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dicomtrolley.datastructures

Additional datastructures that do not belong to any specific dicomtrolley class or function

ExpiringCollection

A collection of objects that expires after a set time

Collects expired items in .expired_items list.

Source code in dicomtrolley/datastructures.py 
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class ExpiringCollection:
    """A collection of objects that expires after a set time

    Collects expired items in .expired_items list.
    """

    def __init__(self, expire_after_seconds: int):
        self.expire_after_seconds = expire_after_seconds
        self.stamped_items = LastUpdatedOrderedDict()
        self.expired_items: List[Any] = []

    @staticmethod
    def _now():
        return datetime.now()

    def add(self, item):
        self.stamped_items[item] = self._now()

    def add_all(self, items: Iterable[Hashable]):
        for item in items:
            self.add(item)

    @property
    def items(self):
        self.check_expired()
        return list(self.stamped_items.keys())

    def check_expired(self):
        """Move expired to expired_items list"""
        expired = []
        for item, timestamp in self.stamped_items.items():
            if (self._now() - timestamp).seconds > self.expire_after_seconds:
                expired.append(item)
            else:
                break  # timestamps should be ordered so we can stop checking

        self.expired_items = self.expired_items + expired
        [self.stamped_items.pop(x) for x in expired]

    def collect_expired(self) -> List[Hashable]:
        """Returns all expired items and removes them from local list"""
        self.check_expired()
        expired = self.expired_items
        self.expired_items = []
        return expired

check_expired()

Move expired to expired_items list

Source code in dicomtrolley/datastructures.py 
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def check_expired(self):
    """Move expired to expired_items list"""
    expired = []
    for item, timestamp in self.stamped_items.items():
        if (self._now() - timestamp).seconds > self.expire_after_seconds:
            expired.append(item)
        else:
            break  # timestamps should be ordered so we can stop checking

    self.expired_items = self.expired_items + expired
    [self.stamped_items.pop(x) for x in expired]

collect_expired()

Returns all expired items and removes them from local list

Source code in dicomtrolley/datastructures.py 
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def collect_expired(self) -> List[Hashable]:
    """Returns all expired items and removes them from local list"""
    self.check_expired()
    expired = self.expired_items
    self.expired_items = []
    return expired

LastUpdatedOrderedDict

Bases: OrderedDict[Any, Any]

Store items in the order the keys were last added

Source code in dicomtrolley/datastructures.py 
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class LastUpdatedOrderedDict(OrderedDictType[Any, Any]):
    """Store items in the order the keys were last added"""

    def __setitem__(self, key, value):
        super().__setitem__(key, value)
        self.move_to_end(key)

PruneStrategy

Bases: str, Enum

How to handle pruning multiple nodes at once. Consider this tree with five nodes: A / B C / D E

I want to prune node B and E. There are two choices to be made with regard to this. Choice 1: Pruning node B will orphan node D, and make it inaccessible. Is this OK? Choice 2: If orphaning node D is not OK, is it still ok to remove E? Or should we just disallow the whole pruning?

These two choices inform tree strategies: FORCE Just prune. Yes you can prune B. D and E will disappear and that's fine

WHERE_POSSIBLE Let's not get overzealous. You can't prune B, but you can still prune E.

CHECK_FIRST Let's be very careful. Only prune if ALL nodes can be pruned. This assures that a successful prune removes all nodes

Source code in dicomtrolley/datastructures.py 
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class PruneStrategy(str, Enum):
    """How to handle pruning multiple nodes at once.
    Consider this tree with five nodes:
          A
        /  \
       B    C
      / \
     D   E

    I want to prune node B and E.
    There are two choices to be made with regard to this.
    Choice 1:
        Pruning node B will orphan node D, and make it inaccessible. Is this OK?
    Choice 2:
        If orphaning node D is not OK, is it still ok to remove E? Or should we just
        disallow the whole pruning?

    These two choices inform tree strategies:
    FORCE
        Just prune. Yes you can prune B. D and E will disappear and that's fine

    WHERE_POSSIBLE
        Let's not get overzealous. You can't prune B, but you can still prune E.

    CHECK_FIRST
        Let's be very careful. Only prune if ALL nodes can be pruned. This
        assures that a successful prune removes all nodes

    """

    FORCE = "Force"  # prune all nodes, don't check for anything

    WHERE_POSSIBLE = (
        "Where_possible"  # prune nodes without children where you can
    )

    CHECK_FIRST = "Check_first"  # only prune if all targets can be pruned

TreeNode

Bases: DefaultDict[str, 'TreeNode']

Recursive defaultdict with a 'data' property. Helps parse to tree structures.

There is no native tree datastructure in python as far as I know.

Some properties: * Inherits 'access-means-creation' functionality from defaultdict: 

 >>> root = TreeNode()
 >>> root['study1']['series1']['instance1'].data = 'some instance info'
 >>> 'study1' in root
 True
* Address nodes by nested dict notation or by list of strings: 
>>> root = TreeNode()
>>> root['study1']['series1']['instance1'].data = 'some instance info'
>>> 'study1' in root
True

Examples

root = TreeNode() root['study1']['series1']['instance1'].data = 'some instance info' 'study1' in root True root['study1']['series2'].data = 'some series data' list(root['study1'].keys) ['series1', 'series2']

Source code in dicomtrolley/datastructures.py 
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class TreeNode(DefaultDict[str, "TreeNode"]):
    """Recursive defaultdict with a 'data' property. Helps parse to tree structures.

    There is no native tree datastructure in python as far as I know.

    Some properties:
    * Inherits 'access-means-creation' functionality from defaultdict:
      ```
       >>> root = TreeNode()
       >>> root['study1']['series1']['instance1'].data = 'some instance info'
       >>> 'study1' in root
       True
      ```
    * Address nodes by nested dict notation or by list of strings:
      ```
      >>> root = TreeNode()
      >>> root['study1']['series1']['instance1'].data = 'some instance info'
      >>> 'study1' in root
      True
      ```

    Examples
    --------
    >>> root = TreeNode()
    >>> root['study1']['series1']['instance1'].data = 'some instance info'
    >>> 'study1' in root
    True
    >>> root['study1']['series2'].data = 'some series data'
    >>> list(root['study1'].keys)
    ['series1', 'series2']
    """

    def __init__(self, data=None, allow_overwrite=True):
        """

        Parameters
        ----------
        data:
            Optional data to associate with this node
        allow_overwrite: bool, optional
            If False, will raise exception when overwriting data attribute
        """
        super().__init__(lambda: TreeNode(allow_overwrite=allow_overwrite))
        self._data = data
        self.allow_overwrite = allow_overwrite

    @property
    def data(self):
        return self._data

    @data.setter
    def data(self, value):
        if self.allow_overwrite or not self.data:
            self._data = value
        else:
            raise ValueError("Overwriting data is not allowed")

    @classmethod
    def init_from_addresses(cls, addresses: Sequence[TreeAddress]):
        """Create TreeNode and make sure all given addresses exist"""
        root = cls()
        for address in addresses:
            root.get_node(address)
        return root

    def iter_leaf_addresses(
        self,
        address_so_far: Tuple[str, ...] = (),
    ) -> Iterator[TreeAddress]:
        """Generate addresses for all this nodes' children, depth-first"""

        if not self.keys():
            yield address_so_far
        else:
            for key in self.keys():
                yield from self[key].iter_leaf_addresses(
                    address_so_far=address_so_far + tuple(key)
                )

    def exists(self, address: TreeAddress) -> bool:
        """Check whether a node exists at address without creating any new nodes

        Parameters
        ----------
        address:
            subsequent keys. To check TreeNode()['a']['b']['c'], use ['a', 'b', 'c'],
            for example
        """
        if not address:
            return True  # required for recursive calls below to work
        else:
            key, address = address[0], address[1:]
            child = self.get(key)
            if child is not None:
                return child.exists(address)  # recurse
            else:
                return False

    def add(self, object_in: Any, address: TreeAddress):
        self.get_node(address).data = object_in

    def copy(self) -> "TreeNode":
        """Create a copy of this node and all children"""
        copied = TreeNode(data=self.data, allow_overwrite=self.allow_overwrite)
        for key, item in self.items():
            copied[key] = item.copy()

        return copied

    def pop_address(self, address: TreeAddress):
        """Pop off the leaf node at this address. Leave stem nodes.

        Raises
        ------
        KeyError
            If node at address does not exist. Follows dict.pop() behaviour.
        """
        if not address:
            raise KeyError("Address was empty. Cannot pop self!")

        key, address = address[0], address[1:]
        try:
            if not address:  # last key in address has been reached. We can pop
                return self.pop(key)
            else:  #
                return self.get_node(tuple(key), create=False).pop_address(
                    address
                )
        except KeyError as e:
            raise KeyError(f"No node found at {address}.{key}") from e

    def prune(self, address: TreeAddress):
        """Remove the node at this address, including any child nodes

        Raises
        ------
        KeyError
            If node at address does not exist
        """
        _ = self.pop_address(address)

    def is_leaf(self):
        return not self.keys()

    def prune_leaf(self, address: TreeAddress):
        """Prune node at this address only if it has no children

        Raises
        ------
        KeyError
            When the referenced node does not exist
        ValueError
            When referenced node is not a leaf (still has child nodes)
        """

        if not address:
            raise KeyError("Address was empty. Cannot prune self!")

        key, address_rest = address[0], address[1:]
        try:
            child = self.get_node((key,), create=False)
        except KeyError as e:
            raise KeyError(
                f"Cannot prune non-existing node at {address}"
            ) from e

        if address_rest:  # more address to traverse. Recurse
            child.prune_leaf(address_rest)
        else:  # no more address. Child should be a leaf
            if child.is_leaf():
                self.pop(key)
            else:
                raise ValueError(f"Node at {address} is not a child node")

    def prune_all(  # noqa: C901  # not too complex I think. Just elifs
        self,
        addresses: List[TreeAddress],
        strategy: PruneStrategy = PruneStrategy.WHERE_POSSIBLE,
    ):
        """Prune the leaf at each address. You can pass non-leaf addresses as well
        provided that all children of this leaf are passed as well.

        Parameters
        ----------
        addresses
            Prune nodes at these locations
        strategy
            Indicates how to handle child nodes and invalid targets.
            See PruneStrategy docstring

        Raises
        ------
        KeyError
            If strategy is PruneStrategy.CHECK_FIRST and illegal addresses are passed.
            Illegal meaning 'would remove unlisted child nodes'
        """
        if strategy == PruneStrategy.FORCE:
            for address in addresses:
                try:
                    self.prune(address)
                except KeyError:
                    continue
        elif strategy == PruneStrategy.WHERE_POSSIBLE:
            for address in addresses:
                try:
                    self.prune_leaf(address)
                except ValueError:
                    continue
        elif strategy == PruneStrategy.CHECK_FIRST:
            # simulate subtree first to avoid leaving tree in half-pruned state after
            # error
            simtree = self.copy()
            addresses.sort(key=lambda x: len(x), reverse=True)
            try:
                for address in addresses:
                    simtree.prune_leaf(address=address)
            except ValueError as e:
                raise KeyError(
                    f"Cannot prune all addresses: {e}. Pruning cancelled"
                ) from e
            # No exceptions. We can safely remove
            for address in addresses:
                self.pop_address(address)
        else:
            raise ValueError(f"Unknown strategy '{strategy}'")

    def get_node(self, address: TreeAddress, create=True):
        """Get node at given address, creating if it does not exist

        Parameters
        ----------
        address
            Address to get
        create: Bool, optional
            If true, create non-existing address. Else, raise exception
             Defaults to True

        Raises
        ------
        KeyError
            If address does not exist and create is False

        Returns
        -------
        TreeNode
            The treenode at this address
        """
        if not address:
            return self
        else:
            key = address[0]
            if not create and key not in self.keys():
                raise KeyError(f"Key {key} not found")
            return self[key].get_node(address[1:], create=create)

__init__(data=None, allow_overwrite=True)

Parameters

data: Optional data to associate with this node allow_overwrite: bool, optional If False, will raise exception when overwriting data attribute

Source code in dicomtrolley/datastructures.py 
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def __init__(self, data=None, allow_overwrite=True):
    """

    Parameters
    ----------
    data:
        Optional data to associate with this node
    allow_overwrite: bool, optional
        If False, will raise exception when overwriting data attribute
    """
    super().__init__(lambda: TreeNode(allow_overwrite=allow_overwrite))
    self._data = data
    self.allow_overwrite = allow_overwrite

copy()

Create a copy of this node and all children

Source code in dicomtrolley/datastructures.py 
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def copy(self) -> "TreeNode":
    """Create a copy of this node and all children"""
    copied = TreeNode(data=self.data, allow_overwrite=self.allow_overwrite)
    for key, item in self.items():
        copied[key] = item.copy()

    return copied

exists(address)

Check whether a node exists at address without creating any new nodes

Parameters

address: subsequent keys. To check TreeNode()['a']['b']['c'], use ['a', 'b', 'c'], for example

Source code in dicomtrolley/datastructures.py 
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def exists(self, address: TreeAddress) -> bool:
    """Check whether a node exists at address without creating any new nodes

    Parameters
    ----------
    address:
        subsequent keys. To check TreeNode()['a']['b']['c'], use ['a', 'b', 'c'],
        for example
    """
    if not address:
        return True  # required for recursive calls below to work
    else:
        key, address = address[0], address[1:]
        child = self.get(key)
        if child is not None:
            return child.exists(address)  # recurse
        else:
            return False

get_node(address, create=True)

Get node at given address, creating if it does not exist

Parameters

address Address to get create: Bool, optional If true, create non-existing address. Else, raise exception Defaults to True

Raises

KeyError If address does not exist and create is False

Returns

TreeNode The treenode at this address

Source code in dicomtrolley/datastructures.py 
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def get_node(self, address: TreeAddress, create=True):
    """Get node at given address, creating if it does not exist

    Parameters
    ----------
    address
        Address to get
    create: Bool, optional
        If true, create non-existing address. Else, raise exception
         Defaults to True

    Raises
    ------
    KeyError
        If address does not exist and create is False

    Returns
    -------
    TreeNode
        The treenode at this address
    """
    if not address:
        return self
    else:
        key = address[0]
        if not create and key not in self.keys():
            raise KeyError(f"Key {key} not found")
        return self[key].get_node(address[1:], create=create)

init_from_addresses(addresses) classmethod

Create TreeNode and make sure all given addresses exist

Source code in dicomtrolley/datastructures.py 
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@classmethod
def init_from_addresses(cls, addresses: Sequence[TreeAddress]):
    """Create TreeNode and make sure all given addresses exist"""
    root = cls()
    for address in addresses:
        root.get_node(address)
    return root

iter_leaf_addresses(address_so_far=())

Generate addresses for all this nodes' children, depth-first

Source code in dicomtrolley/datastructures.py 
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def iter_leaf_addresses(
    self,
    address_so_far: Tuple[str, ...] = (),
) -> Iterator[TreeAddress]:
    """Generate addresses for all this nodes' children, depth-first"""

    if not self.keys():
        yield address_so_far
    else:
        for key in self.keys():
            yield from self[key].iter_leaf_addresses(
                address_so_far=address_so_far + tuple(key)
            )

pop_address(address)

Pop off the leaf node at this address. Leave stem nodes.

Raises

KeyError If node at address does not exist. Follows dict.pop() behaviour.

Source code in dicomtrolley/datastructures.py 
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def pop_address(self, address: TreeAddress):
    """Pop off the leaf node at this address. Leave stem nodes.

    Raises
    ------
    KeyError
        If node at address does not exist. Follows dict.pop() behaviour.
    """
    if not address:
        raise KeyError("Address was empty. Cannot pop self!")

    key, address = address[0], address[1:]
    try:
        if not address:  # last key in address has been reached. We can pop
            return self.pop(key)
        else:  #
            return self.get_node(tuple(key), create=False).pop_address(
                address
            )
    except KeyError as e:
        raise KeyError(f"No node found at {address}.{key}") from e

prune(address)

Remove the node at this address, including any child nodes

Raises

KeyError If node at address does not exist

Source code in dicomtrolley/datastructures.py 
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def prune(self, address: TreeAddress):
    """Remove the node at this address, including any child nodes

    Raises
    ------
    KeyError
        If node at address does not exist
    """
    _ = self.pop_address(address)

prune_all(addresses, strategy=PruneStrategy.WHERE_POSSIBLE)

Prune the leaf at each address. You can pass non-leaf addresses as well provided that all children of this leaf are passed as well.

Parameters

addresses Prune nodes at these locations strategy Indicates how to handle child nodes and invalid targets. See PruneStrategy docstring

Raises

KeyError If strategy is PruneStrategy.CHECK_FIRST and illegal addresses are passed. Illegal meaning 'would remove unlisted child nodes'

Source code in dicomtrolley/datastructures.py 
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def prune_all(  # noqa: C901  # not too complex I think. Just elifs
    self,
    addresses: List[TreeAddress],
    strategy: PruneStrategy = PruneStrategy.WHERE_POSSIBLE,
):
    """Prune the leaf at each address. You can pass non-leaf addresses as well
    provided that all children of this leaf are passed as well.

    Parameters
    ----------
    addresses
        Prune nodes at these locations
    strategy
        Indicates how to handle child nodes and invalid targets.
        See PruneStrategy docstring

    Raises
    ------
    KeyError
        If strategy is PruneStrategy.CHECK_FIRST and illegal addresses are passed.
        Illegal meaning 'would remove unlisted child nodes'
    """
    if strategy == PruneStrategy.FORCE:
        for address in addresses:
            try:
                self.prune(address)
            except KeyError:
                continue
    elif strategy == PruneStrategy.WHERE_POSSIBLE:
        for address in addresses:
            try:
                self.prune_leaf(address)
            except ValueError:
                continue
    elif strategy == PruneStrategy.CHECK_FIRST:
        # simulate subtree first to avoid leaving tree in half-pruned state after
        # error
        simtree = self.copy()
        addresses.sort(key=lambda x: len(x), reverse=True)
        try:
            for address in addresses:
                simtree.prune_leaf(address=address)
        except ValueError as e:
            raise KeyError(
                f"Cannot prune all addresses: {e}. Pruning cancelled"
            ) from e
        # No exceptions. We can safely remove
        for address in addresses:
            self.pop_address(address)
    else:
        raise ValueError(f"Unknown strategy '{strategy}'")

prune_leaf(address)

Prune node at this address only if it has no children

Raises

KeyError When the referenced node does not exist ValueError When referenced node is not a leaf (still has child nodes)

Source code in dicomtrolley/datastructures.py 
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def prune_leaf(self, address: TreeAddress):
    """Prune node at this address only if it has no children

    Raises
    ------
    KeyError
        When the referenced node does not exist
    ValueError
        When referenced node is not a leaf (still has child nodes)
    """

    if not address:
        raise KeyError("Address was empty. Cannot prune self!")

    key, address_rest = address[0], address[1:]
    try:
        child = self.get_node((key,), create=False)
    except KeyError as e:
        raise KeyError(
            f"Cannot prune non-existing node at {address}"
        ) from e

    if address_rest:  # more address to traverse. Recurse
        child.prune_leaf(address_rest)
    else:  # no more address. Child should be a leaf
        if child.is_leaf():
            self.pop(key)
        else:
            raise ValueError(f"Node at {address} is not a child node")

addr(dot_address)

Convenience method for creating an address with dot notation

Works quick and readable as long as you don't have dots in your address keys. If you do, just use a ['list','of','strings','with.dots.if.you.have.to']

Source code in dicomtrolley/datastructures.py 
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def addr(dot_address: str):
    """Convenience method for creating an address with dot notation

    Works quick and readable as long as you don't have dots in your address keys.
    If you do, just use a ['list','of','strings','with.dots.if.you.have.to']
    """
    return tuple(dot_address.split("."))