/usr/share/pyshared/PyMca/HDF5Widget.py is in pymca 4.5.0-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""
from __future__ import with_statement
import operator
import sys
import os
import shutil
import posixpath
import gc
from operator import itemgetter
import PyQt4.QtCore as QtCore
import PyQt4.QtGui as QtGui
if hasattr(QtCore, 'QStringList'):
MyQVariant = QtCore.QVariant
else:
def MyQVariant(x=None):
return x
import h5py
phynx = h5py
import weakref
DEBUG = 0
#sorting method
def h5py_sorting(object_list):
sorting_list = ['start_time', 'end_time', 'name']
n = len(object_list)
if n < 2:
return object_list
# This implementation only sorts entries
if posixpath.dirname(object_list[0].name) != "/":
return object_list
names = list(object_list[0].keys())
sorting_key = None
for key in sorting_list:
if key in names:
sorting_key = key
break
if sorting_key is None:
if 'name' in sorting_list:
sorting_key = 'name'
else:
return object_list
try:
if sorting_key != 'name':
sorting_list = [(o[sorting_key].value, o)
for o in object_list]
sorted_list = sorted(sorting_list, key=itemgetter(0))
return [x[1] for x in sorted_list]
if sorting_key == 'name':
sorting_list = [(_get_number_list(o.name),o)
for o in object_list]
sorting_list.sort()
return [x[1] for x in sorting_list]
except:
#The only way to reach this point is to have different
#structures among the different entries. In that case
#defaults to the unfiltered case
print("WARNING: Default ordering")
print("Probably all entries do not have the key %s" % sorting_key)
return object_list
def _get_number_list(txt):
rexpr = '[/a-zA-Z:-]'
nbs= [float(w) for w in re.split(rexpr, txt) if w not in ['',' ']]
return nbs
class QRLock(QtCore.QMutex):
"""
"""
def __init__(self):
QtCore.QMutex.__init__(self, QtCore.QMutex.Recursive)
def __enter__(self):
self.lock()
return self
def __exit__(self, type, value, traceback):
self.unlock()
class RootItem(object):
@property
def children(self):
return self._children
@property
def hasChildren(self):
if len(self._children):
return True
else:
return False
@property
def header(self):
return self._header
@property
def parent(self):
return None
def __init__(self, header):
self._header = header
self._children = []
self._identifiers = []
def __iter__(self):
def iter_files(files):
for f in files:
yield f
return iter_files(self.children)
def __len__(self):
return len(self.children)
def appendChild(self, item):
self.children.append(H5FileProxy(item, self))
self._identifiers.append(id(item))
def deleteChild(self, child):
idx = self._children.index(child)
del self._children[idx]
del self._identifiers[idx]
class H5NodeProxy(object):
@property
def children(self):
if not self.hasChildren:
return []
if not self._children:
# obtaining the lock here is necessary, otherwise application can
# freeze if navigating tree while data is processing
if 1: #with self.file.plock:
tmpList = list(self.getNode(self.name).values())
try:
finalList = h5py_sorting(tmpList)
except:
#one cannot afford any error
if DEBUG:
raise
else:
finalList = tmpList
self._children = [H5NodeProxy(self.file, i, self)
for i in finalList]
return self._children
@property
def file(self):
return self._file
@property
def hasChildren(self):
return self._hasChildren
@property
def name(self):
return self._name
@property
def row(self):
if 1:#with self.file.plock:
try:
return self.parent.children.index(self)
except ValueError:
return
@property
def type(self):
return self._type
@property
def shape(self):
if type(self._shape) == type(""):
return self._shape
if len(self._shape) == 1:
return "%d" % self._shape[0]
elif len(self._shape) > 1:
text = "%d" % self._shape[0]
for a in range(1, len(self._shape)):
text += " x %d" % self._shape[a]
return text
else:
return ""
@property
def dtype(self):
return self._dtype
@property
def parent(self):
return self._parent
def __init__(self, ffile, node, parent=None):
if 1:#with ffile.plock:
self._file = ffile
self._parent = parent
self._name = node.name
"""
if hasattr(node, "_sourceName"):
self._name = node._sourceName
else:
self._name = posixpath.basename(node.name)
"""
self._type = type(node).__name__
self._hasChildren = isinstance(node, h5py.Group)
if hasattr(node, 'attrs'):
attrs = list(node.attrs)
for cname in ['class', 'NX_class']:
if cname in attrs:
if sys.version <'3.0':
_type = "%s" % node.attrs[cname]
else:
_type = node.attrs[cname].decode('utf=8')
self._type = _type
break
#self._type = _type[2].upper() + _type[3:]
self._children = []
if hasattr(node, 'dtype'):
self._dtype = str(node.dtype)
else:
self._dtype = ""
if hasattr(node, 'shape'):
if 0:
self._shape = str(node.shape)
else:
self._shape = node.shape
else:
self._shape = ""
def clearChildren(self):
self._children = []
self._hasChildren = False
def getNode(self, name=None):
if not name:
name = self.name
return self.file[name]
def __len__(self):
return len(self.children)
class H5FileProxy(H5NodeProxy):
@property
def name(self):
return '/'
@property
def filename(self):
return self._filename
def __init__(self, ffile, parent=None):
super(H5FileProxy, self).__init__(ffile, ffile, parent)
self._name = ffile.name
self._filename = self.file.name
def close(self):
with self.file.plock:
return self.file.close()
def __getitem__(self, path):
if path == '/':
return self
else:
return H5NodeProxy(self.file, self.file[path], self)
class FileModel(QtCore.QAbstractItemModel):
"""
"""
def __init__(self, parent=None):
QtCore.QAbstractItemModel.__init__(self, parent)
self.rootItem = RootItem(['File/Group/Dataset', 'Description', 'Shape', 'DType'])
self._idMap = {QtCore.QModelIndex().internalId(): self.rootItem}
def clearRows(self, index):
self.getProxyFromIndex(index).clearChildren()
def close(self):
for item in self.rootItem:
item.close()
self._idMap = {}
def columnCount(self, parent):
return 4
def data(self, index, role):
if role != QtCore.Qt.DisplayRole:
return MyQVariant()
item = self.getProxyFromIndex(index)
column = index.column()
if column == 0:
if isinstance(item, H5FileProxy):
return MyQVariant(os.path.basename(item.file.filename))
else:
return MyQVariant(posixpath.basename(item.name))
if column == 1:
showtitle = True
if showtitle:
if hasattr(item, 'type'):
if item.type in ["Entry", "NXentry"]:
children = item.children
names = [posixpath.basename(o.name) for o in children]
if "title" in names:
idx = names.index("title")
if len(children[idx].getNode().shape):
#stored as an array of strings!!!
#return just the first item
return MyQVariant("%s" % children[idx].getNode().value[0])
else:
#stored as a string
return MyQVariant("%s" % children[idx].getNode().value)
return MyQVariant(item.type)
if column == 2:
return MyQVariant(item.shape)
if column == 3:
return MyQVariant(item.dtype)
return MyQVariant()
def getNodeFromIndex(self, index):
try:
return self.getProxyFromIndex(index).getNode()
except AttributeError:
return None
def getProxyFromIndex(self, index):
try:
return self._idMap[index.internalId()]
except KeyError:
try:
#Linux 32-bit problem
return self._idMap[index.internalId() & 0xFFFFFFFF]
except KeyError:
return self.rootItem
def hasChildren(self, index):
return self.getProxyFromIndex(index).hasChildren
def headerData(self, section, orientation, role):
if orientation == QtCore.Qt.Horizontal and \
role == QtCore.Qt.DisplayRole:
return MyQVariant(self.rootItem.header[section])
return MyQVariant()
def hasIndex(self, row, column, parent):
parentItem = self.getProxyFromIndex(parent)
if row >= len(parentItem.children):
return False
return True
def index(self, row, column, parent):
parentItem = self.getProxyFromIndex(parent)
if row >= len(parentItem.children):
return QtCore.QModelIndex()
child = parentItem.children[row]
#force a pointer to child and not use id(child)
index = self.createIndex(row, column, child)
self._idMap.setdefault(index.internalId(), child)
return index
def parent(self, index):
child = self.getProxyFromIndex(index)
parent = child.parent
if parent == self.rootItem:
return QtCore.QModelIndex()
if parent is None:
return QtCore.QModelIndex()
if parent.row is None:
return QtCore.QModelIndex()
else:
return self.createIndex(parent.row, 0, parent)
def rowCount(self, index):
return len(self.getProxyFromIndex(index))
def openFile(self, filename, weakreference=False):
gc.collect()
for item in self.rootItem:
if item.file.filename == filename:
ddict = {}
ddict['event'] = "fileUpdated"
ddict['filename'] = filename
self.emit(QtCore.SIGNAL('fileUpdated'), ddict)
return item.file
phynxFile = phynx.File(filename, 'r')
if weakreference:
def phynxFileInstanceDistroyed(weakrefObject):
idx = self.rootItem._identifiers.index(id(weakrefObject))
child = self.rootItem._children[idx]
child.clearChildren()
del self._idMap[id(child)]
self.rootItem.deleteChild(child)
if not self.rootItem.hasChildren:
self.clear()
return
refProxy = weakref.proxy(phynxFile, phynxFileInstanceDistroyed)
self.rootItem.appendChild(refProxy)
else:
self.rootItem.appendChild(phynxFile)
ddict = {}
ddict['event'] = "fileAppended"
ddict['filename'] = filename
self.emit(QtCore.SIGNAL('fileAppended'), ddict)
return phynxFile
def appendPhynxFile(self, phynxFile, weakreference=True):
"""
I create a weak reference to a phynx file instance, get informed when
the instance disappears, and delete the entry from the view
"""
if hasattr(phynxFile, "_sourceName"):
name = phynxFile._sourceName
else:
name = phynxFile.name
gc.collect()
present = False
for child in self.rootItem:
if child.file.filename == name:
#already present
present = True
break
if present:
ddict = {}
ddict['event'] = "fileUpdated"
ddict['filename'] = name
self.emit(QtCore.SIGNAL('fileUpdated'), ddict)
return
if weakreference:
def phynxFileInstanceDistroyed(weakrefObject):
idx = self.rootItem._identifiers.index(id(weakrefObject))
child = self.rootItem._children[idx]
child.clearChildren()
del self._idMap[id(child)]
self.rootItem.deleteChild(child)
if not self.rootItem.hasChildren:
self.clear()
return
phynxFileProxy = weakref.proxy(phynxFile, phynxFileInstanceDistroyed)
self.rootItem.appendChild(phynxFileProxy)
else:
self.rootItem.appendChild(phynxFile)
ddict = {}
ddict['event'] = "fileAppended"
ddict['filename'] = name
self.emit(QtCore.SIGNAL('fileAppended'), ddict)
def clear(self):
self.reset()
class FileView(QtGui.QTreeView):
def __init__(self, fileModel, parent=None):
QtGui.QTreeView.__init__(self, parent)
self.setModel(fileModel)
self.setColumnWidth(0, 250)
#This removes the children after a double click
#with no possibility to recover them
#self.connect(
# self,
# QtCore.SIGNAL('collapsed(QModelIndex)'),
# fileModel.clearRows
#)
self.connect(
fileModel,
QtCore.SIGNAL('fileAppended'),
self.fileAppended
)
self.connect(
fileModel,
QtCore.SIGNAL('fileUpdated'),
self.fileUpdated
)
def fileAppended(self, ddict=None):
self.doItemsLayout()
if ddict is None:
return
self.fileUpdated(ddict)
def fileUpdated(self, ddict):
rootModelIndex = self.rootIndex()
if self.model().hasChildren(rootModelIndex):
rootItem = self.model().getProxyFromIndex(rootModelIndex)
for row in range(len(rootItem)):
if self.model().hasIndex(row, 0, rootModelIndex):
modelIndex = self.model().index(row, 0, rootModelIndex)
item = self.model().getProxyFromIndex(modelIndex)
if item.name == ddict['filename']:
self.selectionModel().setCurrentIndex(modelIndex,
QtGui.QItemSelectionModel.NoUpdate)
self.scrollTo(modelIndex,
QtGui.QAbstractItemView.PositionAtTop)
break
self.doItemsLayout()
class HDF5Widget(FileView):
def __init__(self, model, parent=None):
FileView.__init__(self, model, parent)
self.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
self._adjust()
if 0:
QtCore.QObject.connect(self,
QtCore.SIGNAL('activated(QModelIndex)'),
self.itemActivated)
QtCore.QObject.connect(self,
QtCore.SIGNAL('clicked(QModelIndex)'),
self.itemClicked)
QtCore.QObject.connect(self,
QtCore.SIGNAL('doubleClicked(QModelIndex)'),
self.itemDoubleClicked)
QtCore.QObject.connect(
self,
QtCore.SIGNAL('collapsed(QModelIndex)'),
self._adjust)
QtCore.QObject.connect(
self,
QtCore.SIGNAL('expanded(QModelIndex)'),
self._adjust)
def _adjust(self, modelIndex=None):
self.resizeColumnToContents(0)
self.resizeColumnToContents(1)
self.resizeColumnToContents(2)
self.resizeColumnToContents(3)
def mousePressEvent(self, e):
button = e.button()
if button == QtCore.Qt.LeftButton:
self._lastMouse = "left"
elif button == QtCore.Qt.RightButton:
self._lastMouse = "right"
elif button == QtCore.Qt.MidButton:
self._lastMouse = "middle"
else:
#Should I set it to no button?
self._lastMouse = "left"
QtGui.QTreeView.mousePressEvent(self, e)
def itemActivated(self, modelIndex):
event ="itemActivated"
self.emitSignal(event, modelIndex)
def itemClicked(self, modelIndex):
event ="itemClicked"
self.emitSignal(event, modelIndex)
def itemDoubleClicked(self, modelIndex):
event ="itemDoubleClicked"
self.emitSignal(event, modelIndex)
def emitSignal(self, event, modelIndex):
if self.model() is None:
return
ddict = {}
item = self.model().getProxyFromIndex(modelIndex)
ddict['event'] = event
ddict['file'] = item.file.filename
ddict['name'] = item.name
ddict['type'] = item.type
ddict['dtype'] = item.dtype
ddict['shape'] = item.shape
ddict['mouse'] = self._lastMouse * 1
self.emit(QtCore.SIGNAL("HDF5WidgetSignal"), ddict)
def getSelectedEntries(self):
modelIndexList = self.selectedIndexes()
entryList = []
analyzedPaths = []
for modelIndex in modelIndexList:
item = self.model().getProxyFromIndex(modelIndex)
path = item.name * 1
if path in analyzedPaths:
continue
else:
analyzedPaths.append(path)
if item.type in ["weakproxy", "File"]:
continue
entry = "/" + path.split("/")[1]
if entry not in entryList:
entryList.append((entry, item.file.filename))
return entryList
if __name__ == "__main__":
import sys
app = QtGui.QApplication(sys.argv)
if len(sys.argv) < 2:
print("Usage:")
print("python HDF5Widget.py path_to_hdf5_file_name")
sys.exit(0)
fileModel = FileModel()
fileView = HDF5Widget(fileModel)
#fileModel.openFile('/home/darren/temp/PSI.hdf')
phynxFile = fileModel.openFile(sys.argv[1])
def mySlot(ddict):
print(ddict)
if ddict['type'].lower() in ['dataset']:
print(phynxFile[ddict['name']].dtype, phynxFile[ddict['name']].shape)
QtCore.QObject.connect(fileView, QtCore.SIGNAL("HDF5WidgetSignal"), mySlot)
fileView.show()
sys.exit(app.exec_())
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