def updateImage(self,mask = False,Stack = False):
# acquire image from camera, this should not be the case, you get images multiple times
# like this
if Stack:
# get the last image that was saved in the folder images
print("Stack")
# experiment_folder_path = self.main_widget.get_experiment_folder_path()
# image_path = experiment_folder_path + '/images/'
# file_names = []
# index = []
# for file in os.listdir(image_path):
# index.append(int(file.split('_')[-1]))
# file_names.append(file)
# print(file_names)
# print(np.argmax(np.asarray(index)))
# max_index = np.argmax(np.asarray(index))
# im = Image.open(experiment_folder_path + '/images/' + file_names[max_index])
# im = np.array(im.getdata()).reshape(im.size[0], im.size[1])
# self.img = im.astype('uint16')
# retval = 1
else:
if mask == False:
self.img,retval = self.main_widget.setup.camera.get_raw_img()
else:
img,retval = self.main_widget.setup.camera.get_raw_img()
self.img = processing.processed_image(img)
self.img *= 1024
retval = None
# if there was an error, display a text box
if retval == -1:
msg = QtGui.QMessageBox()
msg.setWindowTitle("Camera Error")
msg.setIcon(QtGui.QMessageBox.Critical)
msg.setStandardButtons(QtGui.QMessageBox.Ok)
msg.setText("Cannot fetch image from camera")
msg.setInformativeText("You must restart the program to fix the issue, your current position will be saved")
msg.exec_()
else:
self.settings.set_Magnification(int(str(self.microscopy_mag.currentText())))
self.im.set_data(self.img)
self.scale_bar()
#self.molo_circle()
molo_intensity,Airy_disk_radius, bkg_mean,bkg_std = mologram_processing.calc_IntAiryDisk(self.img)
self.molo_intensity.setText(str(molo_intensity))
self.bg_int.setText(str(bkg_mean) + ',' + str(bkg_std))
self.sum_int.setText(str(np.sum(self.img)/(2560*1920)))
self.max_pixel.setText(str(np.max(self.img)))
print(self.settings.magnification)
# draw a circle, where you detect the mologram
# update the image
self.canvas.draw()
