from XSDataFullFieldXAS import XSDataInputFullFieldXAS, XSDataResultFullFieldXAS, \
XSDataInputAlignStack, XSDataHDF5Attributes
from XSDataNormalizeImage import XSDataInputNormalize
from XSDataCommon import XSDataString, XSDataInteger, \
XSDataDictionary, XSDataKeyValuePair, XSDataImageExt
################################################################################
# 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)
h5pyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "H5Py-1.3.0", architecture)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="version.version")
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
h5py = EDFactoryPluginStatic.preImport("h5py", h5pyPath)
class EDPluginControlFullFieldXASv1_0(EDPluginControl):
"""
Plugin to control Full Field XRay Absorption Spectroscopy Experiment, ID21 ESRF
"""
_semaphore = Semaphore()
TITLE = "FullField XANES mapping"
start_time = time.time()
DSenergy = "energy"
DSstack = "data"
energyAttr = {"unit":"keV",
sys.path.append(kernel_src)
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller, installLibrary
from EDFactoryPluginStatic import EDFactoryPluginStatic
moduleName = "numpy"
modulePath = os.path.join(os.environ["EDNA_HOME"], "libraries", "NumPy-1.5.1", EDUtilsPlatform.architecture)
moduleVersion = "1.4.0"
################################################################################
# Import the right version of numpy
################################################################################
oModule = EDFactoryPluginStatic.preImport(moduleName, _strMethodVersion="version.version")
if not oModule:
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath, _strMethodVersion="version.version")
if oModule is None:
installLibrary(modulePath)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath, _strMethodVersion="version.version")
try:
version = oModule.version.version
except AttributeError:
version = "0.0.0"
if version.split(".") < moduleVersion.split("."):
EDVerbose.screen("Wrong %s library: %s " % (moduleName, version))
EDFactoryPluginStatic.unImport(moduleName)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath, moduleVersion, _strMethodVersion="version.version")
sys.path.append(os.path.join(os.environ["EDNA_HOME"], "kernel", "src"))
from EDVerbose import EDVerbose
if "EDNA_SITE" not in os.environ:
os.environ["EDNA_SITE"] = "ESRF"
EDVerbose.WARNING("EDNA_SITE not defined: Resetting to 'ESRF'")
from EDParallelExecute import EDParallelExecute
from EDUtilsPlatform import EDUtilsPlatform
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDJob import EDJob
from EDShare import EDShare
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20090405-Numpy-1.3", EDUtilsPlatform.architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="version.version")
fabioPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7", EDUtilsPlatform.architecture)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath, _strMethodVersion="version")
h5pyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "H5Py-1.3.0", EDUtilsPlatform.architecture)
h5py = EDFactoryPluginStatic.preImport(
"h5py", h5pyPath, _strMethodVersion="version.api_version", _strForceVersion="1.8"
)
from EDShare import EDShare
EDFactoryPluginStatic.loadModule("EDPluginHDF5StackImagesv10")
EDFactoryPluginStatic.loadModule("EDPluginControlAlignStackv1_0")
EDFactoryPluginStatic.loadModule("EDPluginAccumulatorv1_0")
from EDPluginAccumulatorv1_0 import EDPluginAccumulatorv1_0
from EDPluginControlAlignStackv1_0 import EDPluginControlAlignStackv1_0
from EDPluginControlFullFieldXASv1_0 import EDPluginControlFullFieldXASv1_0
from EDPluginHDF5StackImagesv10 import EDPluginHDF5StackImagesv10
from EDUtilsPath import EDUtilsPath
from XSDataCommon import XSDataString, XSDataImage, \
XSDataDouble, XSDataLength, XSDataWavelength, \
XSDataTime, XSDataInteger, XSDataTime
from XSDataBioSaxsv1_0 import XSDataInputBioSaxsMetadatav1_0, \
XSDataResultBioSaxsMetadatav1_0, \
XSDataBioSaxsExperimentSetup, \
XSDataBioSaxsSample
from EDUtilsPlatform import EDUtilsPlatform
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)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
if fabio is None:
EDVerbose.ERROR("Unable to import Fabio: Please re-run the tests EDTestSuiteBioSaxs")
class EDPluginBioSaxsMetadatav1_1(EDPluginExec):
"""
Plugin for reading, updating and writing Metadata.
"""
def __init__(self):
"""
from EDVerbose import EDVerbose
from EDPluginControl import EDPluginControl
from EDUtilsBioSaxs import EDUtilsBioSaxs
from EDUtilsPath import EDUtilsPath
from EDFactoryPluginStatic import EDFactoryPluginStatic
from XSDataCommon import XSDataString, XSDataImage, XSDataDouble, XSDataLength, \
XSDataWavelength
from XSDataBioSaxsv1_0 import XSDataInputBioSaxsMetadatav1_0, XSDataResultBioSaxsMetadatav1_0
EDFactoryPluginStatic.loadModule("XSDataSaxsv1_0")
from XSDataSaxsv1_0 import XSDataInputSaxsAddMetadatav1_0
from EDUtilsPlatform import EDUtilsPlatform
architecture = EDUtilsPlatform.architecture
edfFilePath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "EdfFile",
architecture)
EdfFileMod = EDFactoryPluginStatic.preImport("EdfFile", edfFilePath)
if EdfFileMod is None:
EDVerbose.ERROR(
"Unable to import EdfFile: Please re-run the tests EDTestSuiteBioSaxs")
else:
from EdfFile import EdfFile
class EDPluginBioSaxsMetadatav1_0(EDPluginControl):
"""
Plugin for reading, updating and writing Metadata.
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
sys.path.append(kernel_src)
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller, installLibrary
from EDFactoryPluginStatic import EDFactoryPluginStatic
################################################################################
# Import the right version of Scipy
################################################################################
moduleName = "scipy"
modulePath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20090711-SciPy-0.7.1", EDUtilsPlatform.architecture)
moduleVersion = "0.7.0"
oModule = EDFactoryPluginStatic.preImport(moduleName,
_strMethodVersion="version.version")
if not oModule:
oModule = EDFactoryPluginStatic.preImport(
moduleName, modulePath, _strMethodVersion="version.version")
if oModule is None:
installLibrary(modulePath)
oModule = EDFactoryPluginStatic.preImport(
moduleName, modulePath, _strMethodVersion="version.version")
try:
version = oModule.version.version
except AttributeError:
version = "0.0.0"
if version.split(".") < moduleVersion.split("."):
EDVerbose.screen("Wrong %s library: %s " % (moduleName, version))
EDFactoryPluginStatic.unImport(moduleName)
# BIG FAT WARNING
# HDF5 does not like unicode string and crashes with cryptic error messages
###############################################################################
import os, threading, time, locale
from EDVerbose import EDVerbose
from EDPluginHDF5 import EDPluginHDF5
from EDAssert import EDAssert
from EDUtilsPlatform import EDUtilsPlatform
from XSDataHDF5v1_0 import XSDataInputHDF5MapSpectra, XSDataResultHDF5MapSpectra
from XSDataCommon import XSDataFile, XSDataString
from EDConfiguration import EDConfiguration
from EDUtilsArray import EDUtilsArray
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDPluginHDF5 import numpyPath, h5pyPath, fabioPath
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="__version__")
h5py = EDFactoryPluginStatic.preImport("h5py", h5pyPath, _strMethodVersion="version.version")
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath, _strMethodVersion="version")
class EDPluginHDF5MapOfSpectrav10(EDPluginHDF5):
"""
This plugin is made for putting together 1D spectra comming from a 2D scan in a 3D cube,
read using various libraries ... , and put them together in an NeXus/HDF5 file
"""
HDF5_DATASET_MAPSPECTRA_ATTRIBUTES = {"interpretation": "spectrum", # "spectrum", "scalar", "image" or "vertex"
"signal":"1",
}
def __init__(self):
from XSDataShiftv1_0 import XSDataResultMeasureOffset
from EDAssert import EDAssert
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
################################################################################
# AutoBuilder for Numpy, PIL and Fabio
################################################################################
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "FabIO-0.0.7", architecture)
imagingPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "20090405-Numpy-1.3", architecture)
scipyPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "20090711-SciPy-0.7.1", architecture)
fftw3Path = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "pyfftw3-0.2.1", architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
EDFactoryPluginStatic.preImport("scipy.ndimage", scipyPath)
EDFactoryPluginStatic.preImport("scipy.fftpack", scipyPath)
EDFactoryPluginStatic.preImport("scipy.interpolate", scipyPath)
EDFactoryPluginStatic.preImport("scipy.signal", scipyPath)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
fftw3 = EDFactoryPluginStatic.preImport("fftw3", fftw3Path)
try:
import scipy.ndimage, scipy.fftpack, scipy.interpolate # , scipy.signal
from scipy.ndimage import sobel
except:
EDVerbose.ERROR(
"Error in loading numpy, Scipy, PIL or Fabio,\n\
Please re-run the test suite for EDTestSuitePluginExecShift \
except ImportError:
print("No socket opened for debuging -> please install rfoo")
sys.path.append(os.path.join(os.environ["EDNA_HOME"], "kernel", "src"))
from EDVerbose import EDVerbose
if "EDNA_SITE" not in os.environ:
os.environ["EDNA_SITE"] = "ESRF"
EDVerbose.WARNING("EDNA_SITE not defined: Resetting to 'ESRF'")
from EDParallelExecute import EDParallelExecute
from EDUtilsPlatform import EDUtilsPlatform
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDJob import EDJob
from EDShare import EDShare
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20090405-Numpy-1.3", EDUtilsPlatform.architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="version.version")
fabioPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7", EDUtilsPlatform.architecture)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath, _strMethodVersion="version")
h5pyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "H5Py-1.3.0", EDUtilsPlatform.architecture)
h5py = EDFactoryPluginStatic.preImport("h5py", h5pyPath, _strMethodVersion="version.api_version", _strForceVersion="1.8")
from EDShare import EDShare
EDFactoryPluginStatic.loadModule('EDPluginHDF5StackImagesv10')
EDFactoryPluginStatic.loadModule('EDPluginControlAlignStackv1_0')
EDFactoryPluginStatic.loadModule("EDPluginAccumulatorv1_0")
from EDPluginAccumulatorv1_0 import EDPluginAccumulatorv1_0
from EDPluginControlAlignStackv1_0 import EDPluginControlAlignStackv1_0
from EDPluginControlFullFieldXASv1_0 import EDPluginControlFullFieldXASv1_0
from EDPluginHDF5StackImagesv10 import EDPluginHDF5StackImagesv10
from XSDataFullFieldXAS import MeasureOffset, XSDataInputAlignStack, XSDataInputFullFieldXAS
from XSDataCommon import XSDataTime, XSDataFile, XSDataImageExt, XSDataString, XSDataInteger, XSDataBoolean, XSDataDouble
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
__author__ = "Jerome Kieffer"
__license__ = "GPLv3+"
__copyright__ = "2011, ESRF, Grenoble"
__date__ = "2011/05/09"
import os
from EDPluginControl import EDPluginControl
from XSDataShiftv1_0 import XSDataInputStitchImage, XSDataInteger, \
XSDataResultStitchImage, XSDataFile, XSDataString, XSDataBoolean, XSDataInputMeasureOffset, \
XSDataInputStitchOffsetedImage, OffsetedImage, XSDataDouble, XSDataImageExt, XSDataArray
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20090405-Numpy-1.3", EDUtilsPlatform.architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
class EDPluginControlStitchImagev1_0(EDPluginControl):
"""
Control plugin doing automatic image alignment and stitching.
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStitchImage)
self.__strControlledPluginMeasure = "EDPluginExecMeasureOffsetv1_0"
self.__strControlledPluginStitch = "EDPluginExecStitchOffsetedImagev1_0"
self.lInputFiles = []
try:
import numpy
except ImportError:
numpy = None
TEMPDIR = tempfile.gettempdir()
BACKEND = "numpy" # None
if not BACKEND and os.name in ["posix", "nt"]:
h5pyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "H5Py-1.3.0",
EDUtilsPlatform.architecture)
h5py = EDFactoryPluginStatic.preImport(
"h5py",
_strPath=h5pyPath,
_strForceVersion="1.8",
_strMethodVersion="version.api_version")
if h5py is not None:
BACKEND = "hdf5"
if numpy and not BACKEND:
BACKEND = "numpy"
if not BACKEND:
BACKEND = "dict"
class DirStorage():
"""
Simple class that behaves like like an HDF5 file but as a directory with numpy files.
"""
def __init__(self, filename):
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os, sys
from EDVerbose import EDVerbose
from EDTestCase import EDTestCase
from EDAssert import EDAssert
from EDUtilsArray import EDUtilsArray
from XSDataCommon import XSDataArray
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
#EDVerbose.screen("Check Install Numpy")
EDFactoryPluginStatic.loadModule("EDInstallNumpyv1_3")
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20090405-Numpy-1.3", EDUtilsPlatform.architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="__version__")
if numpy is None:
EDVerbose.WARNING("Numpy is not directly available, I will run all tests without it")
#EDVerbose.screen("Check Install PIL")
EDFactoryPluginStatic.loadModule("EDInstallPILv1_1_7")
#ImagePath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20091115-PIL-1.1.7", EDUtilsPlatform.architecture)
#Image = EDFactoryPluginStatic.preImport("Image", ImagePath, _strMethodVersion="VERSION")
#if Image is None:
# EDVerbose.WARNING("Image is not directly available, I will run all tests without it")
#EDVerbose.screen("Check Install Fabio")
EDFactoryPluginStatic.loadModule("EDInstallFabio_v0_0_7")
#fabioPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7", EDUtilsPlatform.architecture)
#fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath, _strMethodVersion="version")
#
__author__ = "Jerome Kieffer"
__license__ = "GPLv3+"
__copyright__ = "2011, ESRF, Grenoble"
__date__ = "2011/05/09"
import os
from EDPluginControl import EDPluginControl
from XSDataShiftv1_0 import XSDataInputStitchImage, XSDataInteger, \
XSDataResultStitchImage, XSDataFile, XSDataString, XSDataBoolean, XSDataInputMeasureOffset, \
XSDataInputStitchOffsetedImage, OffsetedImage, XSDataDouble, XSDataImageExt, XSDataArray
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20090405-Numpy-1.3", EDUtilsPlatform.architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
class EDPluginControlStitchImagev1_0(EDPluginControl):
"""
Control plugin doing automatic image alignment and stitching.
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStitchImage)
self.__strControlledPluginMeasure = "EDPluginExecMeasureOffsetv1_0"
self.__strControlledPluginStitch = "EDPluginExecStitchOffsetedImagev1_0"
self.lInputFiles = []
self.xDummy = None
from XSDataCommon import XSPluginItem, XSDataDouble
from XSDataShiftv1_0 import XSDataInputMeasureOffset
from XSDataShiftv1_0 import XSDataResultMeasureOffset
from EDAssert import EDAssert
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsPath import EDUtilsPath
from EDThreading import Semaphore
################################################################################
# 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)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
feature = EDFactoryPluginStatic.preImport("feature")
sift_pyocl = EDFactoryPluginStatic.preImport("sift_pyocl")
if not sift_pyocl:
EDVerbose.WARNING("Try to load sift_pyocl from sift: You should update your sift installation")
sift_pyocl = EDFactoryPluginStatic.preImport("sift")
#
if (feature or sift_pyocl) is None:
strErr = "Error in loading feature (https://github.com/kif/imageAlignment) AND sift_pyocl (https://github.com/kif/sift_pyocl)"
EDVerbose.ERROR(strErr)
raise ImportError(strErr)
import scipy.interpolate
srcDir = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "src")
from EDAssert import EDAssert
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsPath import EDUtilsPath
from EDThreading import Semaphore
################################################################################
# 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)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
feature = EDFactoryPluginStatic.preImport("feature")
sift_pyocl = EDFactoryPluginStatic.preImport("sift")
#
if (feature or sift_pyocl) is None:
strErr = "Error in loading feature (https://github.com/kif/imageAlignment) AND sift_pyocl (https://github.com/kif/sift_pyocl)"
EDVerbose.ERROR(strErr)
raise ImportError(strErr)
class EDPluginExecAlignFramev1_0(EDPluginExec):
"""
An exec plugin that taked an images and a reference and alines the frame on the reference based on the SIFT algorithm.
sys.path.append(kernel_src)
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller, installLibrary
from EDFactoryPluginStatic import EDFactoryPluginStatic
moduleName = "fabio"
modulePath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7",
EDUtilsPlatform.architecture)
moduleVersion = "0.0.7"
################################################################################
# Import the good version of FabIO ...
################################################################################
if os.name == "posix":
oModule = EDFactoryPluginStatic.preImport(moduleName)
if not oModule:
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
if oModule is None:
installLibrary(modulePath)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
try:
version = oModule.version
except AttributeError:
version = "0.0.0"
if version.split(".") < moduleVersion.split("."):
EDVerbose.screen("Wrong %s library: %s " % (moduleName, version))
EDFactoryPluginStatic.unImport(moduleName)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath,
moduleVersion)
if kernel_src not in sys.path:
sys.path.append(kernel_src)
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller, installLibrary
from EDFactoryPluginStatic import EDFactoryPluginStatic
moduleName = "fabio"
modulePath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.6", EDUtilsPlatform.architecture)
moduleVersion = "0.0.6"
################################################################################
# Import the good version of FabIO ...
################################################################################
oModule = EDFactoryPluginStatic.preImport(moduleName)
if not oModule:
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
if oModule is None:
installLibrary(modulePath)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
try:
version = oModule.version
except AttributeError:
version = "0.0.0"
if version.split(".") < moduleVersion.split("."):
EDVerbose.screen("Wrong %s library: %s " % (moduleName, version))
EDFactoryPluginStatic.unImport(moduleName)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath, moduleVersion)
__license__ = "LGPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "20120228"
import os, tempfile
from EDLogging import EDLogging
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
from EDSession import EDSession
from EDUtilsPath import EDUtilsPath
TEMPDIR = tempfile.gettempdir()
if os.name in ["posix", "nt"]:
h5pyPath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "H5Py-1.3.0", EDUtilsPlatform.architecture)
h5py = EDFactoryPluginStatic.preImport("h5py", _strPath=h5pyPath, _strForceVersion="1.8", _strMethodVersion="version.api_version")
# h5py = None
if h5py is None:
BACKEND = "dict"
else:
BACKEND = "hdf5"
else:
BACKEND = "dict"
if BACKEND == "dict":
import pickle
class EDShare(EDLogging, EDSession):
"""
This class implements methods to share (large) arrays between plugins.
import os, shutil
from EDVerbose import EDVerbose
from EDPluginControl import EDPluginControl
from EDUtilsBioSaxs import EDUtilsBioSaxs
from EDUtilsPath import EDUtilsPath
from EDFactoryPluginStatic import EDFactoryPluginStatic
from XSDataCommon import XSDataString, XSDataImage, XSDataDouble, XSDataLength, \
XSDataWavelength
from XSDataBioSaxsv1_0 import XSDataInputBioSaxsMetadatav1_0, XSDataResultBioSaxsMetadatav1_0
EDFactoryPluginStatic.loadModule("XSDataSaxsv1_0")
from XSDataSaxsv1_0 import XSDataInputSaxsAddMetadatav1_0
from EDUtilsPlatform import EDUtilsPlatform
architecture = EDUtilsPlatform.architecture
edfFilePath = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "EdfFile", architecture)
EdfFileMod = EDFactoryPluginStatic.preImport("EdfFile", edfFilePath)
if EdfFileMod is None:
EDVerbose.ERROR("Unable to import EdfFile: Please re-run the tests EDTestSuiteBioSaxs")
else:
from EdfFile import EdfFile
class EDPluginBioSaxsMetadatav1_0(EDPluginControl):
"""
Plugin for reading, updating and writing Metadata.
"""
def __init__(self):
"""
"""
from XSDataCommon import XSDataImage, XSDataString
from XSDataImageFilter import XSDataInputMedianFilter
from XSDataImageFilter import XSDataResultMedianFilter
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDUtilsPlatform import EDUtilsPlatform
################################################################################
# AutoBuilder for Numpy, PIL and Fabio
################################################################################
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7", architecture)
imagingPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20090405-Numpy-1.3", architecture)
scipyPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "20090711-SciPy-0.7.1", architecture)
EDFactoryPluginStatic.preImport("numpy", numpyPath)
EDFactoryPluginStatic.preImport("scipy", scipyPath)
EDFactoryPluginStatic.preImport("fabio", fabioPath)
EDFactoryPluginStatic.preImport("Image", imagingPath)
try:
import fabio
import scipy
import numpy
except Exception:
EDVerbose.ERROR(
"Error in loading numpy, Scipy, PIL or Fabio,\n\
Please re-run the test suite for EDTestSuitePluginFilterImage \
to ensure that all modules are compiled for you computer as they don't seem to be installed"
)
import os, sys
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller, installLibrary
from EDFactoryPluginStatic import EDFactoryPluginStatic
################################################################################
# Import the right version of Scipy
################################################################################
moduleName = "matplotlib"
modulePath = os.path.join(os.environ["EDNA_HOME"], "libraries", "Matplotlib-1.0.1", EDUtilsPlatform.architecture)
moduleVersion = "0.9.0" # minimum version to be compatible
oModule = EDFactoryPluginStatic.preImport(moduleName)
if not oModule:
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
if oModule is None:
installLibrary(modulePath)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
try:
version = oModule.__version__
except AttributeError:
version = "0.0.0"
if version.split(".") < moduleVersion.split("."):
EDVerbose.screen("Wrong %s library: %s " % (moduleName, version))
EDFactoryPluginStatic.unImport(moduleName)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath, moduleVersion, _strMethodVersion="__version__")
# HDF5 does not like unicode string and crashes with cryptic error messages
###############################################################################
import os, threading, time, locale
from EDVerbose import EDVerbose
from EDPluginHDF5 import EDPluginHDF5
from EDAssert import EDAssert
from EDUtilsPlatform import EDUtilsPlatform
from XSDataHDF5v1_0 import XSDataInputHDF5MapSpectra, XSDataResultHDF5MapSpectra
from XSDataCommon import XSDataFile, XSDataString
from EDConfiguration import EDConfiguration
from EDUtilsArray import EDUtilsArray
from EDFactoryPluginStatic import EDFactoryPluginStatic
from EDPluginHDF5 import numpyPath, h5pyPath, fabioPath
numpy = EDFactoryPluginStatic.preImport("numpy",
numpyPath,
_strMethodVersion="__version__")
h5py = EDFactoryPluginStatic.preImport("h5py",
h5pyPath,
_strMethodVersion="version.version")
fabio = EDFactoryPluginStatic.preImport("fabio",
fabioPath,
_strMethodVersion="version")
class EDPluginHDF5MapOfSpectrav10(EDPluginHDF5):
"""
This plugin is made for putting together 1D spectra comming from a 2D scan in a 3D cube,
read using various libraries ... , and put them together in an NeXus/HDF5 file
"""
HDF5_DATASET_MAPSPECTRA_ATTRIBUTES = {
sys.path.append(kernel_src)
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsLibraryInstaller import EDUtilsLibraryInstaller, installLibrary
from EDFactoryPluginStatic import EDFactoryPluginStatic
################################################################################
# Import the right version of Scipy
################################################################################
moduleName = "matplotlib"
modulePath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"Matplotlib-1.0.1", EDUtilsPlatform.architecture)
moduleVersion = "0.9.0" #minimum version to be compatible
oModule = EDFactoryPluginStatic.preImport(moduleName)
if not oModule:
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
if oModule is None:
installLibrary(modulePath)
oModule = EDFactoryPluginStatic.preImport(moduleName, modulePath)
try:
version = oModule.__version__
except AttributeError:
version = "0.0.0"
if version.split(".") < moduleVersion.split("."):
EDVerbose.screen("Wrong %s library: %s " % (moduleName, version))
EDFactoryPluginStatic.unImport(moduleName)
oModule = EDFactoryPluginStatic.preImport(moduleName,
modulePath,
import os, threading, time, locale
from EDVerbose import EDVerbose
from EDPluginExec import EDPluginExec
from EDAssert import EDAssert
from EDUtilsPlatform import EDUtilsPlatform
from EDConfiguration import EDConfiguration
from EDModule import EDModule
from XSDataHDF5v1_0 import XSDataInputHDF5Writer
from EDFactoryPluginStatic import EDFactoryPluginStatic
architecture = EDUtilsPlatform.architecture
numpyPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "20090405-Numpy-1.3", architecture)
h5pyPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "H5Py-1.3.0", architecture)
fabioPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "FabIO-0.0.7", architecture)
imagingPath = os.path.join(os.environ["EDNA_HOME"], "edna-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(EDPluginExec):
from EDThreading import Semaphore
################################################################################
# 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)
fftw3Path = os.path.join(EDUtilsPath.EDNA_HOME, "libraries", "pyfftw3-0.2.1",
architecture)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
EDFactoryPluginStatic.preImport("scipy.ndimage", scipyPath)
EDFactoryPluginStatic.preImport("scipy.fftpack", scipyPath)
EDFactoryPluginStatic.preImport("scipy.interpolate", scipyPath)
EDFactoryPluginStatic.preImport("scipy.signal", scipyPath)
Image = EDFactoryPluginStatic.preImport("Image", imagingPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
fftw3 = EDFactoryPluginStatic.preImport("fftw3", fftw3Path)
try:
import scipy.ndimage, scipy.interpolate
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"
)
from EDConfiguration import EDConfiguration
from XSDataCommon import XSPluginItem
# import the DriverFactory - either from edna's xia2core or a separate
# one configured in the environment as XIA2CORE_ROOT.
if "XIA2CORE_ROOT" in os.environ and os.environ['XIA2CORE_ROOT'] != '':
pathxia2core = os.path.join(os.environ['XIA2CORE_ROOT'], 'Python')
else:
pathxia2core = EDFactoryPluginStatic.getModuleLocation('XIA2CoreVersion')
os.environ["XIA2CORE_ROOT"] = os.path.dirname(pathxia2core)
EDVerbose.DEBUG('Found xia2core in %s' % pathxia2core)
EDFactoryPluginStatic.preImport("Driver", pathxia2core)
from Driver.DriverFactory import DriverFactory
class EDPluginExecProcessXIA2CORE(EDPluginExec):
# static class variables
CONF_EXEC_PROCESS_EXECUTABLE = "execProcessExecutable"
CONF_EXEC_PROCESS_XIA2CORE_TYPE = "execProcessXIA2COREType"
CONF_EXEC_PROCESS_VERSION_STRING = "execProcessXIA2COREVersionString"
def __init__ (self):
"""
Initializes process related attributes described above
"""
from XSDataNormalizeImage import XSDataInputNormalize, XSDataResultNormalize
from EDAssert import EDAssert
from EDUtilsPlatform import EDUtilsPlatform
from EDShare import EDShare
from EDUtilsPath import EDUtilsPath
from EDThreading import Semaphore
################################################################################
# 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)
EDFactoryPluginStatic.preImport("Image", imagingPath)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strMethodVersion="version.version")
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
class EDPluginExecNormalizeImagev1_1(EDPluginExec):
"""
Plugin that normalizes an image (subtract dark current and divide by flat-field image, taking into account the exposure time)
v1.1 is compatible with EDShare -> lower memory footprint
"""
dictDark = {} #Nota: the key is a string: str(exposutTime)
# listDarkExposure = []
# listDarkArray = []
semaphore = Semaphore()
dtype = None #
import base64, hashlib, sys, struct, threading, os
from EDVerbose import EDVerbose
from EDObject import EDObject
from XSDataCommon import XSDataArray, XSDataString, XSDataImageExt, XSDataFile
from EDAssert import EDAssert
from EDShare import EDShare
from EDUtilsPlatform import EDUtilsPlatform
from EDFactoryPluginStatic import EDFactoryPluginStatic
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "FabIO-0.0.7", architecture)
imagingPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(os.environ["EDNA_HOME"], "edna-libraries", "20090405-Numpy-1.3", architecture)
EDFactoryPluginStatic.preImport("Image", imagingPath)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath, _strForceVersion="1.2", _strMethodVersion="version.version")
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath, _strForceVersion="0.0.7", _strMethodVersion="version")
if (numpy is not None) and ("floating" in dir(numpy)):
bHaveNumpy = True
floatType = (float, numpy.floating)
else:
bHaveNumpy = False
floatType = float
if fabio is not None:
bHaveFabio = True
else:
bHaveFabio = False
from EDUtilsPlatform import EDUtilsPlatform
################################################################################
# AutoBuilder for Numpy, PIL and Fabio
################################################################################
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7",
architecture)
imagingPath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20090405-Numpy-1.3", architecture)
scipyPath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20090711-SciPy-0.7.1", architecture)
EDFactoryPluginStatic.preImport("numpy", numpyPath)
EDFactoryPluginStatic.preImport("fabio", fabioPath)
EDFactoryPluginStatic.preImport("Image", imagingPath)
EDFactoryPluginStatic.preImport("scipy", scipyPath)
EDFactoryPluginStatic.preImport("scipy.ndimage.morphology", scipyPath)
try:
import numpy, Image, fabio, scipy, scipy.ndimage.morphology
except Exception:
EDVerbose.ERROR("Error in loading numpy, PIL, fabio or scipy,\n\
Please re-run the test suite for EDTestSuitePluginExecThumbnailv10 \
to ensure that all modules are compiled for you computer as they don't seem to be installed"
)
raise
import ImageFile, ImageOps
from EDShare import EDShare
from EDUtilsPlatform import EDUtilsPlatform
EDFactoryPluginStatic.loadModule("EDInstallNumpyv1_3")
EDFactoryPluginStatic.loadModule("EDInstallPILv1_1_7")
EDFactoryPluginStatic.loadModule("EDInstallFabio_v0_0_7")
architecture = EDUtilsPlatform.architecture
fabioPath = os.path.join(os.environ["EDNA_HOME"], "libraries", "FabIO-0.0.7",
architecture)
imagingPath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20091115-PIL-1.1.7", architecture)
numpyPath = os.path.join(os.environ["EDNA_HOME"], "libraries",
"20090405-Numpy-1.3", architecture)
EDFactoryPluginStatic.preImport("Image", imagingPath)
numpy = EDFactoryPluginStatic.preImport("numpy", numpyPath)
fabio = EDFactoryPluginStatic.preImport("fabio", fabioPath)
if "USER" not in os.environ:
os.environ["USER"] = "******"
destDir = os.path.join(tempfile.gettempdir(), "edna-%s" % os.environ["USER"])
EDShare.initialize(destDir)
class EDTestCasePluginExecuteExecMatrixInvertv2_0_path(EDTestCasePluginExecute
):
"""
Those are all execution tests for the EDNA Exec plugin MatrixInvertv2_0 (Using shared arrays via HDF5)
"""
def __init__(self, _strTestName=None):
from EDConfiguration import EDConfiguration
from XSDataCommon import XSPluginItem
# import the DriverFactory - either from edna's xia2core or a separate
# one configured in the environment as XIA2CORE_ROOT.
if "XIA2CORE_ROOT" in os.environ and os.environ['XIA2CORE_ROOT'] != '':
pathxia2core = os.path.join(os.environ['XIA2CORE_ROOT'], 'Python')
else:
pathxia2core = EDFactoryPluginStatic.getModuleLocation('XIA2CoreVersion')
os.environ["XIA2CORE_ROOT"] = os.path.dirname(pathxia2core)
EDVerbose.DEBUG('Found xia2core in %s' % pathxia2core)
EDFactoryPluginStatic.preImport("Driver", pathxia2core)
from Driver.DriverFactory import DriverFactory
class EDPluginExecProcessXIA2CORE(EDPluginExec):
# static class variables
CONF_EXEC_PROCESS_EXECUTABLE = "execProcessExecutable"
CONF_EXEC_PROCESS_XIA2CORE_TYPE = "execProcessXIA2COREType"
CONF_EXEC_PROCESS_VERSION_STRING = "execProcessXIA2COREVersionString"
def __init__(self):
"""
Initializes process related attributes described above
