EDFactoryPluginStatic.loadModule("EDPluginExecMeasureOffsetv1_0")
EDFactoryPluginStatic.loadModule("EDPluginExecShiftImagev1_0")
EDFactoryPluginStatic.loadModule("EDPluginHDF5StackImagesv10")
from EDPluginHDF5 import EDPluginHDF5
################################################################################
# AutoBuilder for Numpy, PIL and Fabio
################################################################################
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "FabIO-0.0.7",
architecture)
imagingPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"20090405-Numpy-1.3", architecture)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
EDVerbose.setTestOff()
class EDPluginControlAlignStackv1_0(EDPluginControl):
"""
This control plugin aligns a stack on images in a single HDF5 3D-structure
"""
__iRefFrame = None
__dictRelShift = {
} #key=frame number N, value= 2-tuple of shift relative to frame N-1
__dictAbsShift = {
} #key=frame number N, value= 2-tuple of shift relative to frame iRefFrame
from EDUtilsPath import EDUtilsPath
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsArray import EDUtilsArray
edFactoryPlugin.loadModule("XSDataBioSaxsv1_0")
edFactoryPlugin.loadModule("XSDataSAS")
edFactoryPlugin.loadModule("XSDataWaitFilev1_0")
edFactoryPlugin.loadModule("XSDataExecCommandLine")
from XSDataBioSaxsv1_0 import XSDataInputBioSaxsToSASv1_0, XSDataResultBioSaxsToSASv1_0
from XSDataSAS import XSDataInputSolutionScattering
from XSDataWaitFilev1_0 import XSDataInputWaitFile
from XSDataExecCommandLine import XSDataInputRsync
from XSDataCommon import XSDataInteger, XSDataDouble, XSDataString, XSDataFile, XSPluginItem
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"20090405-Numpy-1.3", architecture)
numpy = edFactoryPlugin.preImport("numpy", numpyPath)
class EDPluginBioSaxsToSASv1_0(EDPluginControl):
"""
This is basically just a wrapper for Irakli's SAS pipeline, but with parameters optimized for ESRF
"""
CONF_MAX_THREAD = "maxThreads"
CONF_FILE_SIZE = "fileSize"
size = None
maxThreads = None
__strControlledPluginWait = "EDPluginWaitFile"
__strControlledPluginSAS = "EDPluginControlSolutionScatteringv0_4"
__strControlledPluginRsync = "EDPluginExecRsync"
from EDUtilsPath import EDUtilsPath
from EDThreading import Semaphore
from XSDataShiftv1_0 import XSDataInputShiftImage, XSDataResultShiftImage
from XSDataCommon import XSDataImageExt, XSDataString, XSPluginItem
from EDShare import EDShare
################################################################################
# AutoBuilder for Numpy, PIL and Fabio
################################################################################
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "FabIO-0.0.7", architecture)
imagingPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20090405-Numpy-1.3", architecture)
scipyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20090711-SciPy-0.7.1", architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
scipy = EDFactoryPluginStatic.preImport("scipy", scipyPath)
EDFactoryPluginStatic.preImport("Image", imagingPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
try:
from fabio.edfimage import edfimage
import scipy.ndimage
except Exception:
EDVerbose.ERROR("Error in loading numpy, Scipy, PIL or Fabio,\n\
Please re-run the test suite for EDTestSuitePluginExecShift \
to ensure that all modules are compiled for you computer as they don't seem to be installed")
class EDPluginExecShiftImagev1_1(EDPluginExec):
from EDConfiguration import EDConfiguration
from EDUtilsPath import EDUtilsPath
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsArray import EDUtilsArray
edFactoryPlugin.loadModule("XSDataBioSaxsv1_0")
edFactoryPlugin.loadModule("XSDataSAS")
edFactoryPlugin.loadModule("XSDataWaitFilev1_0")
edFactoryPlugin.loadModule("XSDataExecCommandLine")
from XSDataBioSaxsv1_0 import XSDataInputBioSaxsToSASv1_0, XSDataResultBioSaxsToSASv1_0
from XSDataSAS import XSDataInputSolutionScattering
from XSDataWaitFilev1_0 import XSDataInputWaitFile
from XSDataExecCommandLine import XSDataInputRsync
from XSDataCommon import XSDataInteger, XSDataDouble, XSDataString, XSDataFile, XSPluginItem
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20090405-Numpy-1.3", architecture)
numpy = edFactoryPlugin.preImport("numpy", numpyPath)
class EDPluginBioSaxsToSASv1_0(EDPluginControl):
"""
This is basically just a wrapper for Irakli's SAS pipeline, but with parameters optimized for ESRF
"""
CONF_MAX_THREAD = "maxThreads"
CONF_FILE_SIZE = "fileSize"
size = None
maxThreads = None
__strControlledPluginWait = "EDPluginWaitFile"
__strControlledPluginSAS = "EDPluginControlSolutionScatteringv0_4"
__strControlledPluginRsync = "EDPluginExecRsync"
from EDVerbose import EDVerbose
from EDPlugin import EDPlugin
from EDUtilsPlatform import EDUtilsPlatform
from EDConfiguration import EDConfiguration
from EDFactoryPlugin import edFactoryPlugin as EDFactoryPluginStatic
from EDDecorator import deprecated
from EDThreading import Semaphore
from EDUtilsPath import EDUtilsPath
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20090405-Numpy-1.3", architecture)
h5pyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "H5Py-1.3.0", architecture)
fabioPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "FabIO-0.0.7", architecture)
imagingPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20091115-PIL-1.1.7", architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="__version__")
h5py = EDFactoryPluginStatic.preImport("h5py", h5pyPath, _strMethodVersion="version.api_version", _strForceVersion="1.8")
Image = EDFactoryPluginStatic.preImport("Image", imagingPath, _strMethodVersion="VERSION")
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath, _strMethodVersion="version")
if h5py is None:
EDVerbose.error("h5py is None ... please investigate why !!!")
EDVerbose.writeErrorTrace()
# raise ImportError("EDPluginHDF5 cannot work without h5py !!!")
if "EDNA_SITE" not in os.environ:
os.environ["EDNA_SITE"] = "edna-site"
class EDPluginHDF5(EDPlugin):
import os
from StringIO import StringIO
from EDVerbose import EDVerbose
from EDUtilsFile import EDUtilsFile
from EDPluginExecProcessScript import EDPluginExecProcessScript
from XSDataEdnaSaxs import XSDataInputGnom, XSDataResultGnom
from XSDataCommon import XSDataFile, XSDataString, XSDataDouble
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsPath import EDUtilsPath
from EDUtilsArray import EDUtilsArray
from EDFactoryPlugin import edFactoryPlugin as EDFactoryPluginStatic
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "20090405-Numpy-1.3", architecture)
matplotlibPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "Matplotlib-1.0.1", architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
matplotlib = EDFactoryPluginStatic.preImport("matplotlib", matplotlibPath)
matplotlib.use('Agg')
pyplot = EDFactoryPluginStatic.preImport("matplotlib.pyplot", matplotlibPath)
class EDPluginExecGnomv0_2(EDPluginExecProcessScript):
"""
Execution plugin for small angle scattering data processing using GNOM
"""
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputGnom)
from EDFactoryPlugin import edFactoryPlugin as EDFactoryPluginStatic
from EDDecorator import deprecated
from EDThreading import Semaphore
from EDUtilsPath import EDUtilsPath
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"20090405-Numpy-1.3", architecture)
h5pyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "H5Py-1.3.0",
architecture)
fabioPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "FabIO-0.0.7",
architecture)
imagingPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"20091115-PIL-1.1.7", architecture)
numpy = EDFactoryPluginStatic.preImport("numpy",
numpyPath,
_strMethodVersion="__version__")
h5py = EDFactoryPluginStatic.preImport("h5py",
h5pyPath,
_strMethodVersion="version.api_version",
_strForceVersion="1.8")
Image = EDFactoryPluginStatic.preImport("Image",
imagingPath,
_strMethodVersion="VERSION")
fabio = EDFactoryPluginStatic.preImport("fabio",
fabioPath,
_strMethodVersion="version")
if h5py is None:
EDVerbose.error("h5py is None ... please investigate why !!!")
EDVerbose.writeErrorTrace()
from StringIO import StringIO
from EDVerbose import EDVerbose
from EDUtilsFile import EDUtilsFile
from EDPluginExecProcessScript import EDPluginExecProcessScript
from XSDataEdnaSaxs import XSDataInputGnom, XSDataResultGnom
from XSDataCommon import XSDataFile, XSDataString, XSDataDouble
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsPath import EDUtilsPath
from EDFactoryPlugin import edFactoryPlugin as EDFactoryPluginStatic
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"20090405-Numpy-1.3", architecture)
matplotlibPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries",
"Matplotlib-1.0.1", architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
matplotlib = EDFactoryPluginStatic.preImport("matplotlib", matplotlibPath)
matplotlib.use('Agg')
pyplot = EDFactoryPluginStatic.preImport("matplotlib.pyplot", matplotlibPath)
class EDPluginExecGnomv0_2(EDPluginExecProcessScript):
"""
Execution plugin for small angle scattering data processing using GNOM
"""
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputGnom)
self.fAngularScale = 1