diff --git a/mxcubecore/HardwareObjects/Bliss.py b/mxcubecore/HardwareObjects/Bliss.py
index 143217abcf..83eeb2904d 100644
--- a/mxcubecore/HardwareObjects/Bliss.py
+++ b/mxcubecore/HardwareObjects/Bliss.py
@@ -7,10 +7,6 @@
import gevent
import numpy
from bliss.config import static
-from bliss.data.node import (
- DataNode,
- get_or_create_node,
-)
from mxcubecore.BaseHardwareObjects import HardwareObject
diff --git a/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py b/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py
deleted file mode 100644
index 0c801825dd..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/BM14EnergyScan.py
+++ /dev/null
@@ -1,46 +0,0 @@
-import logging
-
-from ESRFEnergyScan import (
- ESRFEnergyScan,
- TunableEnergy,
-)
-
-from mxcubecore.TaskUtils import task
-
-
-class BM14EnergyScan(ESRFEnergyScan):
- def __init__(self, name):
- ESRFEnergyScan.__init__(self, name, TunableEnergy())
-
- @task
- def energy_scan_hook(self, energy_scan_parameters):
- self.energy = energy_scan_parameters["edgeEnergy"]
- if self.energy_scan_parameters["findattEnergy"]:
- ESRFEnergyScan.move_energy(self, energy_scan_parameters["findattEnergy"])
-
- @task
- def move_undulators(self, gaps):
- return
-
- @task
- def set_mca_roi(self, eroi_min, eroi_max):
- self.execute_command("calculateMcaRoi", eroi_min, eroi_max)
-
- @task
- def choose_attenuation(self):
- if self.execute_command("chooseAttenuation") == -1:
- logging.getLogger("user_level_log").error(
- "Cannot find appropriate attenuation"
- )
- raise RuntimeError("Cannot find appropriate attenuation")
- self.energy_scan_parameters["transmissionFactor"] = (
- self.transmission.get_value()
- )
-
- @task
- def execute_energy_scan(self, energy_scan_parameters):
- energy_scan_parameters["exposureTime"] = self.get_property("exposureTime")
- self.execute_command("executeScan", energy_scan_parameters)
- self.energy_scan_parameters["exposureTime"] = energy_scan_parameters[
- "exposureTime"
- ]
diff --git a/mxcubecore/HardwareObjects/ESRF/ESRFSession.py b/mxcubecore/HardwareObjects/ESRF/ESRFSession.py
index 75416e0a98..3835222f9f 100644
--- a/mxcubecore/HardwareObjects/ESRF/ESRFSession.py
+++ b/mxcubecore/HardwareObjects/ESRF/ESRFSession.py
@@ -14,6 +14,7 @@ def __init__(self, name):
def init(self):
Session.Session.init(self)
+ self._use_acronym = self.get_property("use_acronym", True)
archive_base_directory = self["file_info"].get_property(
"archive_base_directory"
@@ -95,7 +96,7 @@ def get_default_subdir(self, sample_data: dict) -> str:
sample_name = sample_data.name
protein_acronym = sample_data.crystals[0].protein_acronym
- if protein_acronym:
+ if self._use_acronym and protein_acronym:
subdir = "%s/%s-%s/" % (protein_acronym, protein_acronym, sample_name)
else:
subdir = "%s/" % sample_name
diff --git a/mxcubecore/HardwareObjects/ESRF/ID231BeamCmds.py b/mxcubecore/HardwareObjects/ESRF/ID231BeamCmds.py
index 9d788b7421..96df834472 100644
--- a/mxcubecore/HardwareObjects/ESRF/ID231BeamCmds.py
+++ b/mxcubecore/HardwareObjects/ESRF/ID231BeamCmds.py
@@ -14,7 +14,7 @@ def __init__(self, *args):
def init(self):
controller = self.get_object_by_role("controller")
detcover = self.get_object_by_role("detcover")
- scintilator = self.get_object_by_role("scintilator")
+ scintillator = self.get_object_by_role("scintillator")
aperture = self.get_object_by_role("aperture")
hutchtrigger = self.get_object_by_role("hutchtrigger")
cryo = self.get_object_by_role("cryostream")
@@ -26,7 +26,7 @@ def init(self):
# self.anneal = ControllerCommand("Anneal", controller.anneal_procedure)
self.detcover = HWObjActuatorCommand("Detector cover", detcover)
- self.scintilator = HWObjActuatorCommand("Scintillator", scintilator)
+ self.scintillator = HWObjActuatorCommand("Scintillator", scintillator)
self.aperture = HWObjActuatorCommand("Aperture", aperture)
self.hutchtrigger = HWObjActuatorCommand("Hutchtrigger", hutchtrigger)
self.cryo = HWObjActuatorCommand("Cryostream", cryo)
@@ -38,7 +38,7 @@ def get_commands(self):
self.quick_realign,
# self.anneal,
self.detcover,
- self.scintilator,
+ self.scintillator,
self.aperture,
self.hutchtrigger,
self.cryo,
diff --git a/mxcubecore/HardwareObjects/ESRF/ID232HutchTrigger.py b/mxcubecore/HardwareObjects/ESRF/ID232HutchTrigger.py
deleted file mode 100644
index 4400b2720f..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID232HutchTrigger.py
+++ /dev/null
@@ -1,147 +0,0 @@
-import logging
-import sys
-import time
-
-import gevent
-import PyTango.gevent
-
-from mxcubecore import BaseHardwareObjects
-from mxcubecore import HardwareRepository as HWR
-
-"""
-Read the state of the hutch from the PSS device server and take actions
-when enter (1) or interlock (0) the hutch.
-0 = The hutch has been interlocked and the sample environment should be made
- ready for data collection. The actions are extract the detector cover,
- move the detector to its previous position, set the MD2 to Centring.
-1 = The interlock is cleared and the user is entering the hutch to change
- the sample(s). The actions are insert the detector cover, move the
- detecto to a safe position, set MD2 to sample Transfer.
-"""
-
-
-class ID232HutchTrigger(BaseHardwareObjects.HardwareObject):
- def __init__(self, name):
- BaseHardwareObjects.HardwareObject.__init__(self, name)
- self._enabled = True
-
- def _do_polling(self):
- while True:
- try:
- self.poll()
- except Exception:
- sys.excepthook(*sys.exc_info())
- time.sleep(self.get_property("interval") / 1000.0 or 1)
-
- def init(self):
- try:
- self.device = PyTango.gevent.DeviceProxy(self.get_property("tangoname"))
- except PyTango.DevFailed as traceback:
- last_error = traceback[-1]
- logging.getLogger("HWR").error(
- "%s: %s", str(self.name()), last_error["desc"]
- )
- self.device = None
-
- try:
- self.flex_device = PyTango.gevent.DeviceProxy(
- self.get_property("flex_tangoname")
- )
- except PyTango.DevFailed as traceback:
- last_error = traceback[-1]
- logging.getLogger("HWR").error(
- "%s: %s", str(self.name()), last_error["desc"]
- )
- self.flex_device = None
-
- self.pollingTask = None
- self.initialized = False
- self.__oldValue = None
- self.card = None
- self.channel = None
-
- PSSinfo = self.get_property("pss")
- try:
- self.card, self.channel = map(int, PSSinfo.split("/"))
- except Exception:
- logging.getLogger().error("%s: cannot find PSS number", self.name())
- return
-
- if self.device is not None:
- self.pollingTask = gevent.spawn(self._do_polling)
- self.connected()
-
- def hutchIsOpened(self):
- return self.hutch_opened
-
- def is_connected(self):
- return True
-
- def connected(self):
- self.emit("connected")
-
- def disconnected(self):
- self.emit("disconnected")
-
- def abort(self):
- pass
-
- def macro(self, entering_hutch, old={"dtox": None}):
- logging.info(
- "%s: %s hutch", self.name(), "entering" if entering_hutch else "leaving"
- )
- dtox = HWR.beamline.detector.distance
- udiff_ctrl = self.get_object_by_role("predefined")
- ctrl_obj = self.get_object_by_role("controller")
- if not entering_hutch:
- if old["dtox"] is not None:
- print("Moving %s to %g" % (dtox.name(), old["dtox"]))
- dtox.set_value(old["dtox"])
- self.flex_device.eval("flex.user_port(0)")
- self.flex_device.eval("flex.robot_port(1)")
- udiff_ctrl.moveToPhase(phase="Centring", wait=True)
- else:
- old["dtox"] = dtox.get_value()
- ctrl_obj.detcover.set_in()
- self.flex_device.eval("flex.robot_port(0)")
- dtox.set_value(815)
- udiff_ctrl.moveToPhase(phase="Transfer", wait=True)
-
- def poll(self):
- a = self.device.GetInterlockState([self.card - 1, 2 * (self.channel - 1)])[0]
- b = self.device.GetInterlockState([self.card - 1, 2 * (self.channel - 1) + 1])[
- 0
- ]
- value = a & b
-
- if value == self.__oldValue:
- return
- else:
- self.__oldValue = value
-
- self.value_changed(value)
-
- def value_changed(self, value, *args):
- if value == 0:
- if self.initialized:
- self.emit("hutchTrigger", (1,))
- elif value == 1 and self.initialized:
- self.emit("hutchTrigger", (0,))
-
- self.hutch_opened = 1 - value
- self.initialized = True
-
- if self._enabled:
- self.macro(self.hutch_opened)
-
- def get_actuator_state(self):
- if self._enabled:
- return "ENABLED"
- else:
- return "DISABLED"
-
- def actuatorIn(self):
- self._enabled = True
-
- def actuatorOut(self):
- self._enabled = False
diff --git a/mxcubecore/HardwareObjects/ESRF/ID23PhotonFlux.py b/mxcubecore/HardwareObjects/ESRF/ID23PhotonFlux.py
deleted file mode 100644
index d998f53841..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID23PhotonFlux.py
+++ /dev/null
@@ -1,92 +0,0 @@
-import logging
-import math
-import time
-
-from calc_flux import CalculateFlux
-from PyTango.gevent import DeviceProxy
-
-from mxcubecore import HardwareRepository as HWR
-from mxcubecore.BaseHardwareObjects import HardwareObject
-from mxcubecore.TaskUtils import task
-
-
-class ID23PhotonFlux(HardwareObject):
- def __init__(self, *args, **kwargs):
- super().__init__(*args, **kwargs)
- self.threshold = []
-
- def init(self):
- self.counter = DeviceProxy(self.get_property("url"))
- try:
- self.threshold = map(float, self.get_property("threshold").split())
- except AttributeError:
- self.threshold = [0, 9999]
- self.shutter = self.get_deviceby_role("shutter")
- self.aperture = self.get_object_by_role("aperture")
- fname = self.get_property("calibrated_diodes_file")
-
- self.flux_calc = CalculateFlux()
- self.flux_calc.init(fname)
- self.shutter.connect("shutterStateChanged", self.shutterStateChanged)
-
- self.counts_reading_task = self._read_counts_task(wait=False)
-
- @task
- def _read_counts_task(self):
- old_counts = None
- while True:
- counts = self._get_counts()
- if counts != old_counts:
- old_counts = counts
- self.countsUpdated(counts)
- time.sleep(1)
-
- def _get_counts(self):
- try:
- self.counter.MeasureSingle()
- counts = abs(self.counter.ReadData)
- if counts < self.threshold[0] or counts > self.threshold[1]:
- counts = 0
- except AttributeError:
- counts = 0
- logging.getLogger("HWR").exception("%s: could not get counts", self.name())
- try:
- egy = HWR.beamline.energy.get_value() * 1000.0
- calib = self.flux_calc.calc_flux_coef(egy)
- except Exception:
- logging.getLogger("HWR").exception("%s: could not get energy", self.name())
- else:
- if self.aperture is None:
- aperture_coef = 1
- else:
- try:
- aperture_coef = self.aperture.getApertureCoef()
- except Exception:
- aperture_coef = 1.0
- counts = math.fabs(counts * calib[0] * aperture_coef) * 10e6
- return counts
-
- def connect_notify(self, signal):
- if signal == "valueChanged":
- self.emitValueChanged()
-
- def shutterStateChanged(self, _):
- self.countsUpdated(self._get_counts())
-
- def updateFlux(self, _):
- self.countsUpdated(self._get_counts(), ignore_shutter_state=False)
-
- def countsUpdated(self, counts, ignore_shutter_state=False):
- self.emitValueChanged("%1.3g" % counts)
-
- def get_value(self):
- self.updateFlux("dummy")
- return self.current_flux
-
- def emitValueChanged(self, flux=None):
- if flux is None:
- self.current_flux = None
- self.emit("valueChanged", ("?",))
- else:
- self.current_flux = flux
- self.emit("valueChanged", (self.current_flux,))
diff --git a/mxcubecore/HardwareObjects/ESRF/ID29BeamCmds.py b/mxcubecore/HardwareObjects/ESRF/ID29BeamCmds.py
index 6a7fae1a93..9bbacf787a 100644
--- a/mxcubecore/HardwareObjects/ESRF/ID29BeamCmds.py
+++ b/mxcubecore/HardwareObjects/ESRF/ID29BeamCmds.py
@@ -13,7 +13,7 @@ def __init__(self, *args):
def init(self):
controller = self.get_object_by_role("controller")
detcover = self.get_object_by_role("detcover")
- scintilator = self.get_object_by_role("scintilator")
+ scintillator = self.get_object_by_role("scintillator")
aperture = self.get_object_by_role("aperture")
hutchtrigger = self.get_object_by_role("hutchtrigger")
cryo = self.get_object_by_role("cryo")
@@ -26,7 +26,7 @@ def init(self):
self.anneal = ControllerCommand("Anneal", controller.anneal_procedure)
self.detcover = HWObjActuatorCommand("Detector cover", detcover)
- self.scintilator = HWObjActuatorCommand("Scintillator", scintilator)
+ self.scintillator = HWObjActuatorCommand("Scintillator", scintillator)
self.aperture = HWObjActuatorCommand("Aperture", aperture)
self.hutchtrigger = HWObjActuatorCommand("Hutchtrigger", hutchtrigger)
self.cryo = HWObjActuatorCommand("Cryo", cryo)
@@ -37,7 +37,7 @@ def get_commands(self):
self.quick_realign,
self.anneal,
self.detcover,
- self.scintilator,
+ self.scintillator,
self.aperture,
self.hutchtrigger,
self.cryo,
diff --git a/mxcubecore/HardwareObjects/ESRF/ID29PhotonFlux.py b/mxcubecore/HardwareObjects/ESRF/ID29PhotonFlux.py
deleted file mode 100644
index bf8845c4d7..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID29PhotonFlux.py
+++ /dev/null
@@ -1,87 +0,0 @@
-import logging
-import math
-import sys
-import time
-
-from calc_flux import CalculateFlux
-
-from mxcubecore import HardwareRepository as HWR
-from mxcubecore.BaseHardwareObjects import HardwareObject
-from mxcubecore.TaskUtils import task
-
-
-class ID29PhotonFlux(HardwareObject):
- def __init__(self, *args, **kwargs):
- super().__init__(*args, **kwargs)
-
- def init(self):
- self.counter = self.get_object_by_role("counter")
- self.shutter = self.get_deviceby_role("shutter")
- self.aperture = self.get_object_by_role("aperture")
- fname = self.get_property("calibrated_diodes_file")
-
- self.flux_calc = CalculateFlux()
- self.flux_calc.init(fname)
- self.shutter.connect("shutterStateChanged", self.shutterStateChanged)
-
- self.counts_reading_task = self._read_counts_task(wait=False)
-
- @task
- def _read_counts_task(self):
- old_counts = None
- while True:
- counts = self._get_counts()
- if counts != old_counts:
- old_counts = counts
- self.countsUpdated(counts)
- time.sleep(1)
-
- def _get_counts(self):
- try:
- counts = self.counter.getCorrectedPhysValue()
- if counts == -9999:
- counts = 0
- except Exception:
- counts = 0
- logging.getLogger("HWR").exception("%s: could not get counts", self.name())
- try:
- egy = HWR.beamline.energy.get_value() * 1000.0
- calib = self.flux_calc.calc_flux_coef(egy)
- except Exception:
- logging.getLogger("HWR").exception("%s: could not get energy", self.name())
- else:
- if self.aperture is None:
- aperture_coef = 1
- else:
- try:
- aperture_coef = self.aperture.getApertureCoef()
- except Exception:
- sys.excepthook(*sys.exc_info())
- aperture_coef = 1
- counts = math.fabs(counts * calib[0] * aperture_coef)
- return counts
-
- def connect_notify(self, signal):
- if signal == "valueChanged":
- self.emitValueChanged()
-
- def shutterStateChanged(self, _):
- self.countsUpdated(self._get_counts())
-
- def updateFlux(self, _):
- self.countsUpdated(self._get_counts(), ignore_shutter_state=False)
-
- def countsUpdated(self, counts, ignore_shutter_state=False):
- self.emitValueChanged("%1.3g" % counts)
-
- def get_value(self):
- self.updateFlux("dummy")
- return self.current_flux
-
- def emitValueChanged(self, flux=None):
- if flux is None:
- self.current_flux = None
- self.emit("valueChanged", ("?",))
- else:
- self.current_flux = flux
- self.emit("valueChanged", (self.current_flux,))
diff --git a/mxcubecore/HardwareObjects/ESRF/ID29XRFSpectrum.py b/mxcubecore/HardwareObjects/ESRF/ID29XRFSpectrum.py
deleted file mode 100644
index 4585b69a6c..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID29XRFSpectrum.py
+++ /dev/null
@@ -1,263 +0,0 @@
-import logging
-import os.path
-
-import numpy
-
-from mxcubecore.HardwareObjects.XRFSpectrum import XRFSpectrum
-
-try:
- from PyMca import (
- ClassMcaTheory,
- ConfigDict,
- QtMcaAdvancedFitReport,
- )
-except ImportError:
- from PyMca5.PyMca import (
- ClassMcaTheory,
- ConfigDict,
- QtMcaAdvancedFitReport,
- )
-
-"""
-Next two lines is a trick to avoid core dump in QtMcaAdvancedFitReport
-"""
-from unittest.mock import MagicMock
-
-QtMcaAdvancedFitReport.qt = MagicMock()
-
-
-class ID29XRFSpectrum(XRFSpectrum):
- def __init__(self, *args, **kwargs):
- XRFSpectrum.__init__(self, *args, **kwargs)
- self.mca_hwobj = self.get_object_by_role("mca")
- self.ctrl_hwobj = self.get_object_by_role("controller")
- self.beamsize = self.get_object_by_role("beamsize")
- self.fname = self.get_property("cfgfile")
- self.config = ConfigDict.ConfigDict()
- self.mcafit = ClassMcaTheory.McaTheory(self.fname)
- self.default_integration_time = self.get_property("default_integration_time", 3.5)
-
- def preset_mca(self, ctime=None, fname=None):
- try:
- ctime = float(ctime)
- except (TypeError, ValueError):
- ctime = self.default_integration_time
-
- self.mca_hwobj.set_roi(2, 15, channel=1)
- self.mca_hwobj.set_presets(erange=1, ctime=ctime, fname=str(fname))
- self.ctrl_hwobj.mca.set_roi(2, 15, channel=1)
- self.ctrl_hwobj.mca.set_presets(erange=1, ctime=ctime, fname=str(fname))
-
- def _doSpectrum(self, ctime, filename, wait=True):
- try:
- ctime = float(ctime)
- except (TypeError, ValueError):
- ctime = self.default_integration_time
- print(f"_doSpectrum ctime {ctime}")
- self.choose_attenuation(ctime, filename)
-
- def choose_attenuation(self, ctime=None, fname=None):
- """Choose appropriate maximum attenuation.
- Args:
- ctime (float): count time [s]
- Kwargs:
- fname (str): Filename to save the MCA data (full path)
- Returns:
- (bool): Procedure executed correcly (True) or error (False)
- """
- try:
- ctime = float(ctime)
- except (TypeError, ValueError):
- ctime = self.default_integration_time
- print(f"ctime {ctime}")
-
- res = True
- if not fname:
- fname = self.spectrumInfo["filename"]
- fname = str(fname)
-
- self.preset_mca(ctime, fname)
-
- self.ctrl_hwobj.detcover.set_in(20)
- try:
- _transm = self.ctrl_hwobj.find_max_attenuation(
- ctime=ctime, fname=fname, roi=[2.0, 15.0]
- )
- self.spectrumInfo["beamTransmission"] = _transm
- except Exception as exp:
- logging.getLogger("user_level_log").exception(str(exp))
- res = False
-
- self.ctrl_hwobj.diffractometer.fldet_out()
- return res
-
- def _findAttenuation(self, ctime=None):
- try:
- ctime = float(ctime)
- except (TypeError, ValueError):
- ctime = self.default_integration_time
- return self.choose_attenuation(ctime)
-
- """
- Next methods are for fitting the data with pymca
- """
-
- def mcafit_configuration(self, config=None):
- """Configure the fitting parameters. The procedure is time consuming.
- It is only executed if the last configuration file is not the same.
- Args:
- config(dict): Configuration dictionary, containing among others the
- configuration file name.
- """
- change = False
- if not config or "file" not in config:
- fname = XRFSpectrum._get_cfgfile(self, self.spectrumInfo["energy"])
- else:
- fname = config["file"]
-
- if self.fname != fname:
- self.fname = fname
- change = True
- self.config.read(self.fname)
- if "concentrations" not in self.config:
- self.config["concentrations"] = {}
- change = True
- if "attenuators" not in self.config:
- self.config["attenuators"] = {"Matrix": [1, "Water", 1.0, 0.01, 45.0, 45.0]}
- change = True
- if "flux" in config:
- self.config["concentrations"]["flux"] = float(config["flux"])
- change = True
- if "time" in config:
- self.config["concentrations"]["time"] = float(config["time"])
- change = True
-
- if change:
- self.mcafit.configure(self.config)
-
- def set_data(self, data, calib=None, config=None):
- """Execute the fitting. Write the fitted data files to pyarch.
- Args:
- data (list): The raw data.
- calib (list): The mca calibration.
- config (dict): The configuration dictionary.
- """
- if config:
- self.mcafit_configuration(config)
- try:
- if data[0].size == 2:
- xdata = numpy.array(data[:, 0]) * 1.0
- ydata = numpy.array(data[:, 1])
- else:
- xdata = data[0] * 1.0
- ydata = data[1]
-
- # xmin and xmax hard coded while waiting for configuration file
- # to be corrected.
- # xmin = 292
- # xmax = 4000
-
- xmin = int(config["min"])
- xmax = int(config["max"])
- self.mcafit.setData(xdata, ydata, xmin=xmin, xmax=xmax, calibration=calib)
-
- self.mcafit.estimate()
- # fitresult = self._fit()
-
- fitresult = self.mcafit.startfit(digest=1)
- if fitresult:
- fitresult = {"fitresult": fitresult[0], "result": fitresult[1]}
-
- # write the csv file to pyarch
- csvname = self.spectrumInfo["fittedDataFileFullPath"]
- self._write_csv_file(fitresult, csvname)
-
- # write html report to pyarch
- fname = os.path.basename(self.spectrumInfo["filename"])
- outfile = fname.split(".")[0]
- outdir = os.path.dirname(self.spectrumInfo["annotatedPymcaXfeSpectrum"])
-
- _kw = {
- "outdir": outdir,
- "outfile": outfile,
- "fitresult": fitresult,
- "plotdict": {"logy": False},
- }
-
- report = QtMcaAdvancedFitReport.QtMcaAdvancedFitReport(**_kw)
- text = report.getText()
- report.writeReport(text=text)
- except Exception as exp:
- logging.getLogger().exception("XRFSpectrum: problem fitting %s" % str(exp))
- raise
-
- def _write_csv_file(self, fitresult, fname=None):
- """Write data to a csv file.
- Args:
- fitresult(dict): Data as dictionary.
- Kwargs:
- fname (str): Filename to write to (full path).
- """
- if not fname:
- fname = self.spectrumInfo["fittedDataFileFullPath"]
- if os.path.exists(fname):
- os.remove(fname)
-
- # get the significant peaks
- peaks_dict = {}
- pars_len = len(fitresult["result"]["parameters"])
- grp_len = len(fitresult["result"]["groups"])
- nglobal = pars_len - grp_len
- parameters = fitresult["result"]["fittedpar"][:nglobal] + [0.0] * grp_len
-
- for grp in fitresult["result"]["parameters"][nglobal:]:
- idx = fitresult["result"]["parameters"].index(grp)
- parameters[idx] = fitresult["result"]["fittedpar"][idx]
- xmatrix = fitresult["result"]["xdata"]
- ymatrix = self.mcafit.mcatheory(parameters, xmatrix)
- ymatrix.shape = [len(ymatrix), 1]
- label = "y" + grp
- if self.mcafit.STRIP:
- peaks_dict[label] = ymatrix + self.mcafit.zz
- else:
- peaks_dict[label] = ymatrix
- peaks_dict[label].shape = (len(peaks_dict[label]),)
- parameters[idx] = 0.0
-
- delimiter = ","
- header = '"channel"%s"Energy"%s"counts"%s"fit"%s"continuum"%s"pileup"' % (
- delimiter,
- delimiter,
- delimiter,
- delimiter,
- delimiter,
- )
-
- # add the peaks labels
- for key in peaks_dict:
- header += delimiter + ('"%s"' % key)
- # logging.getLogger("user_level_log").info("Writing %s" % fname)
- with open(fname, "w") as csv_fd:
- csv_fd.write(header)
- csv_fd.write("\n")
- for i in range(fitresult["result"]["xdata"].size):
- csv_fd.write(
- "%.7g%s%.7g%s%.7g%s%.7g%s%.7g%s%.7g"
- % (
- fitresult["result"]["xdata"][i],
- delimiter,
- fitresult["result"]["energy"][i],
- delimiter,
- fitresult["result"]["ydata"][i],
- delimiter,
- fitresult["result"]["yfit"][i],
- delimiter,
- fitresult["result"]["continuum"][i],
- delimiter,
- fitresult["result"]["pileup"][i],
- )
- )
- for key in peaks_dict:
- csv_fd.write("%s%.7g" % (delimiter, peaks_dict[key][i]))
-
- csv_fd.write("\n")
diff --git a/mxcubecore/HardwareObjects/ESRF/ID30A3PhotonFlux.py b/mxcubecore/HardwareObjects/ESRF/ID30A3PhotonFlux.py
deleted file mode 100644
index 4a55b2ad59..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID30A3PhotonFlux.py
+++ /dev/null
@@ -1,109 +0,0 @@
-import time
-
-from PyTango.gevent import DeviceProxy
-
-from mxcubecore.BaseHardwareObjects import HardwareObject
-from mxcubecore.TaskUtils import task
-
-
-class ID30A3PhotonFlux(HardwareObject):
- def __init__(self, *args, **kwargs):
- super().__init__(*args, **kwargs)
-
- def init(self):
- controller = self.get_object_by_role("controller")
- self.musst = controller.musst
- self.shutter = self.get_deviceby_role("shutter")
- self.factor = self.get_property("current_photons_factor")
-
- self.shutter.connect("shutterStateChanged", self.shutterStateChanged)
-
- self.tg_device = DeviceProxy(self.get_property("tango_device"))
- self.counts_reading_task = self._read_counts_task(wait=False)
-
- @task
- def _read_counts_task(self):
- old_counts = None
- while True:
- counts = self._get_counts()
- if counts != old_counts:
- old_counts = counts
- self.countsUpdated(counts)
- time.sleep(1)
-
- def _get_counts(self):
- """gain = 20 #20uA
- keithley_voltage = 2
- musst_voltage = int("".join([x for x in self.musst.putget("#?CHCFG CH5") if x.isdigit()]))
- musst_fs = float(0x7FFFFFFF)
- counts = abs((gain/keithley_voltage)*musst_voltage*int(self.musst.putget("#?VAL CH5"))/musst_fs)
- """
- # try:
- self.tg_device.MeasureSingle()
- counts = abs(self.tg_device.ReadData) * 1e6
- return counts
-
- def connect_notify(self, signal):
- if signal == "valueChanged":
- self.emitValueChanged()
-
- def shutterStateChanged(self, _):
- self.countsUpdated(self._get_counts())
-
- def updateFlux(self, _):
- self.countsUpdated(self._get_counts(), ignore_shutter_state=True)
-
- def countsUpdated(self, counts, ignore_shutter_state=False):
- if not ignore_shutter_state and self.shutter.getShutterState() != "opened":
- self.emitValueChanged(0)
- return
- flux = counts * self.factor
- self.emitValueChanged("%1.3g" % flux)
-
- """
- try:
- counts = counts[self.index]
- except TypeError:
- logging.getLogger("HWR").error("%s: counts is None", self.name())
- return
- flux = None
-
- try:
- egy = HWR.beamline.energy.get_value()*1000.0
- except:
- logging.getLogger("HWR").exception("%s: could not get energy", self.name())
- else:
- try:
- calib_dict = self.calibration_chan.get_value()
- if calib_dict is None:
- logging.getLogger("HWR").error("%s: calibration is None", self.name())
- else:
- calibs = [(float(c["energy"]), float(c[self.counter])) for c in calib_dict.values()]
- calibs.sort()
- E = [c[0] for c in calibs]
- C = [c[1] for c in calibs]
- except:
- logging.getLogger("HWR").exception("%s: could not get calibration", self.name())
- else:
- try:
- aperture_coef = self.aperture.getApertureCoef()
- except:
- aperture_coef = 1
- if aperture_coef <= 0:
- aperture_coef = 1
- calib = numpy.interp([egy], E, C)
- flux = counts * calib * aperture_coef
- #logging.getLogger("HWR").debug("%s: flux-> %f * %f=%f , calib_dict=%r", self.name(), counts, calib, counts*calib, calib_dict)
- self.emitValueChanged("%1.3g" % flux)
- """
-
- def get_value(self):
- return self.current_flux
-
- def emitValueChanged(self, flux=None):
- if flux is None:
- self.current_flux = None
- self.emit("valueChanged", ("?",))
- else:
- self.current_flux = flux
- self.emit("valueChanged", (self.current_flux,))
diff --git a/mxcubecore/HardwareObjects/ESRF/ID30BPhotonFlux.py b/mxcubecore/HardwareObjects/ESRF/ID30BPhotonFlux.py
deleted file mode 100644
index d1c4cd8901..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID30BPhotonFlux.py
+++ /dev/null
@@ -1,88 +0,0 @@
-# encoding: utf-8
-#
-# 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 Lesser 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 Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU General Lesser Public License
-# along with MXCuBE. If not, see .
-
-""" Photon fluc calculations
-Example xml file:
-
-"""
-import logging
-
-from mxcubecore import HardwareRepository as HWR
-from mxcubecore.HardwareObjects.abstract.AbstractFlux import AbstractFlux
-
-
-class ID30BPhotonFlux(AbstractFlux):
- """Photon flux calculation for ID30B"""
-
- def __init__(self, name):
- super(ID30BPhotonFlux, self).__init__(name)
- self._counter = None
- self._flux_calc = None
- self._aperture = None
-
- def init(self):
- """Initialisation"""
- super(ID30BPhotonFlux, self).init()
- controller = self.get_object_by_role("controller")
- # ultimately it should be HWR.beamline.diffractometer.aperture
- self._aperture = self.get_object_by_role("aperture")
-
- try:
- self._flux_calc = controller.CalculateFlux()
- self._flux_calc.init()
- except AttributeError:
- logging.getLogger("HWR").exception(
- "Could not get flux calculation from BLISS"
- )
-
- counter = self.get_property("counter_name")
- if counter:
- self._counter = getattr(controller, counter)
- else:
- self._counter = self.get_object_by_role("counter")
-
- HWR.beamline.safety_shutter.connect("stateChanged", self.update_value)
-
- def get_value(self):
- """Calculate the flux value as function of a reading
- """
- # counts = self._counter._counter_controller.read_all(self._counter)
- # if isinstance(counts, list):
- # counts = float(counts[0])
- counts = float(self._counter.raw_read)
- if counts == -9999:
- counts = 0.0
-
- egy = HWR.beamline.energy.get_value() * 1000.0
- calib = self._flux_calc.calc_flux_factor(egy)[self._counter.name]
-
- try:
- label = self._aperture.get_value().name
- aperture_factor = self._aperture.get_factor(label)
- except AttributeError:
- aperture_factor = 1
- counts = abs(counts * calib * aperture_factor)
- self._nominal_value = counts
- return counts
diff --git a/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py b/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py
deleted file mode 100644
index 850f666d64..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID30BXRFSpectrum.py
+++ /dev/null
@@ -1,428 +0,0 @@
-import logging
-import os
-import time
-
-import gevent
-import gevent.event
-from qt import copy
-
-from mxcubecore import HardwareRepository as HWR
-from mxcubecore.BaseHardwareObjects import HardwareObject
-
-
-class XrfSpectrum(HardwareObject):
- def init(self):
-
- self.scanning = None
- self.moving = None
- self.ready_event = gevent.event.Event()
-
- try:
- self.config_data = self.get_channel_object("config_data")
- except Exception:
- self.config_data = None
-
- try:
- self.calib_data = self.get_channel_object(" calib_data")
- except Exception:
- self.calib_data = None
-
- try:
- self.energySpectrumArgs = self.get_channel_object("spectrum_args")
- except KeyError:
- logging.getLogger().warning(
- "XRFSpectrum: error initializing energy spectrum arguments (missing channel)"
- )
- self.energySpectrumArgs = None
-
- try:
- self.spectrumStatusMessage = self.get_channel_object("spectrumStatusMsg")
- except KeyError:
- self.spectrumStatusMessage = None
- logging.getLogger().warning(
- "XRFSpectrum: energy messages will not appear (missing channel)"
- )
- else:
- self.spectrumStatusMessage.connect_signal(
- "update", self.spectrumStatusChanged
- )
-
- try:
- self.doSpectrum.connect_signal(
- "commandBeginWaitReply", self.spectrumCommandStarted
- )
- self.doSpectrum.connect_signal("commandFailed", self.spectrumCommandFailed)
- self.doSpectrum.connect_signal(
- "commandAborted", self.spectrumCommandAborted
- )
- self.doSpectrum.connect_signal("commandReady", self.spectrumCommandReady)
- self.doSpectrum.connect_signal(
- "commandNotReady", self.spectrumCommandNotReady
- )
- except AttributeError as diag:
- logging.getLogger().warning(
- "XRFSpectrum: error initializing energy spectrum (%s)" % str(diag)
- )
- self.doSpectrum = None
- else:
- self.doSpectrum.connect_signal("connected", self.sConnected)
- self.doSpectrum.connect_signal("disconnected", self.sDisconnected)
-
- if HWR.beamline.lims is None:
- logging.getLogger().warning(
- "XRFSpectrum: you should specify the database hardware object"
- )
- self.spectrumInfo = None
-
- try:
- self.ctrl_hwobj = self.get_object_by_role("controller")
- except Exception:
- self.ctrl_hwobj = None
-
- try:
- self.mca_hwobj = self.get_object_by_role("mca")
- # self.mca_hwobj.set_calibration(calib_cf=[0,0.008324,2.223e-06])
- self.mca_hwobj.set_calibration(calib_cf=self.mca_hwobj.calib_cf)
- except Exception:
- self.mca_hwobj = None
-
- try:
- self.datapath = self.get_property("datapath")
- except Exception:
- self.datapath = "/data/pyarch/"
-
- try:
- self.cfgpath = self.get_property("cfgpath")
- except Exception:
- self.cfgpath = "/users/blissadm/local/userconf"
-
- if self.is_connected():
- self.sConnected()
-
- def is_connected(self):
- try:
- return self.doSpectrum.is_connected()
- except Exception:
- return False
-
- # Handler for spec connection
- def sConnected(self):
- self.emit("connected", ())
- # curr = self.getSpectrumParams()
-
- # Handler for spec disconnection
- def sDisconnected(self):
- self.emit("disconnected", ())
-
- # Energy spectrum commands
- def canSpectrum(self):
- if not self.is_connected():
- return False
- return self.doSpectrum is not None
-
- def startXrfSpectrum(
- self, ct, directory, prefix, session_id=None, blsample_id=None
- ):
- self.spectrumInfo = {"sessionId": session_id, "blSampleId": blsample_id}
- self.spectrumCommandStarted()
- if not os.path.isdir(directory):
- logging.getLogger().debug("XRFSpectrum: creating directory %s" % directory)
- try:
- os.makedirs(directory)
- except OSError as diag:
- logging.getLogger().error(
- "XRFSpectrum: error creating directory %s (%s)"
- % (directory, str(diag))
- )
- self.spectrumStatusChanged("Error creating directory")
- return False
-
- curr = self.getSpectrumParams()
-
- try:
- curr["escan_dir"] = directory
- curr["escan_prefix"] = prefix
- except TypeError:
- curr = {}
- curr["escan_dir"] = directory
- curr["escan_prefix"] = prefix
-
- a = directory.split(os.path.sep)
- suffix_path = os.path.join(*a[4:])
- if "inhouse" in a:
- a_dir = os.path.join(self.datapath, a[2], suffix_path)
- else:
- a_dir = os.path.join(self.datapath, a[4], a[3], *a[5:])
- if a_dir[-1] != os.path.sep:
- a_dir += os.path.sep
- if not os.path.exists(a_dir):
- try:
- # logging.getLogger().debug("XRFSpectrum: creating %s", a_dir)
- os.makedirs(a_dir)
- except OSError as diag:
- logging.getLogger().error(
- "XRFSpectrum: error creating directory %s (%s)" % (a_dir, str(diag))
- )
- self.spectrumStatusChanged("Error creating directory")
- return False
-
- filename_pattern = os.path.join(
- directory, "%s_%s_%%02d" % (prefix, time.strftime("%d_%b_%Y"))
- )
- aname_pattern = os.path.join(
- "%s/%s_%s_%%02d" % (a_dir, prefix, time.strftime("%d_%b_%Y"))
- )
-
- filename_pattern = os.path.extsep.join((filename_pattern, "dat"))
- html_pattern = os.path.extsep.join((aname_pattern, "html"))
- aname_pattern = os.path.extsep.join((aname_pattern, "png"))
- filename = filename_pattern % 1
- aname = aname_pattern % 1
- htmlname = html_pattern % 1
-
- i = 2
- while os.path.isfile(filename):
- filename = filename_pattern % i
- aname = aname_pattern % i
- htmlname = html_pattern % i
- i = i + 1
-
- self.spectrumInfo["filename"] = filename
- # self.spectrumInfo["scanFileFullPath"] = filename
- self.spectrumInfo["jpegScanFileFullPath"] = aname
- self.spectrumInfo["exposureTime"] = ct
- self.spectrumInfo["annotatedPymcaXfeSpectrum"] = htmlname
- logging.getLogger().debug("XRFSpectrum: archive file is %s", aname)
-
- gevent.spawn(self.reallyStartXrfSpectrum, ct, filename)
-
- return True
-
- def reallyStartXrfSpectrum(self, ct, filename):
-
- if self.doSpectrum:
- try:
- res = self.doSpectrum(ct, filename, wait=True)
- except Exception:
- logging.getLogger().exception("XRFSpectrum: problem calling spec macro")
- self.spectrumStatusChanged("Error problem spec macro")
- else:
- self.spectrumCommandFinished(res)
- else:
- try:
- res = self._doSpectrum(ct, filename, wait=True)
- except Exception:
- logging.getLogger().exception("XRFSpectrum: problem calling procedure")
- self.spectrumStatusChanged("Error problem with spectrum procedure")
- else:
- self.spectrumCommandFinished(res)
-
- def cancelXrfSpectrum(self, *args):
- if self.scanning:
- self.doSpectrum.abort()
-
- def spectrumCommandReady(self):
- if not self.scanning:
- self.emit("xrfSpectrumReady", (True,))
- self.emit("xrfScanReady", (True,))
-
- def spectrumCommandNotReady(self):
- if not self.scanning:
- self.emit("xrfSpectrumReady", (False,))
- self.emit("xrfScanReady", (False,))
-
- def spectrumCommandStarted(self, *args):
- self.spectrumInfo["startTime"] = time.strftime("%Y-%m-%d %H:%M:%S")
- self.scanning = True
- self.emit("xrfSpectrumStarted", ())
- self.emit("xrfScanStarted", ())
-
- def spectrumCommandFailed(self, *args):
- self.spectrumInfo["endTime"] = time.strftime("%Y-%m-%d %H:%M:%S")
- self.scanning = False
- self.storeXrfSpectrum()
- self.emit("xrfSpectrumFailed", ())
- self.emit("xrfScanFailed", ())
- self.ready_event.set()
-
- def spectrumCommandAborted(self, *args):
- self.scanning = False
- self.emit("xrfSpectrumFailed", ())
- self.emit("xrfScanFailed", ())
- self.ready_event.set()
-
- def spectrumCommandFinished(self, result):
- self.spectrumInfo["endTime"] = time.strftime("%Y-%m-%d %H:%M:%S")
- logging.getLogger().debug("XRFSpectrum: XRF spectrum result is %s" % result)
- self.scanning = False
-
- if result:
- try:
- mcaData = self.get_channel_object("mca_data").get_value()
- mcaCalib = self.get_channel_object("calib_data").get_value()
- except Exception:
- mcaData = self.mca_hwobj.read_data(save_data=True)
- mcaCalib = self.mca_hwobj.get_calibration()
- try:
- mcaConfig = self.get_channel_object("config_data").get_value()
- self.spectrumInfo["beamTransmission"] = mcaConfig["att"]
- self.spectrumInfo["energy"] = mcaConfig["energy"]
- self.spectrumInfo["beamSizeHorizontal"] = float(mcaConfig["bsX"])
- self.spectrumInfo["beamSizeVertical"] = float(mcaConfig["bsY"])
- except Exception:
- mcaConfig = {}
- # self.spectrumInfo["beamTransmission"] = self.transmission_hwobj.get_value()
- self.spectrumInfo["energy"] = HWR.beamline.energy.get_value()
- beam_info = HWR.beamline.beam.get_beam_info()
- self.spectrumInfo["beamSizeHorizontal"] = beam_info["size_x"]
- self.spectrumInfo["beamSizeVertical"] = beam_info["size_y"]
- mcaConfig["att"] = self.spectrumInfo["beamTransmission"]
- mcaConfig["energy"] = self.spectrumInfo["energy"]
- mcaConfig["bsX"] = self.spectrumInfo["beamSizeHorizontal"]
- mcaConfig["bsY"] = self.spectrumInfo["beamSizeVertical"]
- roi = self.mca_hwobj.get_roi()
- mcaConfig["min"] = roi["chmin"]
- mcaConfig["max"] = roi["chmax"]
- mcaConfig["legend"] = self.spectrumInfo["annotatedPymcaXfeSpectrum"]
- mcaConfig["htmldir"], _ = os.path.split(mcaConfig["legend"])
- mcaConfig["file"] = self._get_cfgfile(self.spectrumInfo["energy"])
-
- # here move the png file
- pf = self.spectrumInfo["filename"].split(".")
- pngfile = os.path.extsep.join((pf[0], "png"))
- if os.path.isfile(pngfile) is True:
- try:
- copy(pngfile, self.spectrumInfo["jpegScanFileFullPath"])
- except Exception:
- logging.getLogger().error("XRFSpectrum: cannot copy %s", pngfile)
-
- logging.getLogger().debug("finished %r", self.spectrumInfo)
- self.storeXrfSpectrum()
- # self.emit('xrfSpectrumFinished', (mcaData,mcaCalib,mcaConfig))
- self.emit("xrfScanFinished", (mcaData, mcaCalib, mcaConfig))
- else:
- self.spectrumCommandFailed()
- self.ready_event.set()
-
- def spectrumStatusChanged(self, status):
- self.emit("xrfScanStatusChanged", (status,))
- self.emit("spectrumStatusChanged", (status,))
-
- def storeXrfSpectrum(self):
- logging.getLogger().debug("db connection %r", HWR.beamline.lims)
- logging.getLogger().debug("spectrum info %r", self.spectrumInfo)
- if HWR.beamline.lims is None:
- return
- try:
- int(self.spectrumInfo["sessionId"])
- except Exception:
- return
- self.spectrumInfo["blSampleId"]
- self.spectrumInfo.pop("blSampleId")
-
- HWR.beamline.lims.storeXfeSpectrum(self.spectrumInfo)
-
- def updateXrfSpectrum(self, spectrum_id, jpeg_spectrum_filename):
- pass
-
- def getSpectrumParams(self):
- if self.energySpectrumArgs:
- try:
- self.curr = self.energySpectrumArgs.get_value()
- return self.curr
- except Exception:
- logging.getLogger().exception(
- "XRFSpectrum: error getting xrfspectrum parameters"
- )
- self.spectrumStatusChanged("Error getting xrfspectrum parameters")
- return False
- else:
- return True
-
- def setSpectrumParams(self, pars):
- self.energySpectrumArgs.set_value(pars)
-
- def _get_cfgfile(self, energy):
- if energy > 12.0:
- cfgname = "15"
- elif energy > 10.0:
- cfgname = "12"
- elif energy > 7.0:
- cfgname = "10"
- else:
- cfgname = "7"
- return os.path.join(self.cfgpath, "%skeV.cfg" % cfgname)
-
- def _doSpectrum(self, ct, filename, wait=True):
- HWR.beamline.energy.get_value()
- if not ct:
- ct = 5
- safshut = HWR.beamline.safety_shutter
- # stop the procedure if hutch not searched
- stat = safshut.getShutterState()
- if stat == "disabled":
- logging.getLogger("user_level_log").exception(
- "XRFSpectrum: hutch not searched, exiting"
- )
- return False
-
- fluodet_ctrl = self.get_object_by_role("fluodet_ctrl")
- fluodet_ctrl.actuatorIn()
- # open the safety and the fast shutter
- safshut.openShutter()
- init_transm = HWR.beamline.transmission.get_value()
- ret = self._findAttenuation(ct)
- self.ctrl_hwobj.diffractometer.msclose()
- fluodet_ctrl.actuatorOut()
- HWR.beamline.transmission.set_value(init_transm)
- return ret
-
- def _findAttenuation(self, ct):
- tf = [0.1, 0.2, 0.3, 0.9, 1.3, 1.9, 2.6, 4.3, 6, 8, 12, 24, 36, 50, 71]
- min_cnt = self.get_property("min_cnt")
- max_cnt = self.get_property("max_cnt")
- self.mca_hwobj.set_roi(2, 15, channel=1)
- print(self.spectrumInfo["filename"])
- self.mca_hwobj.set_presets(
- erange=1, ctime=ct, fname=self.spectrumInfo["filename"]
- )
-
- # put in max attenuation
- HWR.beamline.transmission.set_value(0)
-
- self.ctrl_hwobj.diffractometer.msopen()
- self.mca_hwobj.start_acq()
- time.sleep(ct)
- ic = sum(self.mca_hwobj.read_roi_data()) / ct
- print(ic)
- if ic > max_cnt:
- self.ctrl_hwobj.diffractometer.msclose()
- logging.getLogger("user_level_log").exception(
- "The detector is saturated, giving up."
- )
- return False
- for i in tf:
- self.mca_hwobj.clear_spectrum()
- logging.getLogger("user_level_log").info("Setting transmission to %g" % i)
- HWR.beamline.transmission.set_value(i)
- self.mca_hwobj.start_acq()
- time.sleep(ct)
- ic = sum(self.mca_hwobj.read_roi_data()) / ct
- print(ic)
- if ic > min_cnt:
- self.ctrl_hwobj.diffractometer.msclose()
- self.spectrumInfo["beamTransmission"] = (
- HWR.beamline.transmission.get_value()
- )
- logging.getLogger("user_level_log").info(
- "Transmission used for spectra: %g"
- % self.spectrumInfo["beamTransmission"]
- )
- break
- self.ctrl_hwobj.diffractometer.msclose()
- if ic < min_cnt:
- logging.getLogger("user_level_log").exception(
- "Could not find satisfactory attenuation (is the mca properly set up?), giving up."
- )
- return False
- return True
diff --git a/mxcubecore/HardwareObjects/ESRF/ID30HutchTrigger.py b/mxcubecore/HardwareObjects/ESRF/ID30HutchTrigger.py
deleted file mode 100644
index 0cc60455cb..0000000000
--- a/mxcubecore/HardwareObjects/ESRF/ID30HutchTrigger.py
+++ /dev/null
@@ -1,113 +0,0 @@
-import logging
-import sys
-import time
-
-import gevent
-import PyTango.gevent
-
-from mxcubecore import BaseHardwareObjects
-
-
-class ID30HutchTrigger(BaseHardwareObjects.HardwareObject):
- def __init__(self, name):
- BaseHardwareObjects.HardwareObject.__init__(self, name)
-
- def _do_polling(self):
- while True:
- try:
- self.poll()
- except Exception:
- sys.excepthook(*sys.exc_info())
- time.sleep(self.get_property("interval") / 1000.0 or 1)
-
- def init(self):
- try:
- self.device = PyTango.gevent.DeviceProxy(self.get_property("tangoname"))
- except PyTango.DevFailed as traceback:
- last_error = traceback[-1]
- logging.getLogger("HWR").error(
- "%s: %s", str(self.name()), last_error["desc"]
- )
- self.device = None
- self.device.imported = False
- else:
- self.device.imported = True
-
- self.pollingTask = None
- self.initialized = False
- self.__oldValue = None
- self.card = None
- self.channel = None
-
- PSSinfo = self.get_property("pss")
- try:
- self.card, self.channel = map(int, PSSinfo.split("/"))
- except Exception:
- logging.getLogger().error("%s: cannot find PSS number", self.name())
- return
-
- if self.device is not None:
- self.pollingTask = gevent.spawn(self._do_polling)
-
- self.connected()
-
- def hutchIsOpened(self):
- return self.hutch_opened
-
- def is_connected(self):
- return True
-
- def connected(self):
- self.emit("connected")
-
- def disconnected(self):
- self.emit("disconnected")
-
- def abort(self):
- pass
-
- def macro(self, entering_hutch, old={"dtox": None, "aperture": None}):
- logging.info(
- "%s: %s hutch", self.name(), "entering" if entering_hutch else "leaving"
- )
- eh_controller = self.get_object_by_role("eh_controller")
- if not entering_hutch:
- if old["dtox"] is not None:
- eh_controller.DtoX.set_value(old["dtox"], wait=False)
- if self.get_object_by_role("aperture") and old["aperture"] is not None:
- self.get_object_by_role("aperture").moveToPosition(old["aperture"])
- self.get_object_by_role("beamstop").moveToPosition("in")
- eh_controller.DtoX.wait_move()
- else:
- old["dtox"] = eh_controller.DtoX.position()
- if self.get_object_by_role("aperture"):
- old["aperture"] = self.get_object_by_role("aperture").get_value()
- eh_controller.DtoX.set_value(700, wait=False)
- if self.get_object_by_role("aperture"):
- self.get_object_by_role("aperture").moveToPosition("Outbeam")
- self.get_object_by_role("beamstop").moveToPosition("out")
- eh_controller.detcover.set_in()
- eh_controller.DtoX.wait_move()
-
- def poll(self):
- a = self.device.GetInterlockState([self.card - 1, 2 * (self.channel - 1)])[0]
- b = self.device.GetInterlockState([self.card - 1, 2 * (self.channel - 1) + 1])[
- 0
- ]
- value = a & b
-
- if value == self.__oldValue:
- return
- else:
- self.__oldValue = value
-
- self.value_changed(value)
-
- def value_changed(self, value, *args):
- if value == 0:
- if self.initialized:
- self.emit("hutchTrigger", (1,))
- elif value == 1 and self.initialized:
- self.emit("hutchTrigger", (0,))
- self.hutch_opened = 1 - value
- self.initialized = True
diff --git a/mxcubecore/HardwareObjects/LimaJungfrauDetector.py b/mxcubecore/HardwareObjects/LimaJungfrauDetector.py
deleted file mode 100644
index 881ecf1f2d..0000000000
--- a/mxcubecore/HardwareObjects/LimaJungfrauDetector.py
+++ /dev/null
@@ -1,217 +0,0 @@
-import logging
-import os
-import subprocess
-import time
-
-import gevent
-
-from mxcubecore.BaseHardwareObjects import HardwareObjectState
-from mxcubecore.CommandContainer import ConnectionError
-from mxcubecore.HardwareObjects.abstract.AbstractDetector import AbstractDetector
-
-
-class LimaJungfrauDetector(AbstractDetector):
- def __init__(self, name):
- AbstractDetector.__init__(self, name)
- self.header = dict()
- self.start_angles = list()
-
- def init(self):
- AbstractDetector.init(self)
- lima_device = self.get_property("lima_device", "")
-
- if not lima_device:
- return
-
- t = lima_device.split("/")
- t[-2] = "mask"
- mask_device = "/".join(t)
-
- try:
- for channel_name in (
- "latency_time",
- "State",
- "acq_status",
- "acq_trigger_mode",
- "saving_mode",
- "acq_nb_frames",
- "acq_expo_time",
- "saving_directory",
- "saving_prefix",
- "saving_suffix",
- "saving_next_number",
- "saving_index_format",
- "saving_format",
- "saving_overwrite_policy",
- "saving_header_delimiter",
- "saving_frame_per_file",
- "last_image_saved",
- "image_roi",
- ):
- self.add_channel(
- {"type": "tango", "name": channel_name, "tangoname": lima_device},
- channel_name,
- )
-
- self.add_channel(
- {"type": "tango", "name": "mask_file", "tangoname": mask_device},
- "MaskFile",
- )
- self.add_channel(
- {"type": "tango", "name": "mask_run_level", "tangoname": mask_device},
- "RunLevel",
- )
- self.add_command(
- {"type": "tango", "name": "start_mask", "tangoname": mask_device},
- "Start",
- )
- self.add_command(
- {"type": "tango", "name": "stop_mask", "tangoname": mask_device},
- "Stop",
- )
-
- self.add_command(
- {"type": "tango", "name": "prepare_acq", "tangoname": lima_device},
- "prepareAcq",
- )
- self.add_command(
- {"type": "tango", "name": "start_acq", "tangoname": lima_device},
- "startAcq",
- )
- self.add_command(
- {"type": "tango", "name": "stop_acq", "tangoname": lima_device},
- "stopAcq",
- )
- self.add_command(
- {"type": "tango", "name": "reset", "tangoname": lima_device}, "reset"
- )
- self.add_command(
- {"type": "tango", "name": "set_image_header", "tangoname": lima_device},
- "SetImageHeader",
- )
-
- # prepareAcq can block after large data transfers (buffered by GPFS): 2 min timeout
- self.get_command_object("prepare_acq").set_device_timeout(2 * 60 * 1000)
- self._emit_status()
-
- except ConnectionError:
- self.update_state(HardwareObjectState.FAULT)
- logging.getLogger("HWR").error(
- "Could not connect to detector %s" % lima_device
- )
- self._emit_status()
-
- def has_shutterless(self):
- return True
-
- def wait_ready(self, timeout=3500):
- with gevent.Timeout(timeout, RuntimeError("Detector not ready")):
- while self.get_channel_value("acq_status") != "Ready":
- time.sleep(1)
-
- def last_image_saved(self):
- try:
- img = self.get_channel_object("last_image_saved").get_value() + 1
- return img
- except Exception:
- return 0
-
- def get_deadtime(self):
- return float(self.get_property("deadtime"))
-
- def prepare_acquisition(self, number_of_images, exptime, data_root_path, prefix):
- self.set_channel_value("acq_trigger_mode", "EXTERNAL_TRIGGER_MULTI")
-
- self.set_channel_value("acq_nb_frames", number_of_images)
- self.set_channel_value("acq_expo_time", exptime)
- self.set_channel_value("latency_time", 990e-6)
- self.set_channel_value("saving_frame_per_file", 1000)
-
- mask_file = self.get_property("mask_file", None)
-
- if mask_file:
- self.set_channel_value("mask_file", mask_file)
-
- self.set_channel_value("mask_run_level", 0)
-
- self.set_detector_filenames(data_root_path, prefix)
-
- def find_next_pedestal_dir(self, data_root_path, subdir):
- _index = 1
- _indes_str = "%04d" % _index
- fpath = os.path.join(data_root_path, f"{subdir}_{_indes_str}")
-
- while os.path.exists(fpath):
- _index += 1
- _indes_str = "%04d" % _index
- fpath = os.path.join(data_root_path, f"{subdir}_{_indes_str}")
-
- return fpath
-
- def set_detector_filenames(self, data_root_path, prefix):
- subprocess.Popen(
- "mkdir --parents %s" % (data_root_path),
- shell=True,
- stdin=None,
- stdout=None,
- stderr=None,
- close_fds=True,
- ).wait()
-
- subprocess.Popen(
- "chmod -R 755 %s" % (data_root_path),
- shell=True,
- stdin=None,
- stdout=None,
- stderr=None,
- close_fds=True,
- ).wait()
-
- self.set_channel_value("saving_mode", "AUTO_FRAME")
- self.set_channel_value("saving_directory", data_root_path)
- self.set_channel_value("saving_prefix", prefix)
- self.set_channel_value("saving_format", "HDF5BS")
-
- def start_acquisition(self):
- self.wait_ready()
- self.execute_command("stop_acq")
- self.execute_command("start_mask")
- self.execute_command("prepare_acq")
- self.execute_command("start_acq")
- self._emit_status()
-
- def stop_acquisition(self):
- try:
- self.execute_command("stop_acq")
- except Exception:
- pass
- finally:
- self.wait_ready()
- self.execute_command("reset")
- self.wait_ready()
- self.execute_command("stop_mask")
-
- self._emit_status()
-
- def reset(self):
- self.stop_acquisition()
-
- @property
- def status(self):
- try:
- acq_status = self.get_channel_value("acq_status")
- except Exception:
- acq_status = "OFFLINE"
-
- status = {
- "acq_satus": acq_status.upper(),
- }
-
- return status
-
- def _emit_status(self):
- self.emit("statusChanged", self.status)
-
- def restart(self) -> None:
- self.reset()
- return None
diff --git a/mxcubecore/HardwareObjects/MicrodiffActuator.py b/mxcubecore/HardwareObjects/MicrodiffActuator.py
index f7314293fc..cc9691f828 100644
--- a/mxcubecore/HardwareObjects/MicrodiffActuator.py
+++ b/mxcubecore/HardwareObjects/MicrodiffActuator.py
@@ -3,7 +3,7 @@
If private_state not specified, True will be send to set in and False for out.
Example xml file: