def showGui(par, title):
"""Updated version discriminates between string and numeric outputs to treat them accordingly"""
numflags = {}
gd = NonBlockingGenericDialog(title)
s_keys = sorted(par.keys())
for nm in s_keys:
if isinstance(par[nm], (int, float, long)):
gd.addNumericField(nm, par[nm], 1)
numflags[nm] = True
else:
gd.addStringField(nm, par[nm])
numflags[nm] = False
gd.setOKLabel("Go on!")
gd.setCancelLabel("Recompute..")
gd.centerDialog(False)
gd.setLocation(50, 100)
gd.showDialog()
if gd.wasCanceled():
rep = True
else:
rep = False
for nm in s_keys:
if numflags[nm]:
par[nm] = gd.getNextNumber()
else:
par[nm] = gd.getNextString().encode("ascii", "replace")
return par, rep
def perform_manual_qc(imp, rois, important_channel=1):
"""given cell rois generated by automatic methods, allow user to delete/add/redraw as appropriate"""
for ch in range(imp.getNChannels()):
imp.setC(ch + 1)
sat_frac = 0.99 if (ch + 1) == important_channel else 0.01
IJ.run(imp, "Enhance Contrast", "saturated={}".format(sat_frac))
imp.setC(important_channel)
IJ.setTool("freehand")
proceed = False
roim = RoiManager()
roim.runCommand("Show all with labels")
for roi in rois:
roim.addRoi(roi)
auto_rois_only = rois
while not proceed:
dialog = NonBlockingGenericDialog("Perform manual segmentation")
dialog.setOKLabel("Proceed to next image...")
dialog.addMessage("Perform manual correction of segmentation: ")
dialog.addMessage(
"Draw around cells and add to the region of interest manager (Ctrl+T). "
)
dialog.addMessage("Delete and redraw cells as appropriate. ")
dialog.addMessage(
"Then press \"proceed to next image\" when all cells have been added. "
)
dialog.showDialog()
if dialog.wasCanceled():
print("Manual segmentation canceled")
return auto_rois_only
elif dialog.wasOKed():
if roim.getCount() == 0:
rois = []
confirm_dialog = GenericDialog("Continue?")
confirm_dialog.addMessage(
"No rois selected in this FOV. Are you sure you want to proceed?"
)
confirm_dialog.setOKLabel("Yes, proceed")
confirm_dialog.setCancelLabel("No, not yet")
confirm_dialog.showDialog()
if confirm_dialog.wasOKed():
proceed = True
else:
rois = roim.getRoisAsArray()
proceed = True
roim.reset()
roim.close()
for ch in range(imp.getNChannels()):
imp.setC(ch + 1)
IJ.run(imp, "Enhance Contrast", "saturated={}".format(0.35))
imp.setC(important_channel)
return rois
def exit_assay():
gd = NonBlockingGenericDialog("Exit Assay")
gd.setCancelLabel("Quit & Save")
gd.setOKLabel("Quit")
gd.showDialog()
if gd.wasCanceled(): # quits
imp = IJ.getImage()
current_title = imp.getTitle()
imp.close()
renamer(dest, current_title, extension)
exit()
elif gd.wasOKed():
exit()
def manual_analysis(imp, file_name, output_folder):
"""perform analysis based on manually drawn cells"""
cal = imp.getCalibration()
channel_imps = ChannelSplitter.split(imp)
gfp_imp = channel_imps[0]
IJ.setTool("freehand")
proceed = False
roim = RoiManager()
roim.runCommand("Show all with labels")
dialog = NonBlockingGenericDialog("Perform manual segmentation")
dialog.setOKLabel("Proceed to next image...")
dialog.addMessage("Perform manual segmentation: ")
dialog.addMessage(
"Draw around cells and add to the region of interest manager (Ctrl+T)")
dialog.addMessage(
"You can see what you've added so far if you check \"show all\" on the ROI manager"
)
dialog.addMessage(
"Then press \"proceed to next image\" when all cells have been added")
dialog.showDialog()
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled")
elif dialog.wasOKed():
rois = roim.getRoisAsArray()
roim.reset()
roim.close()
out_stats = generate_cell_shape_results(rois, gfp_imp, cal, file_name)
print("Number of cells identified = {}".format(len(out_stats)))
# save output
save_qc_image(
imp, rois, "{}_plus_overlay.tiff".format(
os.path.join(output_folder,
os.path.splitext(file_name)[0])))
save_cell_rois(rois, output_folder, os.path.splitext(file_name)[0])
imp.changes = False
imp.close()
save_output_csv(out_stats, output_folder)
return out_stats
return None
class CounterPoint:
def __init__(self,x,y,clonenum):
self.x = x
self.y = y
self.clonenum = clonenum
theImage = IJ.getImage()
stayinloop = True
cloneNum = 1
pointList = []
while (stayinloop):
gd = NonBlockingGenericDialog("Clone counter...")
gd.addNumericField("Clone:",cloneNum,0)
gd.setOKLabel("Finalize clone")
gd.setCancelLabel("Quit")
gd.showDialog()
if (gd.wasOKed()):
roi = theImage.getRoi()
if (not roi is None):
cloneNum = int(gd.getNextNumber())
polygon = roi.getFloatPolygon()
for i in range(polygon.npoints):
pointList.append(CounterPoint(polygon.xpoints[i],polygon.ypoints[i],cloneNum))
IJ.run("Draw","stack")
theImage.deleteRoi()
cloneNum = cloneNum + 1
else:
stayinloop = False
## Sets up main GUI interface for examining found objects
ngd = NonBlockingGenericDialog("Control box")
ngd.addCheckbox("Contained_objects",False)
ngd.addCheckbox("Duplicated_objects",False)
ngd.addCheckbox("Restitched_objects",False)
ngd.addCheckbox("Unique_objects",False)
boxes = ngd.getCheckboxes()
checkboxObjects = []
for i in range(boxes.size()):
checkboxObjects.append(boxes.elementAt(i))
for i in range(len(checkboxObjects)):
checkboxObjects[i].addItemListener(CustomCheckboxListener(objectDB,virginImage,boxImages,boxes))
ngd.setCancelLabel("Exit")
ngd.setOKLabel("Inspect")
ngd.showDialog()
if (ngd.wasCanceled()):
titles = WindowManager.getImageTitles()
p = re.compile(r'^Result')
for title in titles:
m = p.search(title)
if m is not None:
theImage = WindowManager.getImage(title)
theImage.close()
virginImage.show()
for img in boxImages:
img.close()
else:
titles = WindowManager.getImageTitles()
roi = theImage.getRoi()
newip = theImage.getProcessor().duplicate()
newip.setColor(0)
newip.fillOutside(roi)
newip.snapshot()
newip.setThreshold(0,t_line,ImageProcessor.BLACK_AND_WHITE_LUT)
newImage = ImagePlus("toggler",newip)
newImage.show()
doSameSlice = True
while (doSameSlice):
accept_waiter = NonBlockingGenericDialog("Thresholding...")
accept_waiter.addNumericField("Threshold:",t_line,0)
accept_waiter.setCancelLabel("Apply new threshold")
accept_waiter.setOKLabel("Accept threshold")
accept_waiter.showDialog()
if (accept_waiter.wasCanceled()):
newip.reset()
newip.snapshot()
t_line = accept_waiter.getNextNumber()
# if (t_line > 10):
# t_line = t_line - 5
# else:
# t_line = 5
newip.setThreshold(0,t_line,ImageProcessor.BLACK_AND_WHITE_LUT)
newImage.updateAndDraw()
else:
doSameSlice = False
for i in range(newImage.getWidth()):
for j in range(newImage.getHeight()):
height = theImage.getHeight()
newStack = ImageStack(width,height)
for i in range(startSlice,endSlice+1):
theImage.setSlice(i)
theImage.killRoi()
pixels = zeros('b',width*height)
bp = ByteProcessor(width,height,pixels)
bp.setColor(127)
doStaySlice = True
while doStaySlice:
waiter = NonBlockingGenericDialog("Set cast")
waiter.addMessage("Pick 2D ROI")
waiter.setOKLabel("Save and advance")
waiter.setCancelLabel("Save")
waiter.showDialog()
if (waiter.wasOKed()):
roi = theImage.getRoi()
if (roi is None):
doStaySlice = True
else:
bp.fill(roi)
doStaySlice = False
else:
roi = theImage.getRoi()
if (roi is None):
doStaySlice = True
else:
# Read csv files into lists, create nuclei list
T = txt2list(os.path.join(thisdir, 't.csv'))
X = txt2list(os.path.join(thisdir, 'x.csv'))
Y = txt2list(os.path.join(thisdir, 'y.csv'))
nuclei = defaultdict(list)
for i, t in enumerate(T):
nuclei[t] = (X[i], Y[i])
print 'Working on: ', cID
# Add listener to image
listener = PointRoiRefresher(imp, nuclei)
ImagePlus.addImageListener(listener)
# Wait for user to clear current cell
gd = NonBlockingGenericDialog("Advance to next cell?")
gd.setOKLabel('Next')
gd.setCancelLabel('Completely exit')
gd.addCheckbox('Skip this cell?', False)
gd.showDialog()
if gd.wasOKed(): # OK means 'advance'
imp.removeImageListener(listener)
if gd.getNextBoolean():
with open(os.path.join(thisdir, 'skipped.txt'), 'w') as f:
f.write('Skipped')
# Log the cell as done
with open(log_filename, 'a') as f:
f.write(''.join((cID, '\n')))
print "Advancing to next cell..."
continue
if gd.wasCanceled(): # Cancel means 'exit'
return True
theImage = IJ.getImage()
stayinloop = True
# IJ.run("RGB Color")
injuryfirst = True
injuryLengths = []
totalLengths = []
injuryRatios = []
Xpositions = []
while stayinloop:
gd = NonBlockingGenericDialog("Pick points...")
gd.addMessage("Use multipoint tool to pick points along a column (Y-axis).\nAlternate points to mark injured vs uninjured area.")
gd.setCancelLabel("Quit")
gd.setOKLabel("Define column")
gd.addCheckbox("First segment is injury?",injuryfirst)
gd.showDialog()
if (gd.wasOKed()):
roi = theImage.getRoi()
if roi is None:
IJ.error("No ROI selected")
else:
polygon = roi.getFloatPolygon()
# if len(polygon.xpoints) % 2 == 0 and is_monotonic_increasing(polygon.ypoints):
if is_monotonic_increasing(polygon.ypoints):
xset = average(polygon.xpoints)
IJ.setForegroundColor(255,255,0)
IJ.run("Draw","stack")
