def green2():
"""
Displays a duplicate of the active image.
"""
green2 = IJ.getImage()
green2 = green2.duplicate()
ImageWindow.setNextLocation(int(IJ.getScreenSize().width * 1 / 3),
int(IJ.getScreenSize().height * 1 / 14))
green2.show()
def subpixels(pixel):
""" Math: subtraction
duplicates and displayes current image.
Performs puxel subtraction using Math.
"""
green = IJ.getImage()
green = green.duplicate()
IJ.run(green, "Subtract...", "value=" + pixel)
ImageWindow.setNextLocation(int(IJ.getScreenSize().width * 1 / 3),
int(IJ.getScreenSize().height * 1 / 14))
green.show()
bgTitle()
def showTup(temp_output):
if not isinstance(temp_output, tuple):
print "Output is not a tuple and therefore can not be displayed correctly"
return False
size = 300
x = 50
y = 300
d = 50
for el in temp_output:
if isinstance(el, ImagePlus):
print el.title
iw = ImageWindow("")
iw.setNextLocation(x, y) # todo: how to also fix the size?
el.show()
# iw = ImageWindow(el)
# iw.setLocationAndSize(x,y,size,size)
x = x + size + d
def regBf(fn=None, imp=None, refId=None):
"""
Register a time series stack to a specified reference slice,
from a file (imported by BioFormat) or a stack ImagePlus.
Returns a registered ImagePlus.
The stack must have only 1 z layer.
refId is in the format of [int channel, int slice, int frame]
If no refId is supplied, will use the first slice [1,1,1]
Note: since TurboReg is used for registeration, there will be
temporary opened image windows.
"""
## Prepare the right ImagePlus
if imp is None:
if fn is None:
od = OpenDialog("Choose a file", None)
filename = od.getFileName()
if filename is None:
print "User canceled the dialog!"
return
else:
directory = od.getDirectory()
filepath = directory + filename
print "Selected file path:", filepath
else:
if os.path.exists(fn) and os.path.isfile(fn):
filepath = fn
else:
print "File does not exist!"
return
imps = BF.openImagePlus(filepath)
imp = imps[0]
if imp is None:
print "Cannot load file!"
return
else:
if fn is not None:
print "File or ImagePlus? Cannot load both."
return
width = imp.getWidth()
height = imp.getHeight()
# C
nChannels = imp.getNChannels()
# Z
nSlices = imp.getNSlices()
# T
nFrames = imp.getNFrames()
# pixel size
calibration = imp.getCalibration()
# Only supoort one z layer
if nSlices != 1:
print "Only support 1 slice at Z dimension."
return
# set registration reference slice
if refId is None:
refC = 1
refZ = 1
refT = 1
else:
refC = refId[0]
refZ = refId[1]
refT = refId[2]
if (refC not in range(1, nChannels + 1)
or refZ not in range(1, nSlices + 1)
or refT not in range(1, nFrames + 1)):
print "Invalid reference image!"
return
stack = imp.getImageStack()
registeredStack = ImageStack(width, height, nChannels * nFrames * nSlices)
# setup windows, these are needed by TurboReg
tmpip = FloatProcessor(width, height)
refWin = ImageWindow(ImagePlus("ref", tmpip))
bounds = refWin.getBounds()
# refWin.setVisible(False)
toRegWin = ImageWindow(ImagePlus("toReg", tmpip))
toRegWin.setLocation(bounds.width + bounds.x, bounds.y)
# toRegWin.setVisible(False)
toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip))
toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y)
# toTransformWin.setVisible(False)
# get reference image
refImp = ImagePlus("ref",
stack.getProcessor(imp.getStackIndex(refC, refZ, refT)))
refWin.setImage(refImp)
tr = TurboReg_()
for t in xrange(1, nFrames + 1):
IJ.showProgress(t - 1, nFrames)
# print "t ", t
# do TurboReg on reference channel
toRegId = imp.getStackIndex(refC, refZ, t)
toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId))
toRegWin.setImage(toRegImp)
regArg = "-align " +\
"-window " + toRegImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-window " + refImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-rigidBody " +\
str(width / 2) + " " + str(height / 2) + " " +\
str(width / 2) + " " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(regArg)
registeredImp = tr.getTransformedImage()
sourcePoints = tr.getSourcePoints()
targetPoints = tr.getTargetPoints()
registeredStack.setProcessor(registeredImp.getProcessor(), toRegId)
# toRegImp.flush()
# apply transformation on other channels
for c in xrange(1, nChannels + 1):
# print "c ", c
if c == refC:
continue
toTransformId = imp.getStackIndex(c, 1, t)
toTransformImp = ImagePlus("toTransform",
stack.getProcessor(toTransformId))
toTransformWin.setImage(toTransformImp)
transformArg = "-transform " +\
"-window " + toTransformImp.getTitle() + " " +\
str(width) + " " + str(height) + " " +\
"-rigidBody " +\
str(sourcePoints[0][0]) + " " +\
str(sourcePoints[0][1]) + " " +\
str(targetPoints[0][0]) + " " +\
str(targetPoints[0][1]) + " " +\
str(sourcePoints[1][0]) + " " +\
str(sourcePoints[1][1]) + " " +\
str(targetPoints[1][0]) + " " +\
str(targetPoints[1][1]) + " " +\
str(sourcePoints[2][0]) + " " +\
str(sourcePoints[2][1]) + " " +\
str(targetPoints[2][0]) + " " +\
str(targetPoints[2][1]) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(transformArg)
registeredStack.setProcessor(
tr.getTransformedImage().getProcessor(), toTransformId)
# toTransformImp.flush()
sourcePoints = None
targetPoints = None
IJ.showProgress(t, nFrames)
IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames))
refWin.close()
toRegWin.close()
toTransformWin.close()
imp2 = ImagePlus("reg_" + imp.getTitle(), registeredStack)
imp2.setCalibration(imp.getCalibration().copy())
imp2.setDimensions(nChannels, nSlices, nFrames)
# print "type ", imp.getType()
# print "type ", imp2.getType()
# print nChannels, " ", nSlices, " ", nFrames
# print registeredStack.getSize()
for key in imp.getProperties().stringPropertyNames():
imp2.setProperty(key, imp.getProperty(key))
# comp = CompositeImage(imp2, CompositeImage.COLOR)
# comp.show()
# imp2 = imp.clone()
# imp2.setStack(registeredStack)
# imp2.setTitle("reg"+imp.getTitle())
# imp2.show()
# imp.show()
return imp2
def regBf(fn=None, imp=None, refId=None):
"""
Register a time series stack to a specified reference slice,
from a file (imported by BioFormat) or a stack ImagePlus.
Returns a registered ImagePlus.
The stack must have only 1 z layer.
refId is in the format of [int channel, int slice, int frame]
If no refId is supplied, will use the first slice [1,1,1]
Note: since TurboReg is used for registeration, there will be
temporary opened image windows.
"""
## Prepare the right ImagePlus
if imp is None:
if fn is None:
od = OpenDialog("Choose a file", None)
filename = od.getFileName()
if filename is None:
print "User canceled the dialog!"
return
else:
directory = od.getDirectory()
filepath = directory + filename
print "Selected file path:", filepath
else:
if os.path.exists(fn) and os.path.isfile(fn):
filepath = fn
else:
print "File does not exist!"
return
imps = BF.openImagePlus(filepath)
imp = imps[0]
if imp is None:
print "Cannot load file!"
return
else:
if fn is not None:
print "File or ImagePlus? Cannot load both."
return
width = imp.getWidth()
height = imp.getHeight()
# C
nChannels = imp.getNChannels()
# Z
nSlices = imp.getNSlices()
# T
nFrames = imp.getNFrames()
# pixel size
calibration = imp.getCalibration()
# Only supoort one z layer
if nSlices != 1:
print "Only support 1 slice at Z dimension."
return
# set registration reference slice
if refId is None:
refC = 1
refZ = 1
refT = 1
else:
refC = refId[0]
refZ = refId[1]
refT = refId[2]
if (refC not in range(1, nChannels+1) or
refZ not in range(1, nSlices+1) or
refT not in range(1, nFrames+1) ):
print "Invalid reference image!"
return
stack = imp.getImageStack()
registeredStack = ImageStack(width, height, nChannels*nFrames*nSlices)
# setup windows, these are needed by TurboReg
tmpip = FloatProcessor(width, height)
refWin = ImageWindow(ImagePlus("ref", tmpip))
bounds = refWin.getBounds()
# refWin.setVisible(False)
toRegWin = ImageWindow(ImagePlus("toReg", tmpip))
toRegWin.setLocation(bounds.width + bounds.x, bounds.y)
# toRegWin.setVisible(False)
toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip))
toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y)
# toTransformWin.setVisible(False)
# get reference image
refImp = ImagePlus("ref", stack.getProcessor(imp.getStackIndex(refC, refZ, refT)))
refWin.setImage(refImp)
tr = TurboReg_()
for t in xrange(1, nFrames+1):
IJ.showProgress(t-1, nFrames)
# print "t ", t
# do TurboReg on reference channel
toRegId = imp.getStackIndex(refC, refZ, t)
toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId))
toRegWin.setImage(toRegImp)
regArg = "-align " +\
"-window " + toRegImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-window " + refImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-rigidBody " +\
str(width / 2) + " " + str(height / 2) + " " +\
str(width / 2) + " " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(regArg)
registeredImp = tr.getTransformedImage()
sourcePoints = tr.getSourcePoints()
targetPoints = tr.getTargetPoints()
registeredStack.setProcessor(registeredImp.getProcessor(), toRegId)
# toRegImp.flush()
# apply transformation on other channels
for c in xrange(1, nChannels+1):
# print "c ", c
if c == refC:
continue
toTransformId = imp.getStackIndex(c, 1, t)
toTransformImp = ImagePlus("toTransform", stack.getProcessor(toTransformId))
toTransformWin.setImage(toTransformImp)
transformArg = "-transform " +\
"-window " + toTransformImp.getTitle() + " " +\
str(width) + " " + str(height) + " " +\
"-rigidBody " +\
str(sourcePoints[0][0]) + " " +\
str(sourcePoints[0][1]) + " " +\
str(targetPoints[0][0]) + " " +\
str(targetPoints[0][1]) + " " +\
str(sourcePoints[1][0]) + " " +\
str(sourcePoints[1][1]) + " " +\
str(targetPoints[1][0]) + " " +\
str(targetPoints[1][1]) + " " +\
str(sourcePoints[2][0]) + " " +\
str(sourcePoints[2][1]) + " " +\
str(targetPoints[2][0]) + " " +\
str(targetPoints[2][1]) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(transformArg)
registeredStack.setProcessor(tr.getTransformedImage().getProcessor(), toTransformId)
# toTransformImp.flush()
sourcePoints = None
targetPoints = None
IJ.showProgress(t, nFrames)
IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames))
refWin.close()
toRegWin.close()
toTransformWin.close()
imp2 = ImagePlus("reg_"+imp.getTitle(), registeredStack)
imp2.setCalibration(imp.getCalibration().copy())
imp2.setDimensions(nChannels, nSlices, nFrames)
# print "type ", imp.getType()
# print "type ", imp2.getType()
# print nChannels, " ", nSlices, " ", nFrames
# print registeredStack.getSize()
for key in imp.getProperties().stringPropertyNames():
imp2.setProperty(key, imp.getProperty(key))
# comp = CompositeImage(imp2, CompositeImage.COLOR)
# comp.show()
# imp2 = imp.clone()
# imp2.setStack(registeredStack)
# imp2.setTitle("reg"+imp.getTitle())
# imp2.show()
# imp.show()
return imp2
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
import glob
import time
from ij import IJ
from ij import WindowManager
from ij.gui import ImageWindow
inDir = "\\\\cm20st\\data\\images\\QM14-02-12A-Kosydar\\qm-04203-PMH1413\\dm3"
outDir = "C:\\Users\\l837410\\Documents\\work\\proj\\QM14-02-12A-Kosydar\\Sweave\\inc\\png"
for file in os.listdir(inDir):
if file.endswith(".dm3"):
path = inDir + "\\" + file
# print(file)
strLoad = "load=%s" % path
IJ.run("DM3 Reader...", strLoad)
IJ.run("Add Scale Bar", "width=50 height=6 font=24 color=Black location=[Lower Right] bold")
IJ.run("RGB Color")
l = len(file)
name = file[0:l-4]
print(name)
path = outDir + "\\" + name + ".png"
# Get the final map
imp = WindowManager.getCurrentImage()
iw = ImageWindow(imp)
# iw.changed = False
IJ.saveAs("PNG", path)
iw.close()
