def createLabelColorBar():
imp7 = ImagePlus("labelColorBar", ShortProcessor(180, 20))
ip7 = imp7.getProcessor()
pix = ip7.getPixels()
n_pixels = len(pix)
# catch width
w = imp7.getWidth()
# create a ramp gradient from left to right
for i in range(len(pix)):
pix[i] = int((i % w) / 18) + 1
# adjust min and max
ip7.setMinAndMax(0, 255)
font = Font("SansSerif", Font.PLAIN, 12)
overlay = Overlay()
for i in range(len(pix)):
roi = TextRoi(i * 18 + 2, 2, str(i + 1), font)
roi.setStrokeColor(Color.black)
overlay.add(roi)
imp7.setOverlay(overlay)
imp7.show()
IJ.run("glasbey_on_dark")
imp7 = imp7.flatten()
return imp7
def write_roi_numbers(ov, corners, L):
roiID = 1
for [x, y] in corners:
text = TextRoi(x, y, L, L, str(roiID), Font("Arial", Font.PLAIN, 400))
text.setJustification(1)
text.setColor(Color.RED)
ov.add(text)
roiID += 1
return ov
def write_roi_numbers(ov, corners, L):
fontsize = int(L / 1.5)
roiID = 1
for [x, y] in corners:
text = TextRoi(x, y, L, L, str(roiID),
Font("Arial", Font.BOLD, fontsize))
text.setJustification(2)
text.setColor(Color.RED)
ov.add(text)
roiID += 1
return ov
def generate_limit_labels(imp, limits, cb_fraction, params):
"""generate text ROIs in correct positions to label colorbar"""
rois = []
w = imp.getWidth()
h = imp.getHeight()
txt_h_px = float(h) / 15
txt_sz_pt = int(round((18.0 / 24.0) * txt_h_px))
for limit in limits:
roi = TextRoi(1, 1, str(round(limit, 3)),
Font("SansSerif", Font.ITALIC, txt_sz_pt))
roi.setJustification(TextRoi.RIGHT)
roi.setFillColor(Color.BLACK)
roi.setStrokeColor(Color.WHITE)
rois.append(roi)
roim = RoiManager(False)
roim.reset()
imp.show()
mbui.autoset_zoom(imp)
for fridx in range(1, imp.getNSlices() + 1):
imp.setPosition(fridx)
roi_uu = rois[1].clone()
xpos = w - cb_fraction * w - float(w) / 100 - rois[1].getFloatWidth()
roi_uu.setLocation(xpos, 1)
imp.setRoi(roi_uu)
roim.addRoi(roi_uu)
roi_ll = rois[0].clone()
roi_ll.setLocation(xpos, h - rois[0].getFloatHeight())
imp.setRoi(roi_ll)
roim.addRoi(roi_ll)
roim.runCommand("Show All")
FileSaver(imp).saveAsTiff(
os.path.join(params.output_path,
"overlaid curvature nudged labels.tif"))
# nudge positions
roim.reset()
imp.killRoi()
for fridx in range(1, imp.getNSlices() + 1):
imp.setPosition(fridx)
roi_uu = rois[1].clone()
xpos = w - cb_fraction * w - float(w) / 100
roi_uu.setLocation(xpos, 1)
imp.setRoi(roi_uu)
roim.addRoi(roi_uu)
roi_ll = rois[0].clone()
roi_ll.setLocation(xpos, h - rois[0].getFloatHeight())
imp.setRoi(roi_ll)
roim.addRoi(roi_ll)
roim.runCommand("Show All")
FileSaver(imp).saveAsTiff(
os.path.join(params.output_path, "overlaid curvature.tif"))
return imp
def drawLines(imp, points=None):
if points and (len(points) % 2 == 0):
# points is numeric list of even length
pRoi = PointRoi(points[0::2], points[1::2], len(points) / 2)
pRoi.setShowLabels(True)
pRoi.setSize(3)
imp.setRoi(pRoi)
roi = imp.getRoi()
pp = roi.getFloatPolygon()
# print "Added", pp.npoints
if pp.npoints <= 1:
# don't draw if only one point
return
xys = []
for i in xrange(pp.npoints):
xys.append([pp.xpoints[i], pp.ypoints[i]])
ol = Overlay()
x0 = xys[0][0]
y0 = xys[0][1]
cal = imp.getCalibration()
for i in xrange(1, pp.npoints):
xi = xys[i][0]
yi = xys[i][1]
# prepare text label
d = math.sqrt((xi - x0)**2 + (yi - y0)**2) * cal.pixelWidth
dText = String.format("%.2f ", d) + cal.getUnits()
textOffset = 30
xt = xi
yt = yi
# if xi > x0:
# xt += textOffset
if xi < x0:
xt -= textOffset
# if yi > y0:
# yt += textOffset
if yi < y0:
yt -= textOffset
dTextRoi = TextRoi(xt, yt, dText)
ol.add(dTextRoi)
lineRoi = Line(x0, y0, xi, yi)
lineRoi.setStrokeWidth(1)
lineRoi.setStrokeColor(Color(255, 255, 0))
ol.add(lineRoi)
imp.setOverlay(ol)
imp.updateAndDraw()
def createMIP(self):
print "starting createMIP"
for a in self.itemSelected:
ImStack = None
for filename in self.dict1.get(a):
self.savfileName = a
if not filename.endswith(self.fileExt):
continue
path = self.sourceDir + filename
# Upon finding the first image, initialize the VirtualStack
if ImStack is None:
imp = IJ.openImage(path)
ImStack = VirtualStack(imp.width, imp.height, None,
self.sourceDir)
# Add a slice, relative to the sourceDIr
ImStack.addSlice(filename)
#adding text overlay to output images so we can differentiate them. Overlay is non destructive - does not affect pixel values of image, and can be selected and deleted
prefix_overlay = Overlay()
font = Font("SansSerif", Font.PLAIN, 10)
roi = TextRoi(0, 0, a)
roi.setStrokeColor(Color(1.00, 1.00, 1.00))
prefix_overlay.add(roi)
#
OnscreenImage = ImagePlus(self.sourceDir, ImStack)
OnscreenImage.setOverlay(prefix_overlay)
OnscreenImage.show()
print "Generating MIP, waiting..."
self.outimp = self.maxZprojection(
OnscreenImage) #generate max projection
self.outimp.setOverlay(prefix_overlay)
self.outimp.show()
print "Max projection generated"
if self.saveState == "Y":
self.saveMIP()
print "Finished!"
rt = ResultsTable.getResultsTable()
celli = 0
FONT = Font(Font.SANS_SERIF, Font.BOLD, 16)
for cell in cells_hoescht_opn:
area = cell.getStatistics().area * cal.pixelWidth * cal.pixelHeight
if area >= MINA and area <= MAXA:
cell.setStrokeColor(Color.MAGENTA)
ol.add(cell)
edm_sca1_gfp.setRoi(cell)
dist = edm_sca1_gfp.getStatistics().mean * cal.pixelWidth
row = rt.getCounter()
rect = cell.getBounds()
rt.setValue("Image", row, imp.getTitle())
rt.setValue("OPN+ Cell", row, celli)
rt.setValue("X", row, (rect.x + rect.width / 2.0) * cal.pixelWidth)
rt.setValue("Y", row, (rect.y + rect.height / 2.0) * cal.pixelHeight)
rt.setValue(
"OPN+ cell distance from SCA1+ GFP+ (" + u"\u00b5" + "m" + ")",
row, dist)
label = TextRoi(rect.x, rect.y - 16, str(celli), FONT)
label.setStrokeColor(Color.MAGENTA)
ol.add(label)
celli += 1
rt.show("Results")
imp.setOverlay(ol)
impProc.setInterpolationMethod(ImageProcessor.NONE)
impProc = impProc.resize(canvasWidth,canvasHeight)
imp.setProcessor(impProc)
imp.show()
IJ.run(imp, "Rainbow RGB", "");
IJ.run(imp, "Canvas Size...", "width=800 height=1024 position=Top-Center zero");
testROI = Roi(0,canvasHeight,canvasWidth,6)
testROI.setFillColor(Color.WHITE)
imp.setRoi(testROI,True)
overlay = Overlay(testROI)
font = Font("SansSerif",Font.PLAIN,fontSize)
# Write the EmissionWavelengths according
# to the metadata read earlier.
for i in xrange(1,len(pixelInt2[0]),tickInterval):
pixelSize = (canvasWidth/(len(pixelInt2[0])*1.0))
calc = (pixelSize)*(i)
roi = TextRoi(calc+(pixelSize*0.2),canvasHeight+10,str(emissionWL[i]),font)
roi.setStrokeColor(Color(1.00, 1.00, 1.00));
overlay.add(roi)
imp.setOverlay(overlay)
imp.show()
IJ.run(imp, "Calibration Bar...", "location=[Upper Right] fill=None label=White number=3 decimal=1 font=9 zoom=2 bold overlay");
# Saves the output file.
IJ.saveAs(imp,"png",hyperspaceImage)
gfpSum += roiStatsGfp.mean * roiStatsGfp.area
gfp.setStrokeColor(Color.MAGENTA)
gfp.setPosition(0, z, 1)
ol.add(gfp)
gfpMean = gfpSum / gfpA if gfpA > 0 else 0
row = rt.getCounter()
uni = row % 26
cha = chr(ord('A') + uni)
name = ""
while len(name) < (row + 1) / 26.0:
name += cha
label = TextRoi(name, cXbf - 20, cYbf + 20, FONT)
label.setStrokeColor(Color.GREEN)
label.setPosition(0, z, 1)
ol.add(label)
rt.setValue("Organoid", row, name)
rt.setValue("X", row, cXbf * cal.pixelWidth)
rt.setValue("Y", row, cYbf * cal.pixelHeight)
rt.setValue("Area", row,
roiStatsBF.area * cal.pixelWidth * cal.pixelHeight)
rt.setValue("Contained Tomato Area", row,
tomatoA * cal.pixelWidth * cal.pixelHeight)
rt.setValue("Contained GFP Area", row,
gfpA * cal.pixelWidth * cal.pixelHeight)
rt.setValue("Contained GFP Mean", row, gfpMean)
