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 displayInfoDialog(text, title = 'Info'): global infoDialog infoDialog = NonBlockingGenericDialog(title) infoDialog.addMessage(text) infoDialog.setLocation(0,0) infoDialog.setSize(400,800) infoDialog.show() return infoDialog
def measure_gd(src_folder,file_names):
from javax.swing import JButton
gd = NonBlockingGenericDialog("Loci to compartment")
gd.setResizable(True)
gd.pack()
gd.addMessage("Draw a freehand ROI aound loci and closest \n compartment(e.g. speckle) and press 0 on keyboard.")
gd.addMessage("To load next image press Next Image button.")
next_imp_bt = JButton('Next Image', actionPerformed=load_next_image)
gd.add(next_imp_bt)
gd.setLocation(10,10)
gd.setAlwaysOnTop(True)
gd.hideCancelButton()
gd.showDialog()
#
if gd.wasOKed():
IJ.log( "Measurement done! You're welcome!")
def measure_gd():
# Dialouge box for measurements.
# It
from javax.swing import JButton
gd = NonBlockingGenericDialog("Loci to compartment")
gd.setResizable(True)
gd.pack()
gd.addMessage(
"Draw a freehand ROI around the loci and closest \ncompartment(e.g. speckle) and press 0 on keyboard."
)
next_imp_bt = JButton('Analyze active image',
actionPerformed=analyze_image)
gd.add(next_imp_bt)
gd.setLocation(10, 10)
gd.setAlwaysOnTop(True)
gd.hideCancelButton()
gd.showDialog()
#
if gd.wasOKed():
IJ.log("Measurement done! Happy FISHing")
im = IJ.getImage()
if im.getNChannels() == 1:
LUTarray = [LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 2:
LUTarray = [LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 3:
LUTarray = [LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 4:
LUTarray = [LUT.createLutFromColor(Color.BLUE),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 5:
LUTarray = [LUT.createLutFromColor(Color.BLUE),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.YELLOW),LUT.createLutFromColor(Color.WHITE)]
else:
LUTarray = []
nbgd = NonBlockingGenericDialog("Pick freehand ROI")
nbgd.setLocation(0,0)
nbgd.addMessage("OK to run, cancel to exit")
nbgd.showDialog()
isContinue = nbgd.wasOKed()
while isContinue:
roi = im.getRoi()
if (roi is not None):
float_poly = roi.getFloatPolygon()
containing_tiles_superlist = []
for i in range(float_poly.npoints):
containing_tiles_superlist.append(find_containing_tiles([float_poly.xpoints[i],float_poly.ypoints[i],0],coords_vals,scale_info[1],scale_info[2]))
upscaled_coords = upscale_coords(coords,scale_info[0])
containing_tiles_dict = rearrange_tile_list(containing_tiles_superlist)
copy_fullsize_tiles(["tile_"+key for key in containing_tiles_dict.keys()],parentLSMFilePath+"_tiles/",parentLSMFilePath+"_tiles/subtiles/",".ome.tif")
subupcoords_vals = normalize_coords_in_list(get_list_from_dict(["tile_"+key for key in containing_tiles_dict.keys()],upscaled_coords))
hadStitched = False
