''' This script generates a GUI with the different functions supported by the machine (Autofocus, Acquire...) Each function is associated to parameters/variables that can be adjusted Once the parameters are chosen, clicking on the button of the function generates the machine command in the log window This can be repeated to generate the full imaging script (cpoy/paste from the log window then) ''' #@PrefService prefs from java.awt.event import ActionListener from fiji.util.gui import GenericDialogPlus from ij import IJ # We create an event subclasse for each machine function to associate to a button class AutofocusClass(ActionListener): # extends action listener def actionPerformed(this,event): '''Called when 'autofocus' is clicked''' # Recover parameters (converting to int and float allows to get rid of leading 0, or turn -0 in 0 for instance) nSlice = int(NumField[0].text) if nSlice<1 : IJ.log("There should be at least 1 slice") raise Exception("There should be at least 1 slice") dSlice = float(NumField[1].text) if float(dSlice)<0 : IJ.log("The distance between slices should be >=0") raise Exception("The distance between slices should be >=0") Bin = Choice[0].getSelectedItem() PreAF = str(CheckBox[0].getState()) DeferAdapt = str(CheckBox[1].getState()) # Formulate Autofocus command cmd = "Autofocus({},{},{},'{}','{}')".format(nSlice,dSlice,Bin,PreAF,DeferAdapt) # see if dSlice should have a given number of digits print cmd IJ.log(cmd) # Save input for persistence prefs.put("AF_nSlice",nSlice) prefs.put("AF_dSlice",dSlice) prefs.put("AF_bin",Bin) prefs.put("PreAF",PreAF) prefs.put("DeferAdapt",DeferAdapt) class AcquireClass(ActionListener): # extends action listener def actionPerformed(this,event): '''Called when 'Acquire' is clicked''' # Recover parameters (converting to int and float allows to get rid of leading 0, or turn -0 in 0 for instance) nSlice = int(NumField[2].text) if nSlice<1 : IJ.log("There should be at least 1 slice") raise Exception("There should be at least 1 slice") dSlice = float(NumField[3].text) if float(dSlice)<0 : IJ.log("The distance between slices should be >=0") raise Exception("The distance between slices should be >=0") Bin = Choice[1].getSelectedItem() MainPath = StringField[0].text UseMeta = str(CheckBox[2].getState()) # Formulate Autofocus command cmd = "Autofocus({},{},{},'{}','{}')".format(nSlice,dSlice,Bin,MainPath,UseMeta) # see if dSlice should have a given number of digits print cmd IJ.log(cmd) # Save input for persistence prefs.put("Acq_nSlice",nSlice) prefs.put("Acq_dSlice",dSlice) prefs.put("Acq_bin",Bin) prefs.put("MainPath",MainPath) prefs.put("UseMeta",UseMeta) class SetLightClass(ActionListener): def actionPerformed(this,event): '''Called when 'SetLight' is clicked''' #(channel, intensity, integration time, AF offset) # Recover input parameters Channel = Choice[2].getSelectedItem() Power = int(NumField[4].text) if Power<=0 or Power>100 : IJ.log("Power should be in the range 0-100") raise Exception("Power should be in the range 0-100") Exposure = int(NumField[5].text) if Exposure<=0 : IJ.log("Exposure should be positive") raise Exception("Exposure should be positive") AFoffset = float(NumField[6].text) # Formulate Autofocus command cmd = "SetLight({},{},{},{})".format(Channel,Power,Exposure,AFoffset) # see if dSlice should have a given number of digits print cmd IJ.log(cmd) # Save input for persistence prefs.put("Channel",Channel) prefs.put("Power",Power) prefs.put("Exposure",Exposure) prefs.put("AFoffset",AFoffset) # Create class instances associated to GUI Button Autofocus = AutofocusClass() # create an instance of the EventListener class Acquire = AcquireClass() # create an instance of the EventListener class SetLight = SetLightClass() ''' # Initialise counter for index - Maybe in the future N_Box = 0 N_String = 0 N_Num = 0 ''' # Generate GUI Win = GenericDialogPlus('Generate Imaging Machine Script File IMSF') # Autofocus(nSlice,dSlice,Bin,PreAF,DeferAdapt) # Get input fron persistence AF_nSlice = prefs.getInt("AF_nSlice",1) AF_dSlice = prefs.getInt("AF_dSlice",0) AF_bin = prefs.get("AF_bin",'1') PreAF = prefs.getBoolean("PreAF",True) DeferAdapt = prefs.getBoolean("DeferAdapt",True) Win.addButton('Autofocus',Autofocus) # add our event listener to the button. Button clicked -> event -> call actionPerformed(MyEvent) Win.addToSameRow() Win.addNumericField('Number of slices',AF_nSlice,0) # Num[0]=Autofocus>N_Slice Win.addToSameRow() Win.addNumericField('- Distance between slices (um)',AF_dSlice,3) # Num[1]=Autofocus>d_Slice Win.addToSameRow() Win.addChoice('Binning',['1','2','4'],AF_bin) # Choices[0]=Autofocus>Binning Win.addToSameRow() Win.addCheckbox('PreAutofocus',PreAF) # Bool[0]=Autofocus>PreAutofocus Win.addToSameRow() Win.addCheckbox('Defer Adaptative',DeferAdapt) # Bool[1]=Autofocus>DeferAdaptative # Acquire (nSlice,dSlice,Bin,path of main directory, Use meta information for filename) # Get input fron persistence Acq_nSlice = prefs.getInt("Acq_nSlice",1) Acq_dSlice = prefs.getInt("Acq_dSlice",0) Acq_bin = prefs.get("Acq_bin",'1') MainPath = prefs.get("MainPath",r'D:\IMAGING-DATA\IMAGES\SCRIPTS') UseMeta = prefs.getBoolean("UseMeta",True) Win.addButton('Acquire',Acquire) # add our event listener to the button. Button clicked -> event -> call actionPerformed(MyEvent) Win.addToSameRow() Win.addNumericField('Number of slices',Acq_nSlice,0) # Num[2]=Acquire>N_Slice Win.addToSameRow() Win.addNumericField('- Distance between slices (um)',Acq_dSlice,3) # Num[3]=Acquire>d_Slice Win.addToSameRow() Win.addChoice('Binning',['1','2','4'],Acq_bin) # Choices[1]=Acquire>Binning Win.addToSameRow() Win.addStringField("- Main folder",MainPath) # String[0]=Acquire>MainPath Win.addToSameRow() Win.addCheckbox("Use metadata for filename",UseMeta) # Bool[2]=Acquire>Use metadata # SetLight(channel, intensity,exposure, AF offset) # Recover input from persistence Channel = prefs.get("Channel",'6') Power = prefs.getInt("Power",50) Exposure = prefs.getInt("Exposure",100) AFoffset = prefs.getFloat("AFoffset",0.000) Win.addButton('Set Light',SetLight) Win.addToSameRow() Win.addChoice('Channel',['1','2','3','4','5','6'],Channel) # Choices[2]=SetLightChannel Win.addToSameRow() Win.addNumericField('Power(%)',Power,0) # Num[4]=SetLight>Power Win.addToSameRow() Win.addNumericField('Exposure(ms)',Exposure,0) # Num[5]=SetLight>Exposure Win.addToSameRow() Win.addNumericField('AF offset(um)',AFoffset,3) # Num[6]=SetLight>AF offset # Recover vector objects from dialog NumField = Win.getNumericFields() CheckBox = Win.getCheckboxes() StringField = Win.getStringFields() Choice = Win.getChoices() # Display after the vector objects were created Win.showDialog()