def loadtracksjson(self, fileString=''): if fileString != '': filename = fileString else: filename = open_file_gui("Open tracks from json", filetypes='*.json') if filename is None: return None obj_text = codecs.open(filename, 'r', encoding='utf-8').read() pts = json.loads(obj_text) txy_pts = np.array(pts['txy_pts']) self.txy_pts = txy_pts points = Points(txy_pts) points.tracks = pts['tracks'] points.get_tracks_by_frame() self.points = points nTracks = len(points.tracks)
def get_text_file(filename=None): if filename is None: filetypes = '.txt' prompt = 'Open File' filename = open_file_gui(prompt, filetypes=filetypes) if filename is None: return None else: filename = g.settings['filename'] if filename is None: g.alert('No filename selected') return None print("Filename: {}".format(filename)) g.m.statusBar().showMessage('Loading {}'.format( os.path.basename(filename))) return filename
def loadtracksjson(self): filename = open_file_gui("Open tracks from json", filetypes='*.json') if filename is None: return None obj_text = codecs.open(filename, 'r', encoding='utf-8').read() pts = json.loads(obj_text) txy_pts = np.array(pts['txy_pts']) self.txy_pts = txy_pts self.algorithm_gui.showPointsButton.setEnabled(True) self.skip_refinePoints() points = Points(txy_pts) points.tracks = pts['tracks'] points.get_tracks_by_frame() self.points = points nTracks = len(points.tracks) self.algorithm_gui.num_tracks_label.setText(str(nTracks)) self.algorithm_gui.showTracksButton.setEnabled(True) self.algorithm_gui.analyze_tab_widget.setCurrentIndex(3)
#get mean pixels values for 3x3 square self.intensities.append((np.mean(self.dataArray[frame][xMin:xMax,yMin:yMax]))) #update points instance self.points.intensities = self.intensities tracks = Tracks() if __name__ == '__main__': start_flika() #load particle image stack that you want to get intensities from imgStack_filename = open_file_gui() #data_window = open_file(r"C:\Users\g_dic\OneDrive\Desktop\testing\particles.tif") data_window = open_file(imgStack_filename) #load tracks from JSON file tracks.loadtracksjson() #set window to get intensities from tracks.setWindow(data_window) #get intensities from point positions tracks.getIntensities() #save new json file including point intensities + csv of linked track values tracks.savetracks() #load json #tracks.loadtracksjson(r"C:\Users\g_dic\OneDrive\Desktop\AL_55_2020-06-29-TIRFM_Diff_tdt-MEFs_B_4_trackintensities.json") #save csv file #tracks.savetrackscsv(r"C:\Users\g_dic\OneDrive\Desktop\AL_55_2020-06-29-TIRFM_Diff_tdt-MEFs_B_4_trackintensities.csv")