Startup
This commit is contained in:
514
script/__Lib/diffutils_new.py
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514
script/__Lib/diffutils_new.py
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###################################################################################################\
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# Diffcalc utilities
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###################################################################################################
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###################################################################################################\
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# Installaling
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###################################################################################################
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#1- Download from: https://github.com/DiamondLightSource/diffcalc/archive/master.zip
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#2- Extract the contents to {script}/Lib/diffcalc
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#3- Download http://central.maven.org/maven2/gov/nist/math/jama/1.0.3/jama-1.0.3.jar
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# to the extensions folder.
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###################################################################################################\
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# Library loading and Hardware setup
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###################################################################################################
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#1- Create a MotorGroup with the diffractometer motors
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# e.g. 'sixc', containing mu, delta, gam, eta, chi, phi motors (gam = nu)
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# or 'fivec', containing delta, gam, eta, chi, phi motors
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# or 'fourc', containing delta, eta, chi, phi motors
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#2- Create positioner to read/set the energy in kEv, e.g. named 'en'
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#3- Execute: run("diffutils")
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#4- Execute: setup_diff(sixc, en)
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from __future__ import absolute_import
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import traceback
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import Jama.Matrix
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#diffcalc_path = os.path.abspath(get_context().setup.expandPath("{script}/Lib/diffcalc"))
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diffcalc_path = os.path.abspath(get_context().setup.expandPath("{script}/Lib/diffcalc_new"))
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if not diffcalc_path in sys.path:
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sys.path.append(diffcalc_path)
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import diffcalc
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from diffcalc import settings
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from diffcalc.hkl.you.geometry import YouGeometry,SixCircle, FiveCircle, FourCircle, YouPosition
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from diffcalc.hardware import HardwareAdapter
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from diffcalc.ub.persistence import UbCalculationNonPersister
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from diffcalc.gdasupport.minigda.scannable import ScannableBase, ScannableGroup
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#from diffcalc.gdasupport.minigda import command
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from diffcalc.hardware import HardwareAdapter
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import ch.psi.pshell.device.PositionerConfig as PositionerConfig
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import ch.psi.pshell.device.RegisterConfig as RegisterConfig
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import ch.psi.pshell.device.Register as Register
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_difcalc_names = {}
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#
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# Disable error handling designed for interactive use
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#diffcalc.util.DEBUG = True
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###################################################################################################
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# Device mapping to difcalc
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###################################################################################################
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class PositionerScannable(ScannableBase):
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def __init__(self, positioner, name = None):
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self.positioner = positioner
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self.name = positioner.name if name is None else name
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self.inputNames = [self.name]
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self.outputFormat = ['% 6.4f']
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self.level = 3
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def isBusy(self):
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return self.positioner.state == State.Busy
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def waitWhileBusy(self):
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self.positioner.waitReady(-1)
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def asynchronousMoveTo(self, new_position):
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#print "Moving " , self.name, " to: ", new_position
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self.positioner.moveAsync(float(new_position), -1)
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def getPosition(self):
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return self.positioner.getPosition()
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def _get_diffcalc_axis_names():
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nu_name=diffcalc.hkl.you.constraints.NUNAME
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return ("mu", "delta", nu_name, "eta", "chi", "phi")
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class PositionerScannableGroup(ScannableGroup):
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def __init__(self, name, motors, diffcalc_axis_names=None):
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self.name = name
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global _difcalc_names
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_difcalc_names = {}
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positioners = []
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if diffcalc_axis_names is None:
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if len(motors) == 6: diffcalc_axis_names = _get_diffcalc_axis_names()
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elif len(motors) == 5: diffcalc_axis_names = ("delta", "gam", "eta", "chi", " phi")
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elif len(motors) == 4: diffcalc_axis_names = ("delta", "eta", "chi", " phi")
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self.diffcalc_axis_names = diffcalc_axis_names
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for i in range(len(motors)):
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_difcalc_names[motors[i]] = diffcalc_axis_names[i]
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exec('self.' + diffcalc_axis_names[i] + ' = PositionerScannable(' + motors[i].name + ', "' +diffcalc_axis_names[i] + '")')
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exec('positioners.append(self.' + diffcalc_axis_names[i] + ')' )
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#for m in motors:
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# exec('self.' + m.name + ' = PositionerScannable(' + m.name + ', "' + m.name + '")')
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# exec('positioners.append(self.' + m.name + ')' )
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ScannableGroup.__init__(self, self.name, positioners)
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class MotorGroupScannable(PositionerScannableGroup):
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def __init__(self, motor_group, diffcalc_axis_names=None):
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self.motor_group = motor_group
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PositionerScannableGroup.__init__(self, motor_group.name, motor_group.motors, diffcalc_axis_names)
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class ScannableAdapter(HardwareAdapter):
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def __init__(self, diffractometer, energy, energy_multiplier_to_kev=1):
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self.diffractometer = diffractometer
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self.energy = energy
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self.energy_multiplier_to_kev = energy_multiplier_to_kev
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input_names = diffractometer.getInputNames()
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HardwareAdapter.__init__(self, input_names)
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#Returns the current physical POSITIONS
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def get_position(self):
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"""
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pos = getDiffractometerPosition() -- returns the current physical
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diffractometer position as a list in degrees
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"""
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return self.diffractometer.getPosition()
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#returns energy in kEv
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def get_energy(self):
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"""energy = get_energy() -- returns energy in kEv (NOT eV!) """
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multiplier = self.energy_multiplier_to_kev
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energy = self.energy.getPosition() * multiplier
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if energy is None:
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raise DiffcalcException("Energy has not been set")
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return energy
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def get_motor(self,name):
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global _motor_group
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global _difcalc_names
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for m in _difcalc_names.keys():
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if _difcalc_names[m] == name:
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return m
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for m in _motor_group.motors:
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if m.name == name:
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return m
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raise Exception("Invalid axis name: " + str(name))
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def get_lower_limit(self, name):
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'''returns lower limits by axis name. Limit may be None if not set
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'''
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m = self.get_motor(name)
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ret = m.getMinValue()
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if ret == float("NaN"): ret = None
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return ret
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def get_upper_limit(self, name):
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'''returns upper limit by axis name. Limit may be None if not set
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'''
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m = self.get_motor(name)
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ret = m.getMaxValue()
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if ret == float("NaN"): ret = None
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return ret
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def set_lower_limit(self, name, value):
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"""value may be None to remove limit"""
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if value is None: value = float("NaN")
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m = self.get_motor(name)
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m.config.minValue =value
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def set_upper_limit(self, name, value):
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"""value may be None to remove limit"""
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if value is None: value = float("NaN")
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m = self.get_motor(name)
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m.config.maxValue =value
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def is_axis_value_within_limits(self, axis_name, value):
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m = self.get_motor(axis_name)
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upper = self.get_upper_limit(axis_name)
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lower = self.get_lower_limit(axis_name)
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if upper is None: upper = sys.float_info.max
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if lower is None: lower = sys.float_info.min
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return lower <= value <= upper
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@property
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def name(self):
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return self.diffractometer.getName()
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class MotorGroupAdapter(ScannableAdapter):
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def __init__(self, diffractometer, energy, energy_multiplier_to_kev=1, diffcalc_axis_names=None):
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self.diffractometer = MotorGroupScannable(diffractometer, diffcalc_axis_names)
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self.energy = PositionerScannable(energy)
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self.energy.level = 3
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ScannableAdapter.__init__(self, self.diffractometer, self.energy, energy_multiplier_to_kev)
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class Wavelength(RegisterBase):
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def doRead(self):
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try:
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return get_wavelength().getPosition()
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except:
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return None
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def doWrite(self, val):
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get_wavelength().asynchronousMoveTo(val)
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###################################################################################################
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# HKL Pseudo-devices
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###################################################################################################
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class HklPositoner (PositionerBase):
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def __init__(self, name, index, hkl_group):
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PositionerBase.__init__(self, name, PositionerConfig())
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self.setParent(hkl_group)
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self.index = index
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def isReady(self):
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return PositionerBase.isReady(self) and self.getParent().isReady()
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def doRead(self):
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return self.getParent()._setpoint[self.index]
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def doWrite(self, value):
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#print "Setting " , self.getName(), "to: ", value
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pos = [None, None, None]
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pos[self.index] = value
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self.getParent().write(pos)
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def doReadReadback(self):
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if java.lang.Thread.currentThread() != self.getParent()._updating_thread:
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self.getParent().update()
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return self.getParent()._readback[self.index]
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class HklGroup(RegisterBase, Register.RegisterArray):
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def __init__(self, name):
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RegisterBase.__init__(self, name, RegisterConfig())
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self.hkl=get_hkl()
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self.h, self.k, self.l = HklPositoner("h", 0, self), HklPositoner("k", 1, self), HklPositoner("l", 2, self)
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add_device(self.h, True)
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add_device(self.k, True)
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add_device(self.l, True)
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self._setpoint = self.doRead()
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self._updating = False
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def getSize(self):
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return 3
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def doRead(self):
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try:
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self._readback = self.hkl.getPosition()
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self._updating_thread = java.lang.Thread.currentThread()
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self.h.update()
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self.k.update()
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self.l.update()
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except:
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#traceback.print_exc()
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self._readback = (None, None, None)
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finally:
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self._updating_thread = None
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return self._readback
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def doWrite(self, pos):
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self._setpoint = pos
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#print "Moving to: " + str(pos)
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self.hkl.asynchronousMoveTo(pos)
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def sim(self, pos):
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return self.hkl.simulateMoveTo(pos)
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###################################################################################################
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# System setup
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###################################################################################################
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you = None
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dc, ub, hardware, hkl = None, None, None, None
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_motor_group = None
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def setup_diff(diffractometer, energy, diffcalc_axis_names = None, geometry=None):
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"""
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diffractometer: Diffraction motor group
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energy: Positioner having energy in kev
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geometry: YouGeometry extension. If none, uses default
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diffcalc_axis_names: if None use defaults:
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- mu, delta, gam, eta, chi, phi (six circle)
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- delta, gam, eta, chi, phi (ficve circle)
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- delta, eta, chi, phi (four circle)
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"""
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global you, dc, ub, hardware, hkl, _motor_group
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_motor_group = diffractometer
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you = None
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if geometry is not None:
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settings.geometry = geometry
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elif diffcalc_axis_names is not None:
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class CustomGeometry(YouGeometry):
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def __init__(self):
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self.all_axis_names = _get_diffcalc_axis_names()
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self.my_axis_names = diffcalc_axis_names
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fixed_constraints = {}
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for axis in self.all_axis_names:
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if not axis in self.my_axis_names:
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fixed_constraints[axis] = 0
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YouGeometry.__init__(self, diffractometer.name, fixed_constraints)
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def physical_angles_to_internal_position(self, physical_angle_tuple):
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pos=[]
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index = 0
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for axis in self.all_axis_names:
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pos.append(physical_angle_tuple[index] if (axis in self.my_axis_names) else 0)
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index = index+1
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pos.append("DEG")#units
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return YouPosition(*pos)
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def internal_position_to_physical_angles(self, internal_position):
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#pos = internal_position.totuple()
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pos = internal_position.clone()
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pos.changeToDegrees()
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pos = pos.totuple()
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ret = []
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for i in range (len(self.all_axis_names)):
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if self.all_axis_names[i] in self.my_axis_names:
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ret.append(pos[i])
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return tuple(ret)
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settings.geometry = CustomGeometry()
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elif len(diffractometer.motors) == 6:
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settings.geometry = SixCircle()
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elif len(diffractometer.motors) == 5:
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settings.geometry = FiveCircle()
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elif len(diffractometer.motors) == 4:
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settings.geometry = FourCircle()
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else:
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raise Exception("Invalid motor group")
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settings.hardware = MotorGroupAdapter(diffractometer, energy, diffcalc_axis_names = diffcalc_axis_names)
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settings.ubcalc_persister = UbCalculationNonPersister()
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settings.axes_scannable_group = settings.hardware.diffractometer
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settings.energy_scannable = settings.hardware.energy
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settings.ubcalc_strategy = diffcalc.hkl.you.calc.YouUbCalcStrategy()
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settings.angles_to_hkl_function = diffcalc.hkl.you.calc.youAnglesToHkl
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from diffcalc.gdasupport import you
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reload(you)
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# These must be imported AFTER the settings have been configured
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from diffcalc.dc import dcyou as dc
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from diffcalc.ub import ub
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from diffcalc import hardware
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from diffcalc.hkl.you import hkl
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add_device(HklGroup("hkl_group"), True)
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add_device(Wavelength("wavelength", 6), True)
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hkl_group.polling = 250
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wavelength.polling = 250
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def setup_axis(motor, min=None, max=None, cut=None):
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name = _difcalc_names[motor]
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if min is not None: hardware.setmin(name, min)
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if max is not None: hardware.setmax(name, max)
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if cut is not None: hardware.setcut(name, cut)
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def print_axis_setup():
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print "Diffcalc names:"
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for m in _difcalc_names.keys():
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print " \t" + m.name + " = " + _difcalc_names[m]
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print "------------------------------------------------------"
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hardware.hardware()
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###################################################################################################
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# Acceess functions
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###################################################################################################
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def get_diff():
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return settings.hardware.diffractometer
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def get_en():
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return settings.hardware.energy
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def get_motor_group():
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return _motor_group
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def get_wavelength():
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return you.wl
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def get_hkl():
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return you.hkl
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def hkl_to_angles(h, k, l, energy=None):
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return dc.hkl_to_angles(h, k, l, energy)
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def angles_to_hkl(positions, energy=None):
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return dc.angles_to_hkl(positions, energy)
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def hkl_read():
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return hkl_group.read()
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def hkl_write(h, k, l):
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hkl_group.write([h,k,l])
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def hkl_simulate(h, k, l):
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return hkl_group.sim([h,k,l])
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def con(*args):
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hkl.con(*args)
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def uncon(name):
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hkl.uncon(name)
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def print_con():
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hkl.con()
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def get_ub_matrix():
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return ub.ubcalc._UB.tolist()
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###################################################################################################
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||||
# HKL Combined Scan
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###################################################################################################
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def hklscan(vector, readables,latency = 0.0, passes = 1, **pars):
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"""
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HKL Scan:
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Args:
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vector(list of lists): HKL values to be scanned
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readables(list of Readable): Sensors to be sampled on each step.
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latency(float, optional): settling time for each step before readout, defaults to 0.0.
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passes(int, optional): number of passes
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pars(keyworded variable length arguments, optional): scan optional named arguments:
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- title(str, optional): plotting window name.
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- hidden(bool, optional): if true generates no effects on user interface.
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- before_read (function, optional): callback on each step, before sampling. Arguments: positions, scan
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- after_read (function, optional): callback on each step, after sampling. Arguments: record, scan.
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- before_pass (function, optional): callback before each scan pass execution. Arguments: pass_num, scan.
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- after_pass (function, optional): callback after each scan pass execution. Arguments: pass_num, scan.
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- Aditional arguments defined by set_exec_pars.
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Returns:
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ScanResult object.
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"""
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readables=to_list(string_to_obj(readables))
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pars["initial_move"] = False
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scan = ManualScan([h,k,l], readables ,vector[0], vector[-1], [len(vector)-1] * 3, dimensions = 1)
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if not "domain_axis" in pars.keys():
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pars["domain_axis"] = "Index"
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processScanPars(scan, pars)
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||||
scan.start()
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||||
try:
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||||
for pos in vector:
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||||
#print "Writing ", pos
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||||
hkl_group.write(pos)
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||||
time.sleep(0.1) #Make sure is busy
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||||
get_motor_group().update()
|
||||
get_motor_group().waitReady(-1)
|
||||
time.sleep(latency)
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||||
hkl_group.update()
|
||||
scan.append ([h.take(), k.take(), l.take()], [h.getPosition(), k.getPosition(), l.getPosition()], [readable.read() for readable in readables ])
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||||
finally:
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||||
scan.end()
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||||
return scan.result
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||||
|
||||
|
||||
def test_diffcalc():
|
||||
print "Start test"
|
||||
en.move(20.0)
|
||||
delta.config.maxSpeed = 50.0
|
||||
delta.speed = 50.0
|
||||
delta.move(1.0)
|
||||
|
||||
#Setup
|
||||
setup_diff(sixc, en)
|
||||
setup_axis('gam', 0, 179)
|
||||
setup_axis('delta', 0, 179)
|
||||
setup_axis('delta', min=0)
|
||||
setup_axis('phi', cut=-180.0)
|
||||
print_axis_setup()
|
||||
|
||||
#Orientation
|
||||
help(ub.ub)
|
||||
ub.listub()
|
||||
# Create a new ub calculation and set lattice parameters
|
||||
ub.newub('test')
|
||||
ub.setlat('cubic', 1, 1, 1, 90, 90, 90)
|
||||
# Add 1st reflection (demonstrating the hardware adapter)
|
||||
settings.hardware.wavelength = 1
|
||||
ub.c2th([1, 0, 0]) # energy from hardware
|
||||
settings.hardware.position = 0, 60, 0, 30, 0, 0
|
||||
ub.addref([1, 0, 0])# energy and position from hardware
|
||||
# Add 2nd reflection (this time without the harware adapter)
|
||||
ub.c2th([0, 1, 0], 12.39842)
|
||||
ub.addref([0, 1, 0], [0, 60, 0, 30, 0, 90], 12.39842)
|
||||
# check the state
|
||||
ub.ub()
|
||||
ub.checkub()
|
||||
|
||||
#Constraints
|
||||
help(hkl.con)
|
||||
hkl.con('qaz', 90)
|
||||
hkl.con('a_eq_b')
|
||||
hkl.con('mu', 0)
|
||||
hkl.con()
|
||||
|
||||
#Motion
|
||||
print angles_to_hkl((0., 60., 0., 30., 0., 0.))
|
||||
print hkl_to_angles(1, 0, 0)
|
||||
sixc.write([0, 60, 0, 30, 90, 0])
|
||||
print "sixc=" , sixc.position
|
||||
wavelength.write(1.0)
|
||||
print "wavelength = ", wavelength.read()
|
||||
ub.lastub()
|
||||
ub.setu ([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
|
||||
ub.showref()
|
||||
ub.swapref(1,2)
|
||||
#print you.hkl
|
||||
#pos(get_hkl())
|
||||
hkl_group.read()
|
||||
#you.hkl.simulateMoveTo([0,1,1])
|
||||
#sim(get_hkl(), [0,1,1])
|
||||
hkl_group.sim([0.0,1.0,1.0])
|
||||
#pos(get_hkl(), [0,1,1])
|
||||
hkl_group.write([0.0,1.0,1.0])
|
||||
|
||||
#Scans
|
||||
lscan(l, [sin], 1.0, 1.5, 0.1)
|
||||
ascan([k,l], [sin], [1.0, 1.0], [1.2, 1.3], [0.1, 0.1], zigzag=True, parallel_positioning = False)
|
||||
vector = [[1.0,1.0,1.0], [1.0,1.0,1.1], [1.0,1.0,1.2], [1.0,1.0,1.4]]
|
||||
hklscan(vector, [sin, arr], 0.9)
|
||||
Reference in New Issue
Block a user