def exportSegmentation(evt=None):
display = Display.getFront()
canvas = display.getCanvas()
numLayer = display.getLayerSet().size();
exportMask(evt)
files = []
for l in display.getLayerSet().getLayers():
for p in l.getDisplayables(Patch):
files.append(p.getFilePath())
# Create virtual stack 'vs'
vs = None
for f in files:
# if first image...
if vs is None:
imp = IJ.openImage(f)
vs = VirtualStack(imp.width, imp.height, None, "/")
vs.addSlice(f)
ImagePlus("VSeg", vs).show()
IJ.run("Duplicate...", "title=Segmentation duplicate range=1-30");
WindowManager.getImage("VSeg").close()
ic = ImageCalculator()
ic.run("Multiply stack", WindowManager.getImage("Segmentation"), WindowManager.getImage("Labels"));
WindowManager.getImage("Labels").close()
def openStack(evt=None):
display = Display.getFront()
canvas = display.getCanvas()
numLayer = display.getLayerSet().size();
files = []
for l in display.getLayerSet().getLayers():
for p in l.getDisplayables(Patch):
files.append(p.getFilePath())
# Create virtual stack 'vs'
vs = None
for f in files:
# if first image...
if vs is None:
imp = IJ.openImage(f)
vs = VirtualStack(imp.width, imp.height, None, "/")
vs.addSlice(f)
layerset = display.getLayerSet()
p = layerset.getProject()
ImagePlus("VSeg", vs).show()
IJ.run("Duplicate...", "title=" + p.getTitle() + " duplicate range=1-30");
WindowManager.getImage("VSeg").close()
return p.getTitle()
def createMIP(self):
print "starting createMIP"
for a in self.itemSelected:
ImStack = None
for filename in self.dict1.get(a):
self.savfileName = a
if not filename.endswith(self.fileExt):
continue
path = self.sourceDir + filename
# Upon finding the first image, initialize the VirtualStack
if ImStack is None:
imp = IJ.openImage(path)
ImStack = VirtualStack(imp.width, imp.height, None,
self.sourceDir)
# Add a slice, relative to the sourceDIr
ImStack.addSlice(filename)
#adding text overlay to output images so we can differentiate them. Overlay is non destructive - does not affect pixel values of image, and can be selected and deleted
prefix_overlay = Overlay()
font = Font("SansSerif", Font.PLAIN, 10)
roi = TextRoi(0, 0, a)
roi.setStrokeColor(Color(1.00, 1.00, 1.00))
prefix_overlay.add(roi)
#
OnscreenImage = ImagePlus(self.sourceDir, ImStack)
OnscreenImage.setOverlay(prefix_overlay)
OnscreenImage.show()
print "Generating MIP, waiting..."
self.outimp = self.maxZprojection(
OnscreenImage) #generate max projection
self.outimp.setOverlay(prefix_overlay)
self.outimp.show()
print "Max projection generated"
if self.saveState == "Y":
self.saveMIP()
print "Finished!"
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."""
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
# 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)
def run(title):
gd = GenericDialog("Record Window")
gd.addMessage("Maximum number of frames to record.\nZero means infinite, interrupt with ESC key.")
gd.addNumericField("Max. frames:", 50, 0)
gd.addNumericField("Milisecond interval:", 300, 0)
gd.addSlider("Start in (seconds):", 0, 20, 5)
frames = []
titles = []
for f in Frame.getFrames():
if f.isEnabled() and f.isVisible():
frames.append(f)
titles.append(f.getTitle())
gd.addChoice("Window:", titles, titles[0])
gd.addCheckbox("To file", False)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
frame = frames[gd.getNextChoiceIndex()]
delay = int(gd.getNextNumber())
tofile = gd.getNextBoolean()
dir = None
if tofile:
dc = DirectoryChooser("Directory to store image frames")
dir = dc.getDirectory()
if dir is None:
return # dialog canceled
snaps = []
borders = None
executors = Executors.newFixedThreadPool(1)
try:
while delay > 0:
IJ.showStatus("Starting in " + str(delay) + "s.")
time.sleep(1) # one second
delay -= 1
IJ.showStatus("Capturing frame borders...")
bounds = frame.getBounds()
robot = Robot()
frame.toFront()
time.sleep(0.5) # half a second
borders = robot.createScreenCapture(bounds)
IJ.showStatus("Recording " + frame.getTitle())
# Set box to the inside borders of the frame
insets = frame.getInsets()
box = bounds.clone()
box.x = insets.left
box.y = insets.top
box.width -= insets.left + insets.right
box.height -= insets.top + insets.bottom
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
i = 1
fus = None
if tofile:
fus = []
# 0 n_frames means continuous acquisition
while 0 == n_frames or (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
img = snapshot(frame, box)
if tofile:
fus.append(executors.submit(Saver(i, dir, bounds, borders, img, insets))) # will flush img
i += 1
else:
snaps.append(img)
intervals.append(real_interval)
else:
time.sleep(interval / 5)
# interrupt capturing:
if IJ.escapePressed():
IJ.showStatus("Recording user-interrupted")
break
# debug:
# print "insets:", insets
# print "bounds:", bounds
# print "box:", box
# print "snap dimensions:", snaps[0].getWidth(), snaps[0].getHeight()
# Create stack
stack = None
if tofile:
for fu in snaps:
fu.get() # wait on all
stack = VirtualStack(bounds.width, bounds.height, None, dir)
files = File(dir).list(TifFilter())
Arrays.sort(files)
for f in files:
stack.addSlice(f)
else:
stack = ImageStack(bounds.width, bounds.height, None)
t = 0
for snap, real_interval in zip(snaps, intervals):
bi = BufferedImage(bounds.width, bounds.height, BufferedImage.TYPE_INT_RGB)
g = bi.createGraphics()
g.drawImage(borders, 0, 0, None)
g.drawImage(snap, insets.left, insets.top, None)
stack.addSlice(str(IJ.d2s(t, 3)), ImagePlus("", bi).getProcessor())
t += real_interval
snap.flush()
bi.flush()
borders.flush()
ImagePlus(frame.getTitle() + " recording", stack).show()
IJ.showStatus("Done recording " + frame.getTitle())
except Exception, e:
print "Some error ocurred:"
print e.printStackTrace()
IJ.showStatus("")
if borders is not None:
borders.flush()
for snap in snaps:
snap.flush()
def run(title):
gd = GenericDialog('Record Window')
gd.addMessage(
"Maximum number of frames to record.\nZero means infinite, interrupt with ESC key."
)
gd.addNumericField('Max. frames:', 50, 0)
gd.addNumericField('Milisecond interval:', 300, 0)
gd.addSlider('Start in (seconds):', 0, 20, 5)
frames = []
titles = []
for f in Frame.getFrames():
if f.isEnabled() and f.isVisible():
frames.append(f)
titles.append(f.getTitle())
gd.addChoice('Window:', titles, titles[0])
gd.addCheckbox("To file", False)
gd.showDialog()
if gd.wasCanceled():
return
n_frames = int(gd.getNextNumber())
interval = gd.getNextNumber() / 1000.0 # in seconds
frame = frames[gd.getNextChoiceIndex()]
delay = int(gd.getNextNumber())
tofile = gd.getNextBoolean()
dir = None
if tofile:
dc = DirectoryChooser("Directory to store image frames")
dir = dc.getDirectory()
if dir is None:
return # dialog canceled
snaps = []
borders = None
executors = Executors.newFixedThreadPool(1)
try:
while delay > 0:
IJ.showStatus('Starting in ' + str(delay) + 's.')
time.sleep(1) # one second
delay -= 1
IJ.showStatus('Capturing frame borders...')
bounds = frame.getBounds()
robot = Robot()
frame.toFront()
time.sleep(0.5) # half a second
borders = robot.createScreenCapture(bounds)
IJ.showStatus("Recording " + frame.getTitle())
# Set box to the inside borders of the frame
insets = frame.getInsets()
box = bounds.clone()
box.x = insets.left
box.y = insets.top
box.width -= insets.left + insets.right
box.height -= insets.top + insets.bottom
start = System.currentTimeMillis() / 1000.0 # in seconds
last = start
intervals = []
real_interval = 0
i = 1
fus = None
if tofile:
fus = []
# 0 n_frames means continuous acquisition
while 0 == n_frames or (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
img = snapshot(frame, box)
if tofile:
fus.append(
executors.submit(
Saver(i, dir, bounds, borders, img,
insets))) # will flush img
i += 1
else:
snaps.append(img)
intervals.append(real_interval)
else:
time.sleep(interval / 5)
# interrupt capturing:
if IJ.escapePressed():
IJ.showStatus("Recording user-interrupted")
break
# debug:
#print "insets:", insets
#print "bounds:", bounds
#print "box:", box
#print "snap dimensions:", snaps[0].getWidth(), snaps[0].getHeight()
# Create stack
stack = None
if tofile:
for fu in snaps:
fu.get() # wait on all
stack = VirtualStack(bounds.width, bounds.height, None, dir)
files = File(dir).list(TifFilter())
Arrays.sort(files)
for f in files:
stack.addSlice(f)
else:
stack = ImageStack(bounds.width, bounds.height, None)
t = 0
for snap, real_interval in zip(snaps, intervals):
bi = BufferedImage(bounds.width, bounds.height,
BufferedImage.TYPE_INT_RGB)
g = bi.createGraphics()
g.drawImage(borders, 0, 0, None)
g.drawImage(snap, insets.left, insets.top, None)
stack.addSlice(str(IJ.d2s(t, 3)),
ImagePlus('', bi).getProcessor())
t += real_interval
snap.flush()
bi.flush()
borders.flush()
ImagePlus(frame.getTitle() + " recording", stack).show()
IJ.showStatus('Done recording ' + frame.getTitle())
except Exception, e:
print "Some error ocurred:"
print e.printStackTrace()
IJ.showStatus('')
if borders is not None: borders.flush()
for snap in snaps:
snap.flush()
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)
test_virtual_stack_mac.py
"""
from ij import IJ, VirtualStack, ImagePlus
import os
git_home = os.getenv("GIT_HOME")
img_dir = git_home + "/tips/ImageJ/py/test_virtual_stack/"
print(img_dir)
IJ.run("Close All")
filtFiles = ["spheres-1.tif", "spheres-2.tif", "spheres-3.tif"]
vs = None
for f in filtFiles:
if vs is None:
path = img_dir + f
imp = IJ.openImage(path)
print(imp)
imp.show()
vs = VirtualStack(imp.width, imp.height, None, "/")
vs.addSlice(path)
else:
path = img_dir + f
vs.addSlice(path)
imPlus = ImagePlus("Stack from subdirectories", vs)
print imPlus
imPlus.show()
def tiffImageFilenames(directory):
for filename in sorted(os.listdir(directory)):
if filename.lower().endswith(".tif"):
yield filename
# Read the dimensions from the first image
first_path = os.path.join(sourceDir, tiffImageFilenames(sourceDir).next())
width, height = dimensionsOf(first_path)
# Create the VirtualStack without a specific ColorModel
# (which will be set much later upon loading any slice)
vstack = VirtualStack(width, height, None, sourceDir)
# Add all TIFF images in sourceDir as slices in vstack
for filename in tiffImageFilenames(sourceDir):
vstack.addSlice(filename)
# Visualize the VirtualStack
imp = ImagePlus("virtual stack of images in " + os.path.basename(sourceDir), vstack)
# imp.show()
from mpicbg.ij.plugin import NormalizeLocalContrast
from ij.io import FileSaver
# slice마다 process 후 targetDir에 save
for i in xrange(0, vstack.size()):
ip = vstack.getProcessor(i+1) # slice list는 1부터 시작 (1-based listing)
# NormalizeLocalContrast plugin을 ImageProcessor에 적용
NormalizeLocalContrast.run(ip, 200, 200, 3, True, True)
# 결과 저장
name = vstack.getFileName(i+1)
exit() # If you do not select a directory, terminates program
# Assumes all files have the same size
ImStack = None
#print "os.walk: ", list(os.walk(sourceDir))
for root, directories, filenames in os.walk(sourceDir):
for filename in filenames:
# Skip non-TIFF files
if not filename.endswith(".tif"):
continue
path = os.path.join(root, filename)
# Upon finding the first image, initialize the VirtualStack
if ImStack is None:
imp = IJ.openImage(path)
ImStack = VirtualStack(imp.width, imp.height, None, sourceDir)
# Add a slice, relative to the sourceDIr
ImStack.addSlice(path[len(sourceDir):])
OnscreenImage = ImagePlus(sourceDir, ImStack)
OnscreenImage.show()
print "Generating MIP, waiting..."
outimp = maxZprojection(OnscreenImage) #generate max projection
outimp.show()
print "Max projection generated"
###To remove save functionality, just remove all beyond here-
SaveQuery = JOptionPane.showInputDialog(
None,
"Would you like to save the max proj? y = save, anything else = don't save"
)
