class PX1Collect(AbstractCollect, HardwareObject):
"""Main data collection class. Inherited from AbstractMulticollect
Collection is done by setting collection parameters and
executing collect command
"""
adxv_host = '127.0.0.1'
adxv_port = 8100
adxv_interval = 2.0 # minimum time (in seconds) between image refresh on adxv
goimg_dir = "/nfs/ruche/share-temp/Proxima/.goimgpx1"
goimg_filename = "goimg.db"
characterization_nb_merged_images = 10
def __init__(self, name):
"""
:param name: name of the object
:type name: string
"""
AbstractCollect.__init__(self)
HardwareObject.__init__(self, name)
self._error_msg = ""
self.owner = None
self.osc_id = None
self._collecting = None
self.diffractometer_hwobj = None
self.omega_hwobj = None
self.kappa_hwobj = None
self.phi_hwobj = None
self.lims_client_hwobj = None
self.machine_info_hwobj = None
self.energy_hwobj = None
self.resolution_hwobj = None
self.transmission_hwobj = None
self.detector_hwobj = None
self.beam_info_hwobj = None
self.autoprocessing_hwobj = None
self.graphics_manager_hwobj = None
self.mxlocal = None
self.helical_positions = None
def init(self):
"""
Init method
"""
self.collect_devname = self.getProperty("tangoname")
self.collect_device = DeviceProxy(self.collect_devname)
self.collect_state_chan = self.getChannelObject("state")
self.px1env_hwobj = self.getObjectByRole("environment")
self.fastshut_hwobj = self.getObjectByRole("fastshut")
self.frontend_hwobj = self.getObjectByRole("frontend")
self.safshut_hwobj = self.getObjectByRole("safshut")
self.lightarm_hwobj = self.getObjectByRole("lightarm")
self.diffractometer_hwobj = self.getObjectByRole("diffractometer")
self.mxlocal_object = self.getObjectByRole("beamline_configuration")
self.omega_hwobj = self.getObjectByRole("omega")
self.kappa_hwobj = self.getObjectByRole("kappa")
self.phi_hwobj = self.getObjectByRole("phi")
self.lims_client_hwobj = self.getObjectByRole("lims_client")
self.machine_info_hwobj = self.getObjectByRole("machine_info")
self.energy_hwobj = self.getObjectByRole("energy")
self.resolution_hwobj = self.getObjectByRole("resolution")
self.transmission_hwobj = self.getObjectByRole("transmission")
self.detector_hwobj = self.getObjectByRole("detector")
self.beam_info_hwobj = self.getObjectByRole("beam_info")
# self.autoprocessing_hwobj = self.getObjectByRole("auto_processing")
self.graphics_manager_hwobj = self.getObjectByRole("graphics_manager")
self.flux_hwobj = self.getObjectByRole("flux")
self.img2jpeg = self.getProperty("imgtojpeg")
undulators = self.get_undulators()
self.exp_type_dict = {'Mesh': 'raster',
'Helical': 'Helical'}
det_px, det_py = self.detector_hwobj.get_pixel_size()
self.set_beamline_configuration(\
synchrotron_name="SOLEIL",
directory_prefix=self.getProperty("directory_prefix"),
default_exposure_time=self.detector_hwobj.get_default_exposure_time(),
minimum_exposure_time=self.detector_hwobj.get_minimum_exposure_time(),
detector_fileext=self.detector_hwobj.get_file_suffix(),
detector_type=self.detector_hwobj.get_detector_type(),
detector_manufacturer=self.detector_hwobj.get_manufacturer(),
detector_model=self.detector_hwobj.get_model(),
detector_px=det_px,
detector_py=det_py,
undulators=undulators,
focusing_optic=self.getProperty('focusing_optic'),
monochromator_type=self.getProperty('monochromator'),
beam_divergence_vertical=self.beam_info_hwobj.get_beam_divergence_hor(),
beam_divergence_horizontal=self.beam_info_hwobj.get_beam_divergence_ver(),
polarisation=self.getProperty('polarisation'),
input_files_server=self.getProperty("input_files_server"))
self.emit("collectConnected", (True,))
self.emit("collectReady", (True, ))
def data_collection_hook(self):
"""Main collection hook
"""
collection_type = self.current_dc_parameters['experiment_type']
logging.getLogger("HWR").info("PX1Collect: Running PX1 data collection hook. Type is %s" % collection_type )
if self.aborted_by_user:
self.emit_collection_failed("Aborted by user")
self.aborted_by_user = False
return
ready = self.prepare_devices_for_collection()
if not ready:
self.collection_failed("Cannot prepare collection")
self.stop_collect()
return
if collection_type != 'Characterization': # standard
prepare_ok = self.prepare_standard_collection()
else:
prepare_ok = self.prepare_characterization()
self._collecting = True
osc_seq = self.current_dc_parameters['oscillation_sequence'][0]
# for progressBar brick
self.emit("progressInit", "Collection", osc_seq['number_of_images'])
#
# Run
#
self.prepare_directories()
if collection_type != 'Characterization': # standard
self.start_standard_collection()
self.follow_collection_progress()
else:
self.start_characterization()
# includes
self.data_collection_end()
self.collection_finished()
def prepare_standard_collection(self):
osc_seq = self.current_dc_parameters['oscillation_sequence'][0]
fileinfo = self.current_dc_parameters['fileinfo']
basedir = fileinfo['directory']
logging.getLogger("HWR").info("PX1Collect: fileinfo is %s " % str(fileinfo))
imgname = fileinfo['template'] % osc_seq['start_image_number']
# move omega to start angle
start_angle = osc_seq['start']
nb_images = osc_seq['number_of_images']
osc_range = osc_seq['range']
exp_time = osc_seq['exposure_time']
logging.getLogger("HWR").info("PX1Collect: nb_images: %s / osc_range: %s / exp_time: %s" % \
(nb_images, osc_range, exp_time))
self.collect_device.exposurePeriod = exp_time
self.collect_device.numberOfImages = nb_images
self.collect_device.imageWidth = osc_range
# self.collect_device.collectAxis = "Omega"
self.collect_device.startAngle = start_angle
self.collect_device.triggerMode = 2
self.collect_device.imagePath = basedir
self.collect_device.imageName = imgname
time.sleep(0.2)
self.collect_device.PrepareCollect()
ret = self.wait_collect_standby()
if ret is False:
logging.getLogger("user_level_log").info("Collect server prepare error. Aborted")
return False
self.prepare_headers()
return True
def start_standard_collection(self):
self.emit("collectStarted", (self.owner, 1))
self.detector_hwobj.start_collection()
self.collect_device.Start()
def follow_collection_progress(self):
osc_seq = self.current_dc_parameters['oscillation_sequence'][0]
fileinfo = self.current_dc_parameters['fileinfo']
basedir = fileinfo['directory']
archive_dir = fileinfo['archive_directory']
template = fileinfo['template']
jpeg_template = os.path.splitext(template)[0] + ".jpeg"
thumb_template = os.path.splitext(template)[0] + ".thumb.jpeg"
osc_range = osc_seq['range']
osc_start = osc_seq['start']
nb_images = osc_seq['number_of_images']
first_imgno = osc_seq['start_image_number']
first_image_fullpath = os.path.join(basedir,template % first_imgno)
first_image_jpegpath = os.path.join(archive_dir, jpeg_template % first_imgno)
first_image_thumbpath = os.path.join(archive_dir, thumb_template % first_imgno)
last_imgno = first_imgno + nb_images -1
last_image_fullpath = os.path.join(basedir,template % last_imgno)
last_image_jpegpath = os.path.join(archive_dir, jpeg_template % last_imgno)
last_image_thumbpath = os.path.join(archive_dir, thumb_template % last_imgno)
# wait for first image
self.adxv_latest_refresh = 0
self.is_firstimg = True
self.file_waiting_display = first_image_fullpath # for showing on adxv
self.wait_image_on_disk(first_image_fullpath)
thumbs_up = self.generate_thumbnails(first_image_fullpath, first_image_jpegpath, first_image_thumbpath)
if thumbs_up:
self.store_image_in_lims(first_imgno)
# update display while collect is running
while self.is_moving() or self.is_firstimg:
self.adxv_show_latest(fileinfo)
time.sleep(0.1)
# wait for last image
self.wait_image_on_disk(last_image_fullpath)
thumbs_up = self.generate_thumbnails(last_image_fullpath, last_image_jpegpath, last_image_thumbpath)
self.adxv_sync_image(first_image_fullpath)
if thumbs_up:
self.store_image_in_lims(last_imgno)
def prepare_characterization(self):
osc_seq = self.current_dc_parameters['oscillation_sequence'][0]
fileinfo = self.current_dc_parameters['fileinfo']
basedir = fileinfo['directory']
merged_images = self.characterization_nb_merged_images
osc_range = float( osc_seq['range'] )/ merged_images
exp_time = float( osc_seq['exposure_time'] )/ merged_images
self.collect_device.numberOfImages = int(merged_images)
self.collect_device.exposurePeriod = exp_time
self.collect_device.imagePath = basedir
self.collect_device.imageWidth = osc_range
self.detector_hwobj.set_image_headers(["Angle_increment %.4f" % osc_range])
return True
def start_characterization(self):
osc_seq = self.current_dc_parameters['oscillation_sequence'][0]
fileinfo = self.current_dc_parameters['fileinfo']
start_angle = osc_seq['start']
nb_images = osc_seq['number_of_images']
merged_images = self.characterization_nb_merged_images
wedge_range = osc_seq['range'] / merged_images
image_template = fileinfo['template']
oscil_image_template = image_template[:3] + '_wdg' + image_template[3:]
start = start_angle
self.emit("collectStarted", (self.owner, 1))
for imgno in range(nb_images):
image_filename = image_template % (imgno + 1)
image_fullpath = os.path.join(fileinfo['directory'], image_filename)
series_first_image = oscil_image_template % ((start-start_angle)/wedge_range + 1)
series_last_image = oscil_image_template % ((start-start_angle)/wedge_range + merged_images)
series_last_fullpath = os.path.join( fileinfo['directory'], series_last_image )
logging.info("PX1Collect: start image series for angle %s - first image name is %s" % (start, series_first_image))
self.collect_device.imageName = series_first_image
self.collect_device.startAngle = start
self.wait_collect_ready()
self.collect_device.prepareCollect()
self.wait_collect_ready()
self.detector_hwobj.set_image_headers(["Start_angle %.4f" % start])
self.collect_device.Start()
# file names to wait for
# wait for completion
self.wait_collect_ready()
logging.info("PX1Collect: waiting to finish image series for angle %s - waiting for %s" % (start, series_last_fullpath))
self.wait_image_on_disk(series_last_fullpath)
self.adxv_sync_image(series_last_fullpath)
# merge images into one image
merge_images(series_first_image, image_filename, fileinfo['directory'],
start, osc_seq['range'], osc_seq['exposure_time'])
logging.info("PX1Collect: waiting for merged image to appear on disk %s - waiting for %s" % (start, image_fullpath))
self.wait_image_on_disk(image_fullpath)
self.adxv_sync_image(image_fullpath)
start += 90.
def data_collection_end(self):
#
# data collection end (or abort)
#
logging.getLogger("HWR").info("PX1Collect: finishing data collection ")
self.omega_hwobj.stop()
self.fastshut_hwobj.closeShutter()
self.emit("progressStop")
def data_collection_failed(self):
logging.getLogger("HWR").info("PX1Collect: Data collection failed. recovering sequence should go here")
def collect_finished(self, green):
logging.info("PX1Collect: Data collection finished")
def collect_failed(self, par):
logging.exception("PX1Collect: Data collection failed")
self.current_dc_parameters["status"] = 'failed'
exc_type, exc_value, exc_tb = sys.exc_info()
failed_msg = 'Data collection failed!\n%s' % exc_value
self.emit("collectOscillationFailed", (self.owner, False, failed_msg,
self.current_dc_parameters.get('collection_id'), 1))
self.detector_hwobj.stop_collection()
self.omega_hwobj.stop()
self.data_collection_end()
def set_helical_pos(self, arg):
"""
Descript. : 8 floats describe
p1AlignmY, p1AlignmZ, p1CentrX, p1CentrY
p2AlignmY, p2AlignmZ, p2CentrX, p2CentrY
"""
self.helical_positions = [arg["1"]["phiy"], arg["1"]["phiz"],
arg["1"]["sampx"], arg["1"]["sampy"],
arg["2"]["phiy"], arg["2"]["phiz"],
arg["2"]["sampx"], arg["2"]["sampy"]]
def setMeshScanParameters(self, num_lines, num_images_per_line, mesh_range):
"""
Descript. :
"""
pass
def trigger_auto_processing(self, *args):
pass
## generate snapshots and data thumbnails ##
@task
def _take_crystal_snapshot(self, filename):
"""
Descript. :
"""
if not self.is_sampleview_phase():
self.go_to_sampleview()
time.sleep(2) # allow time to refresh display after
self.lightarm_hwobj.adjustLightLevel()
time.sleep(0.3) # allow time to refresh display after
self.graphics_manager_hwobj.save_scene_snapshot(filename)
logging.getLogger("HWR").debug("PX1Collect: - snapshot saved to %s" % filename)
def generate_thumbnails(self, filename, jpeg_filename, thumbnail_filename):
#
# write info on LIMS
try:
logging.info("PX1Collect: Generating thumbnails for %s" % filename)
logging.info("PX1Collect: jpeg file: %s" % jpeg_filename)
logging.info("PX1Collect: thumbnail file: %s" % thumbnail_filename)
self.wait_image_on_disk(filename)
if os.path.exists( filename ):
subprocess.Popen([ self.img2jpeg, filename, jpeg_filename, '0.4' ])
subprocess.Popen([ self.img2jpeg, filename, thumbnail_filename, '0.1' ])
return True
else:
logging.info("PX1Collect: Oopps. Trying to generate thumbs but image is not on disk")
return False
except:
import traceback
logging.error("PX1Collect: Cannot generate thumbnails for %s" % filename)
logging.error(traceback.format_exc())
return False
## generate snapshots and data thumbnails (END) ##
## FILE SYSTEM ##
def wait_image_on_disk(self, filename, timeout=20.0):
start_wait = time.time()
while not os.path.exists(filename):
if time.time() - start_wait > timeout:
logging.info("PX1Collect: Giving up waiting for image. Timeout")
break
time.sleep(0.1)
logging.info("PX1Collect: Waiting for image %s ended in %3.2f secs" % (filename, time.time()-start_wait))
def check_directory(self, basedir):
if not os.path.exists(basedir):
try:
os.makedirs(basedir)
except OSError, e:
if e.errno != errno.EEXIST:
raise
class PX1Collect(AbstractCollect, HardwareObject):
"""Main data collection class. Inherited from AbstractMulticollect
Collection is done by setting collection parameters and
executing collect command
"""
adxv_host = "127.0.0.1"
adxv_port = 8100
adxv_interval = 2.0 # minimum time (in seconds) between image refresh on adxv
goimg_dir = "/nfs/ruche/share-temp/Proxima/.goimgpx1"
goimg_filename = "goimg.db"
characterization_nb_merged_images = 10
def __init__(self, name):
"""
:param name: name of the object
:type name: string
"""
AbstractCollect.__init__(self)
HardwareObject.__init__(self, name)
self._error_msg = ""
self.owner = None
self.osc_id = None
self._collecting = None
self.diffractometer_hwobj = None
self.omega_hwobj = None
self.kappa_hwobj = None
self.phi_hwobj = None
self.lims_client_hwobj = None
self.machine_info_hwobj = None
self.energy_hwobj = None
self.resolution_hwobj = None
self.transmission_hwobj = None
self.detector_hwobj = None
self.beam_info_hwobj = None
self.autoprocessing_hwobj = None
self.graphics_manager_hwobj = None
self.mxlocal = None
self.helical_positions = None
def init(self):
"""
Init method
"""
self.collect_devname = self.getProperty("tangoname")
self.collect_device = DeviceProxy(self.collect_devname)
self.collect_state_chan = self.getChannelObject("state")
self.px1env_hwobj = self.getObjectByRole("environment")
self.fastshut_hwobj = self.getObjectByRole("fastshut")
self.frontend_hwobj = self.getObjectByRole("frontend")
self.safshut_hwobj = self.getObjectByRole("safshut")
self.lightarm_hwobj = self.getObjectByRole("lightarm")
self.diffractometer_hwobj = self.getObjectByRole("diffractometer")
self.mxlocal_object = self.getObjectByRole("beamline_configuration")
self.omega_hwobj = self.getObjectByRole("omega")
self.kappa_hwobj = self.getObjectByRole("kappa")
self.phi_hwobj = self.getObjectByRole("phi")
self.lims_client_hwobj = self.getObjectByRole("lims_client")
self.machine_info_hwobj = self.getObjectByRole("machine_info")
self.energy_hwobj = self.getObjectByRole("energy")
self.resolution_hwobj = self.getObjectByRole("resolution")
self.transmission_hwobj = self.getObjectByRole("transmission")
self.detector_hwobj = self.getObjectByRole("detector")
self.beam_info_hwobj = self.getObjectByRole("beam_info")
# self.autoprocessing_hwobj = self.getObjectByRole("auto_processing")
self.graphics_manager_hwobj = self.getObjectByRole("graphics_manager")
self.flux_hwobj = self.getObjectByRole("flux")
self.img2jpeg = self.getProperty("imgtojpeg")
undulators = self.get_undulators()
self.exp_type_dict = {"Mesh": "raster", "Helical": "Helical"}
det_px, det_py = self.detector_hwobj.get_pixel_size()
self.set_beamline_configuration(
synchrotron_name="SOLEIL",
directory_prefix=self.getProperty("directory_prefix"),
default_exposure_time=self.detector_hwobj.get_default_exposure_time(),
minimum_exposure_time=self.detector_hwobj.get_minimum_exposure_time(),
detector_fileext=self.detector_hwobj.get_file_suffix(),
detector_type=self.detector_hwobj.get_detector_type(),
detector_manufacturer=self.detector_hwobj.get_manufacturer(),
detector_model=self.detector_hwobj.get_model(),
detector_px=det_px,
detector_py=det_py,
undulators=undulators,
focusing_optic=self.getProperty("focusing_optic"),
monochromator_type=self.getProperty("monochromator"),
beam_divergence_vertical=self.beam_info_hwobj.get_beam_divergence_hor(),
beam_divergence_horizontal=self.beam_info_hwobj.get_beam_divergence_ver(),
polarisation=self.getProperty("polarisation"),
input_files_server=self.getProperty("input_files_server"),
)
self.emit("collectConnected", (True,))
self.emit("collectReady", (True,))
def data_collection_hook(self):
"""Main collection hook
"""
collection_type = self.current_dc_parameters["experiment_type"]
logging.getLogger("HWR").info(
"PX1Collect: Running PX1 data collection hook. Type is %s" % collection_type
)
if self.aborted_by_user:
self.emit_collection_failed("Aborted by user")
self.aborted_by_user = False
return
ready = self.prepare_devices_for_collection()
if not ready:
self.collection_failed("Cannot prepare collection")
self.stop_collect()
return
if collection_type != "Characterization": # standard
prepare_ok = self.prepare_standard_collection()
else:
prepare_ok = self.prepare_characterization()
self._collecting = True
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
# for progressBar brick
self.emit("progressInit", "Collection", osc_seq["number_of_images"])
#
# Run
#
self.prepare_directories()
if collection_type != "Characterization": # standard
self.start_standard_collection()
self.follow_collection_progress()
else:
self.start_characterization()
# includes
self.data_collection_end()
self.collection_finished()
def prepare_standard_collection(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
logging.getLogger("HWR").info("PX1Collect: fileinfo is %s " % str(fileinfo))
imgname = fileinfo["template"] % osc_seq["start_image_number"]
# move omega to start angle
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
osc_range = osc_seq["range"]
exp_time = osc_seq["exposure_time"]
logging.getLogger("HWR").info(
"PX1Collect: nb_images: %s / osc_range: %s / exp_time: %s"
% (nb_images, osc_range, exp_time)
)
self.collect_device.exposurePeriod = exp_time
self.collect_device.numberOfImages = nb_images
self.collect_device.imageWidth = osc_range
# self.collect_device.collectAxis = "Omega"
self.collect_device.startAngle = start_angle
self.collect_device.triggerMode = 2
self.collect_device.imagePath = basedir
self.collect_device.imageName = imgname
time.sleep(0.2)
self.collect_device.PrepareCollect()
ret = self.wait_collect_standby()
if ret is False:
logging.getLogger("user_level_log").info(
"Collect server prepare error. Aborted"
)
return False
self.prepare_headers()
return True
def start_standard_collection(self):
self.emit("collectStarted", (self.owner, 1))
self.detector_hwobj.start_collection()
self.collect_device.Start()
def follow_collection_progress(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
archive_dir = fileinfo["archive_directory"]
template = fileinfo["template"]
jpeg_template = os.path.splitext(template)[0] + ".jpeg"
thumb_template = os.path.splitext(template)[0] + ".thumb.jpeg"
osc_range = osc_seq["range"]
osc_start = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
first_imgno = osc_seq["start_image_number"]
first_image_fullpath = os.path.join(basedir, template % first_imgno)
first_image_jpegpath = os.path.join(archive_dir, jpeg_template % first_imgno)
first_image_thumbpath = os.path.join(archive_dir, thumb_template % first_imgno)
last_imgno = first_imgno + nb_images - 1
last_image_fullpath = os.path.join(basedir, template % last_imgno)
last_image_jpegpath = os.path.join(archive_dir, jpeg_template % last_imgno)
last_image_thumbpath = os.path.join(archive_dir, thumb_template % last_imgno)
# wait for first image
self.adxv_latest_refresh = 0
self.is_firstimg = True
self.file_waiting_display = first_image_fullpath # for showing on adxv
self.wait_image_on_disk(first_image_fullpath)
thumbs_up = self.generate_thumbnails(
first_image_fullpath, first_image_jpegpath, first_image_thumbpath
)
if thumbs_up:
self.store_image_in_lims(first_imgno)
# update display while collect is running
while self.is_moving() or self.is_firstimg:
self.adxv_show_latest(fileinfo)
time.sleep(0.1)
# wait for last image
self.wait_image_on_disk(last_image_fullpath)
thumbs_up = self.generate_thumbnails(
last_image_fullpath, last_image_jpegpath, last_image_thumbpath
)
self.adxv_sync_image(first_image_fullpath)
if thumbs_up:
self.store_image_in_lims(last_imgno)
def prepare_characterization(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
merged_images = self.characterization_nb_merged_images
osc_range = float(osc_seq["range"]) / merged_images
exp_time = float(osc_seq["exposure_time"]) / merged_images
self.collect_device.numberOfImages = int(merged_images)
self.collect_device.exposurePeriod = exp_time
self.collect_device.imagePath = basedir
self.collect_device.imageWidth = osc_range
self.detector_hwobj.set_image_headers(["Angle_increment %.4f" % osc_range])
return True
def start_characterization(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
merged_images = self.characterization_nb_merged_images
wedge_range = osc_seq["range"] / merged_images
image_template = fileinfo["template"]
oscil_image_template = image_template[:3] + "_wdg" + image_template[3:]
start = start_angle
self.emit("collectStarted", (self.owner, 1))
for imgno in range(nb_images):
image_filename = image_template % (imgno + 1)
image_fullpath = os.path.join(fileinfo["directory"], image_filename)
series_first_image = oscil_image_template % (
(start - start_angle) / wedge_range + 1
)
series_last_image = oscil_image_template % (
(start - start_angle) / wedge_range + merged_images
)
series_last_fullpath = os.path.join(
fileinfo["directory"], series_last_image
)
logging.info(
"PX1Collect: start image series for angle %s - first image name is %s"
% (start, series_first_image)
)
self.collect_device.imageName = series_first_image
self.collect_device.startAngle = start
self.wait_collect_ready()
self.collect_device.prepareCollect()
self.wait_collect_ready()
self.detector_hwobj.set_image_headers(["Start_angle %.4f" % start])
self.collect_device.Start()
# file names to wait for
# wait for completion
self.wait_collect_ready()
logging.info(
"PX1Collect: waiting to finish image series for angle %s - waiting for %s"
% (start, series_last_fullpath)
)
self.wait_image_on_disk(series_last_fullpath)
self.adxv_sync_image(series_last_fullpath)
# merge images into one image
merge_images(
series_first_image,
image_filename,
fileinfo["directory"],
start,
osc_seq["range"],
osc_seq["exposure_time"],
)
logging.info(
"PX1Collect: waiting for merged image to appear on disk %s - waiting for %s"
% (start, image_fullpath)
)
self.wait_image_on_disk(image_fullpath)
self.adxv_sync_image(image_fullpath)
start += 90.0
def data_collection_end(self):
#
# data collection end (or abort)
#
logging.getLogger("HWR").info("PX1Collect: finishing data collection ")
self.omega_hwobj.stop()
self.fastshut_hwobj.closeShutter()
self.emit("progressStop")
def data_collection_failed(self):
logging.getLogger("HWR").info(
"PX1Collect: Data collection failed. recovering sequence should go here"
)
def collect_finished(self, green):
logging.info("PX1Collect: Data collection finished")
def collect_failed(self, par):
logging.exception("PX1Collect: Data collection failed")
self.current_dc_parameters["status"] = "failed"
exc_type, exc_value, exc_tb = sys.exc_info()
failed_msg = "Data collection failed!\n%s" % exc_value
self.emit(
"collectOscillationFailed",
(
self.owner,
False,
failed_msg,
self.current_dc_parameters.get("collection_id"),
1,
),
)
self.detector_hwobj.stop_collection()
self.omega_hwobj.stop()
self.data_collection_end()
def set_helical_pos(self, arg):
"""
Descript. : 8 floats describe
p1AlignmY, p1AlignmZ, p1CentrX, p1CentrY
p2AlignmY, p2AlignmZ, p2CentrX, p2CentrY
"""
self.helical_positions = [
arg["1"]["phiy"],
arg["1"]["phiz"],
arg["1"]["sampx"],
arg["1"]["sampy"],
arg["2"]["phiy"],
arg["2"]["phiz"],
arg["2"]["sampx"],
arg["2"]["sampy"],
]
def setMeshScanParameters(self, num_lines, num_images_per_line, mesh_range):
"""
Descript. :
"""
pass
def trigger_auto_processing(self, *args):
pass
## generate snapshots and data thumbnails ##
@task
def _take_crystal_snapshot(self, filename):
"""
Descript. :
"""
if not self.is_sampleview_phase():
self.go_to_sampleview()
time.sleep(2) # allow time to refresh display after
self.lightarm_hwobj.adjustLightLevel()
time.sleep(0.3) # allow time to refresh display after
self.graphics_manager_hwobj.save_scene_snapshot(filename)
logging.getLogger("HWR").debug("PX1Collect: - snapshot saved to %s" % filename)
def generate_thumbnails(self, filename, jpeg_filename, thumbnail_filename):
#
# write info on LIMS
try:
logging.info("PX1Collect: Generating thumbnails for %s" % filename)
logging.info("PX1Collect: jpeg file: %s" % jpeg_filename)
logging.info("PX1Collect: thumbnail file: %s" % thumbnail_filename)
self.wait_image_on_disk(filename)
if os.path.exists(filename):
subprocess.Popen([self.img2jpeg, filename, jpeg_filename, "0.4"])
subprocess.Popen([self.img2jpeg, filename, thumbnail_filename, "0.1"])
return True
else:
logging.info(
"PX1Collect: Oopps. Trying to generate thumbs but image is not on disk"
)
return False
except BaseException:
import traceback
logging.error("PX1Collect: Cannot generate thumbnails for %s" % filename)
logging.error(traceback.format_exc())
return False
## generate snapshots and data thumbnails (END) ##
## FILE SYSTEM ##
def wait_image_on_disk(self, filename, timeout=20.0):
start_wait = time.time()
while not os.path.exists(filename):
if time.time() - start_wait > timeout:
logging.info("PX1Collect: Giving up waiting for image. Timeout")
break
time.sleep(0.1)
logging.info(
"PX1Collect: Waiting for image %s ended in %3.2f secs"
% (filename, time.time() - start_wait)
)
def check_directory(self, basedir):
if not os.path.exists(basedir):
try:
os.makedirs(basedir)
except OSError as e:
if e.errno != errno.EEXIST:
raise
def prepare_directories(self):
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
process_dir = basedir.replace("RAW_DATA", "PROCESSED_DATA")
try:
os.chmod(process_dir, 0o777)
except BaseException:
import traceback
logging.getLogger("HWR").error(
"PX1Collect: Error changing permissions for PROCESS directory"
)
logging.getLogger("HWR").error(traceback.format_exc())
self.create_goimg_file(process_dir)
def create_goimg_file(self, dirname):
db_f = os.path.join(self.goimg_dir, self.goimg_filename)
if os.path.exists(db_f):
os.remove(db_f)
with open(db_f, "w") as fd:
fd.write(dirname)
os.chmod(db_f, 0o777)
def create_file_directories(self):
"""
Method create directories for raw files and processing files.
Directorie for xds.input and auto_processing are created
"""
self.create_directories(
self.current_dc_parameters["fileinfo"]["directory"],
self.current_dc_parameters["fileinfo"]["process_directory"],
)
"""create processing directories and img links"""
xds_directory, auto_directory = self.prepare_input_files()
try:
# self.create_directories(xds_directory, auto_directory)
# os.system("chmod -R 777 %s %s" % (xds_directory, auto_directory))
"""todo, create link of imgs for auto_processing
try:
os.symlink(files_directory, os.path.join(process_directory, "img"))
except os.error, e:
if e.errno != errno.EEXIST:
raise
"""
pass
# os.symlink(files_directory, os.path.join(process_directory, "img"))
except BaseException:
logging.exception("PX1Collect: Could not create processing file directory")
return
if xds_directory:
self.current_dc_parameters["xds_dir"] = xds_directory
if auto_directory:
self.current_dc_parameters["auto_dir"] = auto_directory
def prepare_input_files(self):
"""
Descript. :
"""
i = 1
log = logging.getLogger("user_level_log")
while True:
xds_input_file_dirname = "xds_%s_%s_%d" % (
self.current_dc_parameters["fileinfo"]["prefix"],
self.current_dc_parameters["fileinfo"]["run_number"],
i,
)
xds_directory = os.path.join(
self.current_dc_parameters["fileinfo"]["process_directory"],
xds_input_file_dirname,
)
if not os.path.exists(xds_directory):
break
i += 1
self.current_dc_parameters["xds_dir"] = xds_directory
mosflm_input_file_dirname = "mosflm_%s_run%s_%d" % (
self.current_dc_parameters["fileinfo"]["prefix"],
self.current_dc_parameters["fileinfo"]["run_number"],
i,
)
mosflm_directory = os.path.join(
self.current_dc_parameters["fileinfo"]["process_directory"],
mosflm_input_file_dirname,
)
log.info(" - xds: %s / mosflm: %s" % (xds_directory, mosflm_directory))
return xds_directory, mosflm_directory
## FILE SYSTEM (END) ##
def prepare_devices_for_collection(self):
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
self.check_directory(basedir)
# check fast shutter closed. others opened
shutok = self.check_shutters()
shutok = True
if not shutok:
logging.getLogger("user_level_log").info(
" Shutters not ready for collection. Aborted"
)
return False
detok = self.detector_hwobj.prepare_collection(self.current_dc_parameters)
if not detok:
logging.getLogger("user_level_log").info(
"Cannot prepare detector for collection. Aborted"
)
return False
adxv_ok = self.adxv_connect()
diff_ok = self.diffractometer_prepare_collection()
if not diff_ok:
logging.getLogger("user_level_log").info(
"Cannot prepare diffractometer for collection. Aborted"
)
return False
return True
def diffractometer_prepare_collection(self):
self.diffractometer_hwobj.wait_device_ready(timeout=10)
# go to collect phase
if not self.is_collect_phase():
success = self.go_to_collect()
if not success:
logging.getLogger("HWR").info("PX1Collect: Cannot set COLLECT phase")
return False
return True
def prepare_headers(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
ax, ay, bx, by = self.get_beam_configuration()
dist = self.detector_hwobj.get_distance()
wavlen = self.energy_hwobj.get_wavelength()
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
img_range = osc_seq["range"]
exp_time = osc_seq["exposure_time"]
kappa_angle = self.kappa_hwobj.getPosition()
_settings = [
["Wavelength %.5f", wavlen],
["Detector_distance %.4f", dist / 1000.0],
["Beam_x %.2f", ax * dist + bx],
["Beam_y %.2f", ay * dist + by],
["Alpha %.2f", 49.64],
["Start_angle %.4f", start_angle],
["Angle_increment %.4f", img_range],
["Oscillation_axis %s", "Omega"],
["Detector_2theta %.4f", 0.0],
["Polarization %.3f", 0.990],
["Kappa %.4f", kappa_angle],
]
# if self.oscaxis == "Phi":
# _settings.append(["Chi %.4f", self.omega_hwo.getPosition()])
# _settings.append(["Phi %.4f", start])
# elif self.oscaxis == "Omega":
_settings.append(["Phi %.4f", self.phi_hwobj.getPosition()])
_settings.append(["Chi %.4f", start_angle])
self.detector_hwobj.set_image_headers(_settings)
def check_shutters(self):
# Check safety shutter
if self.check_shutter_opened(
self.safshut_hwobj, "Safety shutter"
) and self.check_shutter_opened(self.frontend_hwobj, "Front end"):
return True
else:
return False
def check_shutter_opened(self, shut_hwo, shutter_name="shutter"):
if shut_hwo.isShutterOpened():
return True
if shut_hwo.getState() == "disabled":
logging.getLogger("user_level_log").warning(
"%s disabled. Collect cancelled" % shutter_name
)
return False
elif shut_hwo.getState() in ["fault", "alarm", "error"]:
logging.getLogger("user_level_log").warning(
"%s is in fault state. Collect cancelled" % shutter_name
)
return False
elif shut_hwo.isShutterClosed():
shut_hwo.openShutter()
return shut_hwo.waitShutter("opened")
else:
logging.getLogger("user_level_log").warning(
"%s is in an unhandled state. Collect cancelled" % shutter_name
)
return False
def close_fast_shutter(self):
self.fastshut_hwobj.closeShutter()
def close_safety_shutter(self):
pass
## COLLECT SERVER STATE ##
def wait_collect_standby(self, timeout=10):
t0 = time.time()
while not self.is_standby():
elapsed = time.time() - t0
if elapsed > timeout:
break
time.sleep(0.1)
def wait_collect_moving(self, timeout=10):
t0 = time.time()
while not self.is_moving():
elapsed = time.time() - t0
if elapsed > timeout:
break
time.sleep(0.1)
def wait_collect_ready(self, timeout=10):
t0 = time.time()
while self.is_moving():
elapsed = time.time() - t0
if elapsed > timeout:
break
time.sleep(0.1)
def is_standby(self):
return str(self.collect_state_chan.getValue()) == "STANDBY"
def is_moving(self):
return str(self.collect_state_chan.getValue()) in ["MOVING", "RUNNING"]
## COLLECT SERVER STATE (END) ##
## PX1 ENVIRONMENT PHASE HANDLING ##
def is_collect_phase(self):
return self.px1env_hwobj.isPhaseCollect()
def go_to_collect(self, timeout=180):
self.px1env_hwobj.gotoCollectPhase()
gevent.sleep(0.5)
t0 = time.time()
while True:
env_state = self.px1env_hwobj.getState()
if env_state != "RUNNING" and self.is_collect_phase():
break
if time.time() - t0 > timeout:
logging.getLogger("HWR").debug(
"PX1Collect: timeout sending supervisor to collect phase"
)
break
gevent.sleep(0.5)
return self.px1env_hwobj.isPhaseCollect()
def is_sampleview_phase(self):
return self.px1env_hwobj.isPhaseVisuSample()
def go_to_sampleview(self, timeout=180):
self.px1env_hwobj.gotoSampleViewPhase()
gevent.sleep(0.5)
t0 = time.time()
while True:
env_state = self.px1env_hwobj.getState()
if env_state != "RUNNING" and self.is_sampleview_phase():
break
if time.time() - t0 > timeout:
logging.getLogger("HWR").debug(
"PX1Collect: timeout sending supervisor to sample view phase"
)
break
gevent.sleep(0.5)
self.lightarm_hwobj.adjustLightLevel()
return self.is_sampleview_phase()
## PX1 ENVIRONMENT PHASE HANDLING (END) ##
## OTHER HARDWARE OBJECTS ##
def set_energy(self, value):
"""
Descript. :
"""
self.energy_hwobj.move_energy(value)
def set_wavelength(self, value):
"""
Descript. :
"""
self.energy_hwobj.move_wavelength(value)
def get_energy(self):
return self.energy_hwobj.get_energy()
def set_transmission(self, value):
"""
Descript. :
"""
self.transmission_hwobj.set_value(value)
def set_resolution(self, value):
"""
Descript. : resolution is a motor in out system
"""
return
self.resolution_hwobj.move(value)
def move_detector(self, value):
self.detector_hwobj.move_distance(value)
@task
def move_motors(self, motor_position_dict):
"""
Descript. :
"""
self.diffractometer_hwobj.move_motors(motor_position_dict)
def get_wavelength(self):
"""
Descript. :
Called to save wavelength in lims
"""
if self.energy_hwobj is not None:
return self.energy_hwobj.get_wavelength()
def get_detector_distance(self):
"""
Descript. :
Called to save detector_distance in lims
"""
if self.detector_hwobj is not None:
return self.detector_hwobj.get_distance()
def get_resolution(self):
"""
Descript. :
Called to save resolution in lims
"""
if self.resolution_hwobj is not None:
return self.resolution_hwobj.getPosition()
def get_transmission(self):
"""
Descript. :
Called to save transmission in lims
"""
if self.transmission_hwobj is not None:
return self.transmission_hwobj.getAttFactor()
def get_undulators_gaps(self):
"""
Descript. : return gaps as dict. In our case we have one gap,
others are 0
"""
if self.energy_hwobj:
try:
u20_gap = self.energy_hwobj.getCurrentUndulatorGap()
return {"u20": u20_gap}
except BaseException:
return {}
else:
return {}
def get_beam_size(self):
"""
Descript. :
"""
if self.beam_info_hwobj is not None:
return self.beam_info_hwobj.get_beam_size()
def get_slit_gaps(self):
"""
Descript. :
"""
if self.beam_info_hwobj is not None:
return self.beam_info_hwobj.get_slits_gap()
return None, None
def get_beam_shape(self):
"""
Descript. :
"""
if self.beam_info_hwobj is not None:
return self.beam_info_hwobj.get_beam_shape()
def get_measured_intensity(self):
"""
Descript. :
"""
if self.flux_hwobj is not None:
flux = self.flux_hwobj.getValue()
else:
flux = 0.0
return float("%.3e" % flux)
def get_machine_current(self):
"""
Descript. :
"""
if self.machine_info_hwobj:
return self.machine_info_hwobj.get_current()
else:
return 0
def get_machine_message(self):
"""
Descript. :
"""
if self.machine_info_hwobj:
return self.machine_info_hwobj.get_message()
else:
return ""
def get_machine_fill_mode(self):
"""
Descript. :
"""
if self.machine_info_hwobj:
return self.machine_info_hwobj.get_fill_mode()
else:
return ""
def get_beam_configuration(self):
pars_beam = self.mxlocal_object["SPEC_PARS"]["beam"]
ax = pars_beam.getProperty("ax")
ay = pars_beam.getProperty("ay")
bx = pars_beam.getProperty("bx")
by = pars_beam.getProperty("by")
return [ax, ay, bx, by]
def get_undulators(self):
return [U20()]
def get_flux(self):
"""
Descript. :
"""
return self.get_measured_intensity()
## OTHER HARDWARE OBJECTS (END) ##
## ADXV display images ##
def adxv_connect(self):
# connect every time?? maybe we can do better
try:
res = socket.getaddrinfo(
self.adxv_host, self.adxv_port, 0, socket.SOCK_STREAM
)
af, socktype, proto, canonname, sa = res[0]
self.adxv_socket = socket.socket(af, socktype, proto)
self.adxv_socket.connect((self.adxv_host, self.adxv_port))
logging.getLogger().info("PX1Collect: ADXV Visualization connected.")
except BaseException:
self.adxv_socket = None
logging.getLogger().info("PX1Collect: WARNING: Can't connect to ADXV.")
def adxv_show_latest(self, fileinfo):
now = time.time()
elapsed = now - self.adxv_latest_refresh
template = fileinfo["template"]
basedir = fileinfo["directory"]
if self.file_waiting_display is not None:
if os.path.exists(self.file_waiting_display):
self.adxv_sync_image(self.file_waiting_display)
self.file_waiting_display = None
self.is_firstimg = False
# find next file to display
if elapsed >= self.adxv_interval and self.file_waiting_display is None:
_current_img_no = self.collect_device.currentImageSpi
self.file_waiting_display = os.path.join(
basedir, template % _current_img_no
)
self.adxv_last_refresh = time.time()
def adxv_sync_image(self, filename):
adxv_send_cmd = "\nload_image %s\n" + chr(32)
try:
if not self.adxv_socket:
try:
self.adxv_connect()
except Exception as err:
self.adxv_socket = None
logging.info(
"PX1Collect: ADXV: Warning: Can't connect to adxv socket to follow collect."
)
logging.error("PX1Collect: ADXV0: msg= %s" % err)
else:
logging.info(("PX1Collect: ADXV: " + adxv_send_cmd[1:-2]) % imgname)
self.adxv_socket.send(adxv_send_cmd % imgname)
except BaseException:
try:
del self.adxv_socket
self.adxv_connect()
except Exception as err:
self.adxv_socket = None
logging.error("PX1Collect: ADXV1: msg= %s" % err)
class PX1Collect(AbstractCollect, HardwareObject):
"""Main data collection class. Inherited from AbstractMulticollect
Collection is done by setting collection parameters and
executing collect command
"""
adxv_host = "127.0.0.1"
adxv_port = 8100
adxv_interval = 2.0 # minimum time (in seconds) between image refresh on adxv
goimg_dir = "/nfs/ruche/share-temp/Proxima/.goimgpx1"
goimg_filename = "goimg.db"
characterization_nb_merged_images = 10
def __init__(self, name):
"""
:param name: name of the object
:type name: string
"""
AbstractCollect.__init__(self)
HardwareObject.__init__(self, name)
self._error_msg = ""
self.owner = None
self.osc_id = None
self._collecting = None
self.mxlocal = None
self.helical_positions = None
def init(self):
"""
Init method
"""
self.collect_devname = self.getProperty("tangoname")
self.collect_device = DeviceProxy(self.collect_devname)
self.collect_state_chan = self.get_channel_object("state")
self.px1env_hwobj = self.getObjectByRole("environment")
self.frontend_hwobj = self.getObjectByRole("frontend")
self.lightarm_hwobj = self.getObjectByRole("lightarm")
self.mxlocal_object = self.getObjectByRole("beamline_configuration")
self.img2jpeg = self.getProperty("imgtojpeg")
undulators = self.get_undulators()
self.exp_type_dict = {"Mesh": "raster", "Helical": "Helical"}
det_px, det_py = HWR.beamline.detector.get_pixel_size()
self.set_beamline_configuration(
synchrotron_name="SOLEIL",
directory_prefix=self.getProperty("directory_prefix"),
default_exposure_time=HWR.beamline.detector.get_default_exposure_time(),
minimum_exposure_time=HWR.beamline.detector.get_minimum_exposure_time(),
detector_fileext=HWR.beamline.detector.get_file_suffix(),
detector_type=HWR.beamline.detector.get_detector_type(),
detector_manufacturer=HWR.beamline.detector.get_manufacturer(),
detector_model=HWR.beamline.detector.get_model(),
detector_px=det_px,
detector_py=det_py,
undulators=undulators,
focusing_optic=self.getProperty("focusing_optic"),
monochromator_type=self.getProperty("monochromator"),
beam_divergence_vertical=HWR.beamline.beam.get_beam_divergence_hor(),
beam_divergence_horizontal=HWR.beamline.beam.get_beam_divergence_ver(),
polarisation=self.getProperty("polarisation"),
input_files_server=self.getProperty("input_files_server"),
)
self.emit("collectConnected", (True,))
self.emit("collectReady", (True,))
def data_collection_hook(self):
"""Main collection hook
"""
collection_type = self.current_dc_parameters["experiment_type"]
logging.getLogger("HWR").info(
"PX1Collect: Running PX1 data collection hook. Type is %s" % collection_type
)
if self.aborted_by_user:
self.emit_collection_failed("Aborted by user")
self.aborted_by_user = False
return
ready = self.prepare_devices_for_collection()
if not ready:
self.collection_failed("Cannot prepare collection")
self.stop_collect()
return
if collection_type != "Characterization": # standard
prepare_ok = self.prepare_standard_collection()
else:
prepare_ok = self.prepare_characterization()
self._collecting = True
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
# for progressBar brick
self.emit("progressInit", "Collection", osc_seq["number_of_images"])
#
# Run
#
self.prepare_directories()
if collection_type != "Characterization": # standard
self.start_standard_collection()
self.follow_collection_progress()
else:
self.start_characterization()
# includes
self.data_collection_end()
self.collection_finished()
def prepare_standard_collection(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
logging.getLogger("HWR").info("PX1Collect: fileinfo is %s " % str(fileinfo))
imgname = fileinfo["template"] % osc_seq["start_image_number"]
# move omega to start angle
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
osc_range = osc_seq["range"]
exp_time = osc_seq["exposure_time"]
logging.getLogger("HWR").info(
"PX1Collect: nb_images: %s / osc_range: %s / exp_time: %s"
% (nb_images, osc_range, exp_time)
)
self.collect_device.exposurePeriod = exp_time
self.collect_device.numberOfImages = nb_images
self.collect_device.imageWidth = osc_range
# self.collect_device.collectAxis = "Omega"
self.collect_device.startAngle = start_angle
self.collect_device.triggerMode = 2
self.collect_device.imagePath = basedir
self.collect_device.imageName = imgname
time.sleep(0.2)
self.collect_device.PrepareCollect()
ret = self.wait_collect_standby()
if ret is False:
logging.getLogger("user_level_log").info(
"Collect server prepare error. Aborted"
)
return False
self.prepare_headers()
return True
def start_standard_collection(self):
self.emit("collectStarted", (self.owner, 1))
HWR.beamline.detector.start_collection()
self.collect_device.Start()
def follow_collection_progress(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
archive_dir = fileinfo["archive_directory"]
template = fileinfo["template"]
jpeg_template = os.path.splitext(template)[0] + ".jpeg"
thumb_template = os.path.splitext(template)[0] + ".thumb.jpeg"
osc_range = osc_seq["range"]
osc_start = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
first_imgno = osc_seq["start_image_number"]
first_image_fullpath = os.path.join(basedir, template % first_imgno)
first_image_jpegpath = os.path.join(archive_dir, jpeg_template % first_imgno)
first_image_thumbpath = os.path.join(archive_dir, thumb_template % first_imgno)
last_imgno = first_imgno + nb_images - 1
last_image_fullpath = os.path.join(basedir, template % last_imgno)
last_image_jpegpath = os.path.join(archive_dir, jpeg_template % last_imgno)
last_image_thumbpath = os.path.join(archive_dir, thumb_template % last_imgno)
# wait for first image
self.adxv_latest_refresh = 0
self.is_firstimg = True
self.file_waiting_display = first_image_fullpath # for showing on adxv
self.wait_image_on_disk(first_image_fullpath)
thumbs_up = self.generate_thumbnails(
first_image_fullpath, first_image_jpegpath, first_image_thumbpath
)
if thumbs_up:
self.store_image_in_lims(first_imgno)
# update display while collect is running
while self.is_moving() or self.is_firstimg:
self.adxv_show_latest(fileinfo)
time.sleep(0.1)
# wait for last image
self.wait_image_on_disk(last_image_fullpath)
thumbs_up = self.generate_thumbnails(
last_image_fullpath, last_image_jpegpath, last_image_thumbpath
)
self.adxv_sync_image(first_image_fullpath)
if thumbs_up:
self.store_image_in_lims(last_imgno)
def prepare_characterization(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
merged_images = self.characterization_nb_merged_images
osc_range = float(osc_seq["range"]) / merged_images
exp_time = float(osc_seq["exposure_time"]) / merged_images
self.collect_device.numberOfImages = int(merged_images)
self.collect_device.exposurePeriod = exp_time
self.collect_device.imagePath = basedir
self.collect_device.imageWidth = osc_range
HWR.beamline.detector.set_image_headers(["Angle_increment %.4f" % osc_range])
return True
def start_characterization(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
fileinfo = self.current_dc_parameters["fileinfo"]
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
merged_images = self.characterization_nb_merged_images
wedge_range = osc_seq["range"] / merged_images
image_template = fileinfo["template"]
oscil_image_template = image_template[:3] + "_wdg" + image_template[3:]
start = start_angle
self.emit("collectStarted", (self.owner, 1))
for imgno in range(nb_images):
image_filename = image_template % (imgno + 1)
image_fullpath = os.path.join(fileinfo["directory"], image_filename)
series_first_image = oscil_image_template % (
(start - start_angle) / wedge_range + 1
)
series_last_image = oscil_image_template % (
(start - start_angle) / wedge_range + merged_images
)
series_last_fullpath = os.path.join(
fileinfo["directory"], series_last_image
)
logging.info(
"PX1Collect: start image series for angle %s - first image name is %s"
% (start, series_first_image)
)
self.collect_device.imageName = series_first_image
self.collect_device.startAngle = start
self.wait_collect_ready()
self.collect_device.prepareCollect()
self.wait_collect_ready()
HWR.beamline.detector.set_image_headers(["Start_angle %.4f" % start])
self.collect_device.Start()
# file names to wait for
# wait for completion
self.wait_collect_ready()
logging.info(
"PX1Collect: waiting to finish image series for angle %s - waiting for %s"
% (start, series_last_fullpath)
)
self.wait_image_on_disk(series_last_fullpath)
self.adxv_sync_image(series_last_fullpath)
# merge images into one image
merge_images(
series_first_image,
image_filename,
fileinfo["directory"],
start,
osc_seq["range"],
osc_seq["exposure_time"],
)
logging.info(
"PX1Collect: waiting for merged image to appear on disk %s - waiting for %s"
% (start, image_fullpath)
)
self.wait_image_on_disk(image_fullpath)
self.adxv_sync_image(image_fullpath)
start += 90.0
def data_collection_end(self):
#
# data collection end (or abort)
#
logging.getLogger("HWR").info("PX1Collect: finishing data collection ")
HWR.beamline.diffractometer.omega.stop()
HWR.beamline.fast_shutter.closeShutter()
self.emit("progressStop")
def data_collection_failed(self):
logging.getLogger("HWR").info(
"PX1Collect: Data collection failed. recovering sequence should go here"
)
def collect_finished(self, green):
logging.info("PX1Collect: Data collection finished")
def collect_failed(self, par):
logging.exception("PX1Collect: Data collection failed")
self.current_dc_parameters["status"] = "failed"
exc_type, exc_value, exc_tb = sys.exc_info()
failed_msg = "Data collection failed!\n%s" % exc_value
self.emit(
"collectOscillationFailed",
(
self.owner,
False,
failed_msg,
self.current_dc_parameters.get("collection_id"),
1,
),
)
HWR.beamline.detector.stop_collection()
HWR.beamline.diffractometer.omega.stop()
self.data_collection_end()
def set_helical_pos(self, arg):
"""
Descript. : 8 floats describe
p1AlignmY, p1AlignmZ, p1CentrX, p1CentrY
p2AlignmY, p2AlignmZ, p2CentrX, p2CentrY
"""
self.helical_positions = [
arg["1"]["phiy"],
arg["1"]["phiz"],
arg["1"]["sampx"],
arg["1"]["sampy"],
arg["2"]["phiy"],
arg["2"]["phiz"],
arg["2"]["sampx"],
arg["2"]["sampy"],
]
def setMeshScanParameters(self, num_lines, num_images_per_line, mesh_range):
"""
Descript. :
"""
pass
def trigger_auto_processing(self, *args):
pass
## generate snapshots and data thumbnails ##
@task
def _take_crystal_snapshot(self, filename):
"""
Descript. :
"""
if not self.is_sampleview_phase():
self.go_to_sampleview()
time.sleep(2) # allow time to refresh display after
self.lightarm_hwobj.adjustLightLevel()
time.sleep(0.3) # allow time to refresh display after
HWR.beamline.sample_view.save_snapshot(filename)
logging.getLogger("HWR").debug("PX1Collect: - snapshot saved to %s" % filename)
def generate_thumbnails(self, filename, jpeg_filename, thumbnail_filename):
#
# write info on LIMS
try:
logging.info("PX1Collect: Generating thumbnails for %s" % filename)
logging.info("PX1Collect: jpeg file: %s" % jpeg_filename)
logging.info("PX1Collect: thumbnail file: %s" % thumbnail_filename)
self.wait_image_on_disk(filename)
if os.path.exists(filename):
subprocess.Popen([self.img2jpeg, filename, jpeg_filename, "0.4"])
subprocess.Popen([self.img2jpeg, filename, thumbnail_filename, "0.1"])
return True
else:
logging.info(
"PX1Collect: Oopps. Trying to generate thumbs but image is not on disk"
)
return False
except BaseException:
import traceback
logging.error("PX1Collect: Cannot generate thumbnails for %s" % filename)
logging.error(traceback.format_exc())
return False
## generate snapshots and data thumbnails (END) ##
## FILE SYSTEM ##
def wait_image_on_disk(self, filename, timeout=20.0):
start_wait = time.time()
while not os.path.exists(filename):
if time.time() - start_wait > timeout:
logging.info("PX1Collect: Giving up waiting for image. Timeout")
break
time.sleep(0.1)
logging.info(
"PX1Collect: Waiting for image %s ended in %3.2f secs"
% (filename, time.time() - start_wait)
)
def check_directory(self, basedir):
if not os.path.exists(basedir):
try:
os.makedirs(basedir)
except OSError as e:
if e.errno != errno.EEXIST:
raise
def prepare_directories(self):
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
process_dir = basedir.replace("RAW_DATA", "PROCESSED_DATA")
try:
os.chmod(process_dir, 0o777)
except BaseException:
import traceback
logging.getLogger("HWR").error(
"PX1Collect: Error changing permissions for PROCESS directory"
)
logging.getLogger("HWR").error(traceback.format_exc())
self.create_goimg_file(process_dir)
def create_goimg_file(self, dirname):
db_f = os.path.join(self.goimg_dir, self.goimg_filename)
if os.path.exists(db_f):
os.remove(db_f)
with open(db_f, "w") as fd:
fd.write(dirname)
os.chmod(db_f, 0o777)
def create_file_directories(self):
"""
Method create directories for raw files and processing files.
Directorie for xds.input and auto_processing are created
"""
self.create_directories(
self.current_dc_parameters["fileinfo"]["directory"],
self.current_dc_parameters["fileinfo"]["process_directory"],
)
"""create processing directories and img links"""
xds_directory, auto_directory = self.prepare_input_files()
try:
# self.create_directories(xds_directory, auto_directory)
# os.system("chmod -R 777 %s %s" % (xds_directory, auto_directory))
"""todo, create link of imgs for auto_processing
try:
os.symlink(files_directory, os.path.join(process_directory, "img"))
except os.error, e:
if e.errno != errno.EEXIST:
raise
"""
pass
# os.symlink(files_directory, os.path.join(process_directory, "img"))
except BaseException:
logging.exception("PX1Collect: Could not create processing file directory")
return
if xds_directory:
self.current_dc_parameters["xds_dir"] = xds_directory
if auto_directory:
self.current_dc_parameters["auto_dir"] = auto_directory
def prepare_input_files(self):
"""
Descript. :
"""
i = 1
log = logging.getLogger("user_level_log")
while True:
xds_input_file_dirname = "xds_%s_%s_%d" % (
self.current_dc_parameters["fileinfo"]["prefix"],
self.current_dc_parameters["fileinfo"]["run_number"],
i,
)
xds_directory = os.path.join(
self.current_dc_parameters["fileinfo"]["process_directory"],
xds_input_file_dirname,
)
if not os.path.exists(xds_directory):
break
i += 1
self.current_dc_parameters["xds_dir"] = xds_directory
mosflm_input_file_dirname = "mosflm_%s_run%s_%d" % (
self.current_dc_parameters["fileinfo"]["prefix"],
self.current_dc_parameters["fileinfo"]["run_number"],
i,
)
mosflm_directory = os.path.join(
self.current_dc_parameters["fileinfo"]["process_directory"],
mosflm_input_file_dirname,
)
log.info(" - xds: %s / mosflm: %s" % (xds_directory, mosflm_directory))
return xds_directory, mosflm_directory
## FILE SYSTEM (END) ##
def prepare_devices_for_collection(self):
fileinfo = self.current_dc_parameters["fileinfo"]
basedir = fileinfo["directory"]
self.check_directory(basedir)
# check fast shutter closed. others opened
shutok = self.check_shutters()
shutok = True
if not shutok:
logging.getLogger("user_level_log").info(
" Shutters not ready for collection. Aborted"
)
return False
detok = HWR.beamline.detector.prepare_collection(self.current_dc_parameters)
if not detok:
logging.getLogger("user_level_log").info(
"Cannot prepare detector for collection. Aborted"
)
return False
adxv_ok = self.adxv_connect()
diff_ok = self.diffractometer_prepare_collection()
if not diff_ok:
logging.getLogger("user_level_log").info(
"Cannot prepare diffractometer for collection. Aborted"
)
return False
return True
def diffractometer_prepare_collection(self):
HWR.beamline.diffractometer.wait_device_ready(timeout=10)
# go to collect phase
if not self.is_collect_phase():
success = self.go_to_collect()
if not success:
logging.getLogger("HWR").info("PX1Collect: Cannot set COLLECT phase")
return False
return True
def prepare_headers(self):
osc_seq = self.current_dc_parameters["oscillation_sequence"][0]
ax, ay, bx, by = self.get_beam_configuration()
dist = HWR.beamline.detector.distance.get_value()
wavlen = HWR.beamline.energy.get_wavelength()
start_angle = osc_seq["start"]
nb_images = osc_seq["number_of_images"]
img_range = osc_seq["range"]
exp_time = osc_seq["exposure_time"]
kappa_angle = HWR.beamline.diffractometer.kappa.get_value()
_settings = [
["Wavelength %.5f", wavlen],
["Detector_distance %.4f", dist / 1000.0],
["Beam_x %.2f", ax * dist + bx],
["Beam_y %.2f", ay * dist + by],
["Alpha %.2f", 49.64],
["Start_angle %.4f", start_angle],
["Angle_increment %.4f", img_range],
["Oscillation_axis %s", "Omega"],
["Detector_2theta %.4f", 0.0],
["Polarization %.3f", 0.990],
["Kappa %.4f", kappa_angle],
]
# if self.oscaxis == "Phi":
# _settings.append(["Chi %.4f", self.omega_hwo.get_value()])
# _settings.append(["Phi %.4f", start])
# elif self.oscaxis == "Omega":
_settings.append(
["Phi %.4f", HWR.beamline.diffractometer.kappa_phi.get_value()]
)
_settings.append(["Chi %.4f", start_angle])
HWR.beamline.detector.set_image_headers(_settings)
def check_shutters(self):
# Check safety shutter
if self.check_shutter_opened(
HWR.beamline.safety_shutter, "Safety shutter"
) and self.check_shutter_opened(self.frontend_hwobj, "Front end"):
return True
else:
return False
def check_shutter_opened(self, shut_hwo, shutter_name="shutter"):
if shut_hwo.isShutterOpened():
return True
if shut_hwo.get_state() == "disabled":
logging.getLogger("user_level_log").warning(
"%s disabled. Collect cancelled" % shutter_name
)
return False
elif shut_hwo.get_state() in ["fault", "alarm", "error"]:
logging.getLogger("user_level_log").warning(
"%s is in fault state. Collect cancelled" % shutter_name
)
return False
elif shut_hwo.isShutterClosed():
shut_hwo.openShutter()
return shut_hwo.waitShutter("opened")
else:
logging.getLogger("user_level_log").warning(
"%s is in an unhandled state. Collect cancelled" % shutter_name
)
return False
def close_fast_shutter(self):
HWR.beamline.fast_shutter.closeShutter()
def close_safety_shutter(self):
pass
## COLLECT SERVER STATE ##
def wait_collect_standby(self, timeout=10):
t0 = time.time()
while not self.is_standby():
elapsed = time.time() - t0
if elapsed > timeout:
break
time.sleep(0.1)
def wait_collect_moving(self, timeout=10):
t0 = time.time()
while not self.is_moving():
elapsed = time.time() - t0
if elapsed > timeout:
break
time.sleep(0.1)
def wait_collect_ready(self, timeout=10):
t0 = time.time()
while self.is_moving():
elapsed = time.time() - t0
if elapsed > timeout:
break
time.sleep(0.1)
def is_standby(self):
return str(self.collect_state_chan.getValue()) == "STANDBY"
def is_moving(self):
return str(self.collect_state_chan.getValue()) in ["MOVING", "RUNNING"]
## COLLECT SERVER STATE (END) ##
## PX1 ENVIRONMENT PHASE HANDLING ##
def is_collect_phase(self):
return self.px1env_hwobj.isPhaseCollect()
def go_to_collect(self, timeout=180):
self.px1env_hwobj.gotoCollectPhase()
gevent.sleep(0.5)
t0 = time.time()
while True:
env_state = self.px1env_hwobj.get_state()
if env_state != "RUNNING" and self.is_collect_phase():
break
if time.time() - t0 > timeout:
logging.getLogger("HWR").debug(
"PX1Collect: timeout sending supervisor to collect phase"
)
break
gevent.sleep(0.5)
return self.px1env_hwobj.isPhaseCollect()
def is_sampleview_phase(self):
return self.px1env_hwobj.isPhaseVisuSample()
def go_to_sampleview(self, timeout=180):
self.px1env_hwobj.gotoSampleViewPhase()
gevent.sleep(0.5)
t0 = time.time()
while True:
env_state = self.px1env_hwobj.get_state()
if env_state != "RUNNING" and self.is_sampleview_phase():
break
if time.time() - t0 > timeout:
logging.getLogger("HWR").debug(
"PX1Collect: timeout sending supervisor to sample view phase"
)
break
gevent.sleep(0.5)
self.lightarm_hwobj.adjustLightLevel()
return self.is_sampleview_phase()
## PX1 ENVIRONMENT PHASE HANDLING (END) ##
@task
def move_motors(self, motor_position_dict):
"""
Descript. :
"""
HWR.beamline.diffractometer.move_motors(motor_position_dict)
def get_undulators_gaps(self):
"""
Descript. : return gaps as dict. In our case we have one gap,
others are 0
"""
if HWR.beamline.energy:
try:
u20_gap = HWR.beamline.energy.getCurrentUndulatorGap()
return {"u20": u20_gap}
except BaseException:
return {}
else:
return {}
def get_slit_gaps(self):
"""
Descript. :
"""
if HWR.beamline.beam is not None:
return HWR.beamline.beam.get_slits_gap()
return None, None
def get_beam_shape(self):
"""
Descript. :
"""
if HWR.beamline.beam is not None:
return HWR.beamline.beam.get_beam_shape()
def get_machine_current(self):
"""
Descript. :
"""
if HWR.beamline.machine_info:
return HWR.beamline.machine_info.get_current()
else:
return 0
def get_machine_message(self):
"""
Descript. :
"""
if HWR.beamline.machine_info:
return HWR.beamline.machine_info.get_message()
else:
return ""
def get_machine_fill_mode(self):
"""
Descript. :
"""
if HWR.beamline.machine_info:
return HWR.beamline.machine_info.get_fill_mode()
else:
return ""
def get_beam_configuration(self):
pars_beam = self.mxlocal_object["SPEC_PARS"]["beam"]
ax = pars_beam.getProperty("ax")
ay = pars_beam.getProperty("ay")
bx = pars_beam.getProperty("bx")
by = pars_beam.getProperty("by")
return [ax, ay, bx, by]
def get_undulators(self):
return [U20()]
## OTHER HARDWARE OBJECTS (END) ##
## ADXV display images ##
def adxv_connect(self):
# connect every time?? maybe we can do better
try:
res = socket.getaddrinfo(
self.adxv_host, self.adxv_port, 0, socket.SOCK_STREAM
)
af, socktype, proto, canonname, sa = res[0]
self.adxv_socket = socket.socket(af, socktype, proto)
self.adxv_socket.connect((self.adxv_host, self.adxv_port))
logging.getLogger().info("PX1Collect: ADXV Visualization connected.")
except BaseException:
self.adxv_socket = None
logging.getLogger().info("PX1Collect: WARNING: Can't connect to ADXV.")
def adxv_show_latest(self, fileinfo):
now = time.time()
elapsed = now - self.adxv_latest_refresh
template = fileinfo["template"]
basedir = fileinfo["directory"]
if self.file_waiting_display is not None:
if os.path.exists(self.file_waiting_display):
self.adxv_sync_image(self.file_waiting_display)
self.file_waiting_display = None
self.is_firstimg = False
# find next file to display
if elapsed >= self.adxv_interval and self.file_waiting_display is None:
_current_img_no = self.collect_device.currentImageSpi
self.file_waiting_display = os.path.join(
basedir, template % _current_img_no
)
self.adxv_last_refresh = time.time()
def adxv_sync_image(self, filename):
adxv_send_cmd = "\nload_image %s\n" + chr(32)
try:
if not self.adxv_socket:
try:
self.adxv_connect()
except Exception as err:
self.adxv_socket = None
logging.info(
"PX1Collect: ADXV: Warning: Can't connect to adxv socket to follow collect."
)
logging.error("PX1Collect: ADXV0: msg= %s" % err)
else:
logging.info(("PX1Collect: ADXV: " + adxv_send_cmd[1:-2]) % imgname)
self.adxv_socket.send(adxv_send_cmd % imgname)
except BaseException:
try:
del self.adxv_socket
self.adxv_connect()
except Exception as err:
self.adxv_socket = None
logging.error("PX1Collect: ADXV1: msg= %s" % err)