def run(self, inData):
outData = {}
hdf5File = pathlib.Path(inData['hdf5File'])
# Read the header
inDataReadImageHeader = {
"imagePath": [inData['hdf5File']],
"isFastMesh": False
}
readImageHeader = ReadImageHeader(inData=inDataReadImageHeader)
readImageHeader.execute()
if readImageHeader.isSuccess():
firstSubWedge = readImageHeader.outData["subWedge"][0]
experimentalCondition = firstSubWedge["experimentalCondition"]
detector = experimentalCondition["detector"]
beam = experimentalCondition["beam"]
goniostat = experimentalCondition["goniostat"]
beamX = detector["beamPositionX"] / 2.0 / detector["pixelSizeX"]
beamY = detector["beamPositionY"] / 2.0 / detector["pixelSizeY"]
directory = hdf5File.parent
prefix = UtilsImage.getPrefix(hdf5File)
hdf5ImageNumber = 1
if 'master' in str(hdf5File):
masterFile = hdf5File
else:
if UtilsConfig.isEMBL():
fileName = '{0}_master.h5'.format(prefix)
else:
fileName = '{0}_{1}_master.h5'.format(
prefix, hdf5ImageNumber)
masterFile = directory / fileName
image = fabio.open(str(masterFile))
image.data = image.data.reshape(2181, 2, 2074, 2).sum(3).sum(1)
cbfImage = image.convert("cbf")
pilatus_headers = fabio.cbfimage.PilatusHeader(
"Silicon sensor, thickness 0.000750 m")
pilatus_headers["Start_angle"] = goniostat["rotationAxisStart"]
pilatus_headers["Angle_increment"] = goniostat["oscillationWidth"]
pilatus_headers["Detector"] = "Eiger2 16M binned to 4M"
pilatus_headers["Pixel_size"] = (detector["pixelSizeY"] * 2,
detector["pixelSizeX"] * 2)
pilatus_headers["Exposure_time"] = beam["exposureTime"]
pilatus_headers["Wavelength"] = beam["wavelength"]
pilatus_headers[
"Detector_distance"] = detector["distance"] / 1000.0
pilatus_headers["Beam_xy"] = (beamY, beamX)
pilatus_headers["Count_cutoff"] = 1009869
cbfImage.pilatus_headers = pilatus_headers
directory = inData.get("forcedOutputDirectory",
str(self.getWorkingDirectory()))
cbfImagePath = os.path.join(
directory,
os.path.basename(inData['hdf5File']).replace(".h5", ".cbf"))
cbfImage.save(cbfImagePath)
outData["outputCBFFile"] = cbfImagePath
return outData
def run(self, inData):
input_file = inData['input_file']
output_file = inData['output_file']
commandLine = 'pointless'
if UtilsConfig.isEMBL():
commandLine += ' -c'
commandLine += " xdsin {0} hklout {1}".format(input_file, output_file)
listCommand = ['setting symmetry-based']
if 'choose_spacegroup' in inData:
listCommand += 'choose spacegroup {0}'.format(
inData['choose_spacegroup'])
self.setLogFileName('pointless.log')
self.runCommandLine(commandLine, listCommand=listCommand)
outData = self.parsePointlessOutput(self.getLogPath())
return outData
def generateCommandsWithImageNumber(cls, inData, directory, prefix,
hdf5File):
"""
This method creates a list of commands for the converter
"""
imageNumber = inData['imageNumber']
if 'hdf5ImageNumber' in inData:
hdf5ImageNumber = inData['hdf5ImageNumber']
else:
hdf5ImageNumber = imageNumber
if 'master' in str(hdf5File):
masterFile = hdf5File
else:
if UtilsConfig.isEMBL():
fileName = '{0}_master.h5'.format(prefix)
else:
fileName = '{0}_{1}_master.h5'.format(prefix, hdf5ImageNumber)
masterFile = directory / fileName
if 'forcedOutputImageNumber' in inData:
cbfFileName = prefix + \
"_%04d" % inData['forcedOutputImageNumber'] + ".cbf"
imageNumberInHdf5File = imageNumber
else:
cbfFileName = prefix + "_%04d" % imageNumber + ".cbf"
imageNumberInHdf5File = imageNumber - hdf5ImageNumber + 1
if not 'forcedOutputDirectory' in inData:
cbfFile = directory / cbfFileName
else:
forcedOutputDirectory = \
pathlib.Path(inData['forcedOutputDirectory'])
if not forcedOutputDirectory.exists():
forcedOutputDirectory.mkdir(parents=True, mode=0o755)
cbfFile = forcedOutputDirectory / cbfFileName
commandLine = "{0} {1} {2}".format(masterFile, imageNumberInHdf5File,
cbfFile)
return commandLine, cbfFile
def createPyarchFilePath(filePath):
"""
This method translates from an ESRF "visitor" path to a "pyarch" path:
/data/visitor/mx415/id14eh1/20100209 -> /data/pyarch/2010/id14eh1/mx415/20100209
"""
pyarchFilePath = None
if isinstance(filePath, str):
filePath = pathlib.Path(filePath)
listOfDirectories = filePath.parts
if UtilsConfig.isEMBL():
if 'p13' in listOfDirectories[0:3] or 'P13' in listOfDirectories[0:3]:
pyarchFilePath = os.path.join('/data/ispyb/p13',
*listOfDirectories[4:])
else:
pyarchFilePath = os.path.join('/data/ispyb/p14',
*listOfDirectories[4:])
return pyarchFilePath
listBeamlines = ['bm30a', 'id14eh1', 'id14eh2', 'id14eh3', 'id14eh4',
'id23eh1', 'id23eh2', 'id29', 'id30a1',
'id30a2', 'id30a3', 'id30b']
# Check that we have at least four levels of directories:
if len(listOfDirectories) > 5:
dataDirectory = listOfDirectories[1]
secondDirectory = listOfDirectories[2]
thirdDirectory = listOfDirectories[3]
fourthDirectory = listOfDirectories[4]
fifthDirectory = listOfDirectories[5]
year = fifthDirectory[0:4]
proposal = None
beamline = None
if dataDirectory == 'data' and secondDirectory == 'gz':
if thirdDirectory == 'visitor':
proposal = fourthDirectory
beamline = fifthDirectory
elif fourthDirectory == 'inhouse':
proposal = fifthDirectory
beamline = thirdDirectory
else:
raise RuntimeError(
'Illegal path for UtilsPath.createPyarchFilePath: ' +
'{0}'.format(filePath))
listOfRemainingDirectories = listOfDirectories[6:]
elif dataDirectory == 'data' and secondDirectory == 'visitor':
proposal = listOfDirectories[3]
beamline = listOfDirectories[4]
listOfRemainingDirectories = listOfDirectories[5:]
elif dataDirectory == 'data' and secondDirectory in listBeamlines:
beamline = secondDirectory
proposal = listOfDirectories[4]
listOfRemainingDirectories = listOfDirectories[5:]
if proposal is not None and beamline is not None:
pyarchFilePath = pathlib.Path('/data/pyarch') / year / beamline
pyarchFilePath = pyarchFilePath / proposal
for directory in listOfRemainingDirectories:
pyarchFilePath = pyarchFilePath / directory
if pyarchFilePath is None:
logger.warning(
'UtilsPath.createPyarchFilePath: path not converted for' +
' pyarch: %s ' % filePath)
else:
pyarchFilePath = pyarchFilePath.as_posix()
return pyarchFilePath