def maximum_line_profile(imp, roi, pixel_width):
"""return a line profile taking the maximum value over n pixels perpendicular to roi line"""
imp.setRoi(roi)
IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust")
if pixel_width < 1:
pixel_width = 1
pixel_width = int(2 * math.ceil(float(pixel_width) / 2))
ip = Straightener().straightenLine(imp, pixel_width)
# debug
#from ij import ImagePlus
#from ij.gui import WaitForUserDialog
#debug_imp = ImagePlus("debug", ip);
#debug_imp.show();
#WaitForUserDialog("debug").show();
#debug_imp.close();
width = ip.getWidth()
height = ip.getHeight()
max_profile = []
poly = roi.getInterpolatedPolygon(1.0, True)
for idx, (x, y) in enumerate(zip(poly.xpoints, poly.ypoints)):
pix = ip.getLine(idx, 0, idx, height)
max_profile.append(((x, y), max(pix)))
return max_profile
def straighten_vessel(imp, smooth_centres, it=1, save_output=False):
"""use IJ straigtening tool to deal with convoluted vessels"""
print("straighten vessel input image dims = " + str(imp.getWidth()) + "x" +
str(imp.getHeight()))
rot_imp = utils.rot3d(imp, axis='x')
if it == 1:
roi = PolygonRoi([x for x, y, z in smooth_centres],
[z for x, y, z in smooth_centres], Roi.FREELINE)
print("len interp polygon = " +
str(roi.getInterpolatedPolygon().npoints))
elif it == 2:
new_zs = [z for z in range(rot_imp.getWidth())]
new_ys = lin_interp_1d([z for x, y, z in smooth_centres],
[y for x, y, z in smooth_centres], new_zs)
roi = PolygonRoi(new_zs, new_ys, Roi.FREELINE)
split_ch = ChannelSplitter().split(rot_imp)
mch_imp = split_ch[0]
egfp_imp = split_ch[1]
roi_imp = split_ch[2]
roi_imp.setRoi(roi)
for zidx in range(egfp_imp.getNSlices()):
for chidx in range(3):
split_ch[chidx].setZ(zidx + 1)
split_ch[chidx].setRoi(roi)
ip = Straightener().straightenLine(split_ch[chidx], 150)
if chidx == 1:
if zidx == 0:
egfp_straight_stack = ImageStack(ip.getWidth(),
ip.getHeight())
egfp_straight_stack.addSlice(ip)
elif chidx == 0:
if zidx == 0:
mch_straight_stack = ImageStack(ip.getWidth(),
ip.getHeight())
mch_straight_stack.addSlice(ip)
else:
if zidx == 0:
roi_straight_stack = ImageStack(ip.getWidth(),
ip.getHeight())
roi_straight_stack.addSlice(ip)
egfp_out_imp = ImagePlus("Straightened EGFP", egfp_straight_stack)
mch_out_imp = ImagePlus("Straightened mCh", mch_straight_stack)
roi_out_imp = ImagePlus("Straightened ROI", roi_straight_stack)
if it == 2:
egfp_out_imp = utils.rot3d(egfp_out_imp, axis='y')
mch_out_imp = utils.rot3d(mch_out_imp, axis='y')
roi_out_imp = utils.rot3d(roi_out_imp, axis='y')
egfp_out_imp.show()
mch_out_imp.show()
roi_out_imp.show()
IJ.run(
"Merge Channels...",
"c1=[" + mch_out_imp.getTitle() + "] c2=[" + egfp_out_imp.getTitle() +
"] c7=[" + roi_out_imp.getTitle() + "] create keep")
# WaitForUserDialog("pause").show();
# if it==1:
egfp_out_imp.close()
mch_out_imp.close()
roi_out_imp.close()
new_composite = IJ.getImage()
if save_output:
FileSaver(new_composite).saveAsTiffStack(
os.path.join(output_path, "after rotation " + str(it) + ".tif"))
return new_composite
def process_image(imps, rois, ais_chno, nucleus_chno, bg_roino=3, sample_width=3, method='mean', dilations=3, average=1, threshold=0.1):
"""Opens a file and applies a Gaussian filter."""
orig_title = imps[ais_chno-1].getTitle()
print ",".join([i.getTitle() for i in imps])
print "Processing", orig_title
options = IS.MEAN | IS.MEDIAN # many others
nucleus_imp = imps[nucleus_chno-1].duplicate()
IJ.run(nucleus_imp, "Median...", "radius=10")
IJ.setAutoThreshold(nucleus_imp, "Default");
IJ.run(nucleus_imp, "Make Binary", "")
IJ.run(nucleus_imp, "Invert", "")
IJ.run(nucleus_imp, "Options...", "iterations=1 count=1 black do=Nothing");
IJ.run(nucleus_imp, "Watershed", "");
IJ.run(nucleus_imp, "Analyze Particles...", "size=20-Infinity clear add");
rm = RoiManager.getInstance2()
nuclei = rm.getRoisAsArray()
ais_imp = imps[ais_chno-1].duplicate()
print ais_imp.getTitle()
IJ.run(ais_imp, "8-bit","")
IJ.run(ais_imp, "Median...", "radius=1")
bg = 0
for i in range(bg_roino):
bg_roi = rois[i]
ais_imp.setRoi(bg_roi)
stats = ais_imp.getStatistics(options)
bg += stats.mean
print "Bg Roi %s, %s: %s" % (bg_roi.getName(), bg_roi, stats)
background = (int)(bg / bg_roino)
results = []
for i in range(bg_roino, len(rois)):
roiresult = {}
print i, rois[i].getName()
mimp = ais_imp.duplicate()
mimp.setTitle("%s-%s-AIS-Skeleton" % (orig_title, rois[i].getName()))
# IJ.run(mimp, "Median...", "radius=3")
mimp.setRoi(rois[i])
# IJ.setAutoThreshold(mimp, "Huang dark")
IJ.run(mimp, "Auto Local Threshold", "method=Phansalkar radius=15 parameter_1=0 parameter_2=0 white")
IJ.setBackgroundColor(0,0,0)
IJ.run(mimp, "Clear Outside", "")
Prefs.blackBackground = True
for j in range(dilations):
IJ.run(mimp, "Dilate", "")
IJ.run(mimp, "Skeletonize", "")
#IJ.run(mimp, "Analyze Skeleton (2D/3D)", "prune=none prune_0 calculate show display");
ais_skeleton, ais_points, points, orthogonals, ais_roi, nucleus_roi = create_skeleton(mimp, '%s-%s-AIS' % (orig_title, rois[i].getName()), nuclei_rois=nuclei, sample_width=sample_width)
if ais_skeleton is None:
print "Skipping -- AIS skeleton segmentation failed for ROI", rois[i].getName()
continue
#images['ais-skeleton-' + rois[i].getName()] = ais_skeleton
# subtract background
print "Subtracting background: bg=%d" % background
IJ.run(ais_imp, "Subtract...", "value=%d" % int(background))
ais_imp.setRoi(ais_roi)
ip = Straightener().straightenLine(ais_imp, sample_width)
straight_imp = ImagePlus('%s-%s-AIS-Straight' % (orig_title, rois[i].getName()), ip)
straight_imp.setCalibration(imps[ais_chno-1].getCalibration().copy())
IJ.run(straight_imp, "Green Fire Blue", "")
roiresult = {
'roi-name': rois[i].getName(),
'ais-image': straight_imp,
'ais-roi': ais_roi,
'nucleus-roi': nucleus_roi,
}
# plot
if len(points) > 1:
if method == 'sum':
threshold *= sample_width
plot, rt = create_plot(straight_imp, method, average, threshold=threshold)
roiresult['plot'] = plot
roiresult['table'] = rt
results.append(roiresult)
return results, background
#roi = zproj_imp.getRoi();
zproj_imp.changes = False;
zproj_imp.close();
z_planes = egfp_imp.getNSlices();
#straight_stack = Straightener().straightenStack(egfp_imp, roi, 100);
#out_imp = ImagePlus("Straightened", straight_stack);
for zidx in range(z_planes):
for chidx in range(3):
#print("Working on " + str(["egfp", "mCh", "roi"][chidx]));
split_ch[chidx].setZ(zidx+1);
split_ch[chidx].setRoi(roi);
ip = Straightener().straightenLine(split_ch[chidx], 150);
if chidx==1:
if zidx==0:
egfp_straight_stack = ImageStack(ip.getWidth(), ip.getHeight());
egfp_straight_stack.addSlice(ip);
elif chidx==0:
if zidx==0:
mch_straight_stack = ImageStack(ip.getWidth(), ip.getHeight());
mch_straight_stack.addSlice(ip);
else:
if zidx==0:
roi_straight_stack = ImageStack(ip.getWidth(), ip.getHeight());
roi_straight_stack.addSlice(ip);
egfp_out_imp = ImagePlus("Straightened EGFP", egfp_straight_stack);
mch_out_imp = ImagePlus("Straightened mCh", mch_straight_stack);
shell_width = 10
imp = IJ.getImage()
overlay = imp.getOverlay()
raster_shells = []
if imp and overlay:
for i in range(overlay.size()):
roi = overlay.get(i)
if roi.getName() and "Shell" in roi.getName():
imp.setRoi(roi)
IJ.run(imp, "Area to Line", "")
raster = ImagePlus(
roi.getName(),
Straightener().straighten(imp, roi, shell_width))
raster_shells.append(raster)
if raster_shells:
holding_imp = ImagesToStack.run(raster_shells)
IJ.run(holding_imp, "Make Montage...",
"columns=1 rows={} scale=1".format(holding_imp.getNSlices()))
measurable_imp = IJ.getImage()
measurable_imp.setTitle("Rasterized Shells")
IJ.setAutoThreshold(measurable_imp, "Default dark")
IJ.run(measurable_imp, "Analyze Particles...",
" show=[Overlay Masks] display clear overlay")
else:
error()
else:
error()
