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
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()
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")
