IJ.run(imp2, "Find Maxima...", "noise=1800 output=[Single Points]")
return segip
def translate_using_imagescience(imp_tmpstack, dx, dy, dz): translator = Translate() output = translator.run(Image.wrap(imp_tmpstack), dx, dy, dz, Translate.LINEAR) return output.imageplus()
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)
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
# init
shift = shifts[frame-1]
registeredstackthisframe = ImageStack(width, height, imp.getProcessor().getColorModel())
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)))
# Add all slices of this frame
stack = imp.getStack()
for s in range(1, imp.getNSlices()+1):
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, 0, 0)
registeredstackthisframe.addSlice("", ip2)
# Pad the end (in z) of this frame
for s in range(imp.getNSlices(), slices):
for ch in range(1, imp.getNChannels()+1):
registeredstackthisframe.addSlice("", empty)
# Set correct dimensions as below Translate() function needs this
# ..it is important *not* to set the calibration as Translate() works with units if present
registeredstackthisframe_imp = ImagePlus("registered time points", registeredstackthisframe)
registeredstackthisframe_imp.setProperty("Info", imp.getProperty("Info"))
registeredstackthisframe_imp.setDimensions(imp.getNChannels(), slices, 1)
registeredstackthisframe_imp.setOpenAsHyperStack(True)
# Translate and set dimensions to translated result
translator = Translate()
output = translator.run(Image.wrap(registeredstackthisframe_imp),shift.x,shift.y,shift.z,Translate.LINEAR)
imp_translated = output.imageplus()
imp_translated.setProperty("Info", imp.getProperty("Info"))
imp_translated.setDimensions(imp.getNChannels(), slices, 1)
imp_translated.setOpenAsHyperStack(True)
# Add the translated frame to the final time-series
stack = imp_translated.getStack()
for s in range(1, imp_translated.getNSlices()+1):
ss = "_z" + zero_pad(s, len(str(slices)))
for ch in range(1, imp_translated.getNChannels()+1):
ip = stack.getProcessor(imp_translated.getStackIndex(ch, s, 1))
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())
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)
