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"""This package provides a set of helper class and function used by the
package `silx.gui.hdf5` package.
"""
__authors__ = ["V. Valls"]
__license__ = "MIT"
__date__ = "17/01/2019"
from html import escape
import logging
import os.path
from silx.gui import constants
import silx.io.utils
import silx.io.url
from .. import qt
_logger = logging.getLogger(__name__)
def htmlFromDict(dictionary, title=None):
"""Generate a readable HTML from a dictionary
:param dict dictionary: A Dictionary
:rtype: str
"""
result = """<html>
<head>
<style type="text/css">
ul { -qt-list-indent: 0; list-style: none; }
li > b {display: inline-block; min-width: 4em; font-weight: bold; }
</style>
</head>
<body>
"""
if title is not None:
result += "<b>%s</b>" % escape(title)
result += "<ul>"
for key, value in dictionary.items():
result += "<li><b>%s</b>: %s</li>" % (escape(key), escape(value))
result += "</ul>"
result += "</body></html>"
return result
class Hdf5DatasetMimeData(qt.QMimeData):
"""Mimedata class to identify an internal drag and drop of a Hdf5Node."""
MIME_TYPE = "application/x-internal-h5py-dataset"
SILX_URI_TYPE = constants.SILX_URI_MIMETYPE
"""For compatibility with silx <= 1.1"""
def __init__(self, node=None, dataset=None, isRoot=False):
qt.QMimeData.__init__(self)
self.__dataset = dataset
self.__node = node
self.__isRoot = isRoot
self.setData(self.MIME_TYPE, "".encode(encoding="utf-8"))
if node is not None:
h5Node = H5Node(node)
silxUrl = h5Node.url
self.setText(silxUrl)
self.setData(constants.SILX_URI_MIMETYPE, silxUrl.encode(encoding="utf-8"))
def isRoot(self):
return self.__isRoot
def node(self):
return self.__node
def dataset(self):
if self.__node is not None:
return self.__node.obj
return self.__dataset
[docs]
class H5Node(object):
"""Adapter over an h5py object to provide missing informations from h5py
nodes, like internal node path and filename (which are not provided by
:mod:`h5py` for soft and external links).
It also provides an abstraction to reach node type for mimicked h5py
objects.
"""
def __init__(self, h5py_item=None):
"""Constructor
:param Hdf5Item h5py_item: An Hdf5Item
"""
self.__h5py_object = h5py_item.obj
self.__h5py_target = None
self.__h5py_item = h5py_item
def __getattr__(self, name):
if hasattr(self.__h5py_object, name):
attr = getattr(self.__h5py_object, name)
return attr
raise AttributeError("H5Node has no attribute %s" % name)
def __get_target(self, obj):
"""
Return the actual physical target of the provided object.
Objects can contains links in the middle of the path, this function
check each groups and remove this prefix in case of the link by the
link of the path.
:param obj: A valid h5py object (File, group or dataset)
:type obj: h5py.Dataset or h5py.Group or h5py.File
:rtype: h5py.Dataset or h5py.Group or h5py.File
"""
elements = obj.name.split("/")
if obj.name == "/":
return obj
elif obj.name.startswith("/"):
elements.pop(0)
path = ""
subpath = ""
while len(elements) > 0:
e = elements.pop(0)
subpath = path + "/" + e
link = obj.parent.get(subpath, getlink=True)
classlink = silx.io.utils.get_h5_class(link)
if classlink == silx.io.utils.H5Type.EXTERNAL_LINK:
subpath = "/".join(elements)
external_obj = obj.parent.get(self.basename + "/" + subpath)
return self.__get_target(external_obj)
elif classlink == silx.io.utils.H5Type.SOFT_LINK:
# Restart from this stat
root_elements = link.path.split("/")
if link.path == "/":
path = ""
root_elements = []
elif link.path.startswith("/"):
path = ""
root_elements.pop(0)
for name in reversed(root_elements):
elements.insert(0, name)
else:
path = subpath
return obj.file[path]
@property
def h5py_target(self):
if self.__h5py_target is not None:
return self.__h5py_target
self.__h5py_target = self.__get_target(self.__h5py_object)
return self.__h5py_target
@property
def h5py_object(self):
"""Returns the internal h5py node.
:rtype: h5py.File or h5py.Group or h5py.Dataset
"""
return self.__h5py_object
@property
def h5type(self):
"""Returns the node type, as an H5Type.
:rtype: H5Node
"""
return silx.io.utils.get_h5_class(self.__h5py_object)
@property
def ntype(self):
"""Returns the node type, as an h5py class.
:rtype:
:class:`h5py.File`, :class:`h5py.Group` or :class:`h5py.Dataset`
"""
type_ = self.h5type
return silx.io.utils.h5type_to_h5py_class(type_)
@property
def basename(self):
"""Returns the basename of this h5py node. It is the last identifier of
the path.
:rtype: str
"""
return self.__h5py_object.name.split("/")[-1]
@property
def is_broken(self):
"""Returns true if the node is a broken link.
:rtype: bool
"""
if self.__h5py_item is None:
raise RuntimeError("h5py_item is not defined")
return self.__h5py_item.isBrokenObj()
@property
def local_name(self):
"""Returns the path from the master file root to this node.
For links, this path is not equal to the h5py one.
:rtype: str
"""
if self.__h5py_item is None:
raise RuntimeError("h5py_item is not defined")
result = []
item = self.__h5py_item
while item is not None:
# stop before the root item (item without parent)
if item.parent.parent is None:
name = item.obj.name
if name != "/":
result.append(item.obj.name)
break
else:
result.append(item.basename)
item = item.parent
if item is None:
raise RuntimeError("The item does not have parent holding h5py.File")
if result == []:
return "/"
if not result[-1].startswith("/"):
result.append("")
result.reverse()
name = "/".join(result)
return name
def __get_local_file(self):
"""Returns the file of the root of this tree
:rtype: h5py.File
"""
item = self.__h5py_item
while item.parent.parent is not None:
class_ = silx.io.utils.get_h5_class(class_=item.h5pyClass)
if class_ == silx.io.utils.H5Type.FILE:
break
item = item.parent
class_ = silx.io.utils.get_h5_class(class_=item.h5pyClass)
if class_ == silx.io.utils.H5Type.FILE:
return item.obj
else:
return item.obj.file
@property
def local_file(self):
"""Returns the master file in which is this node.
For path containing external links, this file is not equal to the h5py
one.
:rtype: h5py.File
:raises RuntimeException: If no file are found
"""
return self.__get_local_file()
@property
def local_filename(self):
"""Returns the filename from the master file of this node.
For path containing external links, this path is not equal to the
filename provided by h5py.
:rtype: str
:raises RuntimeException: If no file are found
"""
return self.local_file.filename
@property
def local_basename(self):
"""Returns the basename from the master file root to this node.
For path containing links, this basename can be different than the
basename provided by h5py.
:rtype: str
"""
class_ = self.__h5py_item.h5Class
if class_ is not None and class_ == silx.io.utils.H5Type.FILE:
return ""
return self.__h5py_item.basename
@property
def physical_file(self):
"""Returns the physical file in which is this node.
.. versionadded:: 0.6
:rtype: h5py.File
:raises RuntimeError: If no file are found
"""
class_ = silx.io.utils.get_h5_class(self.__h5py_object)
if class_ == silx.io.utils.H5Type.EXTERNAL_LINK:
# It means the link is broken
raise RuntimeError("No file node found")
if class_ == silx.io.utils.H5Type.SOFT_LINK:
# It means the link is broken
return self.local_file
physical_obj = self.h5py_target
return physical_obj.file
@property
def physical_name(self):
"""Returns the path from the location this h5py node is physically
stored.
For broken links, this filename can be different from the
filename provided by h5py.
:rtype: str
"""
class_ = silx.io.utils.get_h5_class(self.__h5py_object)
if class_ == silx.io.utils.H5Type.EXTERNAL_LINK:
# It means the link is broken
return self.__h5py_object.path
if class_ == silx.io.utils.H5Type.SOFT_LINK:
# It means the link is broken
return self.__h5py_object.path
physical_obj = self.h5py_target
return physical_obj.name
@property
def physical_filename(self):
"""Returns the filename from the location this h5py node is physically
stored.
For broken links, this filename can be different from the
filename provided by h5py.
:rtype: str
"""
class_ = silx.io.utils.get_h5_class(self.__h5py_object)
if class_ == silx.io.utils.H5Type.EXTERNAL_LINK:
# It means the link is broken
return self.__h5py_object.filename
if class_ == silx.io.utils.H5Type.SOFT_LINK:
# It means the link is broken
return self.local_file.filename
return self.physical_file.filename
@property
def physical_basename(self):
"""Returns the basename from the location this h5py node is physically
stored.
For broken links, this basename can be different from the
basename provided by h5py.
:rtype: str
"""
return self.physical_name.split("/")[-1]
@property
def data_url(self):
"""Returns a :class:`silx.io.url.DataUrl` object identify this node in the file
system.
:rtype: ~silx.io.url.DataUrl
"""
absolute_filename = os.path.abspath(self.local_filename)
return silx.io.url.DataUrl(
scheme="silx", file_path=absolute_filename, data_path=self.local_name
)
@property
def url(self):
"""Returns an URL object identifying this node in the file
system.
This URL can be used in different ways.
.. code-block:: python
# Parsing the URL
import silx.io.url
dataurl = silx.io.url.DataUrl(item.url)
# dataurl provides access to URL fields
# Open a numpy array
import silx.io
dataset = silx.io.get_data(item.url)
# Open an hdf5 object (URL targetting a file or a group)
import silx.io
with silx.io.open(item.url) as h5:
...your stuff...
:rtype: str
"""
data_url = self.data_url
return data_url.path()
