def uploadReferenceFrame(self, entry):
paths = entry.split(":")
if len(paths) == 1 and os.path.isfile(paths[0]):
obj = fabio.open(paths[0]).data
EDVerbose.WARNING("Got reference frame %s via fabio" % entry)
EDPluginControlAlignStackv1_0.addFrame(-1, obj)
EDPluginAccumulatorv1_0.addItem(XSDataString("raw -001"))
self.updateAttrRefImage(obj)
elif len(paths) == 2 and os.path.isfile(paths[0]):
hdf = h5py.File(paths[0])
if paths[1] in hdf:
obj = hdf[paths[1]]
if obj.__class__.__name__ == "Group":
if self.REFERENCE_FRAME_NAME in obj:
data = obj[self.REFERENCE_FRAME_NAME][:]
EDPluginControlAlignStackv1_0.addFrame(-1, data)
EDPluginAccumulatorv1_0.addItem("raw -001")
self.updateAttrRefImage(data)
else:
EDVerbose.ERROR(
"HDF5: No '%s' in group %s from %s" % (self.REFERENCE_FRAME_NAME, paths[1], paths[0])
)
elif obj.__class__.__name__ == "Dataset":
data = obj[:]
EDPluginControlAlignStackv1_0.addFrame(-1, data)
EDPluginAccumulatorv1_0.addItem(XSDataString("raw -001"))
self.updateAttrRefImage(data)
else:
EDVerbose.ERROR("HDF5: No such internal path %s in %s" % (paths[1], paths[0]))
else:
EDVerbose.ERROR("No such entry %s" % entry)
def uploadReferenceFrame(self, entry):
paths = entry.split(":")
if len(paths) == 1 and os.path.isfile(paths[0]):
obj = fabio.open(paths[0]).data
EDVerbose.WARNING("Got reference frame %s via fabio" % entry)
EDPluginControlAlignStackv1_0.addFrame(-1, obj)
EDPluginAccumulatorv1_0.addItem(XSDataString("raw -001"))
self.updateAttrRefImage(obj)
elif len(paths) == 2 and os.path.isfile(paths[0]):
hdf = h5py.File(paths[0])
if paths[1] in hdf:
obj = hdf[paths[1]]
if obj.__class__.__name__ == "Group":
if self.REFERENCE_FRAME_NAME in obj:
data = obj[self.REFERENCE_FRAME_NAME][:]
EDPluginControlAlignStackv1_0.addFrame(-1, data)
EDPluginAccumulatorv1_0.addItem("raw -001")
self.updateAttrRefImage(data)
else:
EDVerbose.ERROR("HDF5: No '%s' in group %s from %s" % (self.REFERENCE_FRAME_NAME, paths[1], paths[0]))
elif obj.__class__.__name__ == "Dataset":
data = obj[:]
EDPluginControlAlignStackv1_0.addFrame(-1, data)
EDPluginAccumulatorv1_0.addItem(XSDataString("raw -001"))
self.updateAttrRefImage(data)
else:
EDVerbose.ERROR("HDF5: No such internal path %s in %s" % (paths[1], paths[0]))
else:
EDVerbose.ERROR("No such entry %s" % entry)
else:
ffx = FullFieldXas()
if os.path.isfile(".XSDataInputFullFieldXAS.xml"):
ffx.load(".XSDataInputFullFieldXAS.xml")
ffx.dontAlign = dontAlign
if dontAlign:
print ("*" * 80)
print ("*" + "Skipping image alignement part".center(78) + "*")
print ("*" * 80)
ffx.setup(_listInput=paths, _mode=mode)
if not isinstance(ffx.reference, int):
ffx.uploadReferenceFrame(ffx.reference)
ffx.save(".XSDataInputFullFieldXAS.xml")
ffx.dump("analysis-%s.json" % time.strftime("%Y%m%d-%Hh%Mm%Ss"))
edna = EDParallelExecute(
ffx.pluginName, ffx.makeXML, _functXMLerr=ffx.error, _bVerbose=True, _bDebug=debug, _iNbThreads=iNbCPU
)
edna.runEDNA(ffx.listInput, ffx.strMode, ffx.bNewerOnly)
EDVerbose.WARNING("Back to main !")
EDJob.synchronizeAll()
ffx.updateAttrRefImage()
EDPluginControlAlignStackv1_0.showData()
if keepShare:
EDShare.close()
elif (ffx.getNrErrors() == 0) and (not EDVerbose.isVerboseDebug()):
EDVerbose.WARNING("All processing finished successfully: Remove EDShare's big HDF5 file")
EDShare.close(remove=True)
else:
EDShare.close()
mode = "dirwatch"
elif i.lower().find("-all") in [0, 1]:
newerOnly = False
elif i.lower().find("-debug") in [0, 1]:
debug = True
elif i.lower().find("-ncpu") in [0, 1]:
iNbCPU = int(i.split("=", 1)[1])
elif os.path.exists(i):
paths.append(os.path.abspath(i))
if len(paths) == 0:
if mode == "OffLine":
print "This is the HDF5 3D image stacker application of EDNA with image alignment, \nplease give a path to process offline or the option:\n\
--online to process online incoming data in the given directory.\n\
--all to process all existing files (unless they will be excluded)\n\
--debug to turn on debugging mod in EDNA"
sys.exit()
else:
paths = [os.getcwd()]
edna = EDParallelExecute(EDNAPluginName,
fileName2xml,
_functXMLerr=XMLerr,
_bVerbose=True,
_bDebug=debug,
_iNbThreads=iNbCPU)
edna.runEDNA(paths, mode, newerOnly)
EDVerbose.screen("Back in main")
EDPluginControlAlignStackv1_0.showData()
# EDPluginHDF5StackImagesv10.closeAll()
