def open(filename): # pylint:disable=redefined-builtin
"""
Open a file as an `h5py`-like object.
Format supported:
- h5 files, if `h5py` module is installed
- SPEC files exposed as a NeXus layout
- raster files exposed as a NeXus layout (if `fabio` is installed)
- fio files exposed as a NeXus layout
- Numpy files ('npy' and 'npz' files)
The filename can be trailled an HDF5 path using the separator `::`. In this
case the object returned is a proxy to the target node, implementing the
`close` function and supporting `with` context.
The file is opened in read-only mode.
:param str filename: A filename which can containt an HDF5 path by using
`::` separator.
:raises: IOError if the file can't be loaded or path can't be found
:rtype: h5py-like node
"""
url = silx.io.url.DataUrl(filename)
if url.scheme() in [None, "file", "silx"]:
# That's a local file
if not url.is_valid():
raise IOError("URL '%s' is not valid" % filename)
h5_file = _open_local_file(url.file_path())
elif url.scheme() in ["fabio"]:
raise IOError("URL '%s' containing fabio scheme is not supported" %
filename)
else:
# That's maybe an URL supported by h5pyd
uri = urllib.parse.urlparse(filename)
if h5pyd is None:
raise IOError("URL '%s' unsupported. Try to install h5pyd." %
filename)
path = uri.path
endpoint = "%s://%s" % (uri.scheme, uri.netloc)
if path.startswith("/"):
path = path[1:]
return h5pyd.File(path, 'r', endpoint=endpoint)
if url.data_slice():
raise IOError("URL '%s' containing slicing is not supported" %
filename)
if url.data_path() in [None, "/", ""]:
# The full file is requested
return h5_file
else:
# Only a children is requested
if url.data_path() not in h5_file:
msg = "File '%s' does not contain path '%s'." % (filename,
url.data_path())
raise IOError(msg)
node = h5_file[url.data_path()]
proxy = _MainNode(node, h5_file)
return proxy
def open(filename): # pylint:disable=redefined-builtin
"""
Open a file as an `h5py`-like object.
Format supported:
- h5 files, if `h5py` module is installed
- SPEC files exposed as a NeXus layout
- raster files exposed as a NeXus layout (if `fabio` is installed)
- Numpy files ('npy' and 'npz' files)
The filename can be trailled an HDF5 path using the separator `::`. In this
case the object returned is a proxy to the target node, implementing the
`close` function and supporting `with` context.
The file is opened in read-only mode.
:param str filename: A filename which can containt an HDF5 path by using
`::` separator.
:raises: IOError if the file can't be loaded or path can't be found
:rtype: h5py-like node
"""
url = silx.io.url.DataUrl(filename)
if url.scheme() in [None, "file", "silx"]:
# That's a local file
if not url.is_valid():
raise IOError("URL '%s' is not valid" % filename)
h5_file = _open_local_file(url.file_path())
elif url.scheme() in ["fabio"]:
raise IOError("URL '%s' containing fabio scheme is not supported" % filename)
else:
# That's maybe an URL supported by h5pyd
uri = six.moves.urllib.parse.urlparse(filename)
if h5pyd is None:
raise IOError("URL '%s' unsupported. Try to install h5pyd." % filename)
path = uri.path
endpoint = "%s://%s" % (uri.scheme, uri.netloc)
if path.startswith("/"):
path = path[1:]
return h5pyd.File(path, 'r', endpoint=endpoint)
if url.data_slice():
raise IOError("URL '%s' containing slicing is not supported" % filename)
if url.data_path() in [None, "/", ""]:
# The full file is requested
return h5_file
else:
# Only a children is requested
if url.data_path() not in h5_file:
msg = "File '%s' does not contain path '%s'." % (filename, url.data_path())
raise IOError(msg)
node = h5_file[url.data_path()]
proxy = _MainNode(node, h5_file)
return proxy
def testSelectNXdataAccepted_Activate(self):
if fabio is None:
self.skipTest("fabio is missing")
dialog = self.createDialog()
browser = utils.findChildren(dialog, qt.QWidget, name="browser")[0]
dialog.show()
self.qWaitForWindowExposed(dialog)
self.assertTrue(dialog.isVisible())
filename = _tmpDirectory + "/data.h5"
dialog.selectFile(os.path.dirname(filename))
self.qWaitForPendingActions(dialog)
# select, then double click on the file
index = browser.rootIndex().model().index(filename)
browser.selectIndex(index)
browser.activated.emit(index)
self.qWaitForPendingActions(dialog)
# select, then double click on the file
index = browser.rootIndex().model().indexFromH5Object(
dialog._AbstractDataFileDialog__h5["/nxdata"])
browser.selectIndex(index)
browser.activated.emit(index)
self.qWaitForPendingActions(dialog)
button = utils.findChildren(dialog, qt.QPushButton, name="open")[0]
self.assertTrue(button.isEnabled())
self.mouseClick(button, qt.Qt.LeftButton)
url = silx.io.url.DataUrl(dialog.selectedUrl())
self.assertEqual(url.data_path(), "/nxdata")
self.assertFalse(dialog.isVisible())
self.assertEqual(dialog.result(), qt.QDialog.Accepted)
def testSelectNXdataAccepted_Activate(self):
dialog = self.createDialog()
browser = testutils.findChildren(dialog, qt.QWidget, name="browser")[0]
dialog.show()
self.qWaitForWindowExposed(dialog)
self.assertTrue(dialog.isVisible())
filename = _tmpDirectory + "/data.h5"
dialog.selectFile(os.path.dirname(filename))
self.qWaitForPendingActions(dialog)
# select, then double click on the file
index = browser.rootIndex().model().index(filename)
browser.selectIndex(index)
browser.activated.emit(index)
self.qWaitForPendingActions(dialog)
# select, then double click on the file
index = browser.rootIndex().model().indexFromH5Object(dialog._AbstractDataFileDialog__h5["/nxdata"])
browser.selectIndex(index)
browser.activated.emit(index)
self.qWaitForPendingActions(dialog)
button = testutils.findChildren(dialog, qt.QPushButton, name="open")[0]
self.assertTrue(button.isEnabled())
self.mouseClick(button, qt.Qt.LeftButton)
url = silx.io.url.DataUrl(dialog.selectedUrl())
self.assertEqual(url.data_path(), "/nxdata")
self.assertFalse(dialog.isVisible())
self.assertEqual(dialog.result(), qt.QDialog.Accepted)
def testSelectRoot_Activate(self):
if fabio is None:
self.skipTest("fabio is missing")
dialog = self.createDialog()
browser = utils.findChildren(dialog, qt.QWidget, name="browser")[0]
dialog.show()
self.qWaitForWindowExposed(dialog)
self.assertTrue(dialog.isVisible())
filename = _tmpDirectory + "/data.h5"
dialog.selectFile(os.path.dirname(filename))
self.qWaitForPendingActions(dialog)
# select, then double click on the file
index = browser.rootIndex().model().index(filename)
browser.selectIndex(index)
browser.activated.emit(index)
self.qWaitForPendingActions(dialog)
button = utils.findChildren(dialog, qt.QPushButton, name="open")[0]
self.assertTrue(button.isEnabled())
self.mouseClick(button, qt.Qt.LeftButton)
url = silx.io.url.DataUrl(dialog.selectedUrl())
self.assertTrue(url.data_path() is not None)
self.assertFalse(dialog.isVisible())
self.assertEquals(dialog.result(), qt.QDialog.Accepted)
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 testSelectRoot_Activate(self):
dialog = self.createDialog()
browser = testutils.findChildren(dialog, qt.QWidget, name="browser")[0]
dialog.show()
self.qWaitForWindowExposed(dialog)
self.assertTrue(dialog.isVisible())
filename = _tmpDirectory + "/data.h5"
dialog.selectFile(os.path.dirname(filename))
self.qWaitForPendingActions(dialog)
# select, then double click on the file
index = browser.rootIndex().model().index(filename)
browser.selectIndex(index)
browser.activated.emit(index)
self.qWaitForPendingActions(dialog)
button = testutils.findChildren(dialog, qt.QPushButton, name="open")[0]
self.assertTrue(button.isEnabled())
self.mouseClick(button, qt.Qt.LeftButton)
url = silx.io.url.DataUrl(dialog.selectedUrl())
self.assertTrue(url.data_path() is not None)
self.assertFalse(dialog.isVisible())
self.assertEqual(dialog.result(), qt.QDialog.Accepted)
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 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
