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|
# /*##########################################################################
#
# Copyright (c) 2016-2019 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
__authors__ = ["V. Valls"]
__license__ = "MIT"
__date__ = "17/01/2019"
import logging
import collections
import enum
from typing import Optional
from .. import qt
from .. import icons
from . import _utils
from .Hdf5Node import Hdf5Node
import silx.io.utils
from silx.gui.data.TextFormatter import TextFormatter
from ..hdf5.Hdf5Formatter import Hdf5Formatter
_logger = logging.getLogger(__name__)
_formatter = TextFormatter()
_hdf5Formatter = Hdf5Formatter(textFormatter=_formatter)
# FIXME: The formatter should be an attribute of the Hdf5Model
class DescriptionType(enum.Enum):
"""List of available kind of description.
"""
ERROR = "error"
DESCRIPTION = "description"
TITLE = "title"
PROGRAM = "program"
NAME = "name"
VALUE = "value"
class Hdf5Item(Hdf5Node):
"""Subclass of :class:`qt.QStandardItem` to represent an HDF5-like
item (dataset, file, group or link) as an element of a HDF5-like
tree structure.
"""
def __init__(
self,
text: Optional[str],
obj,
parent,
key=None,
h5Class=None,
linkClass=None,
populateAll=False,
openedPath: Optional[str] = None,
):
"""
:param text: text displayed
:param object obj: Pointer to a h5py-link object. See the `obj` attribute.
:param openedPath: The path with which the item was opened if any
"""
self.__obj = obj
self.__key = key
self.__h5Class = h5Class
self.__isBroken = obj is None and h5Class is None
self.__error = None
self.__text = text
self.__linkClass = linkClass
self.__description = None
self.__nx_class = None
Hdf5Node.__init__(self, parent, populateAll=populateAll, openedPath=openedPath)
def _getCanonicalName(self):
parent = self.parent
if parent is None:
return self.__text
else:
return "%s/%s" % (parent._getCanonicalName(), self.__text)
@property
def obj(self):
if self.__key:
self.__initH5Object()
return self.__obj
@property
def basename(self):
return self.__text
@property
def h5Class(self):
"""Returns the class of the stored object.
When the object is in lazy loading, this method should be able to
return the type of the future loaded object. It allows to delay the
real load of the object.
:rtype: silx.io.utils.H5Type
"""
if self.__h5Class is None and self.obj is not None:
self.__h5Class = silx.io.utils.get_h5_class(self.obj)
return self.__h5Class
@property
def h5pyClass(self):
"""Returns the class of the stored object.
When the object is in lazy loading, this method should be able to
return the type of the future loaded object. It allows to delay the
real load of the object.
:rtype: h5py.File or h5py.Dataset or h5py.Group
"""
type_ = self.h5Class
return silx.io.utils.h5type_to_h5py_class(type_)
@property
def linkClass(self):
"""Returns the link class object of this node
:rtype: H5Type
"""
return self.__linkClass
def isGroupObj(self):
"""Returns true if the stored HDF5 object is a group (contains sub
groups or datasets).
:rtype: bool
"""
if self.h5Class is None:
return False
return self.h5Class in [silx.io.utils.H5Type.GROUP, silx.io.utils.H5Type.FILE]
def isBrokenObj(self):
"""Returns true if the stored HDF5 object is broken.
The stored object is then an h5py-like link (external or not) which
point to nowhere (tbhe external file is not here, the expected
dataset is still not on the file...)
:rtype: bool
"""
return self.__isBroken
def _getFormatter(self):
"""
Returns an Hdf5Formatter
:rtype: Hdf5Formatter
"""
return _hdf5Formatter
def _expectedChildCount(self):
if self.isGroupObj():
return len(self.obj)
return 0
def __initH5Object(self):
"""Lazy load of the HDF5 node. It is reached from the parent node
with the key of the node."""
parent_obj = self.parent.obj
try:
obj = parent_obj.get(self.__key)
except Exception as e:
_logger.error("Internal error while reaching HDF5 object: %s", str(e))
_logger.debug("Backtrace", exc_info=True)
try:
self.__obj = parent_obj.get(self.__key, getlink=True)
except Exception:
self.__obj = None
self.__error = e.args[0]
self.__isBroken = True
else:
if obj is None:
# that's a broken link
self.__obj = parent_obj.get(self.__key, getlink=True)
# TODO monkey-patch file (ask that in h5py for consistency)
if not hasattr(self.__obj, "name"):
parent_name = parent_obj.name
if parent_name == "/":
self.__obj.name = "/" + self.__key
else:
self.__obj.name = parent_name + "/" + self.__key
# TODO monkey-patch file (ask that in h5py for consistency)
if not hasattr(self.__obj, "file"):
self.__obj.file = parent_obj.file
class_ = silx.io.utils.get_h5_class(self.__obj)
if class_ == silx.io.utils.H5Type.EXTERNAL_LINK:
message = "External link broken. Path %s::%s does not exist" % (self.__obj.filename, self.__obj.path)
elif class_ == silx.io.utils.H5Type.SOFT_LINK:
message = "Soft link broken. Path %s does not exist" % (self.__obj.path)
else:
name = self.__obj.__class__.__name__.split(".")[-1].capitalize()
message = "%s broken" % (name)
self.__error = message
self.__isBroken = True
else:
self.__obj = obj
if silx.io.utils.get_h5_class(obj) not in [silx.io.utils.H5Type.GROUP, silx.io.utils.H5Type.FILE]:
try:
# pre-fetch of the data
if obj.shape is None:
pass
elif obj.shape == tuple():
obj[()]
else:
if obj.compression is None and obj.size > 0:
key = tuple([0] * len(obj.shape))
obj[key]
except Exception as e:
_logger.debug(e, exc_info=True)
message = "%s broken. %s" % (self.__obj.name, e.args[0])
self.__error = message
self.__isBroken = True
self.__key = None
def _populateChild(self, populateAll=False):
if self.isGroupObj():
keys = []
try:
for name in self.obj:
keys.append(name)
except Exception:
lib_name = self.obj.__class__.__module__.split(".")[0]
_logger.error("Internal %s error. The file is corrupted.", lib_name)
_logger.debug("Backtrace", exc_info=True)
if keys == []:
# If the file was open in READ_ONLY we still can reach something
# https://github.com/silx-kit/silx/issues/2262
try:
for name in self.obj:
keys.append(name)
except Exception:
lib_name = self.obj.__class__.__module__.split(".")[0]
_logger.error("Internal %s error (second time). The file is corrupted.", lib_name)
_logger.debug("Backtrace", exc_info=True)
for name in keys:
try:
class_ = self.obj.get(name, getclass=True)
link = self.obj.get(name, getclass=True, getlink=True)
link = silx.io.utils.get_h5_class(class_=link)
except Exception:
lib_name = self.obj.__class__.__module__.split(".")[0]
_logger.error("Internal %s error", lib_name)
_logger.debug("Backtrace", exc_info=True)
class_ = None
try:
link = self.obj.get(name, getclass=True, getlink=True)
link = silx.io.utils.get_h5_class(class_=link)
except Exception:
_logger.debug("Backtrace", exc_info=True)
link = silx.io.utils.H5Type.HARD_LINK
h5class = None
if class_ is not None:
h5class = silx.io.utils.get_h5_class(class_=class_)
if h5class is None:
_logger.error("Class %s unsupported", class_)
item = Hdf5Item(text=name, obj=None, parent=self, key=name, h5Class=h5class, linkClass=link)
self.appendChild(item)
def hasChildren(self):
"""Retuens true of this node have chrild.
:rtype: bool
"""
if not self.isGroupObj():
return False
return Hdf5Node.hasChildren(self)
def _getDefaultIcon(self):
"""Returns the icon displayed by the main column.
:rtype: qt.QIcon
"""
# Pre-fetch the object, in case it is broken
obj = self.obj
style = qt.QApplication.style()
if self.__isBroken:
icon = style.standardIcon(qt.QStyle.SP_MessageBoxCritical)
return icon
class_ = self.h5Class
if class_ == silx.io.utils.H5Type.FILE:
return style.standardIcon(qt.QStyle.SP_FileIcon)
elif class_ == silx.io.utils.H5Type.GROUP:
return style.standardIcon(qt.QStyle.SP_DirIcon)
elif class_ == silx.io.utils.H5Type.SOFT_LINK:
return style.standardIcon(qt.QStyle.SP_DirLinkIcon)
elif class_ == silx.io.utils.H5Type.EXTERNAL_LINK:
return style.standardIcon(qt.QStyle.SP_FileLinkIcon)
elif class_ == silx.io.utils.H5Type.DATASET:
if obj.shape is None:
name = "item-none"
elif len(obj.shape) < 4:
name = "item-%ddim" % len(obj.shape)
else:
name = "item-ndim"
icon = icons.getQIcon(name)
return icon
return None
def _createTooltipAttributes(self):
"""
Add key/value attributes that will be displayed in the item tooltip
:param Dict[str,str] attributeDict: Key/value attributes
"""
attributeDict = collections.OrderedDict()
if self.h5Class == silx.io.utils.H5Type.DATASET:
attributeDict["#Title"] = "HDF5 Dataset"
attributeDict["Name"] = self.basename
attributeDict["Path"] = self.obj.name
attributeDict["Shape"] = self._getFormatter().humanReadableShape(self.obj)
attributeDict["Value"] = self._getFormatter().humanReadableValue(self.obj)
attributeDict["Data type"] = self._getFormatter().humanReadableType(self.obj, full=True)
elif self.h5Class == silx.io.utils.H5Type.GROUP:
attributeDict["#Title"] = "HDF5 Group"
if self.nexusClassName:
attributeDict["NX_class"] = self.nexusClassName
attributeDict["Name"] = self.basename
attributeDict["Path"] = self.obj.name
elif self.h5Class == silx.io.utils.H5Type.FILE:
attributeDict["#Title"] = "HDF5 File"
attributeDict["Name"] = self.basename
attributeDict["Path"] = "/"
elif self.h5Class == silx.io.utils.H5Type.EXTERNAL_LINK:
attributeDict["#Title"] = "HDF5 External Link"
attributeDict["Name"] = self.basename
attributeDict["Path"] = self.obj.name
attributeDict["Linked path"] = self.obj.path
attributeDict["Linked file"] = self.obj.filename
elif self.h5Class == silx.io.utils.H5Type.SOFT_LINK:
attributeDict["#Title"] = "HDF5 Soft Link"
attributeDict["Name"] = self.basename
attributeDict["Path"] = self.obj.name
attributeDict["Linked path"] = self.obj.path
else:
pass
return attributeDict
def _getDefaultTooltip(self):
"""Returns the default tooltip
:rtype: str
"""
if self.__error is not None:
self.obj # lazy loading of the object
return self.__error
attrs = self._createTooltipAttributes()
title = attrs.pop("#Title", None)
if len(attrs) > 0:
tooltip = _utils.htmlFromDict(attrs, title=title)
else:
tooltip = ""
return tooltip
@property
def nexusClassName(self):
"""Returns the Nexus class name"""
if self.__nx_class is None:
obj = self.obj.attrs.get("NX_class", None)
if obj is None:
text = ""
else:
text = self._getFormatter().textFormatter().toString(obj)
text = text.strip('"')
# Check NX_class formatting
lower = text.lower()
formatedNX_class = ""
if lower.startswith('nx'):
formatedNX_class = 'NX' + lower[2:]
if lower == 'nxcansas':
formatedNX_class = 'NXcanSAS' # That's the only class with capital letters...
if text != formatedNX_class:
_logger.error("NX_class: '%s' is malformed (should be '%s')",
text,
formatedNX_class)
text = formatedNX_class
self.__nx_class = text
return self.__nx_class
def dataName(self, role):
"""Data for the name column"""
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
return self.__text
if role == qt.Qt.DecorationRole:
return self._getDefaultIcon()
if role == qt.Qt.ToolTipRole:
return self._getDefaultTooltip()
return None
def dataType(self, role):
"""Data for the type column"""
if role == qt.Qt.DecorationRole:
return None
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
if self.__error is not None:
return ""
class_ = self.h5Class
if self.isGroupObj():
text = self.nexusClassName
elif class_ == silx.io.utils.H5Type.DATASET:
text = self._getFormatter().humanReadableType(self.obj)
else:
text = ""
return text
return None
def dataShape(self, role):
"""Data for the shape column"""
if role == qt.Qt.DecorationRole:
return None
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
if self.__error is not None:
return ""
class_ = self.h5Class
if class_ != silx.io.utils.H5Type.DATASET:
return ""
return self._getFormatter().humanReadableShape(self.obj)
return None
def dataValue(self, role):
"""Data for the value column"""
if role == qt.Qt.DecorationRole:
return None
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
if self.__error is not None:
return ""
if self.h5Class != silx.io.utils.H5Type.DATASET:
return ""
return self._getFormatter().humanReadableValue(self.obj)
return None
_NEXUS_CLASS_TO_VALUE_CHILDREN = {
'NXaperture': (
(DescriptionType.DESCRIPTION, 'description'),
),
'NXbeam_stop': (
(DescriptionType.DESCRIPTION, 'description'),
),
'NXdetector': (
(DescriptionType.NAME, 'local_name'),
(DescriptionType.DESCRIPTION, 'description')
),
'NXentry': (
(DescriptionType.TITLE, 'title'),
),
'NXenvironment': (
(DescriptionType.NAME, 'short_name'),
(DescriptionType.NAME, 'name'),
(DescriptionType.DESCRIPTION, 'description')
),
'NXinstrument': (
(DescriptionType.NAME, 'name'),
),
'NXlog': (
(DescriptionType.DESCRIPTION, 'description'),
),
'NXmirror': (
(DescriptionType.DESCRIPTION, 'description'),
),
'NXpositioner': (
(DescriptionType.NAME, 'name'),
),
'NXprocess': (
(DescriptionType.PROGRAM, 'program'),
),
'NXsample': (
(DescriptionType.TITLE, 'short_title'),
(DescriptionType.NAME, 'name'),
(DescriptionType.DESCRIPTION, 'description')
),
'NXsample_component': (
(DescriptionType.NAME, 'name'),
(DescriptionType.DESCRIPTION, 'description')
),
'NXsensor': (
(DescriptionType.NAME, 'short_name'),
(DescriptionType.NAME, 'name')
),
'NXsource': (
(DescriptionType.NAME, 'name'),
), # or its 'short_name' attribute... This is not supported
'NXsubentry': (
(DescriptionType.DESCRIPTION, 'definition'),
(DescriptionType.PROGRAM, 'program_name'),
(DescriptionType.TITLE, 'title'),
),
}
"""Mapping from NeXus class to child names containing data to use as value"""
def __computeDataDescription(self):
"""Compute the data description of this item
:rtype: Tuple[kind, str]
"""
if self.__isBroken or self.__error is not None:
self.obj # lazy loading of the object
return DescriptionType.ERROR, self.__error
if self.h5Class == silx.io.utils.H5Type.DATASET:
return DescriptionType.VALUE, self._getFormatter().humanReadableValue(self.obj)
elif self.isGroupObj() and self.nexusClassName:
# For NeXus groups, try to find a title or name
# By default, look for a title (most application definitions should have one)
defaultSequence = ((DescriptionType.TITLE, 'title'),)
sequence = self._NEXUS_CLASS_TO_VALUE_CHILDREN.get(self.nexusClassName, defaultSequence)
for kind, child_name in sequence:
for index in range(self.childCount()):
child = self.child(index)
if (isinstance(child, Hdf5Item) and
child.h5Class == silx.io.utils.H5Type.DATASET and
child.basename == child_name):
return kind, self._getFormatter().humanReadableValue(child.obj)
description = self.obj.attrs.get("desc", None)
if description is not None:
return DescriptionType.DESCRIPTION, description
else:
return None, None
def __getDataDescription(self):
"""Returns a cached version of the data description
As the data description have to reach inside the HDF5 tree, the result
is cached. A better implementation could be to use a MRU cache, to avoid
to allocate too much data.
:rtype: Tuple[kind, str]
"""
if self.__description is None:
self.__description = self.__computeDataDescription()
return self.__description
def dataDescription(self, role):
"""Data for the description column"""
if role == qt.Qt.DecorationRole:
kind, _label = self.__getDataDescription()
if kind is not None:
icon = icons.getQIcon("description-%s" % kind.value)
return icon
return None
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
_kind, label = self.__getDataDescription()
return label
if role == qt.Qt.ToolTipRole:
if self.__error is not None:
self.obj # lazy loading of the object
self.__initH5Object()
return self.__error
kind, label = self.__getDataDescription()
if label is not None:
return "<b>%s</b><br/>%s" % (kind.value.capitalize(), label)
else:
return ""
return None
def dataNode(self, role):
"""Data for the node column"""
if role == qt.Qt.DecorationRole:
return None
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
if self.isBrokenObj():
return ""
class_ = self.obj.__class__
text = class_.__name__.split(".")[-1]
return text
if role == qt.Qt.ToolTipRole:
class_ = self.obj.__class__
if class_ is None:
return ""
return "Class name: %s" % self.__class__
return None
def dataLink(self, role):
"""Data for the link column
Overwrite it to implement the content of the 'link' column.
:rtype: qt.QVariant
"""
if role == qt.Qt.DecorationRole:
return None
if role == qt.Qt.TextAlignmentRole:
return qt.Qt.AlignTop | qt.Qt.AlignLeft
if role == qt.Qt.DisplayRole:
# Mark as link
link = self.linkClass
if link is None:
pass
elif link == silx.io.utils.H5Type.HARD_LINK:
pass
elif link == silx.io.utils.H5Type.EXTERNAL_LINK:
return "External"
elif link == silx.io.utils.H5Type.SOFT_LINK:
return "Soft"
else:
return link.__name__
# Mark as external data
if self.h5Class == silx.io.utils.H5Type.DATASET:
obj = self.obj
if hasattr(obj, "is_virtual"):
if obj.is_virtual:
return "Virtual"
if hasattr(obj, "external"):
if obj.external:
return "ExtRaw"
return ""
if role == qt.Qt.ToolTipRole:
return None
return None
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