''' This script can be used to manually classify full images from a stack into N user-defined categories. A first window pops up to request: - the number of categories N - the structure of the table (single/multi category column) - the image browsing mode (stack or directory) - if the category names should be read from an active table (better than having a browse button, then I dont have to handle issue loading the table) A second window follows with N text fields for the category names. Finally the annotation GUI will show up with one button per category. Clicking on the button will generate a new entry in a table with the image name and the category. It will also skip to the next slice for stacks. ''' #@ String (Label="Read categories from", choices={"Text file", "Active table", "Memory"}, value="Memory" ) categorySource #@ File (label="Text file (if selected above)", style="file", required=false) textFile #@ String (label="Browsing mode", choices={"stack", "directory"}) browse_mode #@ String (Label="Table structure", choices={"single category column","one column per category"}) table_structure #@ Boolean (label="Run measure", value=false) run_measure from ij import IJ, WindowManager, Prefs from fiji.util.gui import GenericDialogPlus from java.awt import GridLayout, Button, Panel from java.awt.event import ActionListener from javax.swing import JButton from QualiAnnotations.utils import CustomDialog, getTable, getCategoriesFrom from QualiAnnotations.CategoryDialog import CategoryDialog from QualiAnnotations.Charts import PieChart import os # Make a dictionary for keycode and shortcut name for button F1-F12 listKeyCodes = range(112, 124) # see https://docs.oracle.com/javase/7/docs/api/constant-values.html#java.awt.event.KeyEvent.VK_F1 listF1_F12 = ["F"+str(x) for x in range(1,13) ] # simply F1-F12 dicoShortcuts = dict(zip(listKeyCodes, listF1_F12)) # keyCode:"FX" value class PlotAction(ActionListener): """Display a PieChart of the data in the category column upon click""" def actionPerformed(self, event): if IJ.getFullVersion() < "1.53g": IJ.error("This plugin requires ImageJ version 1.53g minimum.\n Update using Help > Update ImageJ...") return tableWindow = WindowManager.getActiveTable() # this function requires the 1.53g (or at least not working with 1.53c) if not tableWindow: return # Get column Category table = tableWindow.getResultsTable() column = table.getColumnAsVariables("Category") columnString = [str(item) for item in column] # Plot Pie Plot for this column pieChart = PieChart("Category", columnString) pieChart.showFrame("Data-distribution") class CategoryAction(ActionListener): '''Define what happens when a category button is clicked''' def actionPerformed(self, event): '''Update the selected category and defaultActionSequence to fill the table''' winButton.selectedCategory = event.getSource().getLabel() winButton.defaultActionSequence() class SaveAction(ActionListener): """Define what happens when the save category button is pressed.""" def actionPerformed(self, event): outDir = IJ.getDirectory("Save category file in directory...") if not outDir: return # when cancelled filename = IJ.getString("Filename", "categories.txt") if not filename: return # when cancelled outPath = os.path.join(outDir, filename) listButtons = winButton.getPanel().getComponents() with open(outPath, "w") as catFile: for button in listButtons: catFile.write(button.getLabel().encode("utf-8") + "\n") # important to use UTF-8 otherwise troubles # Define global button action listener # Need to be global since the panel is built out of the dialog constructor (ie no access to self) # Surely not the cleanest but it works categoryAction = CategoryAction() saveAction = SaveAction() class ButtonDialog(CustomDialog): ''' Annotation dialog, also define keyboard shortcut and function to fill the table defaultActionSequence() is defined in the mother class customDialog ''' # define constant used for input (must match script parameters above) TABLE_SINGLE_COLUMN = "single category column" TABLE_MULTI_COLUMN = "one column per category" def __init__(self, panel, browseMode="stack", runMeasure=False, tableStructure=TABLE_SINGLE_COLUMN): """ browseMode: "stack" or "directory" tableStructure: "single category column" or anything else, such as "one column per category" """ title = "Qualitative Annotations - single class (buttons)" message = "Click the category of the current image or ROI, or use the F1-F12 keyboard shortcuts.\nTo annotate ROI, draw a new ROI or select some ROI in the RoiManager before clicking the category button." CustomDialog.__init__(self, title, message, panel) self.addButton("Add new category", self) self.addToSameRow() self.addButton("Save categories to file", saveAction) self.addStringField("Comments", "") #self.addButton("Add", self) # no add button for button-plugin self.browseMode = browseMode # important to define it before adding defaultOptions self.runMeasure = runMeasure self.addDefaultOptions() #if choiceIndex == 0: self.addButton("Make PieChart from category column", PlotAction()) # Remov this button: risk of cherry picking to improve the plot #self.addCitation() # Variable used by instance methods self.tableStructure = tableStructure self.selectedCategory = "" def fillTable(self, table): if self.tableStructure == self.TABLE_SINGLE_COLUMN: # single category column table.addValue("Category", self.selectedCategory) else: # 1 column/category with 0/1 for cat in listCat: if cat == self.selectedCategory: table.addValue(cat, 1) else: table.addValue(cat, 0) def keyPressed(self, keyEvent): ''' Map button to keyboard shortcuts (use F1..F12) ie one can press F1 to assign to the first category instead of clicking the button ''' code = keyEvent.getKeyCode() #print "Pressed key", code # just for debugging in case if code in dicoShortcuts: # check if the code is in the dicos keys index = code - 112 # switch back from keyCode index starting at 112 with F1, to 0-based list index else: return # prevent issue otherwise index variable non-existing if index >= 0 and index < len(listCat): self.selectedCategory = listCat[index] self.defaultActionSequence() def makeCategoryComponent(self, category): """Return a button with the new category name, and mapped to the action""" listCat.append(category) # Save the new category in memory Prefs.set("annot.listCat", ",".join(listCat) ) button = JButton(category) button.addActionListener(categoryAction) button.setFocusable(False) # Add button tooltip if fit in the F1-F12 button range nCat = len(listCat) if nCat <= 12: button.setToolTipText("Keyboard shortcut: F" + str(nCat)) # F shortcut labels are 1-based, ie match the len value return button ############### GUI - CATEGORY DIALOG - collect N classes names (N define at first line) ############# textFilePath = textFile.getPath() if textFile else "" listCategories = getCategoriesFrom(categorySource, textFilePath) # initial list, before user-edit catDialog = CategoryDialog(listCategories) catDialog.showDialog() ################# After OK clicking ########### # Recover fields from the formular if catDialog.wasOKed(): # Loop over categories and add a button to the panel for each catPanel = Panel(GridLayout(0,4)) # Unlimited number of rows - fix to 4 columns - not possible to use a JPanel, not supported by GenericDialog listCat = catDialog.getListCategories() listShortcut = range( 112, 112+len(listCat) ) for index, category in enumerate(listCat): # Create a Button button = JButton(category) # button label if index<12: button.setToolTipText( "Keyboard shortcut: F" + str(index+1) ) # index is 0-based, F shortcut are 1-based # Bind action to button button.addActionListener(categoryAction) # Add a button to the gui for this category button.setFocusable(False) # prevent the button to take the focus, only the window should be able to take the keyboard shortcut catPanel.add(button) # Initialize classification gui winButton = ButtonDialog(catPanel, browse_mode, run_measure, table_structure) winButton.showDialog()