def create_empty_imp(imp):
dims = imp.getDimensions()
depth = imp.getBitDepth()
dims = list(dims)
dims.append(depth)
new_imp = IJ.createHyperStack("new", *dims)
return new_imp
def GenerateGallery(imp, CoordinateList):
""" Generates a gallery from a list of coordinates:
input values are:
a coordinate list (x,y as list of tupels)
an image from which the gallery is generated (imp),
Image must (for now) be a 8 or 16 bit composite
a ROI size for the gallery (roisize)"""
if CoordinateList != []:
CellNumber = len(CoordinateList)
channelnumber = imp.getNChannels()
slicenumber = imp.getNSlices()
bitdepth = imp.getBitDepth()
imp2 = IJ.createHyperStack("Gallery", roisize, roisize, channelnumber,
slicenumber, CellNumber, bitdepth)
if bitdepth != 24:
imp2.copyLuts(imp)
timer = 0
for cells in CoordinateList:
timer = timer + 1
roi2 = Roi(cells[0] - (roisize / 2), cells[1] - roisize / 2,
roisize, roisize)
imp.setC(1)
imp.setRoi(roi2)
imp.copy()
imp2.setT(timer)
imp2.setC(1)
imp2.paste()
if channelnumber > 1:
imp.setC(2)
imp.copy()
imp2.setC(2)
imp2.paste()
if channelnumber > 2:
imp.setC(3)
imp.copy()
imp2.setC(3)
imp2.paste()
imp2.show()
if Label_Gallery:
timer2 = 0
for cells in CoordinateList:
timer2 = timer2 + 1
imp2.setT(timer2)
imp2.setC(1)
ip = imp2.getProcessor()
Labelfont = Font("Arial", Font.PLAIN, 12)
ip.setFont(Labelfont)
ip.setColor(65000)
ROINumber = str(cells[2])
ip.drawString(ROINumber[:4], 5, 14)
imp.updateAndDraw()
return imp2
def concatenateImagePlus(files, outfile):
"""Concatenate images contained in files and save in outfile"""
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)
nslices = imageG.getNSlices()
nframes = len(files)
nchannels = imageG.getNChannels()
luts = imageG.getLuts()
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:
print '...', basename(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 Exception, e:
IJ.log("ERROR")
IJ.log(file_ + str(e))
raise
IJ.showProgress(files.index(file_), len(files))
concatImgPlus.setStack(concatStack, nchannels, nslices, nframes)
concatImgPlus.setCalibration(image.getCalibration())
concatImgPlus.setOpenAsHyperStack(True)
concatImgPlus.setLuts(luts)
concatImgPlus.close()
IJ.saveAs(concatImgPlus, "Tiff", outfile)
def ExtractChannel(imp, channel):
imp_height = imp.getHeight()
imp_width = imp.getWidth()
channelnumber = imp.getNChannels()
slicenumber = imp.getNSlices()
timepoints = imp.getNFrames()
imp2 = IJ.createHyperStack("Gallery",imp_width, imp_height, channelnumber, slicenumber, timepoints, 16)
imp2.copyLuts(imp)
for frame in range(1,timepoints+1):
imp.setT(frame)
imp.setC(channel)
imp.copy()
imp2.setT(frame)
imp2.setC(channel)
imp2.paste()
return imp2
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()
imp2.paste()
return imp2
def dist(p0, p1):
""" Calculates the distance between two xy coordinates, each
each coordinated supplied by a tupel"""
return math.sqrt((p0[0] - p1[0])**2 + (p0[1] - p1[1])**2)
## Generates a gallery from multiple point ROIs
imp = IJ.getImage()
roinumber = RoiManager.getInstance().getCount()
channelnumber = imp.getNChannels()
slicenumber = imp.getNSlices()
timer = 0
imp2 = IJ.createHyperStack("Gallery",GalleryROI, GalleryROI, channelnumber, slicenumber, roinumber, 16)
imp2.copyLuts(imp)
MeanChannel1 = []
MeanChannel2 = []
MeanChannel3 = []
XYCoordinates = []
Distance = []
#print roinumber
#for roi in RoiManager.getInstance().getRoisAsArray(): ## Does not work for time, since only xz coordinates are returned
movietime = []
Lastcoordinates = (0,0)
for roi5 in range(roinumber):
#print roi5
RoiManager().getInstance().select(imp, roi5)
roi = imp.getRoi()
movietime.append(imp.getT())
from ij import IJ, ImagePlus
# create a empty image with the same dimensions, bitdepth
imp = IJ.getImage()
dims = imp.getDimensions()
depth = imp.getBitDepth()
dims = list(dims)
dims.append(depth)
new_imp = IJ.createHyperStack("new", *dims)
new_imp.show()