def createAndShowGUI(self):
'''
Create and display the gui.
'''
self.setLayout(FlowLayout())
serverLabel = Label("BIAFlows host: ");
serverField =TextField(30)
serverField.setName('host')
serverField.setText(self.biaflows.getHost())
serverField.addTextListener(self)
publicKeyLabel = Label("public key: ")
publicKeyField=TextField(40)
publicKeyField.setName('publicKey')
publicKeyField.setText(self.biaflows.getPublicKey())
publicKeyField.addTextListener(self)
privateKeyLabel = Label("private key: ")
privateKeyField=TextField(40)
privateKeyField.setName('privateKey')
privateKeyField.setEchoChar('*')
privateKeyField.setText(self.biaflows.getPrivateKey())
privateKeyField.addTextListener(self)
closeButton = Button("Disconnect and close")
closeButton.addActionListener(self)
self.add(serverLabel)
self.add(serverField)
self.add(publicKeyLabel)
self.add(publicKeyField)
self.add(privateKeyLabel)
self.add(privateKeyField)
self.add(closeButton)
self.setSize(400,250)
self.setVisible(True)
#
class TestButtonAction(ActionListener):
def actionPerformed(self, e):
textArea.append("Test Button Clicked!\n")
#
# Create the Frame, Panel, Button,
# TextArea, and TestButtonAction objects.
#
frame = Frame("Hello World")
panel = Panel()
button = Button("Test Button")
buttonAction = TestButtonAction()
textArea = TextArea()
#
# Put everything together and show
# the window.
#
button.addActionListener(buttonAction)
panel.add(button)
panel.add(textArea)
frame.add(panel)
frame.pack()
frame.show()
class TestButtonAction(ActionListener):
def actionPerformed(self, e):
textArea.append("Test Button Clicked!\n")
#
# Create the Frame, Panel, Button,
# TextArea, and TestButtonAction objects.
#
frame = Frame("Hello World")
panel = Panel()
button = Button("Test Button")
buttonAction = TestButtonAction()
textArea = TextArea()
#
# Put everything together and show
# the window.
#
button.addActionListener(buttonAction)
panel.add(button)
panel.add(textArea)
frame.add(panel)
frame.pack()
frame.show()
def perform_user_qc(in_imp, edges, alt_edges, fixed_anchors_list, params):
"""allow the user to intervene to fix erroneously identified membrane edges"""
n_frames = in_imp.getNFrames();
n_channels = in_imp.getNChannels();
output_folder = params.output_path;
current_edges = edges;
rgbstack = ImageStack(in_imp.getWidth(), in_imp.getHeight());
if n_frames > 1:
for tidx in range(n_frames):
in_imp.setT(tidx+1);
ip = in_imp.getProcessor();
rgbip = ip.convertToRGB();
rgbstack.addSlice(rgbip);
else:
for cidx in range(n_channels):
in_imp.setC(cidx+1);
ip = in_imp.getProcessor();
rgbip = ip.convertToRGB();
rgbstack.addSlice(rgbip);
imp = ImagePlus(("RGB " + in_imp.getTitle()), rgbstack);
IJ.run("Colors...", "foreground=red background=white selection=yellow");
for tidx in range(imp.getNSlices()):
imp.setSlice(tidx+1);
for anchor in params.manual_anchor_positions:
imp.setRoi(PointRoi(anchor[0], anchor[1]));
IJ.run(imp, "Draw", "slice");
imp.show();
autoset_zoom(imp);
imp.setPosition(1);
imp.setRoi(current_edges[0]);
if n_frames > 1:
listener = UpdateRoiImageListener(current_edges);
imp.addImageListener(listener);
IJ.setTool("freeline");
do_flip = True;
while do_flip:
dialog = NonBlockingGenericDialog("User quality control");
dialog.enableYesNoCancel("Continue", "Flip all edges");
dialog.setCancelLabel("Cancel analysis");
dialog.addMessage("Please redraw the membrane edges as necessary, \n" +
"making sure to draw beyond anchor points at either end...\n" +
"Click OK when done. ");
p = Panel();
but = Button("Flip this edge");
al = Listener(edges, alt_edges, imp);
but.addActionListener(al);
p.add(but);
dialog.addPanel(p);
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
elif dialog.wasOKed():
do_flip = False;
else:
print("flip edges");
do_flip = True;
if n_frames > 1:
imp.removeImageListener(listener);
current_edges = alt_edges if (current_edges == edges) else edges;
imp.setPosition(1);
imp.setRoi(current_edges[0]);
if n_frames > 1:
listener = UpdateRoiImageListener(current_edges);
imp.addImageListener(listener);
last_roi = imp.getRoi();
if n_frames > 1:
qcd_edges = listener.getRoiList();
if imp.getNFrames() > imp.getNSlices():
qcd_edges[imp.getT() - 1] = last_roi;
else:
qcd_edges[imp.getZ() - 1] = last_roi;
imp.removeImageListener(listener);
else:
qcd_edges = [last_roi];
mbio.save_qcd_edges2(qcd_edges, output_folder);
# next four lines are a quick and dirty hack...
if n_frames > 1:
nframes = imp.getNFrames() if imp.getNFrames()>imp.getNSlices() else imp.getNSlices();
else:
nframes = n_frames;
for fridx in range(0, nframes):
if (qcd_edges[fridx].getType()==Roi.FREELINE) or (qcd_edges[fridx].getType()==Roi.POLYLINE):
if (fridx == 0) or params.constrain_anchors:
anchors = params.manual_anchor_positions;
else:
anchors = fixed_anchors_list[fridx - 1];
fixed_anchors = mb.fix_anchors_to_membrane(anchors, qcd_edges[fridx], params);
fixed_anchors = mb.order_anchors(fixed_anchors, params.manual_anchor_midpoint);
fixed_anchors_list[fridx] = fixed_anchors;
poly = qcd_edges[fridx].getInterpolatedPolygon(0.25, False);
polypoints = [(x,y) for x,y in zip(poly.xpoints, poly.ypoints)];
idx = [polypoints.index(fixed_anchors[0]), polypoints.index(fixed_anchors[1])];
idx.sort();
polypoints = polypoints[idx[0]:idx[1]];
newedge = PolygonRoi([x for (x,y) in polypoints],
[y for (x,y) in polypoints],
Roi.POLYLINE);
newedge = mb.check_edge_order(anchors, newedge);
imp.setPosition(fridx + 1);
imp.setRoi(newedge);
IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust");
IJ.run(imp, "Fit Spline", "");
qcd_edges[fridx] = imp.getRoi();
mbio.save_qcd_edges2(qcd_edges, output_folder);
imp.changes = False;
imp.close();
return qcd_edges, fixed_anchors_list;
def createAndShowGUI(self):
'''
Create and display the gui.
'''
layout = GridBagLayout()
c = GridBagConstraints()
self.setLayout(layout)
projectLabel = Label("Project: ")
c.gridx = 0
c.gridy = 0
c.ipady = 5
c.ipadx = 5
c.anchor = GridBagConstraints.EAST
layout.setConstraints(projectLabel, c)
self.projectChoice = Choice()
for name in self.projectNames:
self.projectChoice.add(name)
c.gridx = 1
c.gridy = 0
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.projectChoice, c)
storageLabel = Label("Storage: ")
c.gridx = 0
c.gridy = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.EAST
layout.setConstraints(storageLabel, c)
self.storageChoice = Choice()
for name in self.storageNames:
self.storageChoice.add(name)
c.gridx = 1
c.gridy = 1
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.storageChoice, c)
self.convertToOMETIFCheckBox = Checkbox("convert to OME-TIF", True)
c.gridx = 1
c.gridy = 2
layout.setConstraints(self.convertToOMETIFCheckBox, c)
self.uploadAsGroundTruthCheckBox = Checkbox("upload as ground-truth images")
c.gridx = 1
c.gridy = 3
layout.setConstraints(self.uploadAsGroundTruthCheckBox, c)
self.folderTextField = TextField("", 15)
self.folderTextField.setText("<Image-Folder>")
c.gridx = 0
c.gridy = 4
layout.setConstraints(self.folderTextField, c)
self.folderTextField.setEditable(False)
browseButton = Button('Browse...')
browseButton.addActionListener(self)
c.gridx = 1
c.gridy = 4
layout.setConstraints(browseButton, c)
statusLabel = Label("Status:")
c.gridy = 5
c.gridx = 0
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.EAST
layout.setConstraints(statusLabel, c)
self.statusTextField = TextField("Select a folder!", 20)
c.gridy = 5
c.gridx = 1
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.statusTextField, c)
self.statusTextField.setEditable(False)
self.uploadButton = Button("Upload Images")
self.uploadButton.addActionListener(self)
c.gridwidth = 2
c.gridheight = 2
c.gridy = 6
c.gridx = 0
c.weighty = 1.0
layout.setConstraints(self.uploadButton, c)
self.add(projectLabel)
self.add(self.projectChoice)
self.add(storageLabel)
self.add(self.storageChoice)
self.add(self.convertToOMETIFCheckBox)
self.add(self.uploadAsGroundTruthCheckBox)
self.add(self.folderTextField)
self.add(browseButton)
self.add(statusLabel)
self.add(self.statusTextField)
self.add(self.uploadButton)
self.setSize(400,300)
self.setVisible(True)
class UploadWindow(Frame, WindowListener, ActionListener):
'''
A window to upload images to the biaflows server.
The images can be uploaded as inut or as ground-truth images. Input images can
be converted to the ome-tif format. Ground-truth images are always converted to
ome-tif, if they are not alread in ome-tif format.
'''
def __init__(self):
'''
Create and display the upload window.
'''
super(UploadWindow, self).__init__("BIAFlows Image Upload")
self.biaflows = ConnectionWindow.getInstance().getBiaflows()
self.nrOfImagesToUpload = 0
projects = Projects()
self.projectNames = projects.getNames()
self.projectIDs = projects.getIDs()
storages = Storages()
self.storageNames = storages.getNames()
self.storageIDs = storages.getIDs()
self.createAndShowGUI()
self.addWindowListener(self)
WindowManager.addWindow(self)
def windowClosing(self, e):
'''
Close the image upload window and dispose of it.
Also remove it from the ij-window-manager.
'''
self.dispose()
WindowManager.removeWindow(self)
def windowActivated(self, e):
'''
Nothing to do.
'''
pass
def windowDeactivated(self, e):
'''
Nothing to do.
'''
pass
def windowClosed(self, e):
'''
Nothing to do.
'''
pass
def createAndShowGUI(self):
'''
Create and display the gui.
'''
layout = GridBagLayout()
c = GridBagConstraints()
self.setLayout(layout)
projectLabel = Label("Project: ")
c.gridx = 0
c.gridy = 0
c.ipady = 5
c.ipadx = 5
c.anchor = GridBagConstraints.EAST
layout.setConstraints(projectLabel, c)
self.projectChoice = Choice()
for name in self.projectNames:
self.projectChoice.add(name)
c.gridx = 1
c.gridy = 0
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.projectChoice, c)
storageLabel = Label("Storage: ")
c.gridx = 0
c.gridy = 1
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.EAST
layout.setConstraints(storageLabel, c)
self.storageChoice = Choice()
for name in self.storageNames:
self.storageChoice.add(name)
c.gridx = 1
c.gridy = 1
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.storageChoice, c)
self.convertToOMETIFCheckBox = Checkbox("convert to OME-TIF", True)
c.gridx = 1
c.gridy = 2
layout.setConstraints(self.convertToOMETIFCheckBox, c)
self.uploadAsGroundTruthCheckBox = Checkbox("upload as ground-truth images")
c.gridx = 1
c.gridy = 3
layout.setConstraints(self.uploadAsGroundTruthCheckBox, c)
self.folderTextField = TextField("", 15)
self.folderTextField.setText("<Image-Folder>")
c.gridx = 0
c.gridy = 4
layout.setConstraints(self.folderTextField, c)
self.folderTextField.setEditable(False)
browseButton = Button('Browse...')
browseButton.addActionListener(self)
c.gridx = 1
c.gridy = 4
layout.setConstraints(browseButton, c)
statusLabel = Label("Status:")
c.gridy = 5
c.gridx = 0
c.fill = GridBagConstraints.NONE
c.anchor = GridBagConstraints.EAST
layout.setConstraints(statusLabel, c)
self.statusTextField = TextField("Select a folder!", 20)
c.gridy = 5
c.gridx = 1
c.fill = GridBagConstraints.HORIZONTAL
layout.setConstraints(self.statusTextField, c)
self.statusTextField.setEditable(False)
self.uploadButton = Button("Upload Images")
self.uploadButton.addActionListener(self)
c.gridwidth = 2
c.gridheight = 2
c.gridy = 6
c.gridx = 0
c.weighty = 1.0
layout.setConstraints(self.uploadButton, c)
self.add(projectLabel)
self.add(self.projectChoice)
self.add(storageLabel)
self.add(self.storageChoice)
self.add(self.convertToOMETIFCheckBox)
self.add(self.uploadAsGroundTruthCheckBox)
self.add(self.folderTextField)
self.add(browseButton)
self.add(statusLabel)
self.add(self.statusTextField)
self.add(self.uploadButton)
self.setSize(400,300)
self.setVisible(True)
def changed(self, sender, aspect, newValue):
if aspect=='image upload':
self.statusTextField.setText('Uploading image ' + str(newValue) + '.')
if aspect=='image upload finished':
self.statusTextField.setText('Upload finished, ' + str(newValue) + ' images uploaded.')
self.removeTmpFiles()
if aspect=='image upload error':
self.statusTextField.setText('Error uploading ' + str(newValue) + '.')
def removeTmpFiles(self):
if self.convertToOMETIFCheckBox.getState():
shutil.rmtree(self.tmpFolder)
def actionPerformed(self, e):
'''
Event handler for the buttons.
'''
cmd = e.getActionCommand()
if cmd=='Browse...':
folder = IJ.getDirectory("Select the image folder")
if not folder:
return
self.folderTextField.setText(folder)
images = Uploader.getImageList(folder)
self.nrOfImagesToUpload = len(images)
self.inputFolder = folder
self.statusTextField.setText(str(self.nrOfImagesToUpload) + ' images to upload...')
if cmd=='Upload Images':
print('upload')
if self.nrOfImagesToUpload < 1:
return
else:
# convert if ome checked. Add _lbl if ground-truth checked. upload
self.statusTextField.setText('Uploading ' + str(self.nrOfImagesToUpload) + ' images...')
imageFolder = self.folderTextField.getText()
uploader = Uploader.getInstance(self.biaflows)
uploader.addObserver(self)
self.tmpFolder = None
if self.convertToOMETIFCheckBox.getState() or self.uploadAsGroundTruthCheckBox.getState():
self.statusTextField.setText('Converting ' + str(self.nrOfImagesToUpload) + ' images...')
# convert and add '_lbl' if ground truth
self.tmpFolder = imageFolder + 'biaflows_tmp/'
suffix = ''
if self.uploadAsGroundTruthCheckBox.getState():
suffix = '_lbl'
uploader.convertImagesInFolderToOME(imageFolder, self.tmpFolder, suffix)
imageFolder = self.tmpFolder
# upload
pid = self.projectIDs[self.projectChoice.getSelectedIndex()]
sid = self.storageIDs[self.storageChoice.getSelectedIndex()]
self.statusTextField.setText('Uploading ' + str(self.nrOfImagesToUpload) + ' images...')
uploader.setInputFolder(imageFolder)
uploader.setProject(str(pid))
uploader.setStorage(str(sid))
thread = Thread(uploader)
thread.start()
# cleanup
self.statusTextField.setText('Upload started.')
