class gui(JFrame):
def __init__(self): # constructor
#origing of coordinates
self.coordx = 10
self.coordy = 10
#inintialize values
self.Canvas = None
#create panel (what is inside the GUI)
self.panel = self.getContentPane()
self.panel.setLayout(GridLayout(9, 2))
self.setTitle('Subdividing ROIs')
#define buttons here:
self.Dapi_files = DefaultListModel()
mylist = JList(self.Dapi_files, valueChanged=self.open_dapi_image)
#mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
mylist.setLayoutOrientation(JList.VERTICAL)
mylist.setVisibleRowCount(-1)
listScroller1 = JScrollPane(mylist)
listScroller1.setPreferredSize(Dimension(300, 80))
self.output_files = DefaultListModel()
mylist2 = JList(self.output_files)
#mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
mylist2.setLayoutOrientation(JList.VERTICAL)
mylist2.setVisibleRowCount(-1)
listScroller2 = JScrollPane(mylist2)
listScroller2.setPreferredSize(Dimension(300, 80))
quitButton = JButton("Quit", actionPerformed=self.quit)
selectInputFolderButton = JButton("Select Input",
actionPerformed=self.select_input)
cubifyROIButton = JButton("Cubify ROI",
actionPerformed=self.cubify_ROI)
saveButton = JButton("Save ROIs", actionPerformed=self.save)
summsaveButton = JButton("Save Summary",
actionPerformed=self.save_summary)
self.textfield1 = JTextField('500')
#add buttons here
self.panel.add(listScroller1)
self.panel.add(listScroller2)
self.panel.add(selectInputFolderButton)
self.panel.add(Label("Adjust the size of the ROIs"))
self.panel.add(self.textfield1)
self.panel.add(cubifyROIButton)
self.panel.add(saveButton)
self.panel.add(summsaveButton)
self.panel.add(quitButton)
#self.panel.add(saveButton)
#self.panel.add(Zslider)
#other stuff to improve the look
self.pack() # packs the frame
self.setVisible(True) # shows the JFrame
self.setLocation(self.coordx, self.coordy)
#define functions for the buttons:
def quit(self, event): #quit the gui
self.dispose()
IJ.run("Close All")
def select_input(self, event):
self.input_path = IJ.getDirectory(
"Select Directory containing your data")
# get the files in that directory
self.input_files = listdir(self.input_path)
self.input_dapi = [s for s in self.input_files if "DAPI.tif" in s]
self.core_names = get_core_names(self.input_dapi)
# create output directory
self.output_path = path.join(
path.dirname(path.dirname(self.input_path)), "Cubified_ROIs")
if path.isdir(self.output_path):
print "Output path already created"
else:
mkdir(self.output_path)
print "Output path created"
# get the processed data
self.processed_files = listdir(self.output_path)
self.out_core_names = get_core_names(
get_core_names(self.processed_files)
) # needs the channel and roi to be removed
# populate the lists
for f in set(self.core_names):
if f not in set(self.out_core_names): # skip if processed
self.Dapi_files.addElement(f)
for f in set(self.out_core_names
): # a set so that only unique ones are shown
self.output_files.addElement(f)
def open_dapi_image(self, e):
sender = e.getSource()
IJ.run("Close All")
if not e.getValueIsAdjusting():
self.name = sender.getSelectedValue()
print self.name
dapi_filename = path.join(self.input_path, self.name + '_DAPI.tif')
#print dapi_filename
if not path.exists(dapi_filename):
print "I don't find the DAPI file, which is weird as I just found it before"
else:
#open stack and make the reslice
self.dapi_image = ImagePlus(dapi_filename) #read the image
# duplicate image to play with that one, and do the real processing in the background
self.imp_main = Duplicator().run(self.dapi_image)
self.imp_main.setTitle(self.name)
self.imp_main.show() #show image on the left
#self.original_image.getWindow().setLocation(self.coordx-self.original_image.getWindow().getWidth()-10,self.coordy-10) #reposition image
def cubify_ROI(self, e):
self.L = int(self.textfield1.text)
# get info
tit = self.imp_main.getTitle()
self.roi = self.imp_main.getRoi()
# get corners
corners = get_corners(self.roi, self.L)
self.corners_cleaned = clean_corners(corners, self.roi, self.L)
print 'found corners'
# get the overlay
self.ov = overlay_corners(self.corners_cleaned, self.L)
self.ov = overlay_roi(self.roi, self.ov)
# write roi name
self.ov = write_roi_numbers(self.ov, self.corners_cleaned, self.L)
# overlay
self.imp_main.setOverlay(self.ov)
self.imp_main.updateAndDraw()
def save(self, e):
# open the other channels
d1_filename = path.join(self.input_path, self.name + '_D1.tif')
d2_filename = path.join(self.input_path, self.name + '_D2.tif')
self.d1_image = ImagePlus(d1_filename) #read the image
print "d1 image opened"
self.d2_image = ImagePlus(d2_filename) #read the image
print "d2 image opened"
for image in [self.dapi_image, self.d1_image, self.d2_image]:
print "saving rois for image " + image.getTitle()
save_rois(image, self.corners_cleaned, self.L, self.output_path)
print "ROIs saved"
def save_summary(self, e):
IJ.selectWindow(self.name)
IJ.run("Flatten")
imp = IJ.getImage()
# downsample
# scale ENLARGING or SHRINKING the canvas dimensions
scale_factor = .2
new_width = str(int(imp.getWidth() * scale_factor))
new_height = str(int(imp.getHeight() * scale_factor))
IJ.selectWindow(self.name + "-1")
str_to_scale = "x=" + str(scale_factor) + " y=" + str(
scale_factor
) + " width=" + new_width + " height=" + new_height + " interpolation=Bilinear average create"
IJ.run("Scale...", str_to_scale)
# save
imp2 = IJ.getImage()
#IJ.saveAs("Tiff", path.join(OUTDIR, self.name + "_summaryOfROIs"))
IJ.saveAsTiff(
imp2, path.join(self.output_path,
self.name + "_summaryOfROIs.tif"))
print "summary image saved"
