def createContainer(roi, imgA, imgB):
rect = roi.getBounds()
ipmask = roi.getMask()
offset = [rect.x, rect.y]
size = [rect.width, rect.height]
if (ipmask != None):
ipslice = ipmask.createProcessor(imgA.getWidth(), imgA.getHeight())
ipslice.setValue(0.0)
ipslice.fill()
ipslice.copyBits(ipmask, rect.x, rect.y, Blitter.COPY)
impmask = ImagePlus("Mask", ipslice)
ipamask = ImagePlusAdapter.wrap(impmask)
container = DataContainer(imgA, imgB, 1, 1, "imageA", "imageB", ipamask, offset, size)
else:
container = DataContainer(imgA, imgB, 1, 1, "imageA", "imageB", offset, size)
return container
def getContainer(self, impA, impB): imgA = ImagePlusAdapter.wrap(impA) imgB = ImagePlusAdapter.wrap(impB) return DataContainer(imgA, imgB, 1, 1, "imageA", "imageB")
from ij import WindowManager
from ij import IJ
from net.imglib2.img import ImagePlusAdapter
from net.imglib2.img.display.imagej import ImageJFunctions
from fiji.process import Image_Expression_Parser
from spimopener import Rename
from ij import measure
listt = []
listt_2 = []
for i in range(0, 3):
listt.append(WindowManager.getImage(i + 1))
listt_2.append(ImagePlusAdapter.wrap(listt[i]))
map = {'A': listt_2[0], 'B': listt_2[1], 'C': listt_2[2]}
expression = '(A+B+C)/3'
# Instantiate plugin
parser = Image_Expression_Parser()
# Configure & execute
parser.setImageMap(map)
parser.setExpression(expression)
parser.process()
result = parser.getResult() # is an ImgLib image
result_imp = ImageJFunctions.show(result)
IJ.run('Rename...', 'title=AverageIMG')
result_img = ImagePlusAdapter.wrap(result_imp)
mean_average = result_imp.getStatistics()
mean_average = mean_average.mean
scaled_list = []
for i in range(0, 3):
imp = listt[i]
img = listt_2[i]
except UnknownFormatException:
continue
preview = getPreview(image)
preview.show()
rm = RoiManager()
dialog = WaitForUserDialog("Action required", "Please select regions of interest in this image. Click OK when done.")
dialog.show()
rm.close()
splitter = ChannelSplitter()
imp1 = ImagePlus("CH1", splitter.getChannel(image, imageA))
imp2 = ImagePlus("CH2", splitter.getChannel(image, imageB))
title = image.getTitle()
title = title[:title.rfind('.')]
image.close()
preview.close()
ch1 = ImagePlusAdapter.wrap(imp1)
ch2 = ImagePlusAdapter.wrap(imp2)
for roi in rm.getRoisAsArray():
container = createContainer(roi, ch1, ch2)
img1 = container.getSourceImage1()
img2 = container.getSourceImage2()
mask = container.getMask()
thr1, thrimp1 = calculateThreshold(imp1, roi, methods[0])
thr2, thrimp2 = calculateThreshold(imp2, roi, methods[1])
cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor())
rtype = img1.randomAccess().get().createVariable()
raw = manders.calculateMandersCorrelation(cursor, rtype)
rthr1 = rtype.copy()
this_file_name = os.path.realpath( inspect.getfile( lambda : None ) ) # inspect.getfile requires method, class, ... as input and returns the file in which input was defined
shutil.copyfile( this_file_name, '%s/%s' % ( home.rstrip('/'), this_file_name.split('/')[-1] ) )
start = 1
stop = img.getStack().getSize()
if False and stackMin != None:
start = stackMin
if False and stackMax != None:
stop = stackMax
startingCoordinates = range( start - 1, stop )
wrappedImage = ImagePlusAdapter.wrap( img )
radii = [ [ width, height ], [ 50, 50 ], [ 20, 20 ], [ 7, 7 ], [ 7, 7 ] ] #,[ 75, 75 ] ]#, [ 30, 30 ], [ 15, 15 ], [ 7, 7 ] ]#, [ 15, 15 ] ]
steps = [ [ width, height ], [ 50, 50 ], [ 20, 20 ], [ 7, 7 ], [ 1, 1 ] ] #,[ 75, 75 ] ]#, [ 30, 30 ], [ 15, 15 ], [ 3, 3 ] ]#, [ 1, 1 ] ]
ranges = [ int( scaleZBy*max(x) ) for x in radii ]
opt = [options]
ratio = 1.0
for idx in xrange(len(radii)-1):
tmpOptions = options2.clone()
tmpOptions.windowRange = int( opt[idx].windowRange * ratio )
opt.append( tmpOptions )
# opt = [ options, options2, options2, options2, options2 ]#, options2 ]
visitor = ListMultiScaleVisitor( ArrayList() )
bp = home.rstrip('/') + '/transformed/%02d.tif'
imageVisitor = RenderImageMultiScaleVisitor( wrappedImage, bp )
# ImagePlus("", ip2a).show()
imp1a = ImagePlus("%s" % patch, Filter.scale(ip1a, scaleFactor))
imp1b = ImagePlus("%s" % overlays[patch], ip1b.resize(Math.round( scaleFactor*ip1b.getWidth() ), Math.round( scaleFactor*ip1b.getHeight() ) ) )
imp2a = ImagePlus("%s" % match[0], Filter.scale(ip2a, scaleFactor))
imp2b = ImagePlus("%s" % overlays[match[0]], ip2b.resize(Math.round( scaleFactor*ip2b.getWidth() ), Math.round( scaleFactor*ip2b.getHeight() ) ) )
# show images for debugging purposes
# imp1a.show()
# imp1b.show()
# imp2a.show()
# imp2b.show()
img1a = ImagePlusAdapter.wrap(imp1a)
img1b = ImagePlusAdapter.wrap(imp1b)
img2a = ImagePlusAdapter.wrap(imp2a)
img2b = ImagePlusAdapter.wrap(imp2b)
pointMatchGenerator.generate(img1a, img2a, img1b, img2b)
pointHashMap = pointMatchGenerator.getPointMatches()
for entryset in pointHashMap.entrySet():
pointMatches = entryset.getValue()
# connect tile at patch/grid position to tile at match/grid position with appropriate pointMatches
# remove outliers first (ransac)
pairWiseModel = AffineModel1D()
inliers = ArrayList()