149 lines
4.9 KiB
Python
Executable File
149 lines
4.9 KiB
Python
Executable File
###################################################################################################
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# Example of using ImageJ functionalities through ijutils.
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###################################################################################################
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from ijutils import *
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import java.awt.Color as Color
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#Image Loading
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ip = load_image("images/img2.png", title="Image2")
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#Basic image manipulation: creation, copying, padding, saving
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resized = resize(ip, 300,300)
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save_image(resized,get_context().setup.expandPath("{images}/resized.tiff") ,"tiff")
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crop=sub_image(ip,10,20,50,30)
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bin_im = binning(ip,2)
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new_im = new_image(256, 256, "color")
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copy_image_to(bin_im, new_im, 20, 20)
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pad_im = pad_image(ip, 1, 2, 3, 4, Color.RED)
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stack=create_stack([ip,resized,crop, bin_im, new_im, pad_im], title = "Basic Functions")
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save_image(stack,get_context().setup.expandPath("{images}/stack.tiff") ,"tiff")
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stack.show()
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#Decomposing color channels
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create_stack([ get_channel(ip, "red"),
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get_channel(ip, "green"),
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get_channel(ip, "blue"),
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get_channel(ip, "alpha"),
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grayscale(get_channel(ip, "brightness"), False)], title = "Color Decomposition").show()
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#Basic functions (in_place)
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aux1 = ip.duplicate()
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aux1.show()
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grayscale(aux1)
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gaussian_blur(aux1); aux1.repaintWindow()
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invert(aux1); aux1.repaintWindow()
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smooth(aux1); aux1.repaintWindow()
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sharpen(aux1); aux1.repaintWindow()
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noise(aux1, 100); aux1.repaintWindow()
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#Changing LUT
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aux = ip.duplicate()
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aux = grayscale(aux, in_place=False)
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r,g,b = [],[],[]
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for i in range(256):
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r.append(0)
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g.append(0)
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b.append(i)
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set_lut(aux, r, g, b)
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aux.show()
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#Histogram
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plot(get_histogram(ip))
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#Binarization and binary operations
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aux = grayscale(ip, in_place = False)
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bin = ip.duplicate()
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ip_bin = auto_threshold(aux, in_place=False)
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create_stack([ ip_bin,
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binary_outline(ip_bin, in_place=False),
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binary_dilate(ip_bin, in_place=False),
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binary_erode(ip_bin, in_place=False),
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binary_open(ip_bin, in_place=False),
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binary_close(ip_bin, in_place=False),
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binary_skeletonize(ip_bin, in_place=False),
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binary_fill_holes(ip_bin, in_place=False),
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binary_outline(ip_bin, in_place=False)], title = "Binarization").show()
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#EDM, const & image operations
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aux = grayscale(ip, in_place = False)
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ip_bin = auto_threshold(aux, in_place=False)
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binary_fill_holes(ip_bin)
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edm = edm(ip_bin, in_place=False)
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ws = watershed(ip_bin, in_place=False)
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up = ultimate_points(ip_bin, in_place=False)
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vr = veronoi(ip_bin, in_place=False)
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edm_disp = remap(edm, in_place=False)
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ws_disp = grayscale(ws, False)
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up_disp = enhance_contrast(up, in_place=False)
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vr_disp = enhance_contrast(vr, in_place=False)
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create_stack([edm_disp, aux, ip_bin, ws_disp, up_disp, vr_disp], title = "EDM Operations").show()
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final = grayscale(ip_bin, in_place = False)
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op_const(final,"add", -200)
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op_image(final, vr_disp, 'or')
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op_image(final, up_disp, 'or')
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final.show()
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aux = grayscale(ip, in_place = False)
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create_stack([ aux,
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subtract_background(aux, in_place=False),
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smooth(aux, False),
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sharpen(aux, False),
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edges(aux, False),
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bandpass_filter(aux,0, 5, in_place=False),
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bandpass_filter(aux,5, 100, in_place=False),
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op_const(aux,"and", 127, False),
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convolve(aux, KERNEL_BLUR, False),
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convolve(aux, KERNEL_SHARPEN, False),
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convolve(aux, KERNEL_SHARPEN_2, False),
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convolve(aux, KERNEL_LIGHT, False),
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convolve(aux, KERNEL_DARK, False),
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convolve(aux, KERNEL_EDGE_DETECT, False),
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convolve(aux, KERNEL_EDGE_DETECT_2, False),
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convolve(aux, KERNEL_DIFFERENTIAL_EDGE_DETECT, False),
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convolve(aux, KERNEL_PREWITT, False),
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convolve(aux, KERNEL_SOBEL, False)
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], title = "General Operations").show()
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#Rank operators
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rank_opers = []
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for op in "mean", "min", "max", "variance", "median", "close_maxima", "open_maxima", "remove_outliers", "remove_nan", "despeckle":
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rank_opers.append(op_rank(aux,op, in_place=False, kernel_radius=1))
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create_stack(rank_opers, title = "Rank Operations").show()
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#Reslicing
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#orig = load_image("{data}/img/img2.png")
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orig = resize(ip, 300,200)
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grayscale(orig)
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images=[]
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for i in range (20):
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images.append(orig.duplicate())
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op_const(orig, "multiply", 0.9)
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stack=create_stack(images, title = "Original Stack")
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#stack.show()
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r1 = reslice(stack, start_at="Left", title="Reslice Horizontally")
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r2 = reslice(stack, start_at="Top", title="Reslice Vertically")
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r1.show()
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r2.show()
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#Particle Analysis
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aux = grayscale(ip, in_place = False)
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auto_threshold(aux)
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#binary_fill_holes(aux)
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#aux.show()
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(results,output_img)=analyse_particles(aux, 100,1000, print_table=True)
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output_img.show()
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