''' Code to process the live-view image in GMS, producing a map of crystalline regions This requires a module FFTArrayAnalysis, which requires scipy, skimage, matplotlib, and tqdm The module is part of a package which can be installed with pip: pip install BenMillerScripts WARNING: Due to a bug in GMS 3.5.0 and 3.5.1, this script will not run in those versions Run the code with the live-view image, containing a rectangular ROI, front-most in GMS The code also works with an IS video played back with the IS player To stop calculation, delete the ROI. New frames are computed as often as possible. Lines of code between #XXXXXXXX... lines can be changed to modify the data processing All other lines of code are general, and can be re-used to produce other kinds of processed maps from a live-view image #Code written by Ben Miller. Last Updated May 2022 ''' from BenMillerScripts import FFTArrayAnalysis as FAA import time import numpy as np import traceback #User editable variables are set here #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #Set FFT Size and Spacing FAA.FFTsize = 128 #(Default 128) FAA.spacing = 32 #(Default 32) map_var = "theta" #Parameter to be mapped ("theta" or "radius") (default "theta") FAA.maskP = 10 #Set Percentage of Radial Profile (from center) to be Ignored (Default 10) FAA.maskC_width = 2 #Set to an integer value to also mask the center vertical and horizontal lines in the FFT, set to 0 to not mask (Default 2) FAA.binning = 2 #Set how much to bin the raw image data prior to computing FFTs higher values save time, but may result in loss of information (Default 1) Scale = 2 #Upscaling factor for the FFT Map. Either an integer >0 or "match" to output same size as input (Default 2) #a scale value of "match" is required for the overlay option Overlay=False #Set whether to overlay the original image intensity on top of the color map (must also set Scale to "match") (Default False) show_cube = False #This should only be used for troubleshooting. This returns a 4D cube of FFTs, which can be processed like a 4DSTEM dataset in GMS (Default False) Display_Initial_Diffractogram = True #If True, this displays a diffractogram of the first frame. This can be useful for determining whether the binning, maskC_width, and maskP are suitable. (Default True) display_scale = True #If True, this displays the color scale for the map, indicating which direction corresponds to each color. print_timing = True # (Default True) Select whether to output the time it takes to compute each frame #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX class CListen(DM.Py_ScriptObject): #Function to find an ROI placed on an image by the user, returning the ROI ID. #If no ROI found, create a new one covering the entire image. def find_ROI(self,image): imageDisplay = image.GetImageDisplay(0) numROIs = imageDisplay.CountROIs() id = None for n in range(numROIs): roi = imageDisplay.GetROI(n) if roi.IsRectangle(): roi.SetVolatile(False) roi.SetResizable(False) id = roi.GetID() break if id is None: #If No ROI is found, create one that covers the whole image. print("\nRectangular ROI not found... using whole image") data_shape = image.GetNumArray().shape roi=DM.NewROI() roi.SetRectangle(0, 0, data_shape[0], data_shape[1]) imageDisplay.AddROI(roi) roi.SetVolatile(False) roi.SetResizable(False) id = roi.GetID() return id #Initialization Function def __init__(self,img): try: #Create an index that is incremented each time data is processed. self.i = 0 #get the original image and assign it to self.imgref self.imgref = img #Get the data from the region within an ROI self.roi = DM.GetROIFromID(self.find_ROI(self.imgref)) val, val2, val3, val4 = self.roi.GetRectangle() self.data = self.imgref.GetNumArray()[int(val):int(val3),int(val2):int(val4)] #get the shape of the original image (input_sizex, input_sizey) = self.data.shape #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #First plot the color scale if display_scale: FAA.DrawColorScale(map_var = map_var) # use the FAA module to calculate the shape of the map which will be produced result_size_x,result_size_y = FAA.FFT_Result_Shape(self.data, scale=Scale) #Use the FAA module to create a new color image to contain the results of processing (it is currently difficult to work with color images in GMS using Python) self.result_image = FAA.CreateDM_RGB(np.zeros((result_size_x,result_size_y,3))) #Process the first frame (processedframe,direction_image,intensity_image,spacing_image,diffractogram_max) = FAA.processframe( self.imgref,map_var,show_cube, scale=Scale, overlay=Overlay, im_data=self.data) #In addition to the live color map, optionally produce and display a static maximum diffractogram image from the first frame if Display_Initial_Diffractogram: diffim = DM.CreateImage(np.copy(diffractogram_max)) diffim.ShowImage() del diffim #Initialize the color map intensity scale maximum self.RGB_scale_max = np.percentile(intensity_image, 95) #Display the result image in GMS self.result_image.ShowImage() #Set the image name which will be displayed in the image window's title bar self.result_image.SetName("FFT spot " + map_var +" map of "+img.GetName()) #Get the ID of the result image self.result_ID = self.result_image.GetID() #Use the FAA module to update the color map (it is currently difficult to work with color images in GMS using Python) FAA.UpdateRGB(self.result_ID, processedframe) #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX DM.Py_ScriptObject.__init__(self) self.stop = 0 except: print(traceback.format_exc()) #This function is run each time the image changes def HandleDataChangedEvent(self, flags, image): try: if not self.stop: #start timing start=time.perf_counter() #Get an (updated) ROI position val, val2, val3, val4 = self.roi.GetRectangle() #Get the data from the ROI area as a numpy array self.data = self.imgref.GetNumArray()[int(val):int(val3),int(val2):int(val4)] #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #compute ROI profile from the image, and place this profile into results image (processedframe,direction_image,intensity_image,spacing_image,diffractogram_max) = FAA.processframe( self.imgref,map_var,show_cube, scale=Scale, overlay=Overlay,im_data = self.data, RGB_scale_max=self.RGB_scale_max ) #Update the color map intensity scale maximum for use with the next frame self.RGB_scale_max = max(self.RGB_scale_max,np.percentile(intensity_image, 95)) #Update the color map with the latest data FAA.UpdateRGB(self.result_ID, processedframe) #XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX #end timing and output time to process this frame end=time.perf_counter() if print_timing: print("Processed Image "+str(self.i)+" Processing Time= "+str(end-start)) #Increment an index each time data is processed. self.i = self.i+1 except: print(traceback.format_exc()) #Function to Delete Image Listener def __del__(self): print("Listener Deleted") DM.Py_ScriptObject.__del__(self) #Function to end processing by deleting or unregistering listener def RemoveListeners(self): try: if not self.stop: self.stop = 1 DM.DoEvents() global listener #DM 3.5.2 and higher have new function for unregistering listeners. #DM 3.4.3 and lower should delete the listener instead #DM 3.5.0 and 3.5.1 have a fatal flaw regarding listeners, so this script is not compatible with those versions if (get_DM_version()[1][0] == "4" and get_DM_version()[0] == "3"): del listener else: listener.UnregisterAllListeners() print("Live Processing Script Ended") except: print(traceback.format_exc()) #Remove listeners if source image window is closed def HandleWindowClosedEvent(self, event_flags, window): print("Window Closed") self.RemoveListeners() #Remove listeners if the ROI is deleted def HandleROIRemovedEvent(self, img_disp_event_flags, img_disp, roi_change_flag, roi_disp_change_flags, roi): print("ROI Removed") self.RemoveListeners() #Function to get the currently used version of DigitalMicrograph def get_DM_version(): #No Python script command exists to get the DM version, #so we first run a DM script to put the values in the global tags dm_script = ('number minor, major, bugVersion\n' 'GetApplicationVersion(major, minor, bugVersion)\n' 'GetPersistentTagGroup().TagGroupSetTagAsLong("Python_Temp:DM_Version_Major",major)\n' 'GetPersistentTagGroup().TagGroupSetTagAsLong("Python_Temp:DM_Version_Minor",minor)\n' 'GetPersistentTagGroup().TagGroupSetTagAsLong("Python_Temp:DM_Version_bugVersion",bugVersion)') DM.ExecuteScriptString(dm_script) #Now get the information stored in the global tags by the DM script version = [0,0,0] _,version[0] = DM.GetPersistentTagGroup().GetTagAsString("Python_Temp:DM_Version_Major") _,version[1] = DM.GetPersistentTagGroup().GetTagAsString("Python_Temp:DM_Version_Minor") _,version[2] = DM.GetPersistentTagGroup().GetTagAsString("Python_Temp:DM_Version_bugVersion") return version #Main Code Starts Here #Check that we are not running 3.5.0 or 3.5.1 which have a known bug affecting this script. if (((get_DM_version()[1] == '51') or (get_DM_version()[1] == '50')) and get_DM_version()[0] == "3"): DM.OkDialog("Due to a bug in DigitalMicrograph 3.5.0 and 3.5.1, this script would cause DM to crash in those versions. \n\nScript Aborted.") exit() #Get front image in GMS img1 = DM.GetFrontImage() #Get the image window, so we can check if it gets closed imageDoc = DM.GetFrontImageDocument() imDocWin = imageDoc.GetWindow() #Get the image display, for the ROI-removed listener imageDisplay = img1.GetImageDisplay(0) #Listeners are started here #initiate the image listener listener = CListen(img1) #check if the source window closes WindowClosedListenerID = listener.WindowHandleWindowClosedEvent(imDocWin, 'pythonplugin') #check if the ROI has been deleted ROIRemovedListenerID = listener.ImageDisplayHandleROIRemovedEvent(imageDisplay,'pythonplugin') #check if the source image changes DataChangedListenerID = listener.ImageHandleDataChangedEvent(img1, 'pythonplugin') #IDs are not used in this script, but could be used to unregister individual listeners in DM 3.5.2 and higher.