def save_shifts(shifts, roi):
sd = SaveDialog('please select shift file for saving', 'shifts', '.txt')
fp = os.path.join(sd.getDirectory(),sd.getFileName())
f = open(fp, 'w')
txt = []
txt.append("ROI zero-based")
txt.append("\nx_min\ty_min\tz_min\tx_max\ty_max\tz_max")
txt.append("\n"+str(roi[0])+"\t"+str(roi[1])+"\t"+str(roi[2])+"\t"+str(roi[3])+"\t"+str(roi[4])+"\t"+str(roi[5]))
txt.append("\nShifts")
txt.append("\ndx\tdy\tdz")
for shift in shifts:
txt.append("\n"+str(shift.x)+"\t"+str(shift.y)+"\t"+str(shift.z))
f.writelines(txt)
f.close()
def save_shifts(shifts, roi):
sd = SaveDialog('please select shift file for saving', 'shifts', '.txt')
fp = os.path.join(sd.getDirectory(),sd.getFileName())
f = open(fp, 'w')
txt = []
txt.append("ROI zero-based")
txt.append("\nx_min\ty_min\tz_min\tx_max\ty_max\tz_max")
txt.append("\n"+str(roi[0])+"\t"+str(roi[1])+"\t"+str(roi[2])+"\t"+str(roi[3])+"\t"+str(roi[4])+"\t"+str(roi[5]))
txt.append("\nShifts")
txt.append("\ndx\tdy\tdz")
for shift in shifts:
txt.append("\n"+str(shift.x)+"\t"+str(shift.y)+"\t"+str(shift.z))
f.writelines(txt)
f.close()
def doSomething(keyEvent):
""" A function to react to key being pressed on an image canvas. """
global iROI, xlist, ylist, zlist, power, profileType, duration, Nturns, hOffset, camTriggerEvery, zStart, zStep, prewait
print "clicked keyCode " + str(keyEvent.getKeyCode())
if keyEvent.getKeyCode() == 10: # Enter is pressed!
sd = SaveDialog('Save ROIs', '.', 'Eprofile', '.txt')
directory = sd.getDirectory()
filename = sd.getFileName()
filepath = directory + filename
print filepath
f = open(filepath, 'w')
for i in range(len(xlist)):
f.write('ENTRY_START\n')
f.write('ABLATION(OFF,200.0)\n')
f.write('PRE_WAIT(' + str(prewait) + ')\n')
f.write('PRE_TRIGGER(OFF,5000,CONTINUE)\n')
f.write('COORDINATES(' + str(xlist[i]) + ',' +
str(hOffset + ylist[i]) + ',' +
str(zStart + (zlist[i] - 1) * zStep) + ')\n')
if (profileType == 'point'):
f.write('SCAN_TYPE(POINT)\n')
if (profileType == 'circle'):
f.write('SCAN_TYPE(CIRCLE,' + str(radius) + ',' +
str(round(duration / Nturns)) + ')\n')
if (profileType == 'spiral'):
f.write('SCAN_TYPE(SPIRAL,' + str(radius) + ',' +
str(duration) + ',0,' + str(Nturns) + ')\n')
f.write('POWER(' + str(power) + ')\n')
f.write('DURATION(' + str(duration) + ')\n')
f.write('POST_TRIGGER(OFF,0, CONTINUE)\n')
f.write('CAMERA_TRIGGER\n')
f.write('ENTRY_END\n\n')
f.close()
manager.runCommand('Save', directory + filename + '.zip')
if keyEvent.getKeyCode() == 27: # Esc is pressed!
reset()
#if keyEvent.getKeyCode() == 127: # DEL is pressed!
# killIt = true
# return
# Prevent further propagation of the key event:
keyEvent.consume()
def doSomething(keyEvent):
""" A function to react to key being pressed on an image canvas. """
global iROI, xlist, ylist, zlist, power, profileType, duration, Nturns, camTriggerEvery, zStart, zStep, prewait, xOffset, yOffset, tmIndex
if keyEvent.getKeyCode() == 10: # Enter is pressed!
sd = SaveDialog('Save ROIs', '.', 'Eprofile', '.txt')
directory = sd.getDirectory()
filename = sd.getFileName()
filepath = directory + filename
f = open(filepath, 'w')
f.write('<zStart units="um">' + str(zStart) + '</zStart>\n')
f.write('<zStep units="um">' + str(zStep) + '</zStep>\n')
f.write('<xOffset units="px">' + str(xOffset) + '</xOffset>\n')
f.write('<yOffset units="px">' + str(yOffset) + '</yOffset>\n')
f.write('<radiusROI units="px">' + str(radius) + '</radiusROI>\n\n')
for i in range(len(xlist)):
f.write('#cell num:' + str(i) + '\n')
f.write('ENTRY_START\n')
f.write('PRE_WAIT(' + str(prewait) + ')\n')
f.write('TM_INDEX(' + str(tmIndex) + ')\n')
f.write('COORDINATES(' + str(xOffset + xlist[i]) + ',' +
str(yOffset + ylist[i]) + ',' +
str(zStart + (zlist[i] - 1) * zStep) + ')\n')
if (profileType == 'point'):
f.write('SCAN_TYPE(POINT)\n')
if (profileType == 'circle'):
f.write('SCAN_TYPE(CIRCLE,' + str(radius) + ',' +
str(round(duration / Nturns)) + ')\n')
if (profileType == 'spiral'):
f.write('SCAN_TYPE(SPIRAL,' + str(radius) + ',' +
str(duration) + ',0,' + str(Nturns) + ')\n')
f.write('POWER(' + str(power) + ')\n')
f.write('DURATION(' + str(duration) + ')\n')
# f.write('POST_TRIGGER(OFF,0, CONTINUE)\n') #never used
f.write('CAMERA_TRIGGER\n')
f.write('ENTRY_END\n\n')
f.close()
manager.runCommand('Save', directory + filename + '.zip')
if keyEvent.getKeyCode() == 27: # Esc is pressed!
reset()
keyEvent.consume()
#run("Save");
#run ("Jpeg...");
from ij.plugin.frame import RoiManager
from ij import IJ
from ij.io import SaveDialog
from ij.io import RoiEncoder
from ij.io import RoiDecoder
rm = RoiManager.getInstance()
imp = IJ.getImage()
roi = imp.getRoi()
rm.addRoi(roi)
sd = SaveDialog("specify", IJ.getDirectory("image"), ".roi")
path = sd.getDirectory() + sd.getFileName()
RoiEncoder.save(roi, path)
x5x = dialog.getNextNumber();
y5x = dialog.getNextNumber();
w5x = dialog.getNextNumber();
h5x = dialog.getNextNumber();
activation_overlay_data.setRoi((x5x,y5x,w5x,h5x));
offsetx = dialog.getNextNumber();
offsety = dialog.getNextNumber();
activation_overlay_data.setLowMagOffsetXY((offsetx,offsety));
panx = dialog.getNextNumber();
pany = dialog.getNextNumber();
activation_overlay_data.setPanUmXY((panx,pany));
interval = dialog.getNextNumber();
activation_overlay_data.setFrameIntervalS(interval);
roi = activation_overlay_data.generateOverlayRoi(imp);
imp.setRoi(roi);
IJ.run(imp, "RGB Color", "");
IJ.run("Colors...", "foreground=cyan background=white selection=yellow");
IJ.run("Draw", "stack");
sd = SaveDialog("Save as AVI...", os.path.splitext(imp.getTitle())[0], ".avi");
if sd.getFileName is not None:
activation_overlay_data.save_to_json(os.path.join(sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] + " metadata.json"));
IJ.saveAs(imp, "Tiff", os.path.join(sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] + " + ROI, no timestamp.tif"));
IJ.run(imp, "Label...", "format=00:00:00 starting=0 interval=" + str(interval) + " x=5 y=20 font=18 text=[] range=1-"+str(imp.getNFrames()));
IJ.run(imp, "AVI... ", "compression=None frame=10 save=[" + os.path.join(sd.getDirectory(), sd.getFileName()) + "]");
IJ.saveAs(imp, "Tiff", os.path.join(sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] + " + ROI.tif"));
def main():
metadatas = []
runagain = True
offsetx = 0
offsety = 0
interval = 50.0
IJ.run(imp, "RGB Color", "")
IJ.run("Colors...", "foreground=cyan background=white selection=yellow")
while runagain:
dialog = GenericDialog("Define 5x ROI parameters...")
dialog.enableYesNoCancel("Continue and quit",
"Continue and add another line")
dialog.addNumericField("Line scan position 1 X, Y: ", 0, 0)
dialog.addToSameRow()
dialog.addNumericField(", ", 0, 0)
dialog.addNumericField("Line scan position 2 X, Y: ", 0, 0)
dialog.addToSameRow()
dialog.addNumericField(", ", 0, 0)
dialog.addNumericField("Reference image crop origin X, Y: ", offsetx,
0)
dialog.addToSameRow()
dialog.addNumericField(", ", offsety, 0)
dialog.addNumericField("Frame interval (s): ", interval, 2)
dialog.showDialog()
p1x = dialog.getNextNumber()
p1y = dialog.getNextNumber()
p2x = dialog.getNextNumber()
p2y = dialog.getNextNumber()
offsetx = dialog.getNextNumber()
offsety = dialog.getNextNumber()
interval = dialog.getNextNumber()
linescan_overlay = LineScanOverlayMetadata(
(p1x, p1y), (p2x, p2y), (offsetx, offsety), interval)
metadatas.append(linescan_overlay)
roi = linescan_overlay.generateOverlayRoi()
imp.setRoi(roi)
IJ.run("Draw", "stack")
if dialog.wasOKed():
runagain = False
elif dialog.wasCanceled():
return
sd = SaveDialog("Save as AVI...",
os.path.splitext(imp.getTitle())[0],
"line scan overlay.avi")
if sd.getFileName is not None:
metadatas[0].save_to_json(
os.path.join(
sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] +
"line scan metadata.json"))
if len(
metadatas
) > 1: # append: multiple writes=slow, but easiest way based on existing framework
for midx in range(1, len(metadatas)):
metadatas[midx].save_to_json(os.path.join(
sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] +
"line scan metadata.json"),
append=True)
IJ.saveAs(
imp, "Tiff",
os.path.join(
sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] +
" + line scan ROI, no timestamp.tif"))
IJ.run(
imp, "Label...",
"format=00:00:00 starting=0 interval=" + str(interval) +
" x=5 y=20 font=18 text=[] range=1-" + str(imp.getNFrames()))
IJ.run(
imp, "AVI... ", "compression=None frame=10 save=[" +
os.path.join(sd.getDirectory(),
(os.path.splitext(sd.getFileName())[0] +
" + line scan ROI.avi")) + "]")
IJ.saveAs(
imp, "Tiff",
os.path.join(
sd.getDirectory(),
os.path.splitext(os.path.basename(sd.getFileName()))[0] +
" + line scan ROI.tif"))
#run("Save");
#run ("Jpeg...");
from ij.plugin.frame import RoiManager
from ij import IJ
from ij.io import SaveDialog
from ij.io import RoiEncoder
from ij.io import RoiDecoder
rm = RoiManager.getInstance()
imp = IJ.getImage();
roi = imp.getRoi();
rm.addRoi(roi);
sd = SaveDialog("specify", IJ.getDirectory("image"), ".zip");
index = rm.getCount()-1;
path = sd.getDirectory() + sd.getFileName();
name = sd.getFileName();
rm.rename(index, name[0:-4]);
rm.deselect() ;
rm.runCommand("Save", path)
#ok = RoiEncoder.save(roi, path);
from ij import IJ
from ij.io import SaveDialog
from ij.gui import WaitForUserDialog
theImage = IJ.getImage()
ip = theImage.getProcessor()
sd = SaveDialog("Select file to save results","injury",".csv")
saveFileName = sd.getFileName()
saveFileDir = sd.getDirectory()
if (saveFileName is not None):
saveFilePath = saveFileDir + saveFileName
savefilehandler = open(saveFilePath,"w")
waitDialog = WaitForUserDialog("Use freeform tool to outline the piece of tissue")
waitDialog.show()
roi = theImage.getRoi()
if (roi is not None):
print type(roi)
thePolygon = roi.getPolygon()
boundRect = thePolygon.getBounds()
for i in range(boundRect.x,boundRect.x+boundRect.width):
pos_pixels = 0
tot_pixels = 0
IJ.showProgress(i-boundRect.x,boundRect.width)
for j in range(boundRect.y,boundRect.y+boundRect.height):
if thePolygon.contains(i,j):
value = ip.getPixelValue(i,j)
tot_pixels = tot_pixels + 1
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
sd = SaveDialog("Save counter file...","",".csv")
fileDir = sd.getDirectory()
fileName = sd.getFileName()
if fileName is not None:
filePath = fileDir + fileName
fileobj = open(filePath,"w")
for item in pointList:
fileobj.write(str(item.x)+","+str(item.y)+","+str(item.clonenum)+"\n")
fileobj.close()
plot.setColor(Color.BLACK)
plot.addPoints(x, y, Plot.LINE)
plot.addPoints(x, y, PlotWindow.X)
plot.setColor(Color.black)
plot_window = plot.show()
###############################
# Save data as a json file
###############################
# Ask for filename
savename_temp = os.path.splitext(stack_title)[0] + '_cell_XX'
save_file = SaveDialog('Please choose a location to save results', file_dir,
savename_temp, '.json')
# Prepare data for export
file_info = {'source_file': stack_title, 'source_file_dir': file_dir}
roi_info = {
'roi_type': roi_type,
'roi_bounds_pixel': roi_bounds_list,
'roi_area': roi_area
}
calb = {'pixel_size': calibration.pixelHeight, 'unit': calibration.getXUnit()}
data_out = {
'file_info': file_info,
'roi_info': roi_info,
'intensities': intensities,
'calibration': calb