def change_composite_display(imp, luts): ''' luts = [["green",0,1],["red",0,1]] ''' # make Luts grayLut = LUT.createLutFromColor(Color.white) #grayLut.min = luts[0][1]; grayLut.max = luts[0][2] #print grayLut greenLut = LUT.createLutFromColor(Color.green) #greenLut.min = luts[1][1]; greenLut.max = luts[1][2] #print greenLut # change display mode (otherwise the Lut changes do not work) imp.setDisplayMode(IJ.COLOR) # set Luts print "imp.isComposite()",imp.isComposite() imp.setC(1); imp.setChannelLut(grayLut) imp.setDisplayRange(luts[0][1], luts[0][2]) imp.setC(2); imp.setChannelLut(greenLut) #IJ.run(imp, "Fire", ""); #IJ.setMinAndMax(imp, 100, 255); imp.setDisplayRange(luts[1][1], luts[1][2]) #imp.getProcessor().invertLut() # check that it worked print imp.getLuts() imp.setDisplayMode(IJ.COMPOSITE) return imp
def apply_lut(cs, cmap):
# type: (CellStack, str) -> None
"""
Apply a different Look Up Table according to the given cmap name
:param cmap: Can be 'fire'
"""
stats = StackStatistics(cs)
ll = LutLoader()
if cmap == 'fire':
cm = ll.open('luts/fire.lut')
# print("Stats.max " + str(stats.max))
lut = LUT(cm, stats.min, stats.max)
cs.setLut(lut)
else:
IJ.error('Invalid color map: ' + cmap + '\nDefault LUT applied')
def analyze_homogeneity(image_title):
IJ.selectWindow(image_title)
raw_imp = IJ.getImage()
IJ.run(raw_imp, "Duplicate...", "title=Homogeneity duplicate")
IJ.selectWindow('Homogeneity')
hg_imp = IJ.getImage()
# Get a 2D image
if hg_imp.getNSlices() > 1:
IJ.run(hg_imp, "Z Project...", "projection=[Average Intensity]")
hg_imp.close()
IJ.selectWindow('MAX_Homogeneity')
hg_imp = IJ.getImage()
hg_imp.setTitle('Homogeneity')
# Blur and BG correct the image
IJ.run(hg_imp, 'Gaussian Blur...', 'sigma=' + str(HOMOGENEITY_RADIUS) + ' stack')
# Detect the spots
IJ.setAutoThreshold(hg_imp, HOMOGENEITY_THRESHOLD + " dark")
rm = RoiManager(True)
table = ResultsTable()
pa = ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER,
ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES,
Measurements.AREA, # measurements
table, # Output table
0, # MinSize
500, # MaxSize
0.0, # minCirc
1.0) # maxCirc
pa.setHideOutputImage(True)
pa.analyze(hg_imp)
areas = table.getColumn(table.getHeadings().index('Area'))
median_areas = compute_median(areas)
st_dev_areas = compute_std_dev(areas, median_areas)
thresholds_areas = (median_areas - (2 * st_dev_areas), median_areas + (2 * st_dev_areas))
roi_measurements = {'integrated_density': [],
'max': [],
'area': []}
IJ.setForegroundColor(0, 0, 0)
for roi in rm.getRoisAsArray():
hg_imp.setRoi(roi)
if REMOVE_CROSS and hg_imp.getStatistics().AREA > thresholds_areas[1]:
rm.runCommand('Fill')
else:
roi_measurements['integrated_density'].append(hg_imp.getStatistics().INTEGRATED_DENSITY)
roi_measurements['max'].append(hg_imp.getStatistics().MIN_MAX)
roi_measurements['integrated_densities'].append(hg_imp.getStatistics().AREA)
rm.runCommand('Delete')
measuremnts = {'mean_integrated_density': compute_mean(roi_measurements['integrated_density']),
'median_integrated_density': compute_median(roi_measurements['integrated_density']),
'std_dev_integrated_density': compute_std_dev(roi_measurements['integrated_density']),
'mean_max': compute_mean(roi_measurements['max']),
'median_max': compute_median(roi_measurements['max']),
'std_dev_max': compute_std_dev(roi_measurements['max']),
'mean_area': compute_mean(roi_measurements['max']),
'median_area': compute_median(roi_measurements['max']),
'std_dev_area': compute_std_dev(roi_measurements['max']),
}
# generate homogeinity image
# calculate interpoint distance in pixels
nr_point_columns = int(sqrt(len(measuremnts['mean_max'])))
# TODO: This is a rough estimation that does not take into account margins or rectangular FOVs
inter_point_dist = hg_imp.getWidth() / nr_point_columns
IJ.run(hg_imp, "Maximum...", "radius="+(inter_point_dist*1.22))
# Normalize to 100
IJ.run(hg_imp, "Divide...", "value=" + max(roi_measurements['max'] / 100))
IJ.run(hg_imp, "Gaussian Blur...", "sigma=" + (inter_point_dist/2))
hg_imp.getProcessor.setMinAndMax(0, 255)
# Create a LUT based on a predefined threshold
red = zeros(256, 'b')
green = zeros(256, 'b')
blue = zeros(256, 'b')
acceptance_threshold = HOMOGENEITY_ACCEPTANCE_THRESHOLD * 256 / 100
for i in range(256):
red[i] = (i - acceptance_threshold)
green[i] = (i)
homogeneity_LUT = LUT(red, green, blue)
hg_imp.setLut(homogeneity_LUT)
return hg_imp, measuremnts
IJ.run(mergedImage,"Refractive Signal Loss Correction",params)
dataImage = WindowManager.getImage("App Corrected")
mergedImage.close()
refCorrectedImage = WindowManager.getImage("Ref Corrected")
refCorrectedImage.close()
else:
dataImage = channelImages[analysisChannel-1]
if (refChannel > 0):
params = ("reference_channel=" + str(refChannel) +
" application_channel=" + str(analysisChannel) + " automatic_operation" +
" generate_log max_slice=43 surface_slice=87")
IJ.run(theImage,"Refractive Signal Loss Correction",params)
dataImage = WindowManager.getImage("App Corrected")
refCorrectedImage = WindowManager.getImage("Ref Corrected")
refCorrectedImage.close()
dataImage.setLut(LUT.createLutFromColor(Color.WHITE))
#dataImage.setCalibration(calibration)
dataImage.show()
if (processFilter > 0):
if processFilter == 1:
IJ.run(dataImage,"Minimum...", "radius=2 stack")
if processFilter == 2:
IJ.run(dataImage,"Median...", "radius=2 stack")
theImage.close()
## Now runs the object counter on the processed tile
params = ("volume surface nb_of_obj._voxels " +
"nb_of_surf._voxels integrated_density mean_gray_value " +
"std_dev_gray_value median_gray_value minimum_gray_value " +
"maximum_gray_value centroid mean_distance_to_surface " +
"std_dev_distance_to_surface median_distance_to_surface centre_of_mass " +
Canceled = False
if not Canceled:
for f in file_path:
# Hyperstackの作成
imp = IJ.openImage(f)
nFrame = imp.getNSlices(
) / n_Channel # 元画像のAttributionがなぜかFrame が Z sliceとなっている
# File 保存のための文字列作成
save_file = imp.getTitle().replace(".tif", "-stack.tif")
save_path = os.path.join(save_dir, save_file)
# Hyper Stackに変換
h_imp = HyperStackConverter.toHyperStack(imp, n_Channel, 1, nFrame,
"Composite")
del imp
# Hyper Stack の Channelカラー変更
for i, color in enumerate(user_color):
h_imp.setC(i + 1)
h_imp.setLut(LUT.createLutFromColor(Colors[color]))
# ファイルを保存
IJ.saveAsTiff(h_imp, save_path)
# IJ.log(save_path)
del h_imp
active_image.setRoi(proi)
return active_image
## Main body of script starts here
od = OpenDialog("Select parent LSM file...")
parentLSMFilePath = od.getPath()
if parentLSMFilePath is not None:
tileConfigFilePath = parentLSMFilePath + "_tiles/resized/TileConfiguration.registered.txt"
scale_info = estimate_scale_multiplier(parentLSMFilePath+"_tiles/tile_1.ome.tif",parentLSMFilePath+"_tiles/resized/tile_1.tif")
print scale_info
coords = read_tileconfig_file(tileConfigFilePath)
full_keys = ["tile_"+str(i) for i in range(1,len(coords.keys())+1)]
coords_vals = normalize_coords_in_list(get_list_from_dict(full_keys,coords))
im = IJ.getImage()
if im.getNChannels() == 1:
LUTarray = [LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 2:
LUTarray = [LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 3:
LUTarray = [LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 4:
LUTarray = [LUT.createLutFromColor(Color.BLUE),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 5:
LUTarray = [LUT.createLutFromColor(Color.BLUE),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.YELLOW),LUT.createLutFromColor(Color.WHITE)]
else:
LUTarray = []
nbgd = NonBlockingGenericDialog("Pick freehand ROI")
nbgd.setLocation(0,0)
nbgd.addMessage("OK to run, cancel to exit")
nbgd.showDialog()
# adjust min and max, since we know them
imp.getProcessor().setMinAndMax(0, w-1)
imp.show()
# Create a random 8-bit image the hard way...
width = 512
height = 512
pix = zeros(width * height, 'b')
Random().nextBytes(pix)
channel = zeros(256, 'b')
for i in range(256):
channel[i] = (i -128)
cm = LUT(channel, channel, channel)
imp_rand_hard = ImagePlus("Random", ByteProcessor(width, height, pix, cm))
imp_rand_hard.show()
# random 16 bit the hard way...
imp = IJ.createImage("An Easy Random Image 8 bit image", "8-bit", 512, 512, 1)
Random().nextBytes(imp.getProcessor().getPixels())
imp.show()
print(sys.getsizeof(int))
print(sys.getsizeof(bytes))
# 1 - Obtain an image
blobs = IJ.openImage("http://imagej.net/images/blobs.gif")
blobs.setTitle("blobs")
blobs.show()
if dirPath is not None:
dc2 = DirectoryChooser("Select output directory...")
outPath = dc2.getDirectory()
if outPath is not None:
gd = GenericDialog("Options...")
gd.addCheckbox("Recolor_images",True)
gd.showDialog()
if (gd.wasOKed()):
doRecolor = gd.getNextBoolean()
for f in os.listdir(dirPath):
if f.endswith(".tif") or f.endswith(".tiff"):
theImage = IJ.openImage(dirPath+f)
IJ.log("Loaded " + f)
palette = [Color.GREEN,Color.RED,Color.BLUE]
if (theImage.getNChannels() < 4):
if doRecolor:
for i in range(theImage.getNChannels()):
theImage.setChannelLut(LUT.createLutFromColor(palette[i]),i+1)
try:
sc = StackConverter(theImage)
sc.convertToRGB()
IJ.saveAsTiff(theImage,outPath+os.path.splitext(f)[0]+"_rgb.tif")
IJ.log("Completed " + f)
except:
IJ.log("Exception thrown during RGB conversion, image skipped")
finally:
theImage.close()
else:
IJ.log("Image has too many color channels")