def run(self, in_data):
outData = {}
# First get the list of subWedges
if "subWedge" in in_data:
list_sub_wedge = in_data["subWedge"]
else:
list_sub_wedge = self.getListSubWedge(in_data)
# # Get list of spots from Dozor
# listOutDataControlDozor = self.runControlDozor(listSubWedge)
# listDozorSpotFile = []
# for outDataControlDozor in listOutDataControlDozor:
# if "dozorSpotFile" in outDataControlDozor["imageQualityIndicators"][0]:
# dozorSpotFile = outDataControlDozor["imageQualityIndicators"][0][
# "dozorSpotFile"
# ]
# listDozorSpotFile.append(dozorSpotFile)
# imageDict = listSubWedge[0]
# Run XDS indexing
xds_indexin_in_data = {
"subWedge": list_sub_wedge
# "dozorSpotFile": listDozorSpotFile,
}
xds_indexing_task = XDSIndexing(
inData=xds_indexin_in_data
# workingDirectorySuffix=UtilsImage.getPrefix(imageDict["image"][0]["path"]),
)
xds_indexing_task.execute()
resultIndexing = None
xparm_path = None
spot_path = None
if xds_indexing_task.isSuccess():
xdsIndexingOutData = xds_indexing_task.outData
if os.path.exists(xdsIndexingOutData["xparmXdsPath"]):
xparm_path = xdsIndexingOutData["xparmXdsPath"]
if os.path.exists(xdsIndexingOutData["spotXdsPath"]):
spot_path = xdsIndexingOutData["spotXdsPath"]
resultIndexing = ControlIndexing.getResultIndexingFromXds(
xdsIndexingOutData)
outData = {
"resultIndexing": resultIndexing,
"xparmXdsPath": xparm_path,
"spotXdsPath": spot_path
}
return outData
def run(self, inData):
outData = {}
# First get the list of subWedges
if "subWedge" in inData:
listSubWedge = inData["subWedge"]
else:
listSubWedge = self.getListSubWedge(inData)
# Get list of spots from Dozor
listOutDataControlDozor = self.runControlDozor(listSubWedge)
listDozorSpotFile = []
for outDataControlDozor in listOutDataControlDozor:
if "dozorSpotFile" in outDataControlDozor["imageQualityIndicators"][0]:
dozorSpotFile = outDataControlDozor["imageQualityIndicators"][0]["dozorSpotFile"]
listDozorSpotFile.append(dozorSpotFile)
imageDict = listSubWedge[0]
listXdsIndexingTask = []
listResult = []
listSpaceGroup = []
# Run XDS indexing
xdsIndexinInData = {
"subWedge": listSubWedge,
"dozorSpotFile": listDozorSpotFile
}
xdsIndexingTask = XDSIndexing(
inData=xdsIndexinInData,
workingDirectorySuffix=UtilsImage.getPrefix(imageDict["image"][0]["path"])
)
xdsIndexingTask.execute()
xparmXdsPath = None
if xdsIndexingTask.isSuccess():
xdsIndexingOutData = xdsIndexingTask.outData
xparmXdsPath = xdsIndexingOutData["xparmXdsPath"]
resultIndexing = ControlIndexing.getResultIndexingFromXds(xdsIndexingOutData)
outData = {
"resultIndexing": resultIndexing,
"resultDozor": listOutDataControlDozor,
"xparmXdsPath": xparmXdsPath
}
return outData
def test_execute_XDSIndexing(self):
referenceDataPath = self.dataPath / 'inDataXDSIndexing.json'
inData = UtilsTest.loadAndSubstitueTestData(referenceDataPath)
xdsIndexing = XDSIndexing(inData=inData)
xdsIndexing.execute()
self.assertTrue(xdsIndexing.isSuccess())