def SaveCoverFromFs(tiles, newwidth, newheight, cols, rows):
tilewidth = int(newwidth / cols)
tileheight = int(newheight / rows)
newwidth = int(newwidth / tilewidth) * tilewidth
newheight = int(newheight / tileheight) * tileheight
hiresoutip = ColorProcessor(newwidth, newheight)
hiresout = ImagePlus("hi res output", hiresoutip)
hiresout.show()
x = 0
y = -1
plane = []
# scale the images
for i in sorted(tiles.iterkeys()):
if y < rows - 1:
y += 1
else:
y = 0
x += 1
imp = IJ.openImage(str(tiles[i]))
scale = Scale(imp.getProcessor())
ipscaled = ScaleImageToSize(scale, tilewidth, tileheight)
hiresoutip.copyBits(ipscaled, x * tilewidth, y * tileheight, 0)
hiresout.draw()
def SaveCoverFromFs(tiles, newwidth, newheight, cols, rows):
tilewidth = int(newwidth/cols)
tileheight = int(newheight/rows)
newwidth = int(newwidth/tilewidth) * tilewidth
newheight = int(newheight/tileheight) * tileheight
hiresoutip = ColorProcessor(newwidth, newheight)
hiresout = ImagePlus("hi res output", hiresoutip)
hiresout.show()
x = 0
y = -1
plane = []
# scale the images
for i in sorted(tiles.iterkeys()):
if y < rows-1:
y += 1
else:
y = 0
x += 1
imp = IJ.openImage(str(tiles[i]))
scale = Scale(imp.getProcessor())
ipscaled = ScaleImageToSize(scale, tilewidth, tileheight)
hiresoutip.copyBits(ipscaled, x*tilewidth, y*tileheight, 0)
hiresout.draw()
def SaveCoverFromZip(tileIndex, newwidth, newheight, cols, rows,
originalspath):
baseDir = re.sub(r'\/originals.zip', "", originalspath)
#print baseDir
zf = zipfile.ZipFile(originalspath, mode='r')
tilewidth = int(newwidth / cols)
tileheight = int(newheight / rows)
newwidth = int(newwidth / tilewidth) * tilewidth
newheight = int(newheight / tileheight) * tileheight
hiresoutip = ColorProcessor(newwidth, newheight)
hiresout = ImagePlus("hi res output", hiresoutip)
hiresout.show()
x = 0
y = -1
plane = []
# scale the images
for i in sorted(tileIndex.iterkeys()):
if y < rows - 1:
y += 1
else:
y = 0
x += 1
#bi = bir.openImage(tileIndex[i]);
#ip = ColorProcessor(bi)
image = zf.read(str(tileIndex[i]) + ".jpeg")
#IJ.log("Placing image :" + str(tileIndex[i]) + ".jpeg")
my_file = open(baseDir + 'temporary.jpeg', 'w')
my_file.write(image)
my_file.close()
imp = IJ.openImage(baseDir + "/temporary.jpeg")
ip = imp.getProcessor()
scale = Scale(ip)
ipscaled = ScaleImageToSize(scale, tilewidth, tileheight)
hiresoutip.copyBits(ipscaled, x * tilewidth, y * tileheight, 0)
hiresout.draw()
def SaveCoverFromZip(tileIndex, newwidth, newheight, cols, rows, originalspath):
baseDir = re.sub(r'\/originals.zip', "", originalspath)
#print baseDir
zf = zipfile.ZipFile(originalspath, mode='r')
tilewidth = int(newwidth/cols)
tileheight = int(newheight/rows)
newwidth = int(newwidth/tilewidth) * tilewidth
newheight = int(newheight/tileheight) * tileheight
hiresoutip = ColorProcessor(newwidth, newheight)
hiresout = ImagePlus("hi res output", hiresoutip)
hiresout.show()
x = 0
y = -1
plane = []
# scale the images
for i in sorted(tileIndex.iterkeys()):
if y < rows-1:
y += 1
else:
y = 0
x += 1
#bi = bir.openImage(tileIndex[i]);
#ip = ColorProcessor(bi)
image = zf.read(str(tileIndex[i]) + ".jpeg")
#IJ.log("Placing image :" + str(tileIndex[i]) + ".jpeg")
my_file = open(baseDir + 'temporary.jpeg','w')
my_file.write(image)
my_file.close()
imp = IJ.openImage(baseDir + "/temporary.jpeg")
ip = imp.getProcessor()
scale = Scale(ip)
ipscaled = ScaleImageToSize(scale, tilewidth, tileheight)
hiresoutip.copyBits(ipscaled, x*tilewidth, y*tileheight, 0)
hiresout.draw()
# make a gradient image
ip = screenshot.getProcessor()
w = ip.getWidth()
h = ip.getHeight()
u = int(0.99 * 255)
l = int(0.5 * 255)
def gray2rgb(value):
return (value << 16) | (value << 8) | value
# This is a trick: make a 1xh image (because calculation is slow in Python) and resize it to wxh
from jarray import array
maskPixels = array([gray2rgb(int(u + (l + 1 - u) * i / (h))) for i in range(0, h)], 'i')
mask = ColorProcessor(1, h, maskPixels).resize(w, h)
# "blend" mask with original image
mask.copyBits(ip, 0, 0, Blitter.MAX)
mask.flipVertical()
# instantiate the 3D viewer
univ = Image3DUniverse()
univ.show()
# add the images
cImage = univ.addOrthoslice(ImagePlus("screenshot", ip), \
None, "image", 0, [1, 1, 1], 1)
def chartAsImagePlus(chart, frame):
""" Given a JFreeChart and its JFrame, return an ImagePlus of type COLOR_RGB. """
panel = frame.getContentPane().getComponent(0) # a ChartPanel
dimensions = panel.getSize()
bimg = chart.createBufferedImage(dimensions.width, dimensions.height)
return ImagePlus(str(chart.getTitle()), ColorProcessor(bimg))
# Open the Drosophila larval brain sample RGB image stack
#imp = IJ.openImage("https://samples.imagej.net/samples/first-instar-brain.zip")
imp = IJ.getImage()
stack1 = imp.getStack() # of ColorProcessor
# Scale up by 1.5x
scale = 1.5
model = AffineModel2D()
model.set(scale, 0, 0, scale, 0, 0)
# An arbitrary affine, obtained from Plugins - Transform - Interactive Affine (push enter key to print it)
#model.set(1.16, 0.1484375, -0.375, 1.21875, 38.5, -39.5)
# New stack, larger
stack2 = ImageStack(int(imp.getWidth() * scale), int(imp.getHeight() * scale))
for index in xrange(1, stack1.getSize() + 1):
stack2.addSlice(ColorProcessor(stack2.getWidth(), stack2.getHeight()))
imp2 = ImagePlus("larger (push)", stack2)
# Map data from stack to stack2 using the model transform
position = zeros(2, 'd')
"""
# First approach: push (WRONG!)
width1, height1 = stack1.getWidth(), stack1.getHeight()
for index in xrange(1, 3): #stack1.size() + 1):
cp1 = stack1.getProcessor(index)
cp2 = stack2.getProcessor(index)
for y in xrange(height1):
for x in xrange(width1):
position[1] = y
def CreateCover(ip, width, height, dbpath):
# split input image into appropriate tiles
stackt = SplitImage(ip, width, height)
impt = ImagePlus("template", stackt)
nSlicestmp = impt.getNSlices()
# open the preprocessed database
print dbpath
impd = IJ.openImage(dbpath)
stackd = impd.getImageStack()
nSlicesdb = impd.getNSlices()
#associate index with image names
imageNames = impd.getProperty('Info')
imageList = imageNames.split(';')
# set up preview output
outputip = ColorProcessor(ip.width, ip.height)
outputimp = ImagePlus("output", outputip)
outputimp.show()
cols = ip.width / width
rows = ip.height / height
print str(cols) + "," + str(rows)
x = 0
y = 0
arrays = [None, None] # a list of two elements
cruncher = Inline(arrays)
tileNames = {}
tileIndex = {}
placed = {}
used = {}
while len(placed) < nSlicestmp:
randomTileIndex = random.randint(1, nSlicestmp)
if randomTileIndex in placed:
continue
# transform to row adn column coordinate
if randomTileIndex % rows == 0:
y = rows - 1
x = (randomTileIndex / rows) - 1
else:
y = (randomTileIndex % rows) - 1
x = int(randomTileIndex / rows)
pixelst = stackt.getPixels(randomTileIndex)
minimum = Float.MAX_VALUE
#iterate through database images
j = 1
indexOfBestMatch = 0
arrays[0] = pixelst
while j < nSlicesdb:
if j in used:
j += 1
continue
arrays[1] = stackd.getPixels(j)
diff = cruncher.call()
if diff < minimum:
minimum = diff
indexOfBestMatch = j
j += 1
ip = stackd.getProcessor(indexOfBestMatch)
outputip.copyBits(ip, x * width, y * height, 0)
used[indexOfBestMatch] = 1
tileNames[randomTileIndex] = imageList[indexOfBestMatch - 1]
tileIndex[randomTileIndex] = indexOfBestMatch - 1
outputimp.draw()
placed[randomTileIndex] = 1
return tileNames, tileIndex, cols, rows
from ij.process import ColorProcessor
from java.awt.image import BufferedImage as BI
from java.lang import Thread
f = ImagePlus.getDeclaredField("listeners")
f.setAccessible(True)
listeners = f.get(None)
imp = IJ.getImage()
canvas = imp.getWindow().getCanvas()
# Define range of slices to capture
slices = xrange(1, imp.getNSlices() + 1)
w, h = canvas.getWidth(), canvas.getHeight()
capture = ImageStack(w, h)
for i in slices:
imp.setSlice(i)
for l in listeners:
l.imageUpdated(imp)
Thread.sleep(50) # wait for repaints to happen, triggered by listeners, if any.
bi = BI(w, h, BI.TYPE_INT_ARGB)
g = bi.createGraphics()
canvas.paint(g)
g.dispose()
capture.addSlice(ColorProcessor(bi))
bi.flush()
ImagePlus("capture", capture).show()
def CreateCover(ip, width, height, dbpath):
# split input image into appropriate tiles
stackt = SplitImage(ip, width, height)
impt = ImagePlus("template", stackt)
nSlicestmp = impt.getNSlices()
# open the preprocessed database
print dbpath
impd = IJ.openImage(dbpath)
stackd = impd.getImageStack()
nSlicesdb = impd.getNSlices()
#associate index with image names
imageNames = impd.getProperty('Info')
imageList = imageNames.split(';')
# set up preview output
outputip = ColorProcessor(ip.width, ip.height)
outputimp = ImagePlus("output", outputip)
outputimp.show()
cols = ip.width/width
rows = ip.height/height
print str(cols) + "," + str(rows)
x = 0
y = 0
arrays = [None, None] # a list of two elements
cruncher = Inline(arrays)
tileNames = {}
tileIndex = {}
placed = {}
used = {}
while len(placed) < nSlicestmp:
randomTileIndex = random.randint(1, nSlicestmp)
if randomTileIndex in placed:
continue
# transform to row adn column coordinate
if randomTileIndex%rows == 0:
y = rows-1
x = (randomTileIndex/rows)-1
else:
y = (randomTileIndex%rows)-1
x = int(randomTileIndex/rows)
pixelst = stackt.getPixels(randomTileIndex)
minimum = Float.MAX_VALUE
#iterate through database images
j = 1
indexOfBestMatch = 0
arrays[0] = pixelst
while j < nSlicesdb:
if j in used:
j +=1
continue
arrays[1] = stackd.getPixels(j)
diff = cruncher.call()
if diff < minimum:
minimum = diff
indexOfBestMatch = j
j += 1
ip = stackd.getProcessor(indexOfBestMatch)
outputip.copyBits(ip, x*width, y*height, 0)
used[indexOfBestMatch] = 1
tileNames[randomTileIndex] = imageList[indexOfBestMatch-1]
tileIndex[randomTileIndex] = indexOfBestMatch-1
outputimp.draw()
placed[randomTileIndex] = 1
return tileNames, tileIndex, cols, rows
# # print 'fitGoodness', cv.getFitGoodness()
# # print 'formula', cv.getFormula()
# # fit_params = cv.getParams()
# # print 'fit_params', fit_params
# print all_pc
# print 'mean_cc', sum(all_pc)/len(all_pc)
# Create the 2D visualization of the fit plots
stack_w, stack_h = plot_images[0].getWidth(), plot_images[0].getHeight()
stack_plot = ImageStack(stack_w, stack_h)
# add all the plots in a stack
for id, plot_image in enumerate(plot_images):
for i in range(HEXAGON_SPACINGS[id]):
stack_plot.addSlice(
'plot_' + str(id).zfill(2),
ImagePlus('empty', ColorProcessor(stack_w,
stack_h)).getProcessor())
stack_plot.addSlice('plot_' + str(id).zfill(2), plot_image.getProcessor())
imp = ImagePlus('Plot_stack', stack_plot)
montageMaker = MontageMaker()
montage = montageMaker.makeMontage2(imp, 17, 9, 1, 1, imp.getNSlices(), 1, 3,
False)
IJ.save(montage, fit_montage_path)
montage.show()
IJ.log('Done')