def test_context_manager(self):
camera = Camera()
with camera.recording():
self.assertEqual(camera.state, 'recording')
camera.grab()
self.assertEqual(camera.state, 'standby')
async def test_context_manager(self):
camera = Camera()
async with camera.recording():
self.assertEqual(await camera.get_state(), 'recording')
await camera.grab()
self.assertEqual(await camera.get_state(), 'standby')
def test_tomo_scanner(self):
class Stage(object):
def __init__(self):
self.angles = []
self.angle = 0.0 * q.deg
def move(self, value):
self.angle += value
self.angles.append(self.angle)
class PrepareChecker(object):
def __init__(self):
self.prepared = []
def prepare_dark_scan(self):
self.prepared.append('dark')
def prepare_flat_scan(self):
self.prepared.append('flat')
def prepare_proj_scan(self):
self.prepared.append('proj')
camera = Camera()
stage = Stage()
checker = PrepareChecker()
scanner = StepTomoScanner(camera, stage, checker.prepare_dark_scan,
checker.prepare_flat_scan,
checker.prepare_proj_scan)
scanner.angle = 0.5 * q.deg
darks, flats, projections = scanner.run().result()
self.assertEqual(len(projections), len(stage.angles))
compare(checker.prepared, ['dark', 'flat', 'proj'])
def __init__(self,
tomo_axis=None,
flat_axis=None,
vertical_axis=None,
source=None):
self.tomo_axis = tomo_axis
self.flat_axis = flat_axis
self.vertical_axis = vertical_axis
self.source = source
self._last_tomo_axis_position = None
self._last_tomo_axis_velocity = None
self._last_flat_axis_position = None
self._last_flat_axis_velocity = None
self._last_vertical_axis_position = None
self._last_vertical_axis_velocity = None
self._last_source_state = None
Camera.__init__(self)
self.exposure_time = 0.001 * q.s
def connect_to_camera(self):
"""
TODO: call you function connecting to camera
:return: None
"""
self.connect_to_camera_status.setText("CONNECTING...")
self.connect_to_camera_status.setStyleSheet("color: orange")
try:
self.camera = UcaCamera('pcoclhs')
except:
self.on_camera_connect_failure()
# try:
# self.camera = UcaCamera('pcoclhs')
# except:
# self.on_camera_connect_failure()
if self.camera is not None:
self.on_camera_connect_success()
def connect_to_dummy_camera(self):
self.camera = DummyCamera()
self.connect_to_camera_status.setText("CONNECTED")
self.connect_to_camera_status.setStyleSheet("color: orange")
self.camera_model_label.setText("Dummy camera")
self.exposure_entry.setText("{:.02f}".format(
self.camera.exposure_time.magnitude * 1000))
self.fps_entry.setText("{:.02f}".format(int(1000.0 / self.exp_time)))
self.roi_height_entry.setText("{}".format(
self.camera.roi_height.magnitude))
self.roi_width_entry.setText("{}".format(
self.camera.roi_width.magnitude))
self.roi_y0_entry.setText("{}".format(self.camera.roi_y0.magnitude))
self.roi_x0_entry.setText("{}".format(self.camera.roi_x0.magnitude))
self.live_preview_thread.camera = self.camera
self.camera_connected_signal.emit(self.camera)
self.live_on_button.setEnabled(True)
self.live_off_button.setEnabled(True)
self.save_one_image_button.setEnabled(True)
self.camera.acquire_mode = None
class CameraControlsGroup(QGroupBox):
"""
Camera controls
"""
camera_connected_signal = pyqtSignal(object)
def __init__(self, viewer, *args, **kwargs):
# Timer - just as example
super(CameraControlsGroup, self).__init__(*args, **kwargs)
self.timer = QTimer()
self.camera = None
self.log = None
# Buttons
self.live_on_button = QPushButton("LIVE ON")
self.live_on_button.clicked.connect(self.live_on_func)
self.live_on_button.setEnabled(False)
self.lv_duration = 0.0
self.frames_in_last_lv_seq = 0
self.live_on_button_stream2disk = QPushButton(
"LIVE ON -> STREAM TO DISK")
self.live_on_button_stream2disk.clicked.connect(
self.live_on_func_stream2disk)
self.live_on_button_stream2disk.setEnabled(False)
self.live_on_stream_select_file_button = QPushButton(
"Select directory to save streams")
self.live_on_stream_select_file_button.setEnabled(False)
self.live_on_stream_select_file_button.clicked.connect(
self.live_on_stream2disk_prepare)
self.lv_writer = None
self.lv_dirwalker = None
self.lv_experiment = None
self.lv_acquisitions = None
self.lv_stream2disk_on = False
self.cons_viewer = None
self.cons_writer = None
self.fname = None
self.live_off_button = QPushButton("LIVE OFF")
self.live_off_button.setEnabled(False)
self.live_off_button.clicked.connect(self.live_off_func)
self.live_off_button.setEnabled(False)
self.save_lv_sequence_button = QPushButton(
"SAVE live-view sequence from Dimax")
self.save_lv_sequence_button.clicked.connect(self.save_lv_seq)
self.save_lv_sequence_button.setEnabled(False)
self.frames_grabbed_so_far = 0
self.abort_transfer_button = QPushButton("Abort transfer")
self.abort_transfer_button.clicked.connect(self.abort_transfer_func)
self.abort_transfer_button.setEnabled(False)
self.abort_transfer = True
self.lv_session_info = QLabel()
#self.buffer_livev
self.save_one_image_button = QPushButton("SAVE 1 image")
self.save_one_image_button.clicked.connect(self.save_one_image)
self.save_one_image_button.setEnabled(False)
self.QFD = QFileDialog()
self.nim = 0
self.last_dir = "/data/image-"
# Connect to camera
self.connect_to_camera_button = QPushButton("Connect to camera")
self.connect_to_camera_button.clicked.connect(self.connect_to_camera)
self.connect_to_dummy_camera_button = QPushButton(
"Connect to dummy camera")
self.connect_to_dummy_camera_button.clicked.connect(
self.connect_to_dummy_camera)
self.connect_to_camera_status = QLabel()
self.connect_to_camera_status.setText("NOT CONNECTED")
self.connect_to_camera_status.setStyleSheet("color: red")
self.camera_model_label = QLabel()
# Camera object
self.camera = None
self.viewer = viewer
self.live_on = False
# external camera software switch
self.ttl_scan = QCheckBox("External camera controls")
self.ttl_scan.setChecked(False)
# EXPOSURE
self.exposure_label = QLabel()
self.exposure_label.setText("EXPOSURE [msec]")
self.exposure_entry = QLineEdit()
self.exposure_units = QLabel()
self.exposure_units.setText("msec")
# FPS
self.fps_label = QLabel()
self.fps_label.setText("FRAMES PER SECOND")
self.fps_entry = QLineEdit()
self.fps_label_max = QLabel()
self.fps_label_max.setText("Max fps, estimate")
self.fps_label_max_val = QLabel()
# DELAY
self.delay_label = QLabel()
self.delay_label.setText("Dead time [msec]")
self.delay_entry = QLineEdit()
self.delay_entry.setText("10")
self.delay_units = QLabel()
self.delay_units.setText("msec")
# viewer limits
self.viewer_lowlim_label = QLabel()
self.viewer_lowlim_label.setText("Viewer low limit")
self.viewer_lowlim_entry = QLineEdit()
self.viewer_lowlim_entry.setText("20")
self.viewer_highlim_label = QLabel()
self.viewer_highlim_label.setText("Viewer high limit")
self.viewer_highlim_entry = QLineEdit()
self.viewer_highlim_entry.setText("50")
# ROI
# y0
self.roi_y0_label = QLabel()
self.roi_y0_label.setText("ROI first line")
self.roi_y0_entry = QLineEdit()
# height
self.roi_height_label = QLabel()
self.roi_height_label.setText("ROI height, lines")
self.roi_height_entry = QLineEdit()
# x0
self.roi_x0_label = QLabel()
self.roi_x0_label.setText("ROI first column")
self.roi_x0_entry = QLineEdit()
# width
self.roi_width_label = QLabel()
self.roi_width_label.setText("ROI width, columns")
self.roi_width_entry = QLineEdit()
# sensor_vertical_binning
self.sensor_ver_bin_label = QLabel()
self.sensor_ver_bin_label.setText("Vertical binning")
self.sensor_ver_bin_entry = QLineEdit()
self.sensor_ver_bin_entry.setText("1")
# sensor_horizontal_binning
self.sensor_hor_bin_label = QLabel()
self.sensor_hor_bin_label.setText("Horizontal binning")
self.sensor_hor_bin_entry = QLineEdit()
self.sensor_hor_bin_entry.setText("1")
# BUFFERED
self.buffered_label = QLabel()
self.buffered_label.setText("BUFFERED")
self.buffered_entry = QComboBox()
self.buffered_entry.addItems(["NO", "YES"])
# N BUFFERS
self.n_buffers_label = QLabel()
self.n_buffers_label.setText("N BUFFERS")
self.n_buffers_entry = QLineEdit()
self.n_buffers_entry.setText("0")
# TRIGGER
self.trigger_label = QLabel()
self.trigger_label.setText("TRIGGER")
self.trigger_entry = QComboBox()
self.trigger_entry.addItems(["AUTO", "SOFTWARE", "EXTERNAL"])
# ACQUISITION MODE
self.acq_mode_label = QLabel()
self.acq_mode_label.setText("ACQUISITION MODE")
self.acq_mode_entry = QComboBox()
self.acq_mode_entry.addItems(["AUTO", "EXTERNAL"])
self.acq_mode_entry.setEnabled(False)
# STORAGE_MODE
self.storage_mode_label = QLabel()
self.storage_mode_label.setText("STORAGE MODE")
self.storage_mode_entry = QComboBox()
self.storage_mode_entry.addItems(["RECORDER", "FIFO"])
#camera.storage_mode = camera.uca.enum_values.storage_mode.UCA_PCO_CAMERA_STORAGE_MODE_RECORDER
#camera.storage_mode = camera.uca.enum_values.storage_mode.RECORDER
#camera.storage_mode = camera.uca.enum_values.storage_mode.UCA_PCO_CAMERA_STORAGE_MODE_FIFO_BUFFER
# RECORD MODE
self.rec_mode_label = QLabel()
self.rec_mode_label.setText("RECORD MODE")
self.rec_mode_entry = QComboBox()
self.rec_mode_entry.addItems(["RING BUFFER", "SEQUENCE"])
# PIXELRATE line 6
self.sensor_pix_rate_label = QLabel()
self.sensor_pix_rate_label.setText("SENSOR PIXEL RATE, Hz")
self.sensor_pix_rate_entry = QComboBox()
# TIMESTAMP
self.time_stamp = QCheckBox("Add timestamp to camera frames")
self.time_stamp.setChecked(False)
# Thread for live preview
self.live_preview_thread = LivePreviewThread(viewer=self.viewer,
camera=self.camera)
self.live_preview_thread.start()
# Thread for live preview
self.readout_thread = ReadoutThread(camera=self.camera)
self.readout_thread.start()
# signals
self.ttl_scan.clicked.connect(self.extcamera_switched_func)
self.exposure_entry.editingFinished.connect(self.relate_fps_to_exptime)
self.roi_height_entry.editingFinished.connect(
self.get_fps_max_estimate)
# check that dead time is larger than readout time?
self.readout_thread.readout_over_signal.connect(self.readout_over_func)
self.time_stamp.stateChanged.connect(self.set_time_stamp)
self.trigger_entry.currentIndexChanged.connect(
self.restrict_params_depending_on_trigger)
self.all_cam_params_correct = True
self.set_layout()
def constrain_buf_by_trig(self):
if self.trigger_entry.currentText() == 'AUTO':
tmp = self.buffered_entry.findText("NO")
self.buffered_entry.setCurrentIndex(tmp)
if self.trigger_entry.currentText() == 'SOFTWARE':
tmp = self.buffered_entry.findText("NO")
self.buffered_entry.setCurrentIndex(tmp)
self.buffered_entry.setEnabled(False)
if self.trigger_entry.currentText() == 'EXTERNAL':
tmp = self.buffered_entry.findText("YES")
self.buffered_entry.setCurrentIndex(tmp)
self.buffered_entry.setEnabled(False)
def set_layout(self):
layout = QGridLayout()
# Buttons on top
# layout.addWidget(self.live_on_button, 0, 0, 1, 2)
# layout.addWidget(self.live_off_button, 0, 2, 1, 2)
layout.addWidget(self.live_on_button, 0, 0, 1, 2)
layout.addWidget(self.live_off_button, 0, 2)
layout.addWidget(self.save_one_image_button, 0, 3)
layout.addWidget(self.live_on_button_stream2disk, 0, 4)
layout.addWidget(self.live_on_stream_select_file_button, 0, 5)
# Left column of controls
layout.addWidget(self.connect_to_camera_button, 1, 0)
layout.addWidget(self.connect_to_camera_status, 1, 1)
#layout.addWidget(self.camera_model_label, 1, 2)
layout.addWidget(self.connect_to_dummy_camera_button, 1, 2)
layout.addWidget(self.ttl_scan, 1, 3)
layout.addWidget(self.save_lv_sequence_button, 1, 4)
layout.addWidget(self.abort_transfer_button, 1, 5)
# viewer clims
layout.addWidget(self.viewer_lowlim_label, 2, 0)
layout.addWidget(self.viewer_lowlim_entry, 2, 1)
layout.addWidget(self.viewer_highlim_label, 2, 2)
layout.addWidget(self.viewer_highlim_entry, 2, 3)
layout.addWidget(self.exposure_label, 3, 0)
layout.addWidget(self.exposure_entry, 3, 1)
#layout.addWidget(self.exposure_units, 2, 2)
layout.addWidget(self.fps_label, 3, 2)
layout.addWidget(self.fps_entry, 3, 3)
layout.addWidget(self.fps_label_max, 4, 2)
layout.addWidget(self.fps_label_max_val, 4, 3)
layout.addWidget(self.delay_label, 4, 0)
layout.addWidget(self.delay_entry, 4, 1)
#layout.addWidget(self.delay_units, 3, 2)
# Right column of controls
layout.addWidget(self.buffered_label, 2, 4)
layout.addWidget(self.buffered_entry, 2, 5)
# layout.addWidget(self.buffer_location_label, 2, 4)
# layout.addWidget(self.buffer_location_entry, 2, 5)
layout.addWidget(self.n_buffers_label, 3, 4)
layout.addWidget(self.n_buffers_entry, 3, 5)
layout.addWidget(self.trigger_label, 4, 4)
layout.addWidget(self.trigger_entry, 4, 5)
# layout.addWidget(self.acq_mode_label, 5, 4)
# layout.addWidget(self.acq_mode_entry, 5, 5)
layout.addWidget(self.sensor_pix_rate_label, 5, 4)
layout.addWidget(self.sensor_pix_rate_entry, 5, 5)
layout.addWidget(self.time_stamp, 6, 4)
#layout.addWidget(self.lv_session_info, 8, 4, 1, 2)
for column in range(6):
layout.setColumnStretch(column, 1)
# ROI/bin group
layout.addWidget(self.roi_y0_label, 5, 0)
layout.addWidget(self.roi_y0_entry, 5, 1)
layout.addWidget(self.roi_height_label, 6, 0)
layout.addWidget(self.roi_height_entry, 6, 1)
# layout.addWidget(self.sensor_ver_bin_label, 7, 0)
# layout.addWidget(self.sensor_ver_bin_entry, 7, 1)
layout.addWidget(self.roi_x0_label, 5, 2)
layout.addWidget(self.roi_x0_entry, 5, 3)
layout.addWidget(self.roi_width_label, 6, 2)
layout.addWidget(self.roi_width_entry, 6, 3)
# layout.addWidget(self.sensor_hor_bin_label, 7, 2)
# layout.addWidget(self.sensor_hor_bin_entry, 7, 3)
self.setLayout(layout)
def connect_to_camera(self):
"""
TODO: call you function connecting to camera
:return: None
"""
self.connect_to_camera_status.setText("CONNECTING...")
self.connect_to_camera_status.setStyleSheet("color: orange")
try:
self.camera = UcaCamera('pcoclhs')
except:
self.on_camera_connect_failure()
# try:
# self.camera = UcaCamera('pcoclhs')
# except:
# self.on_camera_connect_failure()
if self.camera is not None:
self.on_camera_connect_success()
def connect_to_dummy_camera(self):
self.camera = DummyCamera()
self.connect_to_camera_status.setText("CONNECTED")
self.connect_to_camera_status.setStyleSheet("color: orange")
self.camera_model_label.setText("Dummy camera")
self.exposure_entry.setText("{:.02f}".format(
self.camera.exposure_time.magnitude * 1000))
self.fps_entry.setText("{:.02f}".format(int(1000.0 / self.exp_time)))
self.roi_height_entry.setText("{}".format(
self.camera.roi_height.magnitude))
self.roi_width_entry.setText("{}".format(
self.camera.roi_width.magnitude))
self.roi_y0_entry.setText("{}".format(self.camera.roi_y0.magnitude))
self.roi_x0_entry.setText("{}".format(self.camera.roi_x0.magnitude))
self.live_preview_thread.camera = self.camera
self.camera_connected_signal.emit(self.camera)
self.live_on_button.setEnabled(True)
self.live_off_button.setEnabled(True)
self.save_one_image_button.setEnabled(True)
self.camera.acquire_mode = None
def on_camera_connect_success(self):
"""
TODO: this function should be called from your camera connection software on successful connection
:param camera: Camera object
:return: None
"""
self.connect_to_camera_status.setText("CONNECTED")
self.connect_to_camera_status.setStyleSheet("color: green")
self.connect_to_dummy_camera_button.setEnabled(False)
self.connect_to_camera_button.setEnabled(False)
self.ttl_scan.setEnabled(False)
# identify model
# Dimax must use internal buffer, 4000 only soft trigger
if self.camera.sensor_width.magnitude == 2000:
self.camera_model_label.setText("PCO Dimax")
self.connect_to_camera_status.setText("CONNECTED to PCO Dimax")
####################################
# !!!! can we hardcode it ???
####################################
self.camera.storage_mode = self.camera.uca.enum_values.storage_mode.RECORDER
self.camera.record_mode = self.camera.uca.enum_values.record_mode.RING_BUFFER
####
tmp = self.buffered_entry.findText("NO")
self.buffered_entry.setCurrentIndex(tmp)
self.buffered_entry.setEnabled(False)
self.n_buffers_entry.setEnabled(False)
if self.camera.sensor_width.magnitude == 4008:
self.camera_model_label.setText("PCO 4000")
self.connect_to_camera_status.setText("CONNECTED to PCO 4000")
self.trigger_entry.addItems(["SOFTWARE"])
self.trigger_entry.setEnabled(False)
if self.camera.sensor_width.magnitude == 2560:
self.camera_model_label.setText("PCO Edge")
self.connect_to_camera_status.setText("CONNECTED to PCO Edge")
self.n_buffers_entry.setEnabled(True)
self.live_on_button_stream2disk.setEnabled(True)
self.live_on_stream_select_file_button.setEnabled(True)
####################################
# Hardcoding automode for now
####################################
if self.camera.acquire_mode != self.camera.uca.enum_values.acquire_mode.AUTO:
self.camera.acquire_mode = self.camera.uca.enum_values.acquire_mode.AUTO
self.camera.timestamp_mode = self.camera.uca.enum_values.timestamp_mode.NONE
# set default values
self.exposure_entry.setText("{:.02f}".format(
self.camera.exposure_time.magnitude * 1000))
self.fps_entry.setText("{}".format(int(1000.0 / self.exp_time)))
self.roi_height_entry.setText("{}".format(
self.camera.roi_height.magnitude))
self.roi_height_label.setText("ROI height, lines (max. {})".format(
self.camera.sensor_height.magnitude))
self.roi_width_entry.setText("{}".format(
self.camera.roi_width.magnitude))
self.roi_width_label.setText("ROI width, columns (max. {})".format(
self.camera.sensor_width.magnitude))
self.roi_y0_entry.setText("{}".format(self.camera.roi_y0.magnitude))
self.roi_x0_entry.setText("{}".format(self.camera.roi_x0.magnitude))
self.sensor_pix_rate_entry.addItems(
[str(i) for i in self.camera.sensor_pixelrates])
tmp = self.sensor_pix_rate_entry.findText(
str(self.camera.sensor_pixelrate))
self.sensor_pix_rate_entry.setCurrentIndex(tmp)
#sensor_vertical_binning
# sensor_horizontal_vertical_binning
self.live_preview_thread.camera = self.camera
self.readout_thread.camera = self.camera
self.camera_connected_signal.emit(self.camera)
self.live_on_button.setEnabled(True)
self.live_off_button.setEnabled(True)
self.save_one_image_button.setEnabled(True)
#had to add this in order to avoid that signals
#coming to early can break the matplotlib window
self.live_on_func()
sleep(1)
self.live_off_func()
self.restrict_params_depending_on_trigger()
self.get_fps_max_estimate()
def on_camera_connect_failure(self):
"""
TODO: this function should be called from your camera connection software on connection failure
or on timeout
:return: None
"""
self.connect_to_camera_status.setText("CONNECTION FAILED")
self.connect_to_camera_status.setStyleSheet("color: red")
self.camera = None
self.camera_model_label.setText("")
def set_camera_params(self):
self.log.info("Setting camera parameters")
if self.camera_model_label.text() == 'Dummy camera':
return -1
try:
if self.camera.state == 'recording':
self.camera.stop_recording()
self.camera.exposure_time = self.exp_time * q.msec
if self.camera_model_label.text() == "PCO Dimax":
self.camera.frame_rate = self.fps * q.hertz
else:
self.camera.sensor_pixelrate = int(
self.sensor_pix_rate_entry.currentText())
self.camera.buffered = self.buffered
if self.camera.buffered:
self.camera.num_buffers = self.buffnum
self.set_time_stamp()
self.setROI()
except:
tmp = "Can not set camera parameters"
self.log.error(tmp)
error_message(tmp)
return True
else:
return False
def set_time_stamp(self):
if self.time_stamp.isChecked():
self.camera.timestamp_mode = self.camera.uca.enum_values.timestamp_mode.BINARY
else:
self.camera.timestamp_mode = self.camera.uca.enum_values.timestamp_mode.NONE
def setROI(self):
try:
self.camera.roi_x0 = self.roi_x0 * q.pixels
self.camera.roi_y0 = self.roi_y0 * q.pixels
self.camera.roi_width = self.roi_width * q.pixels
self.camera.roi_height = self.roi_height * q.pixels
except:
error_message(
"ROI is not correctly defined for the sensor, check multipliers and centering"
)
def live_on_func(self):
self.log.info("Live view on with auto trigger")
self.ena_disa_buttons(False)
if self.camera.state == "recording":
self.camera.stop_recording()
if self.camera_model_label.text() == 'Dummy camera':
pass
else:
if self.camera.trigger_source != self.camera.trigger_sources.AUTO:
self.camera.trigger_source = self.camera.trigger_sources.AUTO
self.set_camera_params()
self.camera.start_recording()
self.live_preview_thread.live_on = True
self.lv_duration = time.time()
def live_on_func_ext_trig(self):
self.log.info("Live view on with external trigger")
self.ena_disa_buttons(False)
if self.camera.state == "recording":
self.camera.stop_recording()
if self.camera.trigger_source != self.camera.trigger_sources.EXTERNAL:
self.camera.trigger_source = self.camera.trigger_sources.EXTERNAL
self.set_camera_params()
self.camera.start_recording()
#self.live_preview_thread.live_on = True #not working with external triggers
self.lv_duration = time.time()
def live_on_stream2disk_prepare(self):
self.fname, fext = self.QFD.getSaveFileName(self, 'Select directory',
self.last_dir,
"Image Files (*.tif)")
self.lv_dirwalker = DirectoryWalker(root=os.path.dirname(self.fname),
dsetname="frames_{:>02}.tif",
bytes_per_file=2**37)
self.lv_acquisitions = [Acquisition("Radios", self.acq_lv_stream2disk)]
self.lv_experiment = Experiment(acquisitions=self.lv_acquisitions,
walker=self.lv_dirwalker,
separate_scans=True,
name_fmt="live_view_seq_{:>03}")
self.cons_writer = ImageWriter(self.lv_acquisitions,
self.lv_dirwalker,
async=True)
self.cons_viewer = Consumer(self.lv_acquisitions, self.viewer)
def acq_lv_stream2disk(self):
self.log.info("Streaming lv sequence to disk")
self.ena_disa_buttons(False)
if self.camera.state == "recording":
self.camera.stop_recording()
if self.camera.trigger_source != self.camera.trigger_sources.AUTO:
self.camera.trigger_source = self.camera.trigger_sources.AUTO
self.set_camera_params()
try:
self.camera.start_recording()
while self.lv_stream2disk_on:
yield self.camera.grab()
except Exception as exp:
self.log.error(exp)
def live_on_func_stream2disk(self):
if self.fname == None:
error_message("Select the filename first")
return
self.lv_stream2disk_on = True
self.lv_experiment.run()
def live_off_func(self):
self.log.info("Live off func called")
self.live_preview_thread.live_on = False
self.lv_stream2disk_on = False
self.ena_disa_buttons(True)
try:
self.camera.stop_recording()
except Exception as exp:
self.log.error("Cannot stop recording to stop the live view")
self.log.error(exp)
# if self.camera_model_label.text() != 'Dummy camera':
# error_message("Cannot stop recording")
self.lv_duration = time.time() - self.lv_duration
self.frames_in_last_lv_seq = 0.0
self.live_off_button.setEnabled(False)
self.live_on_button.setEnabled(True)
if self.camera_model_label.text() == 'PCO Dimax': # or self.buffered:
self.save_lv_sequence_button.setEnabled(True)
self.frames_in_last_lv_seq = self.camera.recorded_frames.magnitude
self.setTitle(
"Camera controls. Status: recorded {0} frames in {1:.03f} seconds"
.format(self.frames_in_last_lv_seq, self.lv_duration))
self.log.info("Live view stopped")
def save_lv_seq(self):
self.abort_transfer_button.setEnabled(True)
self.save_lv_sequence_button.setEnabled(False)
self.live_on_button.setEnabled(False)
self.save_one_image_button.setEnabled(False)
# Get file name
f, fext = self.QFD.getSaveFileName(self, 'Select dir and enter prefix',
self.last_dir,
"Image Files (*.tif)")
if f == self.last_dir:
f += "/im-seq-00"
self.last_dir = os.path.dirname(f)
# Start readout
self.readout_thread.filename = f + '.tif'
self.readout_thread.readout_on = True
def abort_transfer_func(self):
## Readuot Thread
self.readout_thread.abort_transfer = True
self.abort_transfer_button.setEnabled(False)
def readout_over_func(self, val):
self.live_on_button.setEnabled(val)
self.save_one_image_button.setEnabled(val)
self.abort_transfer_button.setEnabled(False)
def save_one_image(self):
self.save_one_image_button.setEnabled(False)
f, fext = self.QFD.getSaveFileName(self, 'Save image', self.last_dir,
"Image Files (*.tif)")
if f == self.last_dir:
fname = os.path.join(f, "image-{:>04}.tif".format(self.nim))
self.nim += 1
else:
fname = f + '.tif'
self.last_dir = os.path.dirname(fname)
tmp = False
if self.live_preview_thread.live_on == True:
self.live_off_func()
tmp = True
if self.camera_model_label.text() != 'Dummy camera':
if self.camera.state == 'recording':
self.camera.stop_recording()
self.camera['trigger_source'].stash().join()
self.camera.trigger_source = self.camera.trigger_sources.SOFTWARE
self.set_camera_params()
try:
if self.camera_model_label.text() != 'Dummy camera':
with self.camera.recording():
self.camera.trigger()
im = self.camera.grab()
else:
im = self.camera.grab()
finally:
write_tiff(fname, im)
if self.camera_model_label.text() != 'Dummy camera':
self.camera['trigger_source'].restore().join()
self.save_one_image_button.setEnabled(True)
if tmp == True:
self.live_on_func()
def restrict_params_depending_on_trigger(self):
self.delay_entry.setText('0')
self.delay_entry.setEnabled(False)
if self.trigger_entry.currentText() == 'SOFTWARE':
tmp = self.buffered_entry.findText("NO")
self.buffered_entry.setCurrentIndex(tmp)
self.buffered_entry.setEnabled(False)
self.n_buffers_entry.setEnabled(False)
# delays only applicable in case of external trigger
if self.trigger_entry.currentText() == 'EXTERNAL':
if self.camera_model_label.text() == 'PCO Dimax':
self.delay_entry.setText('1')
self.buffered_entry.setEnabled(False)
self.n_buffers_entry.setEnabled(False)
if self.camera_model_label.text() == 'PCO Edge':
self.delay_entry.setText('{0:d}'.format(
1000 / self.get_fps_max_estimate()))
self.buffered_entry.setEnabled(True)
self.n_buffers_entry.setEnabled(True)
self.delay_entry.setEnabled(True)
def ena_disa_buttons(self, val):
self.live_on_button_stream2disk.setEnabled(val)
self.live_on_stream_select_file_button.setEnabled(val)
self.live_on_button.setEnabled(val)
if self.camera_model_label.text() == 'PCO Dimax':
self.save_lv_sequence_button.setEnabled(val)
self.live_off_button.setEnabled(not val)
# getters/setters
@property
def exp_time(self):
try:
x = float(self.exposure_entry.text())
except ValueError:
error_message("{:}".format(
"Exp. time must be a positive number. Setting to default"))
x = 13
self.all_cam_params_correct = False
if x < 0:
error_message(
"{:}".format("Exp. time must be positive. Setting to default"))
x = 13
self.exposure_entry.setText('13')
self.all_cam_params_correct = False
if self.camera_model_label.text() == 'PCO Dimax' and (x > 40):
error_message("{:}".format("Max exp. time for Dimax is 40 msec"))
self.all_cam_params_correct = False
x = 39.9999
self.exposure_entry.setText('39.9999')
if self.camera_model_label.text() == 'PCO Edge' and (x > 2000):
error_message("{:}".format("Max exp. time for Edge is 2 sec"))
x = 1999.9
self.exposure_entry.setText('1999.9')
self.all_cam_params_correct = False
return x
def relate_fps_to_exptime(self):
if self.trig_mode == "EXTERNAL":
if self.camera_model_label.text() == 'PCO Dimax':
x = int(1000.0 / self.exp_time)
else:
x = int(1000.0 / (self.exp_time + self.dead_time))
else:
x = int(1000.0 / self.exp_time)
self.fps_entry.setText("{:.02f}".format(x))
return x
def get_fps_max_estimate(self):
x = 0
if self.camera_model_label.text() == 'PCO Dimax':
x = 2200 * 2000 / self.roi_height
if self.camera_model_label.text() == 'PCO Edge':
x = 100 * 2160 / self.roi_height
if self.camera_model_label.text() == 'PCO 4000':
x = 4
x = int(x)
self.fps_label_max_val.setText(str(x))
return x
@property
def fps(self):
try:
x = float(self.fps_entry.text())
except ValueError:
warning_message("{:}".format(
"FPS a positive number. Setting FPS based on exp. time"))
x = self.relate_fps_to_exptime()
if x < 0:
error_message("{:}".format("FPS must be positive"))
self.all_cam_params_correct = False
if self.camera_model_label.text() == 'PCO Dimax':
if x < 25:
warning_message(
"{:}".format("Dimax FPS must be greater than 25"))
x = 25
if self.trig_mode == "EXTERNAL" and \
int(x) < int(1000.0 / (self.exp_time + self.dead_time)):
warning_message("{:}".format(
"Dimax FPS must be greater than frequency of external triggers"
))
x = int(1000.0 / self.exp_time)
# if self.camera_model_label.text() == 'PCO Edge' and (x > 100):
# error_message("{:}".format("PCO Edge max FPS is 100"))
# self.all_cam_params_correct = False
# if int(x) < int(1000.0 / (self.exp_time + self.dead_time)): #because of round of errors
# #warning_message("FPS [Hz] cannot exceed 1/exp.time[s]; setting fps=1/exp.time")
# self.relate_fps_to_exptime()
elif self.trig_mode == "EXTERNAL":
x = self.relate_fps_to_exptime()
self.fps_entry.setText("{:.02f}".format(x))
return x
@property
def dead_time(self):
try:
x = float(self.delay_entry.text())
except ValueError:
warning_message(
"{:}".format("Dead time must be a non-negative number"))
x = 0
self.delay_entry.setText('0')
self.all_cam_params_correct = False
if x < 0:
warning_message(
"{:}".format("Dead time must be a non-negative number"))
x = 0
self.delay_entry.setText('0')
self.all_cam_params_correct = False
return x
@property
def roi_height(self):
try:
h = int(self.roi_height_entry.text())
except ValueError:
error_message(
"ROI height must be positive integer number smaller then {}".
format(self.camera.sensor_height.magnitude))
if self.camera_model_label.text() == 'PCO Dimax':
h = int(h / 4) * 4
if h > 2000:
h = 2000
self.roi_height_entry.setText(str(h))
return h
if self.camera_model_label.text() == 'PCO Edge':
h = int(h / 2) * 2
if h > 2160:
h = 2160
self.roi_y0_entry.setText(str(1080 - int(h / 2)))
self.roi_height_entry.setText(str(h))
return h
@property
def roi_y0(self):
try:
h = int(self.roi_y0_entry.text())
except ValueError:
if self.camera_model_label.text() == 'PCO Dimax':
error_message(
"ROI height must be positive integer number divisible by 4 and smaller then {:}"
.format(996))
else:
error_message(
"ROI height must be positive integer number smaller then {:}"
.format(self.camera.sensor_height.magnitude))
if self.camera_model_label.text() == 'PCO Dimax':
h = 1000 - self.roi_height / 2
self.roi_y0_entry.setText(str(h))
return h
else:
return h
@property
def roi_x0(self):
try:
h = int(self.roi_x0_entry.text())
except ValueError:
if self.camera_model_label.text() == 'PCO Dimax':
error_message(
"ROI height must be positive integer number divisible by 4 and smaller then {:}"
.format(996))
else:
error_message(
"ROI height must be positive integer number smaller then {:}"
.format(self.camera.sensor_height.magnitude))
if self.camera_model_label.text() == 'PCO Dimax':
h = 1000 - self.roi_width / 2
self.roi_x0_entry.setText(str(h))
return h
else:
return h
@property
def roi_width(self):
try:
h = int(self.roi_width_entry.text())
except ValueError:
error_message(
"ROI height must be positive integer number smaller then {}".
format(self.camera.sensor_height.magnitude))
if self.camera_model_label.text() == 'PCO Dimax':
h = int(h / 4) * 4
if h > 2000:
h = 2000
self.roi_width_entry.setText(str(h))
return h
else:
return h
@property
def trig_mode(self):
try:
return self.trigger_entry.currentText()
except ValueError:
return None
@property
def acq_mode(self):
try:
return self.acq_mode_entry.currentText()
except ValueError:
return None
@property
def buffered(self):
if self.camera_model_label == "PCO Dimax":
return False
try:
if self.buffered_entry.currentText() == "YES":
return True
else:
return False
except ValueError:
return None
@property
def buffnum(self):
try:
return int(self.n_buffers_entry.text())
except ValueError:
return None
@property
def pix_rate(self):
try:
return int(self.sensor_pix_rate_entry.currentText())
except:
warning_message('Can not get read-out rate')
def extcamera_switched_func(self):
if self.ttl_scan.isChecked():
self.live_on_button.setEnabled(False)
self.live_off_button.setEnabled(False)
self.save_one_image_button.setEnabled(False)
else:
self.live_on_button.setEnabled(True)
self.live_off_button.setEnabled(True)
self.save_one_image_button.setEnabled(True)
def setUp(self):
self.seq = list(range(10))
self.camera = Camera()
self.linear_motor = LinearMotor()
self.linear_motor2 = LinearMotor()
self.rotation_motor = RotationMotor()
def __init__(self, camera=None, magnification=None):
self._camera = Camera() if camera is None else camera
self._magnification = 3 if magnification is None else magnification
super(Detector, self).__init__()
def setUp(self):
self.motor = LinearMotor()
self.camera = Camera()
self.shutter = Shutter()
def setUp(self):
super(TestDummyCamera, self).setUp()
self.background = np.ones((256, 256), dtype=np.uint16)
self.camera = Camera(background=self.background)
async def test_simulate(self):
self.assertTrue(np.any(self.background - await self.camera.grab()))
camera = Camera(background=self.background, simulate=False)
np.testing.assert_equal(self.background, await camera.grab())
class TestDummyCamera(TestCase):
def setUp(self):
super(TestDummyCamera, self).setUp()
self.camera = Camera()
def test_grab(self):
frame = self.camera.grab()
self.assertIsNotNone(frame)
def test_grab_async(self):
frame = self.camera.grab_async().result()
self.assertIsNotNone(frame)
def test_trigger_source(self):
self.camera.trigger_source = self.camera.trigger_sources.EXTERNAL
self.assertEqual(self.camera.trigger_source, 'EXTERNAL')
def test_roi(self):
self.roi_x0 = self.roi_y0 = self.roi_width = self.roi_height = 10 * q.dimensionless
self.assertEqual(self.roi_x0, 10 * q.dimensionless)
self.assertEqual(self.roi_y0, 10 * q.dimensionless)
self.assertEqual(self.roi_width, 10 * q.dimensionless)
self.assertEqual(self.roi_height, 10 * q.dimensionless)
def test_has_sensor_dims(self):
self.assertTrue(hasattr(self.camera, "sensor_pixel_width"))
self.assertTrue(hasattr(self.camera, "sensor_pixel_height"))
def test_buffered_camera(self):
camera = BufferedCamera()
for i, item in enumerate(camera.readout_buffer()):
pass
self.assertEqual(i, 2)
def test_context_manager(self):
camera = Camera()
with camera.recording():
self.assertEqual(camera.state, 'recording')
camera.grab()
self.assertEqual(camera.state, 'standby')
def test_stream(self):
@coroutine
def check():
while True:
yield
check.ok = True
self.camera.stop_recording()
check.ok = False
self.camera.stream(check()).join()
self.assertTrue(check.ok)
def test_grab_convert(self):
def grab():
return np.mgrid[:5, :5][1]
self.camera._grab_real = grab
self.camera.convert = np.fliplr
image = self.camera.grab()
np.testing.assert_equal(image, grab()[:, ::-1])
def setUp(self):
super(TestDummyCamera, self).setUp()
self.camera = Camera()
camera.start_recording()
for i in xrange(num_frames):
yield camera.grab()
def reconstruct_from(camera):
pm = PluginManager()
fft = pm.get_task('fft', dimensions=1)
ifft = pm.get_task('ifft', dimensions=1)
fltr = pm.get_task('filter')
bp = pm.get_task('backproject')
writer = pm.get_task('write')
graph = Ufo.TaskGraph()
graph.connect_nodes(fft, fltr)
graph.connect_nodes(fltr, ifft)
graph.connect_nodes(ifft, bp)
graph.connect_nodes(bp, writer)
with InjectProcess(graph) as process:
for frame in acquire(camera, 10):
process.insert(frame)
if __name__ == '__main__':
camera = Camera()
camera.frame_rate = 10 * q.count / q.s
reconstruct_from(camera)
class TestDummyCamera(TestCase):
def setUp(self):
super(TestDummyCamera, self).setUp()
self.background = np.ones((256, 256), dtype=np.uint16)
self.camera = Camera(background=self.background)
async def test_grab(self):
frame = await self.camera.grab()
self.assertIsNotNone(frame)
def test_trigger_source(self):
self.camera.trigger_source = self.camera.trigger_sources.EXTERNAL
self.assertEqual(self.camera.trigger_source, 'EXTERNAL')
def test_roi(self):
self.roi_x0 = self.roi_y0 = self.roi_width = self.roi_height = 10 * q.dimensionless
self.assertEqual(self.roi_x0, 10 * q.dimensionless)
self.assertEqual(self.roi_y0, 10 * q.dimensionless)
self.assertEqual(self.roi_width, 10 * q.dimensionless)
self.assertEqual(self.roi_height, 10 * q.dimensionless)
def test_has_sensor_dims(self):
self.assertTrue(hasattr(self.camera, "sensor_pixel_width"))
self.assertTrue(hasattr(self.camera, "sensor_pixel_height"))
async def test_buffered_camera(self):
camera = BufferedCamera()
i = 0
async for item in camera.readout_buffer():
i += 1
self.assertEqual(i, 3)
async def test_context_manager(self):
camera = Camera()
async with camera.recording():
self.assertEqual(await camera.get_state(), 'recording')
await camera.grab()
self.assertEqual(await camera.get_state(), 'standby')
async def test_stream(self):
async def check(producer):
async for image in producer:
check.ok = True
await self.camera.stop_recording()
break
check.ok = False
await check(self.camera.stream())
self.assertTrue(check.ok)
async def test_grab_convert(self):
async def grab():
return np.mgrid[:5, :5][1]
self.camera._grab_real = grab
self.camera.convert = np.fliplr
image = await self.camera.grab()
np.testing.assert_equal(image, (await grab())[:, ::-1])
async def test_simulate(self):
self.assertTrue(np.any(self.background - await self.camera.grab()))
camera = Camera(background=self.background, simulate=False)
np.testing.assert_equal(self.background, await camera.grab())
async def test_frames(self):
acc = Accumulate()
await acc(frames(5, Camera()))
assert len(acc.items) == 5