def addItem(self, item):
"""
:param DataItem item: Item to be inserted into the project tree
Item is wrapped in :class:`datahandling.ItemContainer` and inserted into the tree.
The insertion node depdends on the type of item.
**TODO:**
* Add remove functionality here (c.f. RixsTool.Models)
:returns: Container of item
:rtype: ItemContainer
:raises TypeError: if the item type is unknown
:raises ValueError: if the item.key() is already present
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if item.key() in self.__idDict:
raise ValueError("RixsProject.addItem -- Item key '%s' already present" % item.key())
if isinstance(item, ScanItem) or isinstance(item, SpecItem):
node = self.projectRoot.children[0]
elif isinstance(item, ImageItem):
node = self.projectRoot.children[1]
elif isinstance(item, StackItem):
node = self.projectRoot.children[2]
else:
raise TypeError("RixsProject.addItem -- unknown item type '%s'" % type(item))
container = ItemContainer(
item=item,
parent=node
)
node.addChildren([container])
self.__idDict[item.key()] = container.getID()
return container
def addGroup(self, label, node=None):
"""
:param str label: Unique label for the container
:param ItemContainer node: Parent for the new container. Defaults to None, the parent in that case is the root.
Creates a new container object in the parent container node
:returns: The created :class:`datahandling.ItemContainer`
:rtype: ItemContainer
:raises ValueError: if the label is already present in the project
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if label in self.__idDict:
raise ValueError("RixsProject.addItem -- Item key '%s' already present" % label)
if not node:
node = self.projectRoot
container = ItemContainer(
item=None,
parent=node,
label=label
)
node.addChildren([container])
self.__idDict[container.label] = container.getID()
return container
def __init__(self):
#
# Input readers
#
self.inputReaders = IODict.inputReaderDict()
#
# Identifier dict
#
self.__idDict = {}
#
# Data tree
#
self.projectRoot = ItemContainer()
#self.projectRoot.addChildren(
# [ItemContainer(parent=self.projectRoot, label=key)\
# for key in ['Spectra', 'Images', 'Stacks']])
for label in ['Spectra', 'Images', 'Stacks']:
self.addGroup(label)
if DEBUG >= 1:
print('RixsProject.__init__ -- projectRoot.childCount: %d' %
self.projectRoot.childCount())
print('RixsProject.__init__ -- projectRoot.__idDict: %s' %
str(self.__idDict))
def addItem(self, item):
"""
:param DataItem item: Item to be inserted into the project tree
Item is wrapped in :class:`datahandling.ItemContainer` and inserted into the tree.
The insertion node depdends on the type of item.
**TODO:**
* Add remove functionality here (c.f. RixsTool.Models)
:returns: Container of item
:rtype: ItemContainer
:raises TypeError: if the item type is unknown
:raises ValueError: if the item.key() is already present
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if item.key() in self.__idDict:
raise ValueError(
"RixsProject.addItem -- Item key '%s' already present" %
item.key())
if isinstance(item, ScanItem) or isinstance(item, SpecItem):
node = self.projectRoot.children[0]
elif isinstance(item, ImageItem):
node = self.projectRoot.children[1]
elif isinstance(item, StackItem):
node = self.projectRoot.children[2]
else:
raise TypeError("RixsProject.addItem -- unknown item type '%s'" %
type(item))
container = ItemContainer(item=item, parent=node)
node.addChildren([container])
self.__idDict[item.key()] = container.getID()
return container
def __init__(self):
#
# Input readers
#
self.inputReaders = IODict.inputReaderDict()
#
# Identifier dict
#
self.__idDict = {}
#
# Data tree
#
self.projectRoot = ItemContainer()
#self.projectRoot.addChildren(
# [ItemContainer(parent=self.projectRoot, label=key)\
# for key in ['Spectra', 'Images', 'Stacks']])
for label in ['Spectra', 'Images', 'Stacks']:
self.addGroup(label)
if DEBUG >= 1:
print('RixsProject.__init__ -- projectRoot.childCount: %d' %
self.projectRoot.childCount())
print('RixsProject.__init__ -- projectRoot.__idDict: %s' %
str(self.__idDict))
def addGroup(self, label, node=None):
"""
:param str label: Unique label for the container
:param ItemContainer node: Parent for the new container. Defaults to None, the parent in that case is the root.
Creates a new container object in the parent container node
:returns: The created :class:`datahandling.ItemContainer`
:rtype: ItemContainer
:raises ValueError: if the label is already present in the project
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if label in self.__idDict:
raise ValueError(
"RixsProject.addItem -- Item key '%s' already present" % label)
if not node:
node = self.projectRoot
container = ItemContainer(item=None, parent=node, label=label)
node.addChildren([container])
self.__idDict[container.label] = container.getID()
return container
class RixsProject(object):
__doc__ = """The :py:class:`RixsProject` class is used to read raw data related to a RIXS measurement. Internally
it organizes the raw data in instances of type :py:class:`Items.DataItem` and real valued functions in
:py:class:`Items.FunctionItems`. All data items are stored in the project tree, a hierachical data structure.
The tree itself consists of nodes of type :py:class:`datahandling.ItemContainer`.
On the top level, the tree divides the data items in containers depeding on the dimensionality of their data.
Two dimensional input for example is treated as an image.
**TODO**:
* Implement HDF Backend..
"""
def __init__(self):
#
# Input readers
#
self.inputReaders = IODict.inputReaderDict()
#
# Identifier dict
#
self.__idDict = {}
#
# Data tree
#
self.projectRoot = ItemContainer()
#self.projectRoot.addChildren(
# [ItemContainer(parent=self.projectRoot, label=key)\
# for key in ['Spectra', 'Images', 'Stacks']])
for label in ['Spectra', 'Images', 'Stacks']:
self.addGroup(label)
if DEBUG >= 1:
print('RixsProject.__init__ -- projectRoot.childCount: %d' % self.projectRoot.childCount())
print('RixsProject.__init__ -- projectRoot.__idDict: %s' % str(self.__idDict))
def __getitem__(self, key):
result = None
identifier = self.__idDict[key]
for container in self._traverseDFS(self.projectRoot):
if container.getID() == identifier:
result = container
break
if not result:
raise KeyError()
return result
def __contains__(self, item):
"""
:param ItemContainer or str item: Method determines if the given container is already in the tree.
If a string is provided as argument, the function determines if said string is used as a label for a
container in the tree. If an ItemContainer is provided, the function looks if the item ID is already
present in the tree.
:return bool: True or False, depending of item can be found
:raises ValueError: If the provided item is neither of type string nor an ItemContainer
"""
if isinstance(item, str):
llist = self.__idDict.keys()
elif isinstance(item, ItemContainer):
item = item.getID()
llist = self.__idDict.values()
else:
raise ValueError('RixsProject.__contains__ -- Argument must be of type string or ItemContainer')
return item in llist
def getIdDict(self):
# TODO: Function for debugging purposes
return self.__idDict
@staticmethod
def _traverseDFS(root):
yield root
for child in root.children:
for container in RixsProject._traverseDFS(child):
yield container
def groupCount(self):
return self.projectRoot.childCount()
def image(self, key):
"""
:param str key: Identifier of the image
Image -> 2D numpy array. TODO: Try to cast items in form of 2d ndarray?
:returns: Image from the input reader
:rtype: ImageItem
"""
raise NotImplementedError('RixsProject.image -- To be implemented')
def stack(self, key):
"""
Stack -> Sequence of images, i.e. 3D numpy array
"""
raise NotImplementedError('RixsProject.stack -- ..to be implemented')
def spectrum(self, key):
"""
Stack -> Sequence of images, i.e. 3D numpy array
"""
raise NotImplementedError('RixsProject.spectrum -- ..to be implemented')
def addItem(self, item):
"""
:param DataItem item: Item to be inserted into the project tree
Item is wrapped in :class:`datahandling.ItemContainer` and inserted into the tree.
The insertion node depdends on the type of item.
**TODO:**
* Add remove functionality here (c.f. RixsTool.Models)
:returns: Container of item
:rtype: ItemContainer
:raises TypeError: if the item type is unknown
:raises ValueError: if the item.key() is already present
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if item.key() in self.__idDict:
raise ValueError("RixsProject.addItem -- Item key '%s' already present" % item.key())
if isinstance(item, ScanItem) or isinstance(item, SpecItem):
node = self.projectRoot.children[0]
elif isinstance(item, ImageItem):
node = self.projectRoot.children[1]
elif isinstance(item, StackItem):
node = self.projectRoot.children[2]
else:
raise TypeError("RixsProject.addItem -- unknown item type '%s'" % type(item))
container = ItemContainer(
item=item,
parent=node
)
node.addChildren([container])
self.__idDict[item.key()] = container.getID()
return container
def addGroup(self, label, node=None):
"""
:param str label: Unique label for the container
:param ItemContainer node: Parent for the new container. Defaults to None, the parent in that case is the root.
Creates a new container object in the parent container node
:returns: The created :class:`datahandling.ItemContainer`
:rtype: ItemContainer
:raises ValueError: if the label is already present in the project
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if label in self.__idDict:
raise ValueError("RixsProject.addItem -- Item key '%s' already present" % label)
if not node:
node = self.projectRoot
container = ItemContainer(
item=None,
parent=node,
label=label
)
node.addChildren([container])
self.__idDict[container.label] = container.getID()
return container
def removeContainer(self, label):
container = self.__getitem__(label)
if container.childCount():
if DEBUG >= 1:
print('RixsProject.removeContainer -- Has children')
for child in container.children:
self.removeContainer(child.label)
parentContainer = container.parent
idx = container.childNumber()
del(parentContainer.children[idx])
del(self.__idDict[label])
def read(self, fileName):
"""
:param str fileName: File name including path to file
RixsProject stores a number of different reader for all sorts of file formats. The file stored under
file name is registered with a matching reader.
:returns: List of raw data wrapped in :class:`datahandling.ItemContainer`
:rtype: list
:raises TypeError: if the item type is unknown
"""
# Try to guess filetype
name, ext = OsPathSplitext(fileName)
fileType = ext.replace('.', '').lower()
if DEBUG >= 1:
print("RixsProject.read -- Received '%s' file" % fileType)
if fileType in self.inputReaders.keys():
reader = self.inputReaders[fileType]
else:
raise TypeError("RixsProject.read -- Unknown file type '%s'" % fileType)
itemList = reader.itemize(fileName)
return itemList
def crawl(self, directory):
"""
:param str directory: Root directory for the crawler to start
Reads every file of known file type contained in directory and its subdirectories and adds it
to the project.
"""
walk = OsWalk(OsAbsPath(directory))
if DEBUG >= 1:
print("RixsProject.crawl -- crawling '%s'" % directory)
for path, dirs, files in walk:
if DEBUG >= 1:
print('RixsProject.crawl -- current path: %s' % path)
for ffile in files:
absName = OsPathJoin(path, ffile)
try:
itemList = self.read(absName)
except TypeError:
if DEBUG >= 1:
print("RixsProject.crawl -- unkown filetype '%s'" % absName)
continue
for item in itemList:
if DEBUG >= 1:
print("RixsProject.crawl -- adding Item '%s'" % str(item))
self.addItem(item)
class RixsProject(object):
__doc__ = """The :py:class:`RixsProject` class is used to read raw data related to a RIXS measurement. Internally
it organizes the raw data in instances of type :py:class:`Items.DataItem` and real valued functions in
:py:class:`Items.FunctionItems`. All data items are stored in the project tree, a hierachical data structure.
The tree itself consists of nodes of type :py:class:`datahandling.ItemContainer`.
On the top level, the tree divides the data items in containers depeding on the dimensionality of their data.
Two dimensional input for example is treated as an image.
**TODO**:
* Implement HDF Backend..
"""
def __init__(self):
#
# Input readers
#
self.inputReaders = IODict.inputReaderDict()
#
# Identifier dict
#
self.__idDict = {}
#
# Data tree
#
self.projectRoot = ItemContainer()
#self.projectRoot.addChildren(
# [ItemContainer(parent=self.projectRoot, label=key)\
# for key in ['Spectra', 'Images', 'Stacks']])
for label in ['Spectra', 'Images', 'Stacks']:
self.addGroup(label)
if DEBUG >= 1:
print('RixsProject.__init__ -- projectRoot.childCount: %d' %
self.projectRoot.childCount())
print('RixsProject.__init__ -- projectRoot.__idDict: %s' %
str(self.__idDict))
def __getitem__(self, key):
result = None
identifier = self.__idDict[key]
for container in self._traverseDFS(self.projectRoot):
if container.getID() == identifier:
result = container
break
if not result:
raise KeyError()
return result
def __contains__(self, item):
"""
:param ItemContainer or str item: Method determines if the given container is already in the tree.
If a string is provided as argument, the function determines if said string is used as a label for a
container in the tree. If an ItemContainer is provided, the function looks if the item ID is already
present in the tree.
:return bool: True or False, depending of item can be found
:raises ValueError: If the provided item is neither of type string nor an ItemContainer
"""
if isinstance(item, str):
llist = self.__idDict.keys()
elif isinstance(item, ItemContainer):
item = item.getID()
llist = self.__idDict.values()
else:
raise ValueError(
'RixsProject.__contains__ -- Argument must be of type string or ItemContainer'
)
return item in llist
def getIdDict(self):
# TODO: Function for debugging purposes
return self.__idDict
@staticmethod
def _traverseDFS(root):
yield root
for child in root.children:
for container in RixsProject._traverseDFS(child):
yield container
def groupCount(self):
return self.projectRoot.childCount()
def image(self, key):
"""
:param str key: Identifier of the image
Image -> 2D numpy array. TODO: Try to cast items in form of 2d ndarray?
:returns: Image from the input reader
:rtype: ImageItem
"""
raise NotImplementedError('RixsProject.image -- To be implemented')
def stack(self, key):
"""
Stack -> Sequence of images, i.e. 3D numpy array
"""
raise NotImplementedError('RixsProject.stack -- ..to be implemented')
def spectrum(self, key):
"""
Stack -> Sequence of images, i.e. 3D numpy array
"""
raise NotImplementedError(
'RixsProject.spectrum -- ..to be implemented')
def addItem(self, item):
"""
:param DataItem item: Item to be inserted into the project tree
Item is wrapped in :class:`datahandling.ItemContainer` and inserted into the tree.
The insertion node depdends on the type of item.
**TODO:**
* Add remove functionality here (c.f. RixsTool.Models)
:returns: Container of item
:rtype: ItemContainer
:raises TypeError: if the item type is unknown
:raises ValueError: if the item.key() is already present
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if item.key() in self.__idDict:
raise ValueError(
"RixsProject.addItem -- Item key '%s' already present" %
item.key())
if isinstance(item, ScanItem) or isinstance(item, SpecItem):
node = self.projectRoot.children[0]
elif isinstance(item, ImageItem):
node = self.projectRoot.children[1]
elif isinstance(item, StackItem):
node = self.projectRoot.children[2]
else:
raise TypeError("RixsProject.addItem -- unknown item type '%s'" %
type(item))
container = ItemContainer(item=item, parent=node)
node.addChildren([container])
self.__idDict[item.key()] = container.getID()
return container
def addGroup(self, label, node=None):
"""
:param str label: Unique label for the container
:param ItemContainer node: Parent for the new container. Defaults to None, the parent in that case is the root.
Creates a new container object in the parent container node
:returns: The created :class:`datahandling.ItemContainer`
:rtype: ItemContainer
:raises ValueError: if the label is already present in the project
"""
if DEBUG >= 1:
print('RixsProject.addItem -- called')
if label in self.__idDict:
raise ValueError(
"RixsProject.addItem -- Item key '%s' already present" % label)
if not node:
node = self.projectRoot
container = ItemContainer(item=None, parent=node, label=label)
node.addChildren([container])
self.__idDict[container.label] = container.getID()
return container
def removeContainer(self, label):
container = self.__getitem__(label)
if container.childCount():
if DEBUG >= 1:
print('RixsProject.removeContainer -- Has children')
for child in container.children:
self.removeContainer(child.label)
parentContainer = container.parent
idx = container.childNumber()
del (parentContainer.children[idx])
del (self.__idDict[label])
def read(self, fileName):
"""
:param str fileName: File name including path to file
RixsProject stores a number of different reader for all sorts of file formats. The file stored under
file name is registered with a matching reader.
:returns: List of raw data wrapped in :class:`datahandling.ItemContainer`
:rtype: list
:raises TypeError: if the item type is unknown
"""
# Try to guess filetype
name, ext = OsPathSplitext(fileName)
fileType = ext.replace('.', '').lower()
if DEBUG >= 1:
print("RixsProject.read -- Received '%s' file" % fileType)
if fileType in self.inputReaders.keys():
reader = self.inputReaders[fileType]
else:
raise TypeError("RixsProject.read -- Unknown file type '%s'" %
fileType)
itemList = reader.itemize(fileName)
return itemList
def crawl(self, directory):
"""
:param str directory: Root directory for the crawler to start
Reads every file of known file type contained in directory and its subdirectories and adds it
to the project.
"""
walk = OsWalk(OsAbsPath(directory))
if DEBUG >= 1:
print("RixsProject.crawl -- crawling '%s'" % directory)
for path, dirs, files in walk:
if DEBUG >= 1:
print('RixsProject.crawl -- current path: %s' % path)
for ffile in files:
absName = OsPathJoin(path, ffile)
try:
itemList = self.read(absName)
except TypeError:
if DEBUG >= 1:
print("RixsProject.crawl -- unkown filetype '%s'" %
absName)
continue
for item in itemList:
if DEBUG >= 1:
print("RixsProject.crawl -- adding Item '%s'" %
str(item))
self.addItem(item)
