def ReturnColorThresholdedPicture(PICPATH, L_min, L_max, a_min, a_max, b_min,
b_max):
imp = IJ.openImage(PICPATH)
imp.show()
ImageTitle = imp.getTitle()
LabThresold_List = [[L_min, L_max], [a_min, a_max], [b_min, b_max]]
Filt_List = ["pass", "pass", "pass"]
ColorThresholder.RGBtoLab()
IJ.run(imp, "RGB Stack", "")
IJ.run("Stack to Images", "")
IJ.selectWindow("Red")
IJ.run('Rename...', 'title=0') #title=hoge =(equal)の間にスペースを入れてならない。
imp0 = IJ.getImage()
IJ.selectWindow("Green")
IJ.run('Rename...', 'title=1')
imp1 = IJ.getImage()
IJ.selectWindow("Blue")
IJ.run('Rename...', 'title=2')
imp2 = IJ.getImage()
for i in range(3):
WindowTitle = str(i)
MinValue = float(LabThresold_List[i][0])
MaxValue = float(LabThresold_List[i][1])
IJ.selectWindow(WindowTitle)
IJ.setThreshold(MinValue, MaxValue)
IJ.run(IJ.getImage(), "Convert to Mask", "")
if Filt_List[i] == "stop":
ImageProcessor.invert()
#コメントアウトした、imgculcは動かなくなくなった,謎
#imp3 = ImageCalculator.run(imp0, imp1, "and create")
#imp4 = ImageCalculator.run(imp3,imp2, "and create")
imp3 = ImageCalculator().run("and create", imp0, imp1)
imp4 = ImageCalculator().run("and create", imp3, imp2)
imp3.show()
imp4.show()
ResultTitle = imp4.getTitle()
IJ.selectWindow(ResultTitle)
imp4.setTitle(ImageTitle)
#Saveした時点で画像の情報が失われる.
imp.close()
imp0.close()
imp1.close()
imp2.close()
imp3.close()
return imp4
def run_script():
'''Function to be run when this file is used as a script'''
selected_mode, img1_in, img2_in = get_setup()
if not selected_mode:
return
corrected_stack = drift.get_corrected_stack((img1_in, img2_in), mode=selected_mode)
img1, img2 = tools.stack_to_list_of_imp(corrected_stack)
img_ratio = ImageCalculator().run('Divide create', img2, img1)
img_ratio.setTitle('Jump-ratio [%s divided by %s]' % (img2.getShortTitle(),
img1.getShortTitle())
)
img_ratio.changes = True
img_ratio.copyScale(img1_in)
img_ratio.show()
IJ.run(img_ratio, 'Enhance Contrast', 'saturated=0.35')
# We want to optimise the lower displaylimit:
minimum = img_ratio.getProcessor().getMin()
maximum = img_ratio.getProcessor().getMax()
stat = img_ratio.getStatistics(Stats.MEAN + Stats.STD_DEV)
mean = stat.mean
stdv = stat.stdDev
if minimum < mean - stdv:
if mean - stdv >= 0:
img_ratio.getProcessor().setMinAndMax(mean - stdv, maximum)
else:
img_ratio.getProcessor().setMinAndMax(0, maximum)
img_ratio.updateAndDraw()
def mousePressed(self, event):
from ij import IJ, ImagePlus
from ij.process import FloatProcessor
import math
from ij.plugin import ImageCalculator
imp = IJ.getImage()
imp.setSlice(3)
ip = imp.getProcessor().convertToFloat() # as a copy
pixels = ip.getPixels()
imp.setSlice(2)
ip1 = imp.getProcessor().convertToFloat() # as a copy
pixels1 = ip1.getPixels()
imp.setSlice(1)
ip2 = imp.getProcessor().convertToFloat() # as a copy
pixels2 = ip2.getPixels()
canvas = event.getSource()
p = canvas.getCursorLoc()
imp = canvas.getImage()
x = p.x * 1.0000
y = p.y * 1.0000
nx = x - imp.width / 2
ny = y - imp.height / 2
n_y = ny * -1
n_xx = nx / imp.width / 2
n_yy = n_y / imp.height / 2
z = math.sqrt(n_xx * n_xx + n_yy * n_yy)
z1 = math.sqrt(1 - z * z)
Xdir = map(lambda x: x * n_xx, pixels2)
Ydir = map(lambda x: x * n_yy, pixels1)
Zdir = map(lambda x: x * z1, pixels)
ip3 = FloatProcessor(ip.width, ip.height, Xdir, None)
imp3 = ImagePlus("", ip3)
ip4 = FloatProcessor(ip.width, ip.height, Ydir, None)
imp4 = ImagePlus("", ip4)
ip5 = FloatProcessor(ip.width, ip.height, Zdir, None)
imp5 = ImagePlus("", ip4)
imp6 = ImageCalculator().run("Add create 32-bit stack", imp3, imp4)
imp7 = ImageCalculator().run("Add create 32-bit stack", imp5, imp6)
imp7.setTitle("Lighting Direction")
imp7.show()
def ratiometric(LP, org_size, max_Y, min_Y):
""" Generates ratiometric images of dFRET/aFRET for each timepoint. """
source_directory = "D:\\Image_Processing\\Virtualstacks\\Lif_Stack_Split_aligned_all\\"
destination_directory = "D:\\Image_Processing\\Virtualstacks\\Ratiometrics\\"
destination_directory2 = "D:\\Image_Processing\\Virtualstacks\\Ratiometrics_withROI\\"
# As in nested_calculator.
AER = ((8.8764*(LP**2)) + (1.8853*LP)) - 0.1035
DER = 0.1586
# File list of every image in every channel.
channels = []
for root, directory, filenames in os.walk(source_directory):
for filename in filenames:
channels.extend(filename)
# Channel-separator.
IDD, IDA, IAA = channels[0::3], channels[1::3], channels[2::3]
# Create combined ROI.
rm = RoiManager.getInstance()
rm.runCommand("Select All")
rm.runCommand("Combine")
rm.runCommand("Add")
roi = rm.getRoi(rm.getCount())
for timepoint in range(len(IDD)):
# Opens each image, clears outside ROIs.
IDD_base = IJ.openImage(os.path.join(root, IDD[timepoint]))
IDD_base_ip = IDD_base.getProcessor()
IDD_base_ip.fillOutside(roi)
IDA_base = IJ.openImage(os.path.join(root, IDA[timepoint]))
IDA_base_ip = IDA_base.getProcessor()
IDA_base_ip.fillOutside(roi)
IAA_base = IJ.openImage(os.path.join(root, IAA[timepoint]))
IAA_base_ip = IAA_base.getProcessor()
IAA_base_ip.fillOutside(roi)
# Duplicates IDD, IAA for subtraction of cross-talk.
IDD_subtracted = Duplicator().run(IDD_base)
IAA_subtracted = Duplicator().run(IAA_base)
IJ.run(IDD_subtracted, "Multiply...", "value="+str(DER))
IJ.run(IDA_subtracted, "Multiply...", "value="+str(AER))
# Subtracts cross-talk from IDA.
cFRET1 = ImageCalculator().run("Subtract create 32-bit", IDA, IDD_subtracted)
cFRET = ImageCalculator().run("Subtract create 32-bit", cFRET1, IAA_subtracted)
# Corrected donor concentration.
donor_c = ImageCalculator().run("Add create 32-bit", IDD_base, cFRET)
# dFRET.
dFRET = ImageCalculator().run("Divide create 32-bit", cFRET, donorc)
dFRET.setTitle("dFRET")
IJ.run(dFRET, "Rainbow RGB", "")
# aFRET.
aFRET = ImageCalculator().run("Divide create 32-bit", cFRET, IAA_base)
IJ.run(aFRET, "Divide...", "value=4.66")
aFRET.setTitle("aFRET")
IJ.run(aFRET, "Rainbow RGB", "")
# Scalebar.
dimensions = dFRET.getDimensions()
size = dimensions[0] + dimensions[1]
microns = org_size / size
FRET = [aFRET, dFRET]
for i in range(2):
IJ.run(FRET[i], "Set Scale...", "distance=1 known="+str(microns)+" pixel=1 unit=micron")
IJ.run(FRET[i], "Scale Bar...", "width=10 height=4 font=14 color=Yellow background=None location=[Lower Right] bold overlay")
#FRET[i].getProcessor().setMinAndMax(0, 1)
IJ.run(FRET[i], "Calibration Bar...", "location=[Upper Right] fill=None label=White number=3 decimal=2 font=12 zoom=1.5 bold overlay")
IJ.run(FRET[i], "Flatten", "stack")
# Save.
IJ.saveAs(aFRET, "Tiff", os.path.join(destination_directory, IDD[i][0:7]+"aFRET"))
IJ.saveAs(dFRET, "Tiff", os.path.join(destination_directory, IDD[i][0:7]+"dFRET"))
