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")