def getScanAngles(self, scan, angleNames):
"""
This function returns all of the geometry angles for the
for the scan as a N-by-num_geo array, where N is the number of scan
points and num_geo is the number of geometry motors.
:param scan: scan from which to retrieve the angles
:params angleNames: a list of names for the angles to be returned
"""
try:
dataKeys = scan.data.keys()
except IndexError as ie:
logger.exception(str(ie) )
raise ie
except Exception as ex:
logger.exception(str(ex) + "at scan " + str(scan.scanNum))
raise ex
if len(dataKeys) == 0:
raise ScanDataMissingException("No Scan Data Found for scan " +
scan.scanNum)
geoAngles = np.zeros((len(scan.data[dataKeys[0]]), len(angleNames)))
for i, name in enumerate(angleNames):
v = scan.data.get(name)
p = scan.positioner.get(name)
if v != None:
if len(v) == 1:
v = np.ones(len(scan.data[scan.data.keys()[0]])) * v
elif p != None:
v = np.ones(len(scan.data[scan.data.keys()[0]])) * p
else:
raise InstConfigException("Could not find angle " + name + \
" in scan parameters")
geoAngles[:,i] = v
return geoAngles
def getSampleAngleMappingPrimaryAngles(self):
'''
:return: The name of a function to be used in mapping
'''
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " +\
"instrument config file")
angles = []
primaryAngles = function.findall(PRIMARY_ANGLE)
if primaryAngles is None:
raise InstConfigException("No primaryAngle members in " + \
"sampleAngleMapFunction in instrument config")
for angle in primaryAngles:
angles.append(int(angle.attrib[AXIS_NUMBER]))
angles.sort()
return angles
def __init__(self, filename):
'''
'''
self.root = None
try:
tree = ET.parse(filename)
except IOError as ex:
raise (InstConfigException("Bad Instrument Configuration File" + str(ex)))
self.root = tree.getroot()
def getPrimaryBeamDirection(self):
'''
:return: The direction of primary beam
'''
direction = \
self.root.find(PRIMARY_BEAM_DIRECTION)
if direction is None:
raise InstConfigException("Missing primary beam direction " + \
"in instrument config file")
return self._makeReferenceDirection(direction )
def getDetectorCircles(self):
'''
:return: The detector children as and element list. If detector circles
is not included in the file raise an InstConfigException
'''
circles = self.root.find(DETECTOR_CIRCLES)
if circles is None:
raise InstConfigException("Instrument configuration has no " +\
"Detector Circles")
return self.root.find(DETECTOR_CIRCLES).getchildren()
def getSampleAngleMappingReferenceAngles(self):
'''
'''
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " + \
"instrument config file")
angles = {}
angleList = []
referenceAngles = function.findall(REFERENCE_ANGLE)
if referenceAngles is None:
raise InstConfigException("No referenceAngle members in " + \
"sampleAngleMapFunction in instrument config")
for angle in referenceAngles:
angles[int(angle.attrib[AXIS_NUMBER])] = \
angle.attrib[SPEC_MOTOR_NAME]
for i in angles.keys():
angleList.append(angles[i])
return angleList
def getSampleSurfaceNormalDirection(self):
'''
:return: The sample surface normal direction as a list of 3 numbers
'''
direction = \
self.root.find(SAMPLE_SURFACE_NORMAL_DIRECTION)
if direction is None:
raise InstConfigException("Missing sample surface normal " + \
"direction in instrument config file")
return self._makeReferenceDirection(direction )
def getInplaneReferenceDirection(self):
'''
:return: The In-plane reference direction
'''
direction = \
self.root.find(INPLANE_REFERENCE_DIRECTION)
if direction is None:
raise InstConfigException("Missing in-plane reference direction " + \
"in instrument config file")
return self._makeReferenceDirection(direction )
def getSampleCircles(self):
'''
:return: The sample children as and element list. If sample circles
is not included in the file raise an InstConfigException
'''
circles = self.root.find(SAMPLE_CIRCLES)
if circles is None:
raise InstConfigException("Instrument configuration has no Sample" +
" Circles")
return circles.getchildren()
def getCircleAxisNumber(self, circle):
'''
:param circle: specifies the detector who's return value is requested
:return: The axis number for the given circle
'''
try:
axisNumberStr = circle.attrib[AXIS_NUMBER]
except KeyError:
raise InstConfigException("Axis number is empty in \n" + \
ET.tostring(circle) + \
"\nIn the instrument config file")
return int(axisNumberStr)
def _makeReferenceDirection(self, direction):
'''
Create a list of reference directions from the XML
:param direction: the XML representation of the circle
'''
axes = direction.findall(REFERENCE_AXIS)
if len(axes) != 3:
raise InstConfigException("Axes not defined properly in \n" + \
ET.tostring(direction) + \
"\nin instrument config file")
refAxis = {}
for axis in axes:
try:
refAxis[int(axis.attrib[AXIS_NUMBER])] = int(axis.text)
except ValueError:
raise InstConfigException("Values and axis numbers in " + \
ET.tostring(direction) + \
" in instrument configuration file")
return [refAxis[1], refAxis[2], refAxis[3]]
def getProjectionDirection(self):
'''
:return: The direction to be used for constructing Stereographic
projections.
'''
direction = \
self.root.find(PROJECTION_DIRECTION)
if direction is None:
message = PROJECTION_DIRECTION + \
" was not found in the instrument config file"
raise InstConfigException(message)
return self._makeReferenceDirection(direction )
def getSampleAngleMappingAlwaysFix(self):
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " + \
"instrument config file")
alwaysFix = None
try:
alwaysFix = function.attrib[ALWAYS_FIX]
if alwaysFix is None:
return False
except KeyError:
alwaysFix = False
return bool(alwaysFix)
def getSampleAngleMappingCalcOnScannedRef(self):
'''
:return: true to run mapping function only when a reference angle is
scanned
'''
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " + \
"instrument config file")
if function.attrib[CALC_ON_SCANNED_REF] is None:
return False
else:
if function.attrib[CALC_ON_SCANNED_REF].lower() in \
['true', '1', 'yes']:
return True
elif function.attrib[CALC_ON_SCANNED_REF].lower() in \
['false', '0', 'no']:
return False
else:
raise InstConfigException("Error reading value for " + \
"'calcOnScannedRef' from Instrument " + \
"Config : " + \
str(function.attrib[CALC_ON_SCANNED_REF]))
def getSampleAngleMappingReferenceAngleAttrib(self, \
number=None, \
attribName=None):
attribValue = None
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " +\
"instrument config file")
refAngles = function.findall(REFERENCE_ANGLE)
for angle in refAngles:
if angle.attrib[SPEC_MOTOR_NAME] == str(number):
attribValue = angle.attrib[attribName]
if (attribValue is None):
raise(AttributeError("Angle " + str(number) +
" does not have a value for " +
str(attribName)))
return attribValue
def getSampleAngleMappingFunctionModule(self):
'''
:return: The name of a function to be used in mapping
'''
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " +\
"instrument config file")
try:
module = function.attrib[SAMPLE_ANGLE_MAP_MODULE]
except KeyError:
module = None
if module != None and module != "":
print ("Found Module %s" % module)
return module
else:
return None
def getSampleAngleMappingParameter(self, name):
'''
Return a named parameter to be used by the mapping function. This
parameter is unique to the mapping function. This method returns a
string parameter which must be properly cast by the mapping function.
Mapping function needs to deal with error cases. None is returned if
the named parameter is not defined.
:param: name Name of the defined parameter
:return: Parameter defined by the XML element 'name'
'''
function = self.root.find(SAMPLE_ANGLE_MAP_FUNCTION)
if function is None:
raise InstConfigException("No Mapping function defined in " +\
"instrument config file")
param = function.find(NAMESPACE + name)
if param != None and param.text != "":
return param.text
else:
return None
def _makeCircleNames(self, circles):
'''
Create a list of circle names from the XML
:param circles: the XML representation of the circles
'''
data = []
for circle in circles:
try:
motorName = circle.attrib[SPEC_MOTOR_NAME]
axisNumber = circle.attrib[AXIS_NUMBER]
except KeyError:
raise InstConfigException("missing axis number or " + \
"motorName in\n" + \
ET.tostring(circle) + \
"\nIn the instrument config file")
data.append((int(axisNumber), \
motorName))
data.sort()
names = []
for dataum in data:
names.append(dataum[1])
return names
def _makeCircleDirections(self, circles):
'''
Create a list of circle directions from the XML
:param circles: the XML representation of the circles
'''
data = []
for circle in circles:
try:
axisNum = circle.attrib[AXIS_NUMBER]
directionAxis = circle.attrib[DIRECTION_AXIS]
except KeyError:
raise InstConfigException("missing axis number or " + \
"axis direction in\n" + \
ET.tostring(circle) + \
"\nIn the instrument config file")
data.append((int(axisNum), \
directionAxis))
data.sort()
directions = []
for dataum in data:
directions.append(dataum[1])
return directions
