def testSelectImageFromEdf(self):
dialog = self.createDialog()
dialog.show()
self.qWaitForWindowExposed(dialog)
# init state
filename = _tmpDirectory + "/singleimage.edf"
url = silx.io.url.DataUrl(scheme="silx", file_path=filename, data_path="/scan_0/instrument/detector_0/data")
dialog.selectUrl(url.path())
self.assertEqual(dialog._selectedData().shape, (100, 100))
self.assertSamePath(dialog.selectedFile(), filename)
self.assertSamePath(dialog.selectedUrl(), url.path())
def testSelectImageFromEdf(self):
dialog = self.createDialog()
dialog.show()
self.qWaitForWindowExposed(dialog)
# init state
filename = _tmpDirectory + "/singleimage.edf"
url = silx.io.url.DataUrl(scheme="silx", file_path=filename, data_path="/scan_0/instrument/detector_0/data")
dialog.selectUrl(url.path())
self.assertTrue(dialog._selectedData().shape, (100, 100))
self.assertSamePath(dialog.selectedFile(), filename)
self.assertSamePath(dialog.selectedUrl(), url.path())
def test_silx_scheme(self):
url = silx.io.url.DataUrl(scheme="silx",
file_path=self.h5_filename,
data_path="/")
with utils.open(url.path()) as f:
self.assertIsNotNone(f)
self.assertTrue(silx.io.utils.is_file(f))
def test_fabio_scheme(self):
if h5py is None:
self.skipTest("H5py is missing")
if fabio is None:
self.skipTest("Fabio is missing")
url = silx.io.url.DataUrl(scheme="fabio", file_path=self.edf_filename)
self.assertRaises(IOError, utils.open, url.path())
def test_fabio_scheme(self):
if h5py is None:
self.skipTest("H5py is missing")
if fabio is None:
self.skipTest("Fabio is missing")
url = silx.io.url.DataUrl(scheme="fabio", file_path=self.edf_filename)
self.assertRaises(IOError, utils.open, url.path())
def test_silx_scheme(self):
if h5py is None:
self.skipTest("H5py is missing")
url = silx.io.url.DataUrl(scheme="silx", file_path=self.h5_filename, data_path="/")
with utils.open(url.path()) as f:
self.assertIsNotNone(f)
self.assertTrue(silx.io.utils.is_file(f))
def testBadSubpath(self):
dialog = self.createDialog()
self.qWaitForPendingActions(dialog)
browser = testutils.findChildren(dialog, qt.QWidget, name="browser")[0]
filename = _tmpDirectory + "/data.h5"
url = silx.io.url.DataUrl(scheme="silx", file_path=filename, data_path="/group/foobar")
dialog.selectUrl(url.path())
self.qWaitForPendingActions(dialog)
self.assertIsNotNone(dialog._selectedData())
# an existing node is browsed, but the wrong path is selected
index = browser.rootIndex()
obj = index.model().data(index, role=Hdf5TreeModel.H5PY_OBJECT_ROLE)
self.assertEqual(obj.name, "/group")
url = silx.io.url.DataUrl(dialog.selectedUrl())
self.assertEqual(url.data_path(), "/group")
def testBadSubpath(self):
dialog = self.createDialog()
self.qWaitForPendingActions(dialog)
browser = testutils.findChildren(dialog, qt.QWidget, name="browser")[0]
filename = _tmpDirectory + "/data.h5"
url = silx.io.url.DataUrl(scheme="silx", file_path=filename, data_path="/group/foobar")
dialog.selectUrl(url.path())
self.qWaitForPendingActions(dialog)
self.assertIsNotNone(dialog._selectedData())
# an existing node is browsed, but the wrong path is selected
index = browser.rootIndex()
obj = index.model().data(index, role=Hdf5TreeModel.H5PY_OBJECT_ROLE)
self.assertEqual(obj.name, "/group")
url = silx.io.url.DataUrl(dialog.selectedUrl())
self.assertEqual(url.data_path(), "/group")
def get_data(url):
"""Returns a numpy data from an URL.
Examples:
>>> # 1st frame from an EDF using silx.io.open
>>> data = silx.io.get_data("silx:/users/foo/image.edf::/scan_0/instrument/detector_0/data[0]")
>>> # 1st frame from an EDF using fabio
>>> data = silx.io.get_data("fabio:/users/foo/image.edf::[0]")
Yet 2 schemes are supported by the function.
- If `silx` scheme is used, the file is opened using
:meth:`silx.io.open`
and the data is reach using usually NeXus paths.
- If `fabio` scheme is used, the file is opened using :meth:`fabio.open`
from the FabIO library.
No data path have to be specified, but each frames can be accessed
using the data slicing.
This shortcut of :meth:`silx.io.open` allow to have a faster access to
the data.
.. seealso:: :class:`silx.io.url.DataUrl`
:param Union[str,silx.io.url.DataUrl]: A data URL
:rtype: Union[numpy.ndarray, numpy.generic]
:raises ImportError: If the mandatory library to read the file is not
available.
:raises ValueError: If the URL is not valid or do not match the data
:raises IOError: If the file is not found or in case of internal error of
:meth:`fabio.open` or :meth:`silx.io.open`. In this last case more
informations are displayed in debug mode.
"""
if not isinstance(url, silx.io.url.DataUrl):
url = silx.io.url.DataUrl(url)
if not url.is_valid():
raise ValueError("URL '%s' is not valid" % url.path())
if not os.path.exists(url.file_path()):
raise IOError("File '%s' not found" % url.file_path())
if url.scheme() == "silx":
data_path = url.data_path()
data_slice = url.data_slice()
with open(url.file_path()) as h5:
if data_path not in h5:
raise ValueError("Data path from URL '%s' not found" %
url.path())
data = h5[data_path]
if not silx.io.is_dataset(data):
raise ValueError("Data path from URL '%s' is not a dataset" %
url.path())
if data_slice is not None:
data = h5py_read_dataset(data, index=data_slice)
else:
# works for scalar and array
data = h5py_read_dataset(data)
elif url.scheme() == "fabio":
import fabio
data_slice = url.data_slice()
if data_slice is None:
data_slice = (0, )
if data_slice is None or len(data_slice) != 1:
raise ValueError(
"Fabio slice expect a single frame, but %s found" % data_slice)
index = data_slice[0]
if not isinstance(index, int):
raise ValueError(
"Fabio slice expect a single integer, but %s found" %
data_slice)
try:
fabio_file = fabio.open(url.file_path())
except Exception:
logger.debug("Error while opening %s with fabio",
url.file_path(),
exc_info=True)
raise IOError(
"Error while opening %s with fabio (use debug for more information)"
% url.path())
if fabio_file.nframes == 1:
if index != 0:
raise ValueError(
"Only a single frame available. Slice %s out of range" %
index)
data = fabio_file.data
else:
data = fabio_file.getframe(index).data
# There is no explicit close
fabio_file = None
else:
raise ValueError("Scheme '%s' not supported" % url.scheme())
return data
def test_sliced_url(self):
url = silx.io.url.DataUrl(file_path=self.h5_filename, data_slice=(5, ))
self.assertRaises(IOError, utils.open, url.path())
def test_bad_url(self):
url = silx.io.url.DataUrl(scheme="sil", file_path=self.h5_filename)
self.assertRaises(IOError, utils.open, url.path())
def test_fabio_scheme(self):
url = silx.io.url.DataUrl(scheme="fabio", file_path=self.edf_filename)
self.assertRaises(IOError, utils.open, url.path())
def test_sliced_url(self):
url = silx.io.url.DataUrl(file_path=self.h5_filename, data_slice=(5,))
self.assertRaises(IOError, utils.open, url.path())
def test_bad_url(self):
url = silx.io.url.DataUrl(scheme="sil", file_path=self.h5_filename)
self.assertRaises(IOError, utils.open, url.path())
def test_fabio_scheme(self):
url = silx.io.url.DataUrl(scheme="fabio", file_path=self.edf_filename)
self.assertRaises(IOError, utils.open, url.path())
def get_data(url):
"""Returns a numpy data from an URL.
Examples:
>>> # 1st frame from an EDF using silx.io.open
>>> data = silx.io.get_data("silx:/users/foo/image.edf::/scan_0/instrument/detector_0/data[0]")
>>> # 1st frame from an EDF using fabio
>>> data = silx.io.get_data("fabio:/users/foo/image.edf::[0]")
Yet 2 schemes are supported by the function.
- If `silx` scheme is used, the file is opened using
:meth:`silx.io.open`
and the data is reach using usually NeXus paths.
- If `fabio` scheme is used, the file is opened using :meth:`fabio.open`
from the FabIO library.
No data path have to be specified, but each frames can be accessed
using the data slicing.
This shortcut of :meth:`silx.io.open` allow to have a faster access to
the data.
.. seealso:: :class:`silx.io.url.DataUrl`
:param Union[str,silx.io.url.DataUrl]: A data URL
:rtype: Union[numpy.ndarray, numpy.generic]
:raises ImportError: If the mandatory library to read the file is not
available.
:raises ValueError: If the URL is not valid or do not match the data
:raises IOError: If the file is not found or in case of internal error of
:meth:`fabio.open` or :meth:`silx.io.open`. In this last case more
informations are displayed in debug mode.
"""
if not isinstance(url, silx.io.url.DataUrl):
url = silx.io.url.DataUrl(url)
if not url.is_valid():
raise ValueError("URL '%s' is not valid" % url.path())
if not os.path.exists(url.file_path()):
raise IOError("File '%s' not found" % url.file_path())
if url.scheme() == "silx":
data_path = url.data_path()
data_slice = url.data_slice()
with open(url.file_path()) as h5:
if data_path not in h5:
raise ValueError("Data path from URL '%s' not found" % url.path())
data = h5[data_path]
if not silx.io.is_dataset(data):
raise ValueError("Data path from URL '%s' is not a dataset" % url.path())
if data_slice is not None:
data = data[data_slice]
else:
# works for scalar and array
data = data[()]
elif url.scheme() == "fabio":
import fabio
data_slice = url.data_slice()
if data_slice is None:
data_slice = (0, )
if data_slice is None or len(data_slice) != 1:
raise ValueError("Fabio slice expect a single frame, but %s found" % data_slice)
index = data_slice[0]
if not isinstance(index, int):
raise ValueError("Fabio slice expect a single integer, but %s found" % data_slice)
try:
fabio_file = fabio.open(url.file_path())
except Exception:
logger.debug("Error while opening %s with fabio", url.file_path(), exc_info=True)
raise IOError("Error while opening %s with fabio (use debug for more information)" % url.path())
if fabio_file.nframes == 1:
if index != 0:
raise ValueError("Only a single frame availalbe. Slice %s out of range" % index)
data = fabio_file.data
else:
data = fabio_file.getframe(index).data
# There is no explicit close
fabio_file = None
else:
raise ValueError("Scheme '%s' not supported" % url.scheme())
return data
