class GalvoRegistrator: def __init__(self, *args, **kwargs): self.cam = CamActuator() self.cam.initializeCamera() def registration(self, grid_points_x=3, grid_points_y=3): galvothread = DAQmission() readinchan = [] x_coords = np.linspace(-10, 10, grid_points_x + 2)[1:-1] y_coords = np.linspace(-10, 10, grid_points_y + 2)[1:-1] xy_mesh = np.reshape(np.meshgrid(x_coords, y_coords), (2, -1), order='F').transpose() galvo_coordinates = xy_mesh camera_coordinates = np.zeros((galvo_coordinates.shape)) for i in range(galvo_coordinates.shape[0]): galvothread.sendSingleAnalog('galvosx', galvo_coordinates[i, 0]) galvothread.sendSingleAnalog('galvosy', galvo_coordinates[i, 1]) time.sleep(1) image = self.cam.SnapImage(0.06) plt.imsave( os.getcwd() + '/CoordinatesManager/Registration_Images/2P/image_' + str(i) + '.png', image) camera_coordinates[i, :] = readRegistrationImages.gaussian_fitting( image) print('Galvo Coordinate') print(galvo_coordinates) print('Camera coordinates') print(camera_coordinates) del galvothread self.cam.Exit() transformation = CoordinateTransformations.polynomial2DFit( camera_coordinates, galvo_coordinates, order=1) print('Transformation found for x:') print(transformation[:, :, 0]) print('Transformation found for y:') print(transformation[:, :, 1]) return transformation
class DMDRegistator: def __init__(self, parent): self.DMD = DMDActuator.DMDActuator() self.cam = CamActuator() self.cam.initializeCamera() def registration(self, laser='640', points=6): x_coords = np.linspace(0, 1024, 5)[1:-1] y_coords = np.linspace(0, 768, 4)[1:-1] dmd_coordinates = np.vstack((x_coords, y_coords)) camera_coordinates = np.zeros(dmd_coordinates.shape) cnt = 0 for i in range(points): for j in range(y_coords.shape[0]): mask = create_registration_image(i, j) self.DMD.send_data_to_DMD(mask) self.DMD.start_projection() image = self.cam.SnapImage(0.4) camera_coordinates[cnt, :] = touchingCoordinateFinder( image, method='curvefit') cnt += 1 self.DMD.stop_projection() self.DMD.free_memory() self.DMD.disconnect_DMD() transformation = findTransformationCurvefit(camera_coordinates, dmd_coordinates, kx=3, ky=2) return transformation def create_registration_image(x, y, sigma=75): array = np.zeros((1024, 768)) array[skd.draw.rectangle((x - sigma, y - sigma), (x, y))] = 255 array[skd.draw.rectangle((x + sigma, y + sigma), (x, y))] = 255 return array
class DMDRegistator: def __init__(self, DMD, *args, **kwargs): self.DMD = DMD self.cam = CamActuator() self.cam.initializeCamera() def registration(self, laser='640', grid_points_x=2, grid_points_y=3, registration_pattern='circles'): x_coords = np.linspace(0, 768, grid_points_x + 2)[1:-1] y_coords = np.linspace(0, 1024, grid_points_y + 2)[1:-1] x_mesh, y_mesh = np.meshgrid(x_coords, y_coords) x_coords = np.ravel(x_mesh) y_coords = np.ravel(y_mesh) dmd_coordinates = np.stack((x_coords, y_coords), axis=1) camera_coordinates = np.zeros(dmd_coordinates.shape) for i in range(dmd_coordinates.shape[0]): x = int(dmd_coordinates[i, 0]) y = int(dmd_coordinates[i, 1]) if registration_pattern == 'squares': mask = DMDRegistator.create_registration_image_touching_squares( x, y) else: mask = DMDRegistator.create_registration_image_circle(x, y) self.DMD.send_data_to_DMD(mask) self.DMD.start_projection() image = self.cam.SnapImage(0.01) plt.imsave( os.getcwd() + '/CoordinatesManager/Registration_Images/TouchingSquares/image_' + str(i) + '.png', image) camera_coordinates[ i, :] = readRegistrationImages.touchingCoordinateFinder( image, method='curvefit') self.DMD.stop_projection() print('DMD coordinates:') print(dmd_coordinates) print('Found camera coordinates:') print(camera_coordinates) self.DMD.free_memory() self.cam.Exit() transformation = CoordinateTransformations.polynomial2DFit( camera_coordinates, dmd_coordinates, order=1) print('Transformation found for x:') print(transformation[:, :, 0]) print('Transformation found for y:') print(transformation[:, :, 1]) return transformation def create_registration_image_touching_squares(x, y, sigma=75): array = np.zeros((768, 1024)) array[skimage.draw.rectangle((x - sigma, y - sigma), (x, y))] = 255 array[skimage.draw.rectangle((x + sigma, y + sigma), (x, y))] = 255 return array def create_registration_image_circle(x, y, sigma=75): array = np.zeros((768, 1024)) array[skimage.draw.circle(x, y, sigma)] = 255 return array
class RegistrationThread(QThread): sig_finished_registration = pyqtSignal(dict) def __init__(self, parent, laser=None): QThread.__init__(self) self.flag_finished = [0, 0, 0] self.backend = parent self.dmd = self.backend.DMD if not isinstance(laser, list): self.laser_list = [laser] else: self.laser_list = laser self.dict_transformators = {} self.dict_transformations = {} self.dtype_ref_co = np.dtype([('camera', int, (3, 2)), ('dmd', int, (3, 2)), ('galvos', int, (3, 2)), ('stage', int, (3, 2))]) self.reference_coordinates = {} def set_device_to_register(self, device_1, device_2='camera'): self.device_1 = device_1 self.device_2 = device_2 def run(self): #Make sure registration can only start when camera is connected try: self.cam = CamActuator() self.cam.initializeCamera() except: print(sys.exc_info()) self.backend.ui_widget.normalOutputWritten( 'Unable to connect Hamamatsu camera') return self.cam.setROI(0, 0, 2048, 2048) if self.device_1 == 'galvos': reference_coordinates = self.gather_reference_coordinates_galvos() self.dict_transformations['camera-galvos'] = findTransform(reference_coordinates[0], \ reference_coordinates[1]) elif self.device_1 == 'dmd': reference_coordinates = self.gather_reference_coordinates_dmd() for laser in self.laser_list: self.dict_transformations['camera-dmd-'+laser] = findTransform(reference_coordinates[0], \ reference_coordinates[1]) elif self.device_1 == 'stage': reference_coordinates = self.gather_reference_coordinates_stage() self.dict_transformations['camera-stage'] = findTransform(reference_coordinates[0], \ reference_coordinates[1]) self.cam.Exit() ## Save transformation to file with open('CoordinatesManager/Registration/transformation.txt', 'w') as json_file: dict_transformations_list_format = {} for key, value in self.dict_transformations.items(): dict_transformations_list_format[key] = value.tolist() json.dump(dict_transformations_list_format, json_file) self.sig_finished_registration.emit(self.dict_transformations) def gather_reference_coordinates_stage(self): image = np.zeros((2048, 2048, 3)) stage_coordinates = np.array([[-2800, 100], [-2500, 400], [-1900, -200]]) self.backend.loadMask(mask=np.ones((768, 1024))) self.backend.startProjection() for idx, pos in enumerate(stage_coordinates): stage_movement_thread = StagemovementAbsoluteThread(pos[0], pos[1]) stage_movement_thread.start() time.sleep(0.5) stage_movement_thread.quit() stage_movement_thread.wait() image[:, :, idx] = self.cam.SnapImage(0.04) camera_coordinates = find_subimage_location(image, save=True) self.backend.stopProjection() self.backend.freeMemory() return np.array([camera_coordinates, stage_coordinates]) def gather_reference_coordinates_galvos(self): galvothread = DAQmission() readinchan = [] camera_coordinates = np.zeros((3, 2)) galvo_coordinates = np.array([[0, 3], [3, -3], [-3, -3]]) for i in range(3): pos_x = galvo_coordinates[i, 0] pos_y = galvo_coordinates[i, 1] galvothread.sendSingleAnalog('galvosx', pos_x) galvothread.sendSingleAnalog('galvosy', pos_y) image = self.cam.SnapImage(0.04) camera_coordinates[i, :] = gaussian_fitting(image) del galvothread return np.array([camera_coordinates, galvo_coordinates]) def gather_reference_coordinates_dmd(self): galvo_coordinates = np.zeros((3, 2)) for laser in self.laser_list: self.flag_finished = [0, 0, 0] self.backend.ui_widget.sig_control_laser.emit(laser, 5) self.registration_single_laser(laser) self.backend.ui_widget.sig_control_laser.emit(laser, 0) return np.array( [self.camera_coordinates, self.dmd_coordinates, galvo_coordinates]) def registration_single_laser(self, laser): date_time = datetime.datetime.now().timetuple() image_id = '' for i in range(5): image_id += str(date_time[i]) + '_' image_id += str(date_time[5]) + '_l' + laser self.camera_coordinates = np.zeros((3, 2)) self.touchingCoordinateFinder = [] for i in range(3): self.touchingCoordinateFinder.append( touchingCoordinateFinder_Thread(i, method='curvefit')) self.touchingCoordinateFinder[ i].sig_finished_coordinatefinder.connect( self.touchingCoordinateFinder_finished) for i in range(3): self.loadFileName = './CoordinatesManager/Registration_Images/TouchingSquares/registration_mask_' + str( i) + '.png' # Transpose because mask in file is rotated by 90 degrees. mask = np.transpose(plt.imread(self.loadFileName)) self.backend.loadMask(mask) self.backend.startProjection() time.sleep(0.5) self.image = self.cam.SnapImage(0.0015) time.sleep(0.5) self.backend.stopProjection() self.backend.freeMemory() # Start touchingCoordinateFinder thread self.touchingCoordinateFinder[i].put_image(self.image) self.touchingCoordinateFinder[i].start() self.dmd_coordinates = self.read_dmd_coordinates_from_file() # Block till all touchingCoordinateFinder_Thread threads are finished while np.prod(self.flag_finished) == 0: time.sleep(0.1) def read_dmd_coordinates_from_file(self): file = open( './CoordinatesManager/Registration_Images/TouchingSquares/positions.txt', 'r') self.dmd_coordinates = [] for ln in file.readlines(): self.dmd_coordinates.append(ln.strip().split(',')) file.close() return np.asarray(self.dmd_coordinates).astype(int) def touchingCoordinateFinder_finished(self, sig): self.camera_coordinates[sig, :] = np.flip( self.touchingCoordinateFinder[sig].coordinates) self.flag_finished[sig] = 1
class StageWidget(QWidget): def __init__(self, parent=None, *args, **kwargs): super().__init__(*args, **kwargs) self.main_application = parent self.set_image_saving_location( os.getcwd() + '/CoordinatesManager/Registration_Images/StageRegistration/') self.init_gui() self.ludlStage = LudlStage("COM12") def init_gui(self): layout = QGridLayout() # self.setFixedSize(320,100) self.box = roundQGroupBox() self.box.setTitle("Stage") box_layout = QGridLayout() self.box.setLayout(box_layout) self.setLayout(layout) self.collect_data_button = QPushButton('Collect data') self.collect_data_button.clicked.connect(self.start_aqcuisition) box_layout.addWidget(self.collect_data_button) layout.addWidget(self.box) def set_image_saving_location(self, filepath): self.image_file_path = filepath def start_aqcuisition(self): global_pos = np.array( ((-5000, -5000), (-5000, 5000), (5000, -5000), (5000, 5000))) global_pos_name = ['A', 'B', 'C', 'D'] delta = 200 local_pos = np.transpose( np.reshape( np.meshgrid(np.array((-delta, 0, delta)), np.array((-delta, 0, delta))), (2, -1))) local_pos_name = [str(i) for i in range(9)] self.cam = CamActuator() self.cam.initializeCamera() # Offset variables are used to generate replicates for good statistics offset_y = offset_x = delta cnt = 0 for i in range(global_pos.shape[0]): for j in range(local_pos.shape[0]): x = global_pos[i, 0] + local_pos[j, 0] + offset_x y = global_pos[i, 1] + local_pos[j, 1] + offset_y self.ludlStage.moveAbs(x=x, y=y) # stage_movement_thread = StagemovementAbsoluteThread(x, y) # stage_movement_thread.start() # time.sleep(2) # stage_movement_thread.quit() # stage_movement_thread.wait() image = self.cam.SnapImage(0.04) filename = global_pos_name[i] + local_pos_name[j] self.save_image(filename, image) cnt += 1 print( str(cnt) + '/' + str(len(local_pos_name) * len(global_pos_name))) self.cam.Exit() def save_image(self, filename, image): plt.imsave(self.image_file_path + filename + '.png', image)
class CoordinatesWidgetUI(QWidget): sig_cast_mask_coordinates_to_dmd = pyqtSignal(list) sig_cast_mask_coordinates_to_galvo = pyqtSignal(list) sig_start_registration = pyqtSignal() sig_finished_registration = pyqtSignal() sig_cast_camera_image = pyqtSignal(np.ndarray) def __init__(self, parent=None, *args, **kwargs): super().__init__(*args, **kwargs) self.main_application = parent self.init_gui() def closeEvent(self, event): try: self.DMD except: pass else: self.DMD.disconnect_DMD() QtWidgets.QApplication.quit() event.accept() def init_gui(self): self.setWindowTitle("Coordinate control") self.layout = QGridLayout() self.setMinimumSize(1250, 1000) self.setLayout(self.layout) self.image_mask_stack = QTabWidget() self.selection_view = DrawingWidget(self) self.selection_view.enable_drawing(True) self.selection_view.getView().setLimits(xMin=0, xMax=2048, yMin=0, yMax=2048, minXRange=2048, minYRange=2048, maxXRange=2048, maxYRange=2048) self.selection_view.ui.roiBtn.hide() self.selection_view.ui.menuBtn.hide() self.selection_view.ui.normGroup.hide() self.selection_view.ui.roiPlot.hide() # self.selection_view.setImage(plt.imread('CoordinatesManager/Registration_Images/StageRegistration/Distance200_Offset0/A1.png')) self.mask_view = SquareImageView() self.mask_view.getView().setLimits(xMin=0, xMax=2048, yMin=0, yMax=2048, minXRange=2048, minYRange=2048, maxXRange=2048, maxYRange=2048) self.mask_view.ui.roiBtn.hide() self.mask_view.ui.menuBtn.hide() self.mask_view.ui.normGroup.hide() self.mask_view.ui.roiPlot.hide() self.mask_view.ui.histogram.hide() self.image_mask_stack.addTab(self.selection_view, 'Select') self.image_mask_stack.addTab(self.mask_view, 'Mask') self.layout.addWidget(self.image_mask_stack, 0, 0, 5, 1) # ---------------------- Mask generation Container -------------- self.maskGeneratorContainer = roundQGroupBox() self.maskGeneratorContainer.setFixedSize(320, 220) self.maskGeneratorContainer.setTitle("Mask generator") self.maskGeneratorContainerLayout = QGridLayout() self.maskGeneratorLayout = QGridLayout() self.maskGeneratorContainer.setLayout( self.maskGeneratorContainerLayout) self.loadMaskFromFileButton = QPushButton('Open mask') self.loadMaskFromFileButton.clicked.connect(self.load_mask_from_file) self.addRoiButton = QPushButton("Add ROI") self.createMaskButton = QPushButton("Create mask") self.removeSelectionButton = QPushButton("Remove ROIs") self.addRoiButton.clicked.connect(self.add_polygon_roi) self.createMaskButton.clicked.connect(self.create_mask) self.removeSelectionButton.clicked.connect(self.remove_selection) self.maskGeneratorContainerLayout.addWidget(self.addRoiButton, 1, 0) self.maskGeneratorContainerLayout.addWidget(self.createMaskButton, 2, 0) self.maskGeneratorContainerLayout.addWidget(self.removeSelectionButton, 1, 1) self.selectionOptionsContainer = roundQGroupBox() self.selectionOptionsContainer.setTitle('Options') self.selectionOptionsLayout = QGridLayout() self.fillContourButton = QCheckBox() self.invertMaskButton = QCheckBox() self.thicknessSpinBox = QSpinBox() self.thicknessSpinBox.setRange(1, 25) self.selectionOptionsLayout.addWidget(QLabel('Fill contour:'), 0, 0) self.selectionOptionsLayout.addWidget(self.fillContourButton, 0, 1) self.selectionOptionsLayout.addWidget(QLabel('Invert mask:'), 1, 0) self.selectionOptionsLayout.addWidget(self.invertMaskButton, 1, 1) self.selectionOptionsLayout.addWidget(QLabel('Thickness:'), 2, 0) self.selectionOptionsLayout.addWidget(self.thicknessSpinBox, 2, 1) self.selectionOptionsContainer.setLayout(self.selectionOptionsLayout) self.snapFovButton = QPushButton('Image FOV') self.snapFovButton.clicked.connect(self.snap_fov) self.maskGeneratorContainerLayout.addWidget(self.snapFovButton, 0, 0, 1, 1) self.maskGeneratorContainerLayout.addWidget( self.loadMaskFromFileButton, 0, 1, 1, 1) self.maskGeneratorContainerLayout.addWidget( self.selectionOptionsContainer, 2, 1, 2, 1) self.layout.addWidget(self.maskGeneratorContainer, 0, 1) self.DMDWidget = DMDWidget.DMDWidget() self.layout.addWidget(self.DMDWidget, 1, 1) self.DMDWidget.sig_request_mask_coordinates.connect( lambda: self.cast_mask_coordinates('dmd')) self.sig_cast_mask_coordinates_to_dmd.connect( self.DMDWidget.receive_mask_coordinates) self.DMDWidget.sig_start_registration.connect( lambda: self.sig_start_registration.emit()) self.DMDWidget.sig_finished_registration.connect( lambda: self.sig_finished_registration.emit()) self.GalvoWidget = GalvoWidget.GalvoWidget() self.layout.addWidget(self.GalvoWidget, 2, 1) self.GalvoWidget.sig_request_mask_coordinates.connect( lambda: self.cast_mask_coordinates('galvo')) self.sig_cast_mask_coordinates_to_galvo.connect( self.GalvoWidget.receive_mask_coordinates) self.GalvoWidget.sig_start_registration.connect( lambda: self.sig_start_registration.emit()) self.GalvoWidget.sig_finished_registration.connect( lambda: self.sig_finished_registration.emit()) self.ManualRegistrationWidget = ManualRegistration.ManualRegistrationWidget( self) self.ManualRegistrationWidget.sig_request_camera_image.connect( self.cast_camera_image) self.sig_cast_camera_image.connect( self.ManualRegistrationWidget.receive_camera_image) self.layout.addWidget(self.ManualRegistrationWidget, 3, 1) self.StageRegistrationWidget = StageRegistrationWidget.StageWidget( self) self.layout.addWidget(self.StageRegistrationWidget, 4, 1) def cast_transformation_to_DMD(self, transformation, laser): self.DMDWidget.transform[laser] = transformation self.DMDWidget.save_transformation() def cast_transformation_to_galvos(self, sig): transformation = sig self.GalvoWidget.transform = transformation self.GalvoWidget.save_transformation() def cast_camera_image(self): image = self.selection_view.image if type(image) == np.ndarray: self.sig_cast_camera_image.emit(image) def snap_fov(self): self.DMDWidget.interupt_projection() self.DMDWidget.project_full_white() self.cam = CamActuator() self.cam.initializeCamera() image = self.cam.SnapImage(0.04) self.cam.Exit() self.selection_view.setImage(image) def cast_mask_coordinates(self, receiver): list_of_rois = self.get_list_of_rois() sig = [ list_of_rois, self.fillContourButton.isChecked(), self.thicknessSpinBox.value(), self.invertMaskButton.isChecked() ] if receiver == 'dmd': self.sig_cast_mask_coordinates_to_dmd.emit(sig) else: self.sig_cast_mask_coordinates_to_galvo.emit(sig) def get_list_of_rois(self): view = self.selection_view list_of_rois = [] for roi in view.roilist: roi_handle_positions = roi.getLocalHandlePositions() roi_origin = roi.pos() for idx, pos in enumerate(roi_handle_positions): roi_handle_positions[idx] = pos[1] num_vertices = len(roi_handle_positions) vertices = np.zeros([num_vertices, 2]) for idx, vertex in enumerate(roi_handle_positions): vertices[idx, :] = np.array( [vertex.x() + roi_origin.x(), vertex.y() + roi_origin.y()]) list_of_rois.append(vertices) return list_of_rois def create_mask(self): flag_fill_contour = self.fillContourButton.isChecked() flag_invert_mode = self.invertMaskButton.isChecked() contour_thickness = self.thicknessSpinBox.value() list_of_rois = self.get_list_of_rois() self.mask = ProcessImage.CreateBinaryMaskFromRoiCoordinates(list_of_rois, \ fill_contour = flag_fill_contour, \ contour_thickness = contour_thickness, \ invert_mask = flag_invert_mode) self.mask_view.setImage(self.mask) def remove_selection(self): self.selection_view.clear_rois() def set_camera_image(self, sig): self.selection_view.setImage(sig) def add_polygon_roi(self): view = self.selection_view x = (view.getView().viewRect().x()) * 0.3 y = (view.getView().viewRect().y()) * 0.3 a = (view.getView().viewRect().width() + x) * 0.3 b = (view.getView().viewRect().height() + y) * 0.3 c = (view.getView().viewRect().width() + x) * 0.7 d = (view.getView().viewRect().height() + y) * 0.7 polygon_roi = pg.PolyLineROI([[a, b], [c, b], [c, d], [a, d]], pen=view.pen, closed=True, movable=True, removable=True) view.getView().addItem(polygon_roi) view.append_to_roilist(polygon_roi) def load_mask_from_file(self): """ Open a file manager to browse through files, load image file """ self.loadFileName, _ = QtWidgets.QFileDialog.getOpenFileName( self, 'Select file', './CoordinateManager/Images/', "(*.png, *.tiff, *.jpg)") try: image = plt.imread(self.loadFileName) self.mask = image self.mask_view.setImage(self.mask) except: print('fail to load file.')
class FocusFinder(): def __init__(self, source_of_image = "PMT", init_search_range = 0.010, total_step_number = 5, imaging_conditions = {'edge_volt':5}, \ motor_handle = None, camera_handle = None, twophoton_handle = None, *args, **kwargs): """ Parameters ---------- source_of_image : string, optional The input source of image. The default is PMT. init_search_range : int, optional The step size when first doing coarse searching. The default is 0.010. total_step_number : int, optional Number of steps in total to find optimal focus. The default is 5. imaging_conditions : list Parameters for imaging. For PMT, it specifies the scanning voltage. For camera, it specifies the AOTF voltage and exposure time. motor_handle : TYPE, optional Handle to control PI motor. The default is None. twophoton_handle : TYPE, optional Handle to control Insight X3. The default is None. Returns ------- None. """ super().__init__(*args, **kwargs) # The step size when first doing coarse searching. self.init_search_range = init_search_range # Number of steps in total to find optimal focus. self.total_step_number = total_step_number # Parameters for imaging. self.imaging_conditions = imaging_conditions if motor_handle == None: # Connect the objective if the handle is not provided. self.pi_device_instance = PIMotor() else: self.pi_device_instance = motor_handle # Current position of the focus. self.current_pos = self.pi_device_instance.GetCurrentPos() # Number of steps already tried. self.steps_taken = 0 # The focus degree of previous position. self.previous_degree_of_focus = 0 # Number of going backwards. self.turning_point = 0 # The input source of image. self.source_of_image = source_of_image if source_of_image == "PMT": self.galvo = RasterScan(Daq_sample_rate = 500000, edge_volt = self.imaging_conditions['edge_volt']) elif source_of_image == "Camera": if camera_handle == None: # If no camera instance fed in, initialize camera. self.HamamatsuCam_ins = CamActuator() self.HamamatsuCam_ins.initializeCamera() else: self.HamamatsuCam_ins = camera_handle def gaussian_fit(self, move_to_focus = True): # The upper edge. upper_position = self.current_pos + self.init_search_range # The lower edge. lower_position = self.current_pos - self.init_search_range # Generate the sampling positions. sample_positions = np.linspace(lower_position, upper_position, self.total_step_number) degree_of_focus_list = [] for each_pos in sample_positions: # Go through each position and write down the focus degree. degree_of_focus = self.evaluate_focus(round(each_pos, 6)) degree_of_focus_list.append(degree_of_focus) print(degree_of_focus_list) try: interpolated_fitted_curve = ProcessImage.gaussian_fit(degree_of_focus_list) # Generate the inpterpolated new focus position axis. x_axis_new = np.linspace(lower_position, upper_position, len(interpolated_fitted_curve)) # Generate a dictionary and find the position where has the highest focus degree. max_focus_pos = dict(zip(interpolated_fitted_curve, x_axis_new))[np.amax(interpolated_fitted_curve)] if True: # Plot the fitting. plt.plot(sample_positions, np.asarray(degree_of_focus_list),'b+:',label='data') plt.plot(x_axis_new, interpolated_fitted_curve,'ro:',label='fit') plt.legend() plt.title('Fig. Fit for focus degree') plt.xlabel('Position') plt.ylabel('Focus degree') plt.show() max_focus_pos = round(max_focus_pos, 6) print(max_focus_pos) self.pi_device_instance.move(max_focus_pos) # max_focus_pos_focus_degree = self.evaluate_focus(round(max_focus_pos, 6)) except: print("Fitting failed. Find max in the list.") max_focus_pos = sample_positions[degree_of_focus_list.index(max(degree_of_focus_list))] print(max_focus_pos) if move_to_focus == True: self.pi_device_instance.move(max_focus_pos) return max_focus_pos def bisection(self): """ Bisection way of finding focus. Returns ------- mid_position : float DESCRIPTION. """ # The upper edge in which we run bisection. upper_position = self.current_pos + self.init_search_range # The lower edge in which we run bisection. lower_position = self.current_pos - self.init_search_range for step_index in range(1, self.total_step_number + 1): # In each step of bisection finding. # In the first round, get degree of focus at three positions. if step_index == 1: # Get degree of focus in the mid. mid_position = (upper_position + lower_position)/2 degree_of_focus_mid = self.evaluate_focus(mid_position) print("mid focus degree: {}".format(round(degree_of_focus_mid, 5))) # Break the loop if focus degree is below threshold which means # that there's no cell in image. if not ProcessImage.if_theres_cell(self.galvo_image.astype('float32')): print('no cell') mid_position = False break # Move to top and evaluate. degree_of_focus_up = self.evaluate_focus(obj_position = upper_position) print("top focus degree: {}".format(round(degree_of_focus_up, 5))) # Move to bottom and evaluate. degree_of_focus_low = self.evaluate_focus(obj_position = lower_position) print("bot focus degree: {}".format(round(degree_of_focus_low, 5))) # Sorting dicitonary of degrees in ascending. biesection_range_dic = {"top":[upper_position, degree_of_focus_up], "bot":[lower_position, degree_of_focus_low]} # In the next rounds, only need to go to center and update boundaries. elif step_index > 1: # The upper edge in which we run bisection. upper_position = biesection_range_dic["top"][0] # The lower edge in which we run bisection. lower_position = biesection_range_dic["bot"][0] # Get degree of focus in the mid. mid_position = (upper_position + lower_position)/2 degree_of_focus_mid = self.evaluate_focus(mid_position) print("Current focus degree: {}".format(round(degree_of_focus_mid, 5))) # If sits in upper half, make the middle values new bottom. if biesection_range_dic["top"][1] > biesection_range_dic["bot"][1]: biesection_range_dic["bot"] = [mid_position, degree_of_focus_mid] else: biesection_range_dic["top"] = [mid_position, degree_of_focus_mid] print("The upper pos: {}; The lower: {}".format(biesection_range_dic["top"][0], biesection_range_dic["bot"][0])) return mid_position def evaluate_focus(self, obj_position = None): """ Evaluate the focus degree of certain objective position. Parameters ---------- obj_position : float, optional The target objective position. The default is None. Returns ------- degree_of_focus : float Degree of focus. """ if obj_position != None: self.pi_device_instance.move(obj_position) # Get the image. if self.source_of_image == "PMT": self.galvo_image = self.galvo.run() plt.figure() plt.imshow(self.galvo_image) plt.show() if False: with skimtiff.TiffWriter(os.path.join(r'M:\tnw\ist\do\projects\Neurophotonics\Brinkslab\Data\Xin\2020-11-17 gaussian fit auto-focus cells\trial_11', str(obj_position).replace(".", "_")+ '.tif')) as tif: tif.save(self.galvo_image.astype('float32'), compress=0) degree_of_focus = ProcessImage.local_entropy(self.galvo_image.astype('float32')) elif self.source_of_image == "Camera": # First configure the AOTF. self.AOTF_runner = DAQmission() # Find the AOTF channel key for key in self.imaging_conditions: if 'AO' in key: # like '488AO' AOTF_channel_key = key # Set the AOTF first. self.AOTF_runner.sendSingleDigital('blankingall', True) self.AOTF_runner.sendSingleAnalog(AOTF_channel_key, self.imaging_conditions[AOTF_channel_key]) # Snap an image from camera self.camera_image = self.HamamatsuCam_ins.SnapImage(self.imaging_conditions['exposure_time']) time.sleep(0.5) # Set back AOTF self.AOTF_runner.sendSingleDigital('blankingall', False) self.AOTF_runner.sendSingleAnalog(AOTF_channel_key, 0) plt.figure() plt.imshow(self.camera_image) plt.show() if False: with skimtiff.TiffWriter(os.path.join(r'M:\tnw\ist\do\projects\Neurophotonics\Brinkslab\Data\Xin\2021-03-06 Camera AF\beads', str(obj_position).replace(".", "_")+ '.tif')) as tif: tif.save(self.camera_image.astype('float32'), compress=0) degree_of_focus = ProcessImage.variance_of_laplacian(self.camera_image.astype('float32')) time.sleep(0.2) return degree_of_focus
class MainGUI(QWidget): # signal_DMDmask is cictionary with laser specification as key and binary mask as content. signal_DMDmask = pyqtSignal(dict) signal_DMDcontour = pyqtSignal(list) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) os.chdir('./') # Set directory to current folder. self.setFont(QFont("Arial")) # self.setMinimumSize(900, 1020) self.setWindowTitle("Cell Selection") self.layout = QGridLayout(self) self.roi_list_freehandl_added = [] self.selected_ML_Index = [] self.selected_cells_infor_dict = {} self.mask_color_multiplier = [1, 1, 0] # ============================================================================= # Container for image display # ============================================================================= graphContainer = StylishQT.roundQGroupBox() graphContainerLayout = QGridLayout() self.Imgviewtabs = QTabWidget() MLmaskviewBox = QWidget() MLmaskviewBoxLayout = QGridLayout() self.Matdisplay_Figure = Figure() self.Matdisplay_Canvas = FigureCanvas(self.Matdisplay_Figure) self.Matdisplay_Canvas.setFixedWidth(500) self.Matdisplay_Canvas.setFixedHeight(500) self.Matdisplay_Canvas.mpl_connect('button_press_event', self._onclick) self.Matdisplay_toolbar = NavigationToolbar(self.Matdisplay_Canvas, self) MLmaskviewBoxLayout.addWidget(self.Matdisplay_toolbar, 0, 0) MLmaskviewBoxLayout.addWidget(self.Matdisplay_Canvas, 1, 0) MLmaskviewBox.setLayout(MLmaskviewBoxLayout) self.Imgviewtabs.addTab(MLmaskviewBox, "MaskRCNN") # ============================================================================= # Mask editing tab # ============================================================================= MLmaskEditBox = QWidget() MLmaskEditBoxLayout = QGridLayout() self.Mask_edit_view = DrawingWidget(self) self.Mask_edit_view.enable_drawing(False) # Disable drawing first # self.Mask_edit_view = pg.ImageView() # self.Mask_edit_view.getView().setLimits(xMin = 0, xMax = 2048, yMin = 0, yMax = 2048, minXRange = 2048, minYRange = 2048, maxXRange = 2048, maxYRange = 2048) self.Mask_edit_viewItem = self.Mask_edit_view.getImageItem() # self.ROIitem = pg.PolyLineROI([[0,0], [80,0], [80,80], [0,80]], closed=True) self.Mask_edit_view_getView = self.Mask_edit_view.getView() # self.Mask_edit_view_getView.addItem(self.ROIitem) self.Mask_edit_view.ui.roiBtn.hide() self.Mask_edit_view.ui.menuBtn.hide() self.Mask_edit_view.ui.normGroup.hide() self.Mask_edit_view.ui.roiPlot.hide() MLmaskEditBoxLayout.addWidget(self.Mask_edit_view, 0, 0) MLmaskEditBox.setLayout(MLmaskEditBoxLayout) self.Imgviewtabs.addTab(MLmaskEditBox, "Mask edit") graphContainerLayout.addWidget(self.Imgviewtabs, 0, 0) graphContainer.setLayout(graphContainerLayout) # ============================================================================= # Operation container # ============================================================================= operationContainer = StylishQT.roundQGroupBox() operationContainerLayout = QGridLayout() self.init_ML_button = QPushButton('Initialize ML', self) operationContainerLayout.addWidget(self.init_ML_button, 0, 0) self.init_ML_button.clicked.connect(self.init_ML) #---------------------Load image from file----------------------------- self.textbox_loadimg = QLineEdit(self) operationContainerLayout.addWidget(self.textbox_loadimg, 1, 0) self.button_import_img_browse = QPushButton('Browse', self) operationContainerLayout.addWidget(self.button_import_img_browse, 1, 1) self.button_import_img_browse.clicked.connect(self.get_img_file_tif) self.run_ML_button = QPushButton('Analysis', self) operationContainerLayout.addWidget(self.run_ML_button, 2, 0) self.run_ML_button.clicked.connect(self.run_ML_onImg_and_display) self.generate_MLmask_button = QPushButton('Mask', self) operationContainerLayout.addWidget(self.generate_MLmask_button, 2, 1) self.generate_MLmask_button.clicked.connect(self.generate_MLmask) self.update_MLmask_button = QPushButton('Update mask', self) operationContainerLayout.addWidget(self.update_MLmask_button, 3, 0) self.update_MLmask_button.clicked.connect(self.update_mask) self.enable_modify_MLmask_button = QPushButton('Enable free-hand', self) self.enable_modify_MLmask_button.setCheckable(True) operationContainerLayout.addWidget(self.enable_modify_MLmask_button, 4, 0) self.enable_modify_MLmask_button.clicked.connect(self.enable_free_hand) # self.modify_MLmask_button = QPushButton('Add patch', self) # operationContainerLayout.addWidget(self.modify_MLmask_button, 4, 1) # self.modify_MLmask_button.clicked.connect(self.addedROIitem_to_Mask) self.clear_roi_button = QPushButton('Clear ROIs', self) operationContainerLayout.addWidget(self.clear_roi_button, 5, 0) self.clear_roi_button.clicked.connect(self.clear_edit_roi) # self.maskLaserComboBox = QComboBox() # self.maskLaserComboBox.addItems(['640', '532', '488']) # operationContainerLayout.addWidget(self.maskLaserComboBox, 6, 0) # # self.generate_transformed_mask_button = QPushButton('Transform mask', self) # operationContainerLayout.addWidget(self.generate_transformed_mask_button, 6, 1) # self.generate_transformed_mask_button.clicked.connect(self.generate_transformed_mask) self.emit_transformed_mask_button = QPushButton('Emit mask', self) operationContainerLayout.addWidget(self.emit_transformed_mask_button, 7, 1) self.emit_transformed_mask_button.clicked.connect( self.emit_mask_contour) operationContainer.setLayout(operationContainerLayout) # ============================================================================= # Mask para container # ============================================================================= MaskparaContainer = StylishQT.roundQGroupBox() MaskparaContainerContainerLayout = QGridLayout() #---------------------------------------------------------------------- self.fillContourButton = QCheckBox() self.invertMaskButton = QCheckBox() self.thicknessSpinBox = QSpinBox() self.thicknessSpinBox.setRange(1, 25) MaskparaContainerContainerLayout.addWidget(QLabel('Fill contour:'), 0, 0) MaskparaContainerContainerLayout.addWidget(self.fillContourButton, 0, 1) MaskparaContainerContainerLayout.addWidget(QLabel('Invert mask:'), 1, 0) MaskparaContainerContainerLayout.addWidget(self.invertMaskButton, 1, 1) MaskparaContainerContainerLayout.addWidget(QLabel('Thickness:'), 2, 0) MaskparaContainerContainerLayout.addWidget(self.thicknessSpinBox, 2, 1) MaskparaContainer.setLayout(MaskparaContainerContainerLayout) # ============================================================================= # Device operation container # ============================================================================= deviceOperationContainer = StylishQT.roundQGroupBox() deviceOperationContainerLayout = QGridLayout() #---------------------------------------------------------------------- self.CamExposureBox = QDoubleSpinBox(self) self.CamExposureBox.setDecimals(6) self.CamExposureBox.setMinimum(0) self.CamExposureBox.setMaximum(100) self.CamExposureBox.setValue(0.001501) self.CamExposureBox.setSingleStep(0.001) deviceOperationContainerLayout.addWidget(self.CamExposureBox, 0, 1) deviceOperationContainerLayout.addWidget(QLabel("Exposure time:"), 0, 0) cam_snap_button = QPushButton('Cam snap', self) deviceOperationContainerLayout.addWidget(cam_snap_button, 0, 2) cam_snap_button.clicked.connect(self.cam_snap) cam_snap_button = QPushButton('Cam snap', self) deviceOperationContainerLayout.addWidget(cam_snap_button, 0, 2) cam_snap_button.clicked.connect(self.cam_snap) deviceOperationContainer.setLayout(deviceOperationContainerLayout) self.layout.addWidget(graphContainer, 0, 0, 3, 1) self.layout.addWidget(operationContainer, 0, 1) self.layout.addWidget(MaskparaContainer, 1, 1) self.layout.addWidget(deviceOperationContainer, 2, 1) self.setLayout(self.layout) #%% # ============================================================================= # MaskRCNN detection part # ============================================================================= # @run_in_thread def init_ML(self): # Initialize the detector instance and load the model. self.ProcessML = ProcessImageML() def get_img_file_tif(self): self.img_tif_filePath, _ = QtWidgets.QFileDialog.getOpenFileName( self, 'Single File', 'M:/tnw/ist/do/projects/Neurophotonics/Brinkslab/Data', "(*.tif)") self.textbox_loadimg.setText(self.img_tif_filePath) if self.img_tif_filePath != None: self.Rawimage = imread(self.img_tif_filePath) self.MLtargetedImg_raw = self.Rawimage.copy() self.MLtargetedImg = self.convert_for_MaskRCNN( self.MLtargetedImg_raw) self.show_raw_image(self.MLtargetedImg) self.addedROIitemMask = np.zeros( (self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) self.MLmask = np.zeros( (self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) def show_raw_image(self, image): # display a single image try: self.Matdisplay_Figure.clear() except: pass ax1 = self.Matdisplay_Figure.add_subplot(111) ax1.set_xticks([]) ax1.set_yticks([]) ax1.imshow(image) self.Matdisplay_Figure.tight_layout() self.Matdisplay_Canvas.draw() RGB_image = gray2rgb(image) self.Mask_edit_viewItem.setImage(RGB_image) def convert_for_MaskRCNN(self, input_img): """Convert the image size and bit-depth to make it suitable for MaskRCNN detection.""" if input_img.shape[0] > 1024 or input_img.shape[1] > 1024: resized_img = resize(input_img, [1024, 1024], preserve_range=True).astype(input_img.dtype) minval = np.min(resized_img) maxval = np.max(resized_img) return ((resized_img - minval) / (maxval - minval) * 255).astype( np.uint8) def run_ML_onImg_and_display(self): """Run MaskRCNN on input image""" self.Matdisplay_Figure.clear() ax1 = self.Matdisplay_Figure.add_subplot(111) # Depends on show_mask or not, the returned figure will be input raw image with mask or not. self.MLresults, self.Matdisplay_Figure_axis, self.unmasked_fig = self.ProcessML.DetectionOnImage( self.MLtargetedImg, axis=ax1, show_mask=False, show_bbox=False) self.Mask = self.MLresults['masks'] self.Label = self.MLresults['class_ids'] self.Score = self.MLresults['scores'] self.Bbox = self.MLresults['rois'] self.SelectedCellIndex = 0 self.NumCells = int(len(self.Label)) self.selected_ML_Index = [] self.selected_cells_infor_dict = {} self.Matdisplay_Figure_axis.imshow(self.unmasked_fig.astype(np.uint8)) self.Matdisplay_Figure.tight_layout() self.Matdisplay_Canvas.draw() #%% # ============================================================================= # Configure click event to add clicked cell mask # ============================================================================= def _onclick(self, event): """Highlights the cell selected in the figure by the user when clicked on""" if self.NumCells > 0: ShapeMask = np.shape(self.Mask) # get coorinates at selected location in image coordinates if event.xdata == None or event.ydata == None: return xcoor = min(max(int(event.xdata), 0), ShapeMask[1]) ycoor = min(max(int(event.ydata), 0), ShapeMask[0]) # search for the mask coresponding to the selected cell for EachCell in range(self.NumCells): if self.Mask[ycoor, xcoor, EachCell]: self.SelectedCellIndex = EachCell break # highlight selected cell if self.SelectedCellIndex not in self.selected_ML_Index: # Get the selected cell's contour coordinates and mask patch self.contour_verts, self.Cell_patch = self.get_cell_polygon( self.Mask[:, :, self.SelectedCellIndex]) self.Matdisplay_Figure_axis.add_patch(self.Cell_patch) self.Matdisplay_Canvas.draw() self.selected_ML_Index.append(self.SelectedCellIndex) self.selected_cells_infor_dict['cell{}_verts'.format( str(self.SelectedCellIndex))] = self.contour_verts else: # If click on the same cell self.Cell_patch.remove() self.Matdisplay_Canvas.draw() self.selected_ML_Index.remove(self.SelectedCellIndex) self.selected_cells_infor_dict.pop('cell{}_verts'.format( str(self.SelectedCellIndex))) def get_cell_polygon(self, mask): # Mask Polygon # Pad to ensure proper polygons for masks that touch image edges. padded_mask = np.zeros((mask.shape[0] + 2, mask.shape[1] + 2), dtype=np.uint8) padded_mask[1:-1, 1:-1] = mask contours = find_contours(padded_mask, 0.5) for verts in contours: # Subtract the padding and flip (y, x) to (x, y) verts = np.fliplr(verts) - 1 contour_polygon = mpatches.Polygon( verts, facecolor=self.random_colors(1)[0]) return contours, contour_polygon def random_colors(self, N, bright=True): """ Generate random colors. To get visually distinct colors, generate them in HSV space then convert to RGB. """ brightness = 1.0 if bright else 0.7 hsv = [(i / N, 1, brightness) for i in range(N)] colors = list(map(lambda c: colorsys.hsv_to_rgb(*c), hsv)) random.shuffle(colors) return colors #%% # ============================================================================= # For mask generation # ============================================================================= def generate_MLmask(self): """ Generate binary mask with all selected cells""" self.MLmask = np.zeros( (self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) if len(self.selected_ML_Index) > 0: for selected_index in self.selected_ML_Index: self.MLmask = np.add(self.MLmask, self.Mask[:, :, selected_index]) self.intergrate_into_final_mask() self.add_rois_of_selected() else: self.intergrate_into_final_mask() # self.Mask_edit_viewItem.setImage(gray2rgb(self.MLtargetedImg)) def add_rois_of_selected(self): """ Using find_contours to get list of contour coordinates in the binary mask, and then generate polygon rois based on these coordinates. """ for selected_index in self.selected_ML_Index: contours = self.selected_cells_infor_dict['cell{}_verts'.format( str(selected_index))] # contours = find_contours(self.Mask[:,:,selected_index], 0.5) # Find iso-valued contours in a 2D array for a given level value. for n, contour in enumerate(contours): contour_coord_array = contours[n] #Swap columns contour_coord_array[:, 0], contour_coord_array[:, 1] = contour_coord_array[:, 1], contour_coord_array[:, 0].copy( ) #Down sample the coordinates otherwise it will be too dense. contour_coord_array_del = np.delete( contour_coord_array, np.arange(2, contour_coord_array.shape[0] - 3, 2), 0) self.selected_cells_infor_dict['cell{}_ROIitem'.format(str(selected_index))] = \ pg.PolyLineROI(positions=contour_coord_array_del, closed=True) self.Mask_edit_view.getView().addItem( self.selected_cells_infor_dict['cell{}_ROIitem'.format( str(selected_index))]) def update_mask(self): """ Regenerate the masks for MaskRCNN and free-hand added (in case they are changed), and show in imageview. !!!ISSUE: getLocalHandlePositions: moving handles changes the position read out, dragging roi as a whole doesn't. """ # Binary mask from ML detection if len(self.selected_ML_Index) > 0: # Delete items in dictionary that are not roi items roi_dict = self.selected_cells_infor_dict.copy() del_key_list = [] for key in roi_dict: print(key) if 'ROIitem' not in key: del_key_list.append(key) for key in del_key_list: del roi_dict[key] self.MLmask = ProcessImage.ROIitem2Mask( roi_dict, mask_resolution=(self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) # Binary mask of added rois self.addedROIitemMask = ProcessImage.ROIitem2Mask( self.roi_list_freehandl_added, mask_resolution=(self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) self.intergrate_into_final_mask() # if type(self.roi_list_freehandl_added) is list: # for ROIitem in self.roi_list_freehandl_added: # # ROIitem.sigHoverEvent.connect(lambda: self.show_roi_detail(ROIitem)) # # plt.figure() # plt.imshow(self.addedROIitemMask) # plt.show() # ============================================================================= # For free-hand rois # ============================================================================= def enable_free_hand(self): if self.enable_modify_MLmask_button.isChecked(): self.Mask_edit_view.enable_drawing(True) else: self.Mask_edit_view.enable_drawing(False) def add_freehand_roi(self, roi): # For drawwidget self.roi_list_freehandl_added.append(roi) def clear_edit_roi(self): """ Clean up all the free-hand rois. """ for roi in self.roi_list_freehandl_added: self.Mask_edit_view.getView().removeItem(roi) self.roi_list_freehandl_added = [] if len(self.selected_cells_infor_dict) > 0: # Remove all selected masks for roiItemkey in self.selected_cells_infor_dict: if 'ROIitem' in roiItemkey: self.Mask_edit_view.getView().removeItem( self.selected_cells_infor_dict[roiItemkey]) self.selected_cells_infor_dict = {} self.MLmask = np.zeros( (self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) self.intergrate_into_final_mask() def intergrate_into_final_mask(self): # Binary mask of added rois self.addedROIitemMask = ProcessImage.ROIitem2Mask( self.roi_list_freehandl_added, mask_resolution=(self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) #Display the RGB mask, ML mask plus free-hand added. self.Mask_edit_viewItem.setImage(gray2rgb(self.addedROIitemMask) * self.mask_color_multiplier + \ gray2rgb(self.MLmask) * self.mask_color_multiplier + gray2rgb(self.MLtargetedImg)) self.final_mask = self.MLmask + self.addedROIitemMask # In case the input image is 2048*2048, and it is resized to fit in MaskRCNN, need to convert back to original size for DMD tranformation. if self.final_mask.shape[0] != self.Rawimage.shape[ 0] or self.final_mask.shape[1] != self.Rawimage.shape[1]: self.final_mask = resize( self.final_mask, [self.Rawimage.shape[0], self.Rawimage.shape[1]], preserve_range=True).astype(self.final_mask.dtype) # self.final_mask = np.where(self.final_mask <= 1, self.final_mask, int(1)) plt.figure() plt.imshow(self.final_mask) plt.show() # ============================================================================= # For DMD transformation and mask generation # ============================================================================= def generate_transformed_mask(self): self.read_transformations_from_file() # self.transform_to_DMD_mask(laser = self.maskLaserComboBox.currentText(), dict_transformations = self.dict_transformations) target_laser = self.maskLaserComboBox.currentText() self.final_DMD_mask = self.finalmask_to_DMD_mask( laser=target_laser, dict_transformations=self.dict_transformations) plt.figure() plt.imshow(self.final_DMD_mask) plt.show() def emit_mask_contour(self): """Use find_contours to get a list of (n,2)-ndarrays consisting of n (row, column) coordinates along the contour, and then feed the list of signal:[list_of_rois, flag_fill_contour, contour_thickness, flag_invert_mode] to the receive_mask_coordinates function in DMDWidget. """ contours = find_contours(self.final_mask, 0.5) sig = [ contours, self.fillContourButton.isChecked(), self.thicknessSpinBox.value(), self.invertMaskButton.isChecked() ] self.signal_DMDcontour.emit(sig) def emit_mask(self): target_laser = self.maskLaserComboBox.currentText() final_DMD_mask_dict = {} final_DMD_mask_dict['camera-dmd-' + target_laser] = self.final_DMD_mask self.signal_DMDmask.emit(final_DMD_mask_dict) def read_transformations_from_file(self): try: with open( r'M:\tnw\ist\do\projects\Neurophotonics\Brinkslab\People\Xin Meng\Code\Python_test\DMDManager\Registration\transformation.txt', 'r') as json_file: self.dict_transformations = json.load(json_file) except: print( 'No transformation could be loaded from previous registration run.' ) return # def transform_to_DMD_mask(self, laser, dict_transformations, flag_fill_contour = True, contour_thickness = 1, flag_invert_mode = False, mask_resolution = (1024, 768)): # """ # Get roi vertices from all roi items and perform the transformation, and then create the mask for DMD. # """ # # #list of roi vertices each being (n,2) numpy array for added rois # if len(self.roi_list_freehandl_added) > 0: # self.addedROIitem_vertices = ProcessImage.ROIitem2Vertices(self.roi_list_freehandl_added) # #addedROIitem_vertices needs to be seperated to be inidividual (n,2) np.array # self.ROIitems_mask_transformed = ProcessImage.vertices_to_DMD_mask(self.addedROIitem_vertices, laser, dict_transformations, flag_fill_contour = True, contour_thickness = 1,\ # flag_invert_mode = False, mask_resolution = (1024, 768)) # # #Dictionary with (n,2) numpy array for clicked cells # if len(self.selected_cells_infor_dict) > 0: # #Convert dictionary to np.array # for roiItemkey in self.selected_cells_infor_dict: # #Each one is 'contours' from find_contour # if '_verts' in roiItemkey: # self.selected_cells_infor_dict[roiItemkey] # # self.MLitems_mask_transformed = ProcessImage.vertices_to_DMD_mask(self.selected_cells_infor_dict, laser, dict_transformations, flag_fill_contour = True, contour_thickness = 1,\ # flag_invert_mode = False, mask_resolution = (1024, 768)) # # if len(self.roi_list_freehandl_added) > 0: # self.final_DMD_mask = self.ROIitems_mask_transformed + self.MLitems_mask_transformed # self.final_DMD_mask[self.final_DMD_mask>1] = 1 # else: # self.final_DMD_mask = self.MLitems_mask_transformed # # return self.final_DMD_mask def finalmask_to_DMD_mask(self, laser, dict_transformations, flag_fill_contour=True, contour_thickness=1, flag_invert_mode=False, mask_resolution=(1024, 768)): """ Same goal as transform_to_DMD_mask, with input being the final binary mask and using find_contour to get all vertices and perform transformation, and then coordinates to mask. """ self.final_DMD_mask = ProcessImage.binarymask_to_DMD_mask(self.final_mask, laser, dict_transformations, flag_fill_contour = True, \ contour_thickness = 1, flag_invert_mode = False, mask_resolution = (1024, 768)) return self.final_DMD_mask def closeEvent(self, event): QtWidgets.QApplication.quit() event.accept() # def apply_mask(self, image, mask, color, alpha=0.5): # """Apply the given mask to the image. # """ # for c in range(3): # image[:, :, c] = np.where(mask == 1, # image[:, :, c] * # (1 - alpha) + alpha * color[c] * 255, # image[:, :, c]) # return image #%% # @run_in_thread def cam_snap(self): """Get a image from camera""" self.cam = CamActuator() self.cam.initializeCamera() exposure_time = self.CamExposureBox.value() self.Rawimage = self.cam.SnapImage(exposure_time) self.cam.Exit() print('Snap finished') self.MLtargetedImg_raw = self.Rawimage.copy() self.MLtargetedImg = self.convert_for_MaskRCNN(self.MLtargetedImg_raw) self.show_raw_image(self.MLtargetedImg) self.addedROIitemMask = np.zeros( (self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1])) self.MLmask = np.zeros( (self.MLtargetedImg.shape[0], self.MLtargetedImg.shape[1]))
class GalvoRegistrator: def __init__(self, *args, **kwargs): self.cam = CamActuator() self.cam.initializeCamera() def registration(self, grid_points_x=3, grid_points_y=3): """ By default, generate 9 galvo voltage coordinates from (-5,-5) to (5,5), take the camera images of these points, return a function matrix that transforms camera_coordinates into galvo_coordinates using polynomial transform. Parameters ---------- grid_points_x : TYPE, optional DESCRIPTION. The default is 3. grid_points_y : TYPE, optional DESCRIPTION. The default is 3. Returns ------- transformation : TYPE DESCRIPTION. """ galvothread = DAQmission() readinchan = [] x_coords = np.linspace(-10, 10, grid_points_x + 2)[1:-1] y_coords = np.linspace(-10, 10, grid_points_y + 2)[1:-1] xy_mesh = np.reshape(np.meshgrid(x_coords, y_coords), (2, -1), order='F').transpose() galvo_coordinates = xy_mesh camera_coordinates = np.zeros((galvo_coordinates.shape)) for i in range(galvo_coordinates.shape[0]): galvothread.sendSingleAnalog('galvosx', galvo_coordinates[i, 0]) galvothread.sendSingleAnalog('galvosy', galvo_coordinates[i, 1]) time.sleep(1) image = self.cam.SnapImage(0.06) plt.imsave( os.getcwd() + '/CoordinatesManager/Registration_Images/2P/image_' + str(i) + '.png', image) camera_coordinates[i, :] = readRegistrationImages.gaussian_fitting( image) print('Galvo Coordinate') print(galvo_coordinates) print('Camera coordinates') print(camera_coordinates) del galvothread self.cam.Exit() transformation_cam2galvo = CoordinateTransformations.polynomial2DFit( camera_coordinates, galvo_coordinates, order=1) transformation_galvo2cam = CoordinateTransformations.polynomial2DFit( galvo_coordinates, camera_coordinates, order=1) print('Transformation found for x:') print(transformation_cam2galvo[:, :, 0]) print('Transformation found for y:') print(transformation_cam2galvo[:, :, 1]) print('galvo2cam found for x:') print(transformation_galvo2cam[:, :, 0]) print('galvo2cam found for y:') print(transformation_galvo2cam[:, :, 1]) return transformation_cam2galvo