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 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 draw_scale(image, ticks):
cal = image.getCalibration()
overlay = Overlay()
image.setOverlay(overlay)
TextRoi.setGlobalJustification(TextRoi.CENTER)
offset = image.getHeight() - extend
for tick in ticks:
tick_pos = cal.getRawX(tick)
line = Line(tick_pos, offset, tick_pos, offset + font_size)
line.setWidth(font_size // 8)
line.setStrokeColor(Color(1.00, 1.00, 1.00))
overlay.add(line)
text = TextRoi(tick_pos, offset + font_size, str(tick), font)
text_width = text.getFloatWidth()
text_y = text.getYBase()
text.setLocation(tick_pos - text_width/2, text_y)
text.setStrokeColor(Color(1.00, 1.00, 1.00))
overlay.add(text)
def getCells(dicStack):
outStack = ImageStack(W,H)
cells = [None for t in range(T+1)]
for t in range(1,T+1):
mapp = dicStack.getProcessor(t).convertToFloatProcessor()
mapp.subtract( mapp.getStatistics().mean )
mapp.abs()
RankFilters().rank(mapp, 1.0, RankFilters.VARIANCE)
mapp.sqrt()
mapp.blurGaussian(5)
hist = mapp.getHistogram(256)
stats = mapp.getStatistics()
thresh = AutoThresholder().getThreshold( AutoThresholder.Method.Otsu, hist )
thresh = (thresh/float(255)) * (stats.max-stats.min) + stats.min
mask = ByteProcessor(W,H)
for i in range(W*H):
value = mapp.getf(i)
bite = 255 if value>=thresh else 0
mask.set(i, bite)
fillHoles(mask)
ed = 3
for e in range(ed): mask.erode(1, 0)
for d in range(ed): mask.dilate(1, 0)
watershed(mask)
minA = 5000 #px²
mask.setThreshold(255,255, ImageProcessor.NO_LUT_UPDATE)
composite = ThresholdToSelection().convert(mask)
rois = ShapeRoi(composite).getRois()
keep = []
for roi in rois:
if roi.getStatistics().area >= minA:
if not onEdge(roi):
keep.append(roi)
else:
edgeRoi = ShapeRoi(roi)
edgeRoi.setPosition(0,0,t)
edgeRoi.setStrokeColor(Color.YELLOW)
ol.add(edgeRoi)
print("T"+str(t)+" using "+str(len(keep))+"/"+str(len(rois))+" ROIs")
rois = keep
#rois = [ roi for roi in rois if roi.getStatistics().area >= minA and not onEdge(roi) ] #keep big enough and not on edges
# if there is only one Roi, cut it along the fitted ellipse minor axis
if len(rois)==1:
el = EllipseFitter()
mask.setRoi(rois[0])
el.fit(mask, None)
el.makeRoi(mask)
theta = el.angle * (maths.pi/180.0)
length = el.major/2.0
dy = maths.sin(theta)* length
dx = maths.cos(theta)* length
#major axis
lineX0 = el.xCenter - dx
lineY0 = el.yCenter + dy
lineX1 = el.xCenter + dx
lineY1 = el.yCenter - dy
line = Line(lineX0, lineY0, lineX1, lineY1)
line.setStrokeColor(Color.BLUE)
line.setStrokeWidth(1)
line.setPosition(0,0,t)
ol.add(line)
#minor axis scaled length to make sure cut ends are outside Roi
cutX0 = el.xCenter + dy*100
cutY0 = el.xCenter + dx*100
cutX1 = el.yCenter - dy*100
cutY1 = el.yCenter - dx*100
cut = Line(cutX0,cutY0, cutX1, cutY1)
cut.setStrokeWidth(2)
cut = PolygonRoi( cut.getFloatPolygon(), PolygonRoi.POLYGON )
mask.setColor(0)
mask.fill(cut)
composite = ThresholdToSelection().convert(mask)
rois = ShapeRoi(composite).getRois()
rois = [ roi for roi in rois if roi.getStatistics().area >= minA ]
print(str(t) + ":" + str(len(rois)))
rois = [ PolygonRoi(roi.getInterpolatedPolygon(20, True), PolygonRoi.POLYGON) for roi in rois ]
rois = [ PolygonRoi(roi.getConvexHull(), PolygonRoi.POLYGON) for roi in rois ]
rois = sorted(list(rois), key=lambda roi:roi.getLength() ) #size order
rois = rois[-2:] #keep 2 biggest
rois = sorted(list(rois), key=lambda roi:roi.getStatistics().xCentroid+roi.getStatistics().yCentroid ) #top left to bottom right order
if len(rois)>0:
rois[0].setStrokeColor(Color.RED)
rois[0].setPosition(0, 0, t)
ol.add(rois[0])
if len(rois)>1:
rois[1].setStrokeColor(Color.GREEN)
rois[1].setPosition(0, 0, t)
ol.add(rois[1])
cells[t] = (rois[0], rois[1])
return cells
def main(imp,options):
from ij.plugin import ChannelSplitter
from ij.gui import Roi,PointRoi, PolygonRoi, Overlay, Line
from java.awt import Color
from ij import WindowManager
from ij.measure import ResultsTable
from ij.text import TextWindow
active_z=imp.getZ()
imps = ChannelSplitter.split(imp)
imp.setZ(active_z)
roi_int = imp.getRoi()
comp_imp=Zproj(imps[options["comp_ch"]],
"SUM",
active_z,
options["z_range"])
comp_imp=mode_subtract(comp_imp,roi_int)
loci_imp=Zproj(imps[options["loci_ch"]],
"SUM",
imp.getZ(),
options["z_range"])
loci_imp=mode_subtract(loci_imp,roi_int)
#Finding the boundaries of compartment and loci
comp_roi=thresh(sum_prj=comp_imp,thresh=options["comp_T"],roi=roi_int,method="boundary")
print "ok"
if (options["loci_method"]== "locus center"):
loci_roi=thresh(sum_prj=loci_imp,
thresh=options["loci_T"],
roi=roi_int,
method="point")
elif options["loci_method"]== "locus boundary":
loci_roi=thresh(sum_prj=loci_imp,
thresh=options["loci_T"],
roi=roi_int,
method="boundary")
if options["loci_method"]== "locus center":
dist,xc,yc,xl,yl=get_center_edge_dist(imp,comp_roi, loci_roi)
elif options["loci_method"]== "locus boundary":
dist,xc,yc,xl,yl=get_closest_points(imp,comp_roi,loci_roi)
rt_exist = WindowManager.getWindow("Loci distance to compartment")
if rt_exist==None or not isinstance(rt_exist, TextWindow):
table= ResultsTable()
else:
table = rt_exist.getTextPanel().getOrCreateResultsTable()
table.incrementCounter()
table.addValue("Label", imp.title)
table.addValue("Distance(micron)", dist)
if options['measure_feret']:
feret_roi,loci_feret,loci_area= feret(sum_prj=loci_imp,thresh=options["loci_T"],
roi=roi_int,pixel_size=imp.getCalibration().pixelWidth)
table.addValue("Loci feret", loci_feret)
table.addValue("Loci area", loci_area)
table.show("Loci distance to compartment")
## Adding loci overlay
ov=imp.getOverlay()
if ov==None:
ov=Overlay()
line = Line(xc,yc, xl,yl)
line.setStrokeWidth(0.2)
line.setStrokeColor(Color.PINK)
ov.add(line)
if options["loci_method"]== "locus center":
ov.add(PointRoi(loci_roi["x"],loci_roi["y"]))
elif options["loci_method"]== "locus boundary":
ov.add(loci_roi)
if options['measure_feret']:
ov.add(feret_roi)
ov.add(comp_roi)
imp.setOverlay(ov)
