forked from mxcube/HardwareObjects
/
CollectMockup.py
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/
CollectMockup.py
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# Project: MXCuBE
# https://github.com/mxcube.
#
# This file is part of MXCuBE software.
#
# MXCuBE is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MXCuBE is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with MXCuBE. If not, see <http://www.gnu.org/licenses/>.
import os
import time
import logging
import gevent
from HardwareRepository.TaskUtils import *
from HardwareRepository.BaseHardwareObjects import HardwareObject
from AbstractCollect import AbstractCollect
__credits__ = ["MXCuBE colaboration"]
__version__ = "2.2."
class CollectMockup(AbstractCollect, HardwareObject):
"""
"""
def __init__(self, name):
"""
:param name: name of the object
:type name: string
"""
AbstractCollect.__init__(self)
HardwareObject.__init__(self, name)
self._centring_status = None
self._previous_collect_status = None
self._actual_collect_status = None
self.current_dc_parameters = None
self.osc_id = None
self.owner = None
self._collecting = False
self._error_msg = ""
self._error_or_aborting = False
self.collect_frame = None
self.ready_event = None
self.exp_type_dict = None
self.aborted_by_user = None
self.diffractometer_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
def init(self):
"""Main init method
"""
self.ready_event = gevent.event.Event()
self.diffractometer_hwobj = self.getObjectByRole("diffractometer")
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")
undulators = []
try:
for undulator in self["undulators"]:
undulators.append(undulator)
except:
pass
self.exp_type_dict = {'Mesh': 'raster',
'Helical': 'Helical'}
self.set_beamline_configuration(\
synchrotron_name = "EMBL-HH",
directory_prefix = self.getProperty("directory_prefix"),
default_exposure_time = self.detector_hwobj.getProperty("default_exposure_time"),
minimum_exposure_time = self.detector_hwobj.getProperty("minimum_exposure_time"),
detector_fileext = self.detector_hwobj.getProperty("fileSuffix"),
detector_type = self.detector_hwobj.getProperty("type"),
detector_manufacturer = self.detector_hwobj.getProperty("manufacturer"),
detector_model = self.detector_hwobj.getProperty("model"),
detector_px = self.detector_hwobj.getProperty("px"),
detector_py = self.detector_hwobj.getProperty("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
"""
self.emit("collectStarted", (self.owner, 1))
self.emit("progressInit", ("Data collection", 100))
self.emit("fsmConditionChanged",
"data_collection_started",
True)
self.store_image_in_lims_by_frame_num(1)
number_of_images = self.current_dc_parameters\
['oscillation_sequence'][0]['number_of_images']
for image in range(self.current_dc_parameters["oscillation_sequence"][0]["number_of_images"]):
if self.aborted_by_user:
self.ready_event.set()
return
#Uncomment to test collection failed
#if image == 5:
# self.emit("collectOscillationFailed", (self.owner, False,
# "Failed on 5", self.current_dc_parameters.get("collection_id")))
# self.ready_event.set()
# return
time.sleep(self.current_dc_parameters["oscillation_sequence"][0]["exposure_time"])
self.emit("collectImageTaken", image)
self.emit("progressStep", (int(float(image) / number_of_images * 100)))
self.emit_collection_finished()
def emit_collection_finished(self):
"""Collection finished beahviour
"""
if self.current_dc_parameters['experiment_type'] != "Collect - Multiwedge":
self.update_data_collection_in_lims()
last_frame = self.current_dc_parameters['oscillation_sequence'][0]['number_of_images']
if last_frame > 1:
self.store_image_in_lims_by_frame_num(last_frame)
if (self.current_dc_parameters['experiment_type'] in ('OSC', 'Helical') and
self.current_dc_parameters['oscillation_sequence'][0]['overlap'] == 0 and
last_frame > 19):
self.trigger_auto_processing("after",
self.current_dc_parameters,
0)
success_msg = "Data collection successful"
self.current_dc_parameters["status"] = success_msg
self.emit("collectOscillationFinished", (self.owner, True,
success_msg, self.current_dc_parameters.get('collection_id'),
self.osc_id, self.current_dc_parameters))
self.emit("collectEnded", self.owner, success_msg)
self.emit("collectReady", (True, ))
self.emit("progressStop", ())
self.emit("fsmConditionChanged",
"data_collection_successful",
True)
self.emit("fsmConditionChanged",
"data_collection_started",
False)
self._collecting = None
self.ready_event.set()
def store_image_in_lims_by_frame_num(self, frame, motor_position_id=None):
"""
Descript. :
"""
image_id = None
self.trigger_auto_processing("image", self.current_dc_parameters, frame)
image_id = self.store_image_in_lims(frame)
return image_id
def update_lims_with_workflow(self, workflow_id, grid_snapshot_filename):
"""Updates collection with information about workflow
:param workflow_id: workflow id
:type workflow_id: int
:param grid_snapshot_filename: grid snapshot file path
:type grid_snapshot_filename: string
"""
if self.lims_client_hwobj is not None:
try:
self.current_dc_parameters["workflow_id"] = workflow_id
self.current_dc_parameters["xtalSnapshotFullPath3"] = \
grid_snapshot_filename
self.lims_client_hwobj.update_data_collection(self.current_dc_parameters)
except:
logging.getLogger("HWR").exception("Could not store data collection into ISPyB")
def trigger_auto_processing(self, process_event, params_dict, frame_number):
"""
Descript. :
"""
if self.autoprocessing_hwobj is not None:
self.autoprocessing_hwobj.execute_autoprocessing(process_event,
self.current_dc_parameters, frame_number, self.run_processing_after)
def stopCollect(self, owner="MXCuBE"):
"""
Descript. :
"""
self.aborted_by_user = True
self.cmd_collect_abort()
self.emit_collection_failed("Aborted by user")
@task
def _take_crystal_snapshot(self, filename):
self.graphics_manager_hwobj.save_scene_snapshot(filename)
@task
def _take_crystal_animation(self, animation_filename, duration_sec):
"""Rotates sample by 360 and composes a gif file
Animation is saved as the fourth snapshot
"""
self.graphics_manager_hwobj.save_scene_animation(animation_filename, duration_sec)
@task
def move_motors(self, motor_position_dict):
"""
Descript. :
"""
return
def prepare_input_files(self):
"""
Descript. :
"""
i = 1
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
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)
return xds_directory, mosflm_directory, ""