def __init__(self, dataSource, \
outputFileName, \
nx=200, ny=201, nz=202, \
transform = None, \
gridWriter = None,
appConfig = None):
'''
Constructor
:param dataSource: source of scan data
:param outputFileName: filename for output
:param nx: number of points in x direction for griidder
:param ny: number of points in y direction for griidder
:param nz: number of points in z direction for griidder
:param transform: Transform to be applied to the axes before gridding
'''
self.appConfig = None
if not (appConfig is None):
self.appConfig = appConfig
else:
raise RSMap3DException("no AppConfig object received.")
self.dataSource = dataSource
self.outputFileName = outputFileName
self.nx = nx
self.ny = ny
self.nz = nz
self.haltMap = False
self.progressUpdater = None
self.gridWriter = gridWriter
if transform is None:
self.transform = UnityTransform3D()
else:
self.transform = transform
def __init__(self,
dataSource,
outputFileName,
transform=None,
gridWriter=None,
appConfig=None,
dataCoord=X_COORD_OPTIONS[0],
xCoordMin=None,
xCoordMax=None,
xCoordStep=None,
plotResults=False,
yScaling=Y_SCALING_OPTIONS[0],
writeXyeFile=True):
self.dataSource = dataSource
self.outputFileName = outputFileName
self.gridWriter = gridWriter
self.appConfig = None
self.progressUpdater = None
if transform is None:
self.transform = UnityTransform3D()
else:
self.transform = transform
if not (appConfig is None):
self.appConfig = appConfig
else:
raise RSMap3DException("No AppConfig object received")
self.dataCoord = dataCoord
self.yScaling = yScaling
self.plotResults = plotResults
self.writeXyeFile = writeXyeFile
self.xCoordMin = xCoordMin
self.xCoordMax = xCoordMax
self.XCoordStep = xCoordStep
def getDataSource(self):
logger.debug(METHOD_ENTER_STR)
if self.getOutputType() == self.SIMPLE_GRID_MAP_STR:
self.transform = UnityTransform3D()
elif self.getOutputType() == self.POLE_MAP_STR:
self.transform = \
PoleMapTransform3D(projectionDirection=\
self.getProjectionDirection())
else:
self.transform = None
self.dataSource = \
Sector33SpecDataSource(str(self.getProjectDir()), \
str(self.getProjectName()), \
str(self.getProjectExtension()), \
str(self.getInstConfigName()), \
str(self.getDetConfigName()), \
transform = self.transform, \
scanList = self.getScanList(), \
roi = self.getDetectorROI(), \
pixelsToAverage = \
self.getPixelsToAverage(), \
badPixelFile = \
self.getBadPixelFileName(), \
flatFieldFile = \
self.getFlatFieldFileName(), \
appConfig = self.appConfig
)
self.dataSource.setProgressUpdater(self.updateProgress)
self.dataSource.setCurrentDetector(self.currentDetector)
self.dataSource.loadSource(mapHKL=self.getMapAsHKL())
logger.debug(METHOD_EXIT_STR)
return self.dataSource
def testS1HighEnergyDiffractionDS(self):
projectDir = os.path.join(configDir, "../1-idscan")
projectName = "fastpar_startup_oct16_FF1"
projectExtension = ".par"
instConfig = os.path.join(projectDir, "1-ID-E_AeroTable.xml")
detConfig = os.path.join(projectDir, "1-ID-GE.xml")
transform = UnityTransform3D()
pixelsToAverage = [1, 1]
scanList = [
3,
]
detRoi = [1, 2048, 1, 2048]
imageDirName = "" #fake since not used here.
appConfig = RSMap3DConfigParser()
ds = S1HighEnergyDiffractionDS(str(projectDir),
str(projectName),
str(projectExtension),
str(instConfig),
str(detConfig),
imageDirName,
transform=transform,
scanList=scanList,
pixelsToAverage=pixelsToAverage,
badPixelFile=None,
flatFieldFile=None,
appConfig=appConfig)
ds.setCurrentDetector('ge3')
ds.loadSource()
availableScans = ds.getAvailableScans()
self.assertEquals(availableScans, [
3,
])
def __init__(self,
transform=None,
scanList=None,
roi=None,
pixelsToAverage=[1, 1],
badPixelFile=None,
flatFieldFile=None,
**kwargs):
'''
Constructor
'''
super(AbstractXrayutilitiesDataSource, self).__init__(**kwargs)
self.sampleCircleDirections = None
self.detectorCircleDirections = None
self.primaryBeamDirection = None
self.incidentWavelength = float('nan')
self.incidentEnergy = None
self.sampleInplaneReferenceDirection = None
self.sampleSurfaceNormalDirection = None
self.detectorCenterChannel = None
self.distanceToDetector = float('nan')
self.detectorPixelWidth = None
self.detectorChannelPerDegree = None
self.numPixelsToAverage = pixelsToAverage
self.detectorROI = roi
self.detectorAngles = None
self.sampleAngles = None
self.detectorAngleNames = None
self.sampleAngleNames = None
self.detectorPixelDirection1 = None
self.detectorPixelDirection2 = None
self.imageToBeUsed = {}
self.availableScans = []
self.ubMatrix = {}
self.badPixels = []
self.rangeBounds = None
self.cancelLoad = False
self.monitorName = None
self.monitorScaleFactor = 1.0
self.projectionDirection = None
self.filterName = None
self.filterScaleFactor = 1.0
if transform is None:
self.transform = UnityTransform3D()
else:
self.transform = transform
self.badPixelFile = badPixelFile
self.flatFieldFile = flatFieldFile
self.flatFieldData = None
self.progressUpdater = None
def loadScanFile(self):
'''
Set up to load the scan file
'''
self.blockTabsForLoad.emit()
if self.fileFormWidget.getOutputType(
) == self.fileFormWidget.SIMPLE_GRID_MAP_STR:
self.transform = UnityTransform3D()
elif self.fileFormWidget.getOutputType(
) == self.fileFormWidget.POLE_MAP_STR:
self.transform = \
PoleMapTransform3D(projectionDirection=\
self.fileFormWidget.getProjectionDirection())
else:
self.transform = None
try:
self.dataSource = \
self.fileFormWidget.getDataSource()
except LoadCanceledException as e:
self.blockTabsForLoad.emit()
self.setScanLoadOK.emit()
#self.fileForm.setLoadOK()
return
except ScanDataMissingException as e:
self.fileError.emit(str(e))
return
except DetectorConfigException as e:
self.fileError.emit(str(e))
return
except InstConfigException as e:
self.fileError.emit(str(e))
return
except Transform3DException as e:
self.fileError.emit(str(e))
return
except ScanDataMissingException as e:
self.fileError.emit(str(e))
return
except RSMap3DException as e:
self.fileError.emit(str(e))
return
except Exception as e:
self.fileError.emit(str(e) + "\n" + str(traceback.format_exc()))
return
self.loadDataSourceToScanForm.emit()
self.setScanLoadOK.emit()
def getDataSource(self):
if self.getOutputType() == self.SIMPLE_GRID_MAP_STR:
self.transform = UnityTransform3D()
elif self.getOutputType() == self.POLE_MAP_STR:
self.transform = \
PoleMapTransform3D(projectionDirection=\
self.fileForm.getProjectionDirection())
else:
self.transform = None
self.dataSource = \
Sector34NexusEscanSource(str(self.getProjectDir()), \
str(self.getProjectName()), \
str(self.getProjectExtension()), \
str(self.getDetConfigName()), \
appConfig = self.appConfig)
self.dataSource.setProgressUpdater(self.updateProgress)
self.dataSource.loadSource()
return self.dataSource
def getDataSource(self):
logger.debug(METHOD_ENTER_STR)
if self.getOutputType() == self.SIMPLE_GRID_MAP_STR:
self.transform = UnityTransform3D()
elif self.getOutputType() == self.POLE_MAP_STR:
self.transform = \
PoleMapTransform3D(projectionDirection=\
self.getProjectionDirection())
else:
self.transform = None
self.dataSource = \
S1HighEnergyDiffractionDS(str(self.getProjectDir()), \
str(self.getProjectName()), \
str(self.getProjectExtension()), \
str(self.getInstConfigName()), \
str(self.getDetConfigName()), \
str(self.getImageDirName()), \
transform = self.transform, \
scanList = self.getScanList(), \
roi = self.getDetectorROI(), \
pixelsToAverage = \
[1,1], \
badPixelFile = None, \
flatFieldFile = None, \
detectorDistanceOverride = \
self.getDetectorDistanceOverride(), \
incidentEnergyOverride =
self.getIncidentEnergyOverride(), \
offsetAngle = self.getOffsetAngle(), \
appConfig = self.appConfig
)
self.dataSource.setProgressUpdater(self.updateProgress)
self.dataSource.setCurrentDetector(self.currentDetector)
self.dataSource.loadSource(mapHKL=self.getMapAsHKL())
logger.debug(METHOD_EXIT_STR)
return self.dataSource
def getDataSource(self):
if self.getOutputType() == self.SIMPLE_GRID_MAP_STR:
self.transform = UnityTransform3D()
elif self.getOutputType() == self.POLE_MAP_STR:
self.transform = \
PoleMapTransform3D(projectionDirection=\
self.fileForm.getProjectionDirection())
else:
self.transform = None
pathToReplaceStr = str(self.pathToReplaceTxt.text())
replacePathWithStr = str(self.replacePathWithTxt.text())
if (pathToReplaceStr == ""):
pathToReplace = None
else:
pathToReplace = pathToReplaceStr
if (replacePathWithStr == ""):
replacePathWith = None
else:
replacePathWith = replacePathWithStr
self.dataSource = \
XPCSSpecDataSource(str(self.getProjectDir()), \
str(self.getProjectName()), \
str(self.getProjectExtension()), \
str(self.getInstConfigName()), \
str(self.getDetConfigName()), \
# str(self.getImmFileName()), \
scanList = self.getScanList(), \
transform = self.transform, \
appConfig = self.appConfig,
pathToReplace = pathToReplace,
replacePathWith = replacePathWith
)
self.dataSource.setProgressUpdater(self.updateProgress)
self.dataSource.setCurrentDetector(self.currentDetector)
self.dataSource.loadSource(mapHKL=self.getMapAsHKL())
return self.dataSource
ds.setRangeBounds(ds.getOverallRanges())
imageToBeUsed = ds.getImageToBeUsed()
print("imageToBeUsed %s" % imageToBeUsed)
# wavelen = ENERGY_WAVELENGTH_CONVERT_FACTOR/ds.getIncidentEnergy()[scans[0]]
imageSize = np.prod(ds.getDetectorDimensions())
print scanRange[0]
for imageInScan in range(1, len(imageToBeUsed[scanRange[0]])+1):
print ("Scan Line %d" % imageInScan)
outputFileName = os.path.join(projectDir, specName + \
('_N%d.vti' % imageInScan))
gridWriter = VTIGridWriter()
tmpImageUsed = imageToBeUsed[scanRange[0]]
savImageUsed = imageToBeUsed[scanRange[0]]
tmpImageUsed[imageInScan] = False
ds.imageToBeUsed[scanRange[0]] = [not i for i in tmpImageUsed]
gridMapper = QGridMapper(ds,
outputFileName,
outputType=BINARY_OUTPUT,
transform=UnityTransform3D(),
gridWriter=gridWriter,
appConfig=appConfig,
nx=nx, ny=ny, nz=nz)
gridMapper.setProgressUpdater(updateMapperProgress)
gridMapper.doMap()
ds.imageToBeUsed[scanRange[0]] = savImageUsed