def test_getShiftData(self):
mrcFilePath = "/scisoft/pxsoft/data/cryoem/testRunData/20171113/Runs/000056_ProtMotionCorr/extra/FoilHole_9208892_Data_9209286_9209287_20171109_1540-0539_aligned_mic.mrc"
dictResult = UtilsPath.getShiftData(mrcFilePath)
dictRef = {
'averageMotionPerFrame': 6.3,
'noPoints': 40,
'totalMotion': 250.6
}
self.assertEqual(dictRef, dictResult)
def uploadAlignMovies(self, prot):
self.info("ESRF ISPyB upload motion corr results")
for micrograph in self.iter_updated_set(prot.outputMicrographs):
micrographFullPath = os.path.join(self.currentDir, micrograph.getFileName())
#self.info("Motion corr micrographFullPath: {0}".format(micrographFullPath))
dictFileNameParameters = UtilsPath.getMovieFileNameParametersFromMotioncorrPath(micrographFullPath)
movieName = dictFileNameParameters["movieName"]
#self.info("Motion corr movie name: {0}".format(movieName))
if movieName in self.allParams and not "motionCorrectionId" in self.allParams[movieName]:
self.info("Align movies: movie {0}".format(os.path.basename(self.allParams[movieName]["movieFullPath"])))
movieFullPath = self.allParams[movieName]["movieFullPath"]
dictResult = UtilsPath.getAlignMoviesPngLogFilePath(micrographFullPath)
driftPlotFullPath = dictResult["globalShiftPng"]
if "doseWeightMrc" in dictResult:
correctedDoseMicrographFullPath = dictResult["doseWeightMrc"]
else:
correctedDoseMicrographFullPath = None
if "thumbnailPng" in dictResult:
micrographSnapshotFullPath = dictResult["thumbnailPng"]
else:
micrographSnapshotFullPath = None
dictShift = UtilsPath.getShiftData(micrographFullPath)
if "totalMotion" in dictShift:
totalMotion = dictShift["totalMotion"]
else:
totalMotion = None
if "averageMotionPerFrame" in dictShift:
averageMotionPerFrame = dictShift["averageMotionPerFrame"]
else:
averageMotionPerFrame = None
logFileFullPath = dictResult["logFileFullPath"]
firstFrame = 1
lastFrame = self.allParams[movieName]["imagesCount"]
dosePerFrame = self.allParams[movieName]["dosePerFrame"]
doseWeight = None
driftPlotPyarchPath = UtilsPath.copyToPyarchPath(driftPlotFullPath)
micrographPyarchPath = None
correctedDoseMicrographPyarchPath = None
micrographSnapshotPyarchPath = UtilsPath.copyToPyarchPath(micrographSnapshotFullPath)
logFilePyarchPath = UtilsPath.copyToPyarchPath(logFileFullPath)
shutil.copy(micrographFullPath, self.allParams[movieName]["processDir"])
shutil.copy(correctedDoseMicrographFullPath, self.allParams[movieName]["processDir"])
shutil.copy(logFileFullPath, self.allParams[movieName]["processDir"])
try:
motionCorrectionObject = self.client.service.addMotionCorrection(proposal=self.proposal,
movieFullPath=movieFullPath,
firstFrame=firstFrame,
lastFrame=lastFrame,
dosePerFrame=dosePerFrame,
doseWeight=doseWeight,
totalMotion=totalMotion,
averageMotionPerFrame=averageMotionPerFrame,
driftPlotFullPath=driftPlotPyarchPath,
micrographFullPath=micrographPyarchPath,
correctedDoseMicrographFullPath=correctedDoseMicrographPyarchPath,
micrographSnapshotFullPath=micrographSnapshotPyarchPath,
logFileFullPath=logFilePyarchPath)
except:
self.info("ERROR uploading motion correction for movie {0}".format(movieFullPath))
traceback.print_exc()
motionCorrectionObject = None
if motionCorrectionObject is not None:
motionCorrectionId = motionCorrectionObject.motionCorrectionId
else:
self.info("ERROR: motionCorrectionObject is None!")
motionCorrectionId = None
self.allParams[movieName]["motionCorrectionId"] = motionCorrectionId
self.allParams[movieName]["totalMotion"] = totalMotion
self.allParams[movieName]["averageMotionPerFrame"] = averageMotionPerFrame
self.info("Align movies done, motionCorrectionId = {0}".format(motionCorrectionId))