def setup(self, _listInput=[], _mode="offline"):
"""Configure the various options"""
bOK = False
if _listInput == []:
_listInput = [os.getcwd()]
while not bOK:
strtmp = raw_input(
"What are the input directories (mandatory, space separated) %s: "
% _listInput).strip()
if len(strtmp) > 0:
bAllExists = True
lstTemp = shlex.split(strtmp)
for oneDir in shlex.split(strtmp):
if not os.path.exists(oneDir):
EDVerbose.screen("No such file or directory: %s" %
oneDir)
bAllExists = False
if bAllExists is True:
self.listInput = lstTemp
bOK = True
else:
self.listInput = _listInput
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is operation mode [offline|online|all] (mandatory: %s): "
% _mode).strip().lower()
if len(strtmp) > 0:
bOK = True
if strtmp == "offline":
self.bNewerOnly = False
self.strMode = "OffLine"
elif strtmp == "online":
self.bNewerOnly = True
self.strMode = "dirwatch"
elif strtmp == "all":
self.bNewerOnly = False
self.strMode = "dirwatch"
else:
bOK = False
bOK = False
while not bOK:
strtmp = raw_input(
"What is the destination directory (mandatory): ").strip()
if os.path.isdir(strtmp):
self.destinationDirectory = XSDataFile()
self.destinationDirectory.setPath(
XSDataString(os.path.abspath(strtmp)))
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is the sinogram filename prefix (mandatory): ").strip()
if strtmp != "":
self.sinogramFileNamePrefix = XSDataString(strtmp)
bOK = True
bOK = False
while not bOK:
strtmp = raw_input(
"What is the powder diffraction subdirectory (mandatory): "
).strip()
if strtmp != "":
self.powderDiffractionSubdirectory = XSDataString(strtmp)
bOK = True
strtmp = raw_input(
"What is the powder diffraction output format (CHI or CIF, if any ): "
).strip().lower()
if strtmp.find("cif") >= 0:
self.powderDiffractionFormat = XSDataString("cif")
elif strtmp.find("chi") >= 0:
self.powderDiffractionFormat = XSDataString("chi")
strtmp = raw_input("Process all files ending with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExtensions.append(oneExt)
strtmp = raw_input("Exclude all files starting with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExcludedPrefix.append(oneExt)
strtmp = raw_input(
"Do you want to over-ride metadata from the headers [y|N]: "
).strip().lower()
if len(strtmp) > 0 and strtmp[0] == "y":
strtmp = raw_input("What is the flat field image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
flatFieldImage = XSDataFile()
flatFieldImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_flat_field(
flatFieldImage)
strtmp = raw_input("What is the dark current image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
darkCurrentImage = XSDataFile()
darkCurrentImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_dark_current(
darkCurrentImage)
strtmp = raw_input("What is the mask file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
maskFile = XSDataFile()
maskFile.setPath(XSDataString(strtmp))
self.forceImage.set_file_correction_image_mask(maskFile)
strtmp = raw_input("What is the spline file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
splineFile = XSDataFile()
splineFile.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_spline_spatial_distortion(
splineFile)
strtmp = raw_input(
"What is the wavelength (like 0.7 A): ").replace(
"(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
wavelength = XSDataWavelength()
wavelength.setValue(f)
if len(w) == 2:
wavelength.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_diffrn_radiation_wavelength(
wavelength)
strtmp = raw_input(
"What is the distance between the sample and the detector along the beam: "
).replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
distance = XSDataLength()
distance.setValue(f)
if len(w) == 2:
distance.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_pd_instr_dist_spec_detc(distance)
strtmp = raw_input(
"What is the pixel size (like 52.8 um 53.2 um): ").replace(
"(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_array_element_size_1(xsdata1)
self.forceImage.set_array_element_size_2(xsdata2)
strtmp = raw_input(
"What is the beam center in distance, not pixels (like 53.5 mm 48.2 mm): "
).strip().replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError, IndexError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_diffrn_detector_element_center_1(
xsdata1)
self.forceImage.set_diffrn_detector_element_center_2(
xsdata2)
strtmp = raw_input("What is the detector tilt angle: ").strip()
tiltAngle = None
try:
tiltAngle = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_angle(
tiltAngle)
strtmp = raw_input("What is the tilt plan rotation: ").strip()
tiltRotation = None
try:
tiltRotation = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_rotation(
tiltRotation)
strtmp = raw_input(
"What is the number of fast motor steps (you will have n+1 points): "
).strip()
try:
self.fastMotorSteps = int(strtmp)
except ValueError:
fastMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_spec_displ_x_max(
XSDataLength(self.fastMotorSteps))
self.forceInstrument.set_tomo_spec_displ_x_min(XSDataLength(0))
self.forceInstrument.set_tomo_spec_displ_x_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input(
"What is the number of slow motor steps (you will have n+1 points): "
).strip()
try:
self.slowMotorSteps = int(strtmp)
except ValueError:
self.slowMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_scan_ampl(
XSDataLength(self.slowMotorSteps))
self.forceInstrument.set_tomo_spec_displ_rotation_inc(
XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input(
"What is the index offset of your images: ").strip()
try:
self.indexOffset = int(strtmp)
except ValueError:
print("unable to understand what you said, skipping")
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(
self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(
self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT"
in self.__dictID11) and (self.__dictID11["DARK CURRENT"]
== "YES"):
if ("DC FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"]
== "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning(
"Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"]
== "YES"):
if ("MASK FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning(
"Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"]
== "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning(
"Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !"
% (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(
XSDataDouble(1 / value))
else:
self.warning(
"Asked for FF SCALE correction but no FF MULTIPLIER provided"
)
if ("SPATIAL DIS."
in self.__dictID11) and (self.__dictID11["SPATIAL DIS."]
== "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(
self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else:
self.warning(
"Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file"
)
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(
self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue(
(float(self.__dictID11["END AZIMUTH"]) -
float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(
XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def populateXSDataInputSPDCake(self, _inputDict=None):
self.DEBUG("EDPluginControlID11v1_0.populateXSDataInputSPDCake")
xsDataInputSPDCake = XSDataInputSPDCake()
if isinstance(_inputDict, dict):
self.__dictID11 = _inputDict
# Angle of tilt
if "ANGLE OF TILT" in self.__dictID11:
xsDataTilt = XSDataAngle()
xsDataTilt.setValue(float(self.__dictID11["ANGLE OF TILT"]))
xsDataTilt.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setAngleOfTilt(xsDataTilt)
if "TILT ROTATION" in self.__dictID11:
xsDataTiltRot = XSDataAngle()
xsDataTiltRot.setValue(float(self.__dictID11["TILT ROTATION"]))
xsDataTiltRot.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setTiltRotation(xsDataTiltRot)
if "X-PIXEL SIZE" in self.__dictID11:
xsDataXPixel = XSDataLength()
xsDataXPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataXPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeX(xsDataXPixel)
if "Y-PIXEL SIZE" in self.__dictID11:
xsDataYPixel = XSDataLength()
xsDataYPixel.setValue(float(self.__dictID11["Y-PIXEL SIZE"]))
xsDataYPixel.setUnit(XSDataString("micron"))
xsDataInputSPDCake.setPixelSizeY(xsDataYPixel)
if "DISTANCE" in self.__dictID11:
xsDataDistance = XSDataLength()
xsDataDistance.setValue(float(self.__dictID11["DISTANCE"]))
xsDataDistance.setUnit(XSDataString("mm"))
xsDataInputSPDCake.setSampleToDetectorDistance(xsDataDistance)
if "WAVELENGTH" in self.__dictID11:
xsDataWaweLength = XSDataWavelength()
xsDataWaweLength.setValue(float(self.__dictID11["WAVELENGTH"]))
xsDataWaweLength.setUnit(XSDataString("A"))
xsDataInputSPDCake.setWavelength(xsDataWaweLength)
if "DIM1_DATA" in self.__dictID11:
xsDataBufferSizeX = XSDataInteger(int(self.__dictID11["DIM1_DATA"]))
xsDataInputSPDCake.setBufferSizeX(xsDataBufferSizeX)
if "DIM2_DATA" in self.__dictID11:
xsDataBufferSizeY = XSDataInteger(int(self.__dictID11["DIM2_DATA"]))
xsDataInputSPDCake.setBufferSizeY(xsDataBufferSizeY)
# Dark current
if ("DARK CURRENT" in self.__dictID11) and (self.__dictID11["DARK CURRENT"] == "YES") :
if ("DC FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["DC FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["DC FILE"]))
xsDataInputSPDCake.setDarkCurrentImageFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FLAT-FIELD" in self.__dictID11) and (self.__dictID11["FLAT-FIELD"] == "YES"):
if ("FF FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["FF FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["FF FILE"]))
xsDataInputSPDCake.setFlatFieldImageFile(xsDataFile)
else:
self.warning("Asked for FLAT-FIELD correction but no FLAT-FIELD file")
if ("MASK FILE" in self.__dictID11) and (self.__dictID11["USE MASK"] == "YES") :
if ("MASK FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["MASK FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["MASK FILE"]))
xsDataInputSPDCake.setMaskFile(xsDataFile)
else:
self.warning("Asked for DC Current correction but no DC current file")
if ("FF SCALE" in self.__dictID11) and (self.__dictID11["FF SCALE"] == "YES"):
if ("FF MULTIPLIER" in self.__dictID11):
try:
value = float(self.__dictID11["FF MULTIPLIER"])
except Exception:
self.warning("Asked for FF SCALE correction but FF MULTIPLIER provided (%s) in not float !" % (self.__dictID11["FF MULTIPLIER"]))
else:
xsDataInputSPDCake.setIntensityScaleFactor(XSDataDouble(1 / value))
else:
self.warning("Asked for FF SCALE correction but no FF MULTIPLIER provided")
if ("SPATIAL DIS." in self.__dictID11) and (self.__dictID11["SPATIAL DIS."] == "YES"):
if ("SD FILE" in self.__dictID11) and os.path.isfile(self.__dictID11["SD FILE"]):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.__dictID11["SD FILE"]))
xsDataInputSPDCake.setSpatialDistortionFile(xsDataFile)
else :
self.warning("Asked for SPATIAL DISTORSION correction but no SPATIAL DISTORSION file")
if "START AZIMUTH" in self.__dictID11:
xsDataAzimuthStart = XSDataAngle()
xsDataAzimuthStart.setValue(float(self.__dictID11["START AZIMUTH"]))
xsDataAzimuthStart.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStartAzimuth(xsDataAzimuthStart)
if "END AZIMUTH" in self.__dictID11:
xsDataAzimuthStop = XSDataAngle()
xsDataAzimuthStop.setValue(float(self.__dictID11["END AZIMUTH"]))
xsDataAzimuthStop.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStopAzimuth(xsDataAzimuthStop)
if "AZIMUTH BINS" in self.__dictID11:
xsDataAzimuthStep = XSDataAngle()
xsDataAzimuthStep.setValue((float(self.__dictID11["END AZIMUTH"]) - float(self.__dictID11["START AZIMUTH"])) /
float(self.__dictID11["AZIMUTH BINS"]))
xsDataAzimuthStep.setUnit(XSDataString("deg"))
xsDataInputSPDCake.setStepAzimuth(xsDataAzimuthStep)
if "INNER RADIUS" in self.__dictID11:
xsDataInnerRadius = XSDataDouble()
xsDataInnerRadius.setValue(float(self.__dictID11["INNER RADIUS"]))
xsDataInputSPDCake.setInnerRadius(xsDataInnerRadius)
if "OUTER RADIUS" in self.__dictID11:
xsDataOuterRadius = XSDataDouble()
xsDataOuterRadius.setValue(float(self.__dictID11["OUTER RADIUS"]))
xsDataInputSPDCake.setOuterRadius(xsDataOuterRadius)
if "X-BEAM CENTRE" in self.__dictID11:
xsDataXBeamCentre = XSDataDouble()
xsDataXBeamCentre.setValue(float(self.__dictID11["X-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsX(xsDataXBeamCentre)
if "Y-BEAM CENTRE" in self.__dictID11:
xsDataYBeamCentre = XSDataDouble()
xsDataYBeamCentre.setValue(float(self.__dictID11["Y-BEAM CENTRE"]))
xsDataInputSPDCake.setBeamCentreInPixelsY(xsDataYBeamCentre)
# if "saving_format" in self.__dictID11:
# xsSaveFormat = XSDataString()
# if self.__dictID11["saving_format"] == "SPREAD SHEET":
# xsSaveFormat.setValue("spr")
# elif self.__dictID11["saving_format"] == "CIF":
# xsSaveFormat.setValue("cif")
# elif self.__dictID11["saving_format"] == "CHIPLOT":
# xsSaveFormat.setValue("chi")
# else:
# xsSaveFormat.setValue("edf")
# xsDataInputSPDCake.setOutputFileType(xsSaveFormat)
if "output_dir" in self.__dictID11:
xsOutputDir = XSDataFile()
xsOutputDir.setPath(XSDataString(self.__dictID11["output_dir"]))
xsDataInputSPDCake.setOutputDir(xsOutputDir)
#Default options to SPD
xsDataInputSPDCake.setOutputFileType(XSDataString("azim"))
xsDataInputSPDCake.setDeleteCorImg(XSDataBoolean(not self.isVerboseDebug()))
xsDataInputSPDCake.setCorrectTiltMask(XSDataBoolean(self.bCorrectMask))
return xsDataInputSPDCake
def setup(self, _listInput=[], _mode="offline"):
"""Configure the various options"""
bOK = False
if _listInput == []:
_listInput = [os.getcwd()]
while not bOK:
strtmp = raw_input("What are the input directories (mandatory, space separated) %s: " % _listInput).strip()
if len(strtmp) > 0:
bAllExists = True
lstTemp = shlex.split(strtmp)
for oneDir in shlex.split(strtmp):
if not os.path.exists(oneDir):
EDVerbose.screen("No such file or directory: %s" % oneDir)
bAllExists = False
if bAllExists is True:
self.listInput = lstTemp
bOK = True
else:
self.listInput = _listInput
bOK = True
bOK = False
while not bOK:
strtmp = raw_input("What is operation mode [offline|online|all] (mandatory: %s): " % _mode).strip().lower()
if len(strtmp) > 0:
bOK = True
if strtmp == "offline":
self.bNewerOnly = False
self.strMode = "OffLine"
elif strtmp == "online":
self.bNewerOnly = True
self.strMode = "dirwatch"
elif strtmp == "all":
self.bNewerOnly = False
self.strMode = "dirwatch"
else:
bOK = False
bOK = False
while not bOK:
strtmp = raw_input("What is the destination directory (mandatory): ").strip()
if os.path.isdir(strtmp):
self.destinationDirectory = XSDataFile()
self.destinationDirectory.setPath(XSDataString(os.path.abspath(strtmp)))
bOK = True
bOK = False
while not bOK:
strtmp = raw_input("What is the sinogram filename prefix (mandatory): ").strip()
if strtmp != "":
self.sinogramFileNamePrefix = XSDataString(strtmp)
bOK = True
bOK = False
while not bOK:
strtmp = raw_input("What is the powder diffraction subdirectory (mandatory): ").strip()
if strtmp != "":
self.powderDiffractionSubdirectory = XSDataString(strtmp)
bOK = True
strtmp = raw_input("What is the powder diffraction output format (CHI or CIF, if any ): ").strip().lower()
if strtmp.find("cif") >= 0:
self.powderDiffractionFormat = XSDataString("cif")
elif strtmp.find("chi") >= 0:
self.powderDiffractionFormat = XSDataString("chi")
strtmp = raw_input("Process all files ending with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExtensions.append(oneExt)
strtmp = raw_input("Exclude all files starting with: ").strip()
if len(strtmp) > 0:
for oneExt in shlex.split(strtmp):
self.listExcludedPrefix.append(oneExt)
strtmp = raw_input("Do you want to over-ride metadata from the headers [y|N]: ").strip().lower()
if len(strtmp) > 0 and strtmp[0] == "y":
strtmp = raw_input("What is the flat field image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
flatFieldImage = XSDataFile()
flatFieldImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_flat_field(flatFieldImage)
strtmp = raw_input("What is the dark current image: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
darkCurrentImage = XSDataFile()
darkCurrentImage.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_image_dark_current(darkCurrentImage)
strtmp = raw_input("What is the mask file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
maskFile = XSDataFile()
maskFile.setPath(XSDataString(strtmp))
self.forceImage.set_file_correction_image_mask(maskFile)
strtmp = raw_input("What is the spline file: ").strip()
if os.path.isfile(strtmp):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
splineFile = XSDataFile()
splineFile.setPath(XSDataString(os.path.abspath(strtmp)))
self.forceImage.set_file_correction_spline_spatial_distortion(splineFile)
strtmp = raw_input("What is the wavelength (like 0.7 A): ").replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
wavelength = XSDataWavelength()
wavelength.setValue(f)
if len(w) == 2:
wavelength.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_diffrn_radiation_wavelength(wavelength)
strtmp = raw_input("What is the distance between the sample and the detector along the beam: ").replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
try:
f = float(w[0])
except ValueError:
print("unable to understand what you said, skipping")
else:
distance = XSDataLength()
distance.setValue(f)
if len(w) == 2:
distance.setUnit(XSDataString(w[1]))
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_pd_instr_dist_spec_detc(distance)
strtmp = raw_input("What is the pixel size (like 52.8 um 53.2 um): ").replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_array_element_size_1(xsdata1)
self.forceImage.set_array_element_size_2(xsdata2)
strtmp = raw_input("What is the beam center in distance, not pixels (like 53.5 mm 48.2 mm): ").strip().replace("(", "").replace(")", "").strip()
w = strtmp.split()
if len(w) > 0:
xsdata1 = None
xsdata2 = None
if len(w) == 4:
try:
f1 = float(w[0])
f2 = float(w[2])
except ValueError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata1.setUnit(XSDataString(w[1]))
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
xsdata2.setUnit(XSDataString(w[3]))
elif len(w) == 2:
try:
f1 = float(w[0])
f2 = float(w[1])
except ValueError, IndexError:
print "Unable to convert to float !!! skipping"
else:
xsdata1 = XSDataLength()
xsdata1.setValue(f1)
xsdata2 = XSDataLength()
xsdata2.setValue(f2)
else:
print("unable to understand what you said, skipping")
if (xsdata1 is not None) and (xsdata2 is not None):
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_diffrn_detector_element_center_1(xsdata1)
self.forceImage.set_diffrn_detector_element_center_2(xsdata2)
strtmp = raw_input("What is the detector tilt angle: ").strip()
tiltAngle = None
try:
tiltAngle = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_angle(tiltAngle)
strtmp = raw_input("What is the tilt plan rotation: ").strip()
tiltRotation = None
try:
tiltRotation = XSDataAngle(float(strtmp))
except ValueError:
print("unable to understand what you said, skipping")
else:
if self.forceImage is None:
self.forceImage = XSDataDiffractionCTImage()
self.forceImage.set_pd_instr_special_details_tilt_rotation(tiltRotation)
strtmp = raw_input("What is the number of fast motor steps (you will have n+1 points): ").strip()
try:
self.fastMotorSteps = int(strtmp)
except ValueError:
fastMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_spec_displ_x_max(XSDataLength(self.fastMotorSteps))
self.forceInstrument.set_tomo_spec_displ_x_min(XSDataLength(0))
self.forceInstrument.set_tomo_spec_displ_x_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input("What is the number of slow motor steps (you will have n+1 points): ").strip()
try:
self.slowMotorSteps = int(strtmp)
except ValueError:
self.slowMotorSteps = None
else:
if self.forceInstrument is None:
self.forceInstrument = XSDataDiffractionCTInstrument()
self.forceInstrument.set_tomo_scan_ampl(XSDataLength(self.slowMotorSteps))
self.forceInstrument.set_tomo_spec_displ_rotation_inc(XSDataLength(1))
self.forceInstrument.set_tomo_scan_type(XSDataString("flat"))
strtmp = raw_input("What is the index offset of your images: ").strip()
try:
self.indexOffset = int(strtmp)
except ValueError:
print("unable to understand what you said, skipping")