def make_tiled_imp(imp):
"""generate a ImageProcessor that is the input tiled 3 time horizontally"""
ip = imp.getProcessor()
stack = ImageStack(imp.getWidth(), imp.getHeight())
for idx in range(3):
stack.addSlice(ip)
temp_imp = ImagePlus("temp", stack)
tile_imp = MontageMaker().makeMontage2(temp_imp, 3, 1, 1, 1, 3, 1, 0,
False)
temp_imp.close()
return tile_imp
def make_montage(self, xy="", montage_name=""):
if self.channels_to_montage == None:
channels_to_montage = self.channel_names
else:
channels_to_montage = self.channels_to_montage
w = self.cropped_imps[self.channel_names[0]].width
h = self.cropped_imps[self.channel_names[0]].height
new_stack = ImageStack(w, h)
# print self.cropped_imps.keys()
for channel in channels_to_montage:
img = self.cropped_imps[channel].getProcessor()
new_stack.addSlice(img)
tomontage = ImagePlus("to montage", new_stack)
montager = MontageMaker()
self.montage = montager.makeMontage2(
tomontage, len(channels_to_montage), 1, 1, 1, len(channels_to_montage), 1, 0, 0
)
directory = self.outdir
file_name = self.name
save_as = os.path.join(directory, "%s_%s_montage.tif" % (file_name, xy))
IJ.save(self.montage, save_as)
def _channelmontage(_imp):
"""Makes a montage of a single channel ImagePlus object.
Args:
_imp (ImagePlus): A single channel ImagePlus object.
Returns:
ImagePlus: A montage of the one input channel.
"""
dims = _imp.getDimensions() # width, height, nChannels, nSlices, nFrames
frames = listProduct(dims[2:])
if frames > gridsize: frames = gridsize
_montage = MontageMaker().makeMontage2(_imp, hsize, vsize, 1.00, 1, frames, increment, 0, True)
return _montage
def plotRotation(roi_number, result_path, t, x, y, rotation_speed):
# plot t-x, t-y, x-y, t-rotation_speed and save plot+roi_number.bmp
txplot = Plot('x-t plot','time (s)', 'x (pixel)', t, x)
typlot = Plot('y-t plot','time (s)', 'y (pixel)', t, y)
xyplot = Plot('x-y plot', 'x (pixel)', 'y (pixel)', x, y)
tspeedplot = Plot('Rotation speed-t plot','time (s)', 'Rotaion Speed (Hz)', t, rotation_speed)
graphW = 1000
graphH = 500
txplot.setFrameSize(graphW, graphH)
typlot.setFrameSize(graphW, graphH)
xyplot.setFrameSize(graphW, graphH)
tspeedplot.setFrameSize(graphW, graphH)
#make plots as stack image
tximp = txplot.getImagePlus()
xyimp = xyplot.getImagePlus()
tyimp = typlot.getImagePlus()
tsimp = tspeedplot.getImagePlus()
pstack = ImageStack(tximp.width,tximp.height)
pstack.addSlice(tximp.getProcessor())
pstack.addSlice(tyimp.getProcessor())
pstack.addSlice(xyimp.getProcessor())
pstack.addSlice(tsimp.getProcessor())
pstackimp = ImagePlus('plots', pstack)
pstackM = MontageMaker().makeMontage2(pstackimp, 2, 2, 2, 1, 4, 1, 0, False)
#pstackM.show()
IJ.saveAs(pstackM, 'BMP', os.path.join(result_path,'Plot' + str(roi_number) + '.bmp'))
tximp.close()
xyimp.close()
tyimp.close()
tsimp.close()
pstackM.close()
# testMontageMaker
from ij import IJ, WindowManager, ImageStack, ImagePlus
from ij.io import FileInfo
from ij.plugin import MontageMaker
import jmFijiGen as jmg
IJ.run("Lena (68K)")
lena = IJ.getImage()
lI = [lena, lena, lena]
stack = jmg.makeStackFromListRGB(lI)
mont = MontageMaker()
# starts with a stack (stack) and returns an imp to the montage
# makeMontage2(ImagePlus imp, int columns, int rows, double scale, int first, int last, int inc, int borderWidth, boolean labels)
imp = mont.makeMontage2(stack, 3, 1, 1.0, 1, 3, 1, 0, False)
imp.show()
def __fmosa(self) :
mm = MontageMaker()
imp = mm.makeMontage2(self.__impRes, 1, self.__impRes.getStackSize(), 1, 1, self.__impRes.getStackSize(), 1, 0, False)
imp.setTitle("MONTAGE"+self.__name)
imp.show()
if self.__fire : IJ.run(imp, "Fire", "")
# # 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')
