ratiopath.parsers.ASAPParser

Parser for ASAP format annotation files.

ASAP (Automated Slide Analysis Platform) uses XML format for storing annotations. This parser supports both polygon and point annotations.

Source code in ratiopath/parsers/asap_parser.py

class ASAPParser:
    """Parser for ASAP format annotation files.

    ASAP (Automated Slide Analysis Platform) uses XML format for storing annotations.
    This parser supports both polygon and point annotations.
    """

    def __init__(self, file_path: Path | str | TextIO):
        self.tree = ET.parse(file_path)
        self.root = self.tree.getroot()

    def _get_filtered_annotations(
        self, name: str, part_of_group: str
    ) -> Iterable[ET.Element]:
        """Get annotations that match the provided regex filters.

        Args:
            name: Regex pattern to match annotation names.
            part_of_group: Regex pattern to match annotation groups.

        Yields:
            XML annotation elements that match the filters.
        """
        name_regex = re.compile(name)
        part_of_group_regex = re.compile(part_of_group)

        for annotation in self.root.findall(".//Annotation"):
            if name_regex.match(
                annotation.attrib["Name"]
            ) and part_of_group_regex.match(annotation.attrib["PartOfGroup"]):
                yield annotation

    def _extract_coordinates(self, annotation: ET.Element) -> list[Point]:
        """Extract coordinates from an annotation element.

        Args:
            annotation: XML annotation element.

        Returns:
            List of (x, y) coordinate tuples.
        """
        return [
            Point(float(coordinate.attrib["X"]), float(coordinate.attrib["Y"]))
            for coordinate in annotation.findall(".//Coordinate")
        ]

    def get_polygons(
        self, name: str = ".*", part_of_group: str = ".*"
    ) -> Iterable[Polygon]:
        """Parse polygon annotations from ASAP XML file.

        Args:
            name: Regex pattern to match annotation names.
            part_of_group: Regex pattern to match annotation groups.

        Returns:
            An iterable of shapely Polygon objects.
        """
        for annotation in self._get_filtered_annotations(name, part_of_group):
            if annotation.attrib["Type"] in ["Polygon", "Spline"]:
                yield Polygon(self._extract_coordinates(annotation))

    def get_points(
        self, name: str = ".*", part_of_group: str = ".*"
    ) -> Iterable[Point]:
        """Parse point annotations from ASAP XML file.

        Args:
            name: Regex pattern to match annotation names.
            part_of_group: Regex pattern to match annotation groups.

        Returns:
            An iterable of shapely Point objects.
        """
        for annotation in self._get_filtered_annotations(name, part_of_group):
            if annotation.attrib["Type"] in ["Point", "Dot"]:
                yield from self._extract_coordinates(annotation)

root = self.tree.getroot() instance-attribute

tree = ET.parse(file_path) instance-attribute

__init__(file_path)

Source code in ratiopath/parsers/asap_parser.py

def __init__(self, file_path: Path | str | TextIO):
    self.tree = ET.parse(file_path)
    self.root = self.tree.getroot()

get_points(name='.*', part_of_group='.*')

Parse point annotations from ASAP XML file.

Parameters:

Name	Type	Description	Default
name	str	Regex pattern to match annotation names.	'.*'
part_of_group	str	Regex pattern to match annotation groups.	'.*'

Returns:

Type	Description
Iterable[Point]	An iterable of shapely Point objects.

Source code in ratiopath/parsers/asap_parser.py

def get_points(
    self, name: str = ".*", part_of_group: str = ".*"
) -> Iterable[Point]:
    """Parse point annotations from ASAP XML file.

    Args:
        name: Regex pattern to match annotation names.
        part_of_group: Regex pattern to match annotation groups.

    Returns:
        An iterable of shapely Point objects.
    """
    for annotation in self._get_filtered_annotations(name, part_of_group):
        if annotation.attrib["Type"] in ["Point", "Dot"]:
            yield from self._extract_coordinates(annotation)

get_polygons(name='.*', part_of_group='.*')

Parse polygon annotations from ASAP XML file.

Parameters:

Name	Type	Description	Default
name	str	Regex pattern to match annotation names.	'.*'
part_of_group	str	Regex pattern to match annotation groups.	'.*'

Returns:

Type	Description
Iterable[Polygon]	An iterable of shapely Polygon objects.

Source code in ratiopath/parsers/asap_parser.py

def get_polygons(
    self, name: str = ".*", part_of_group: str = ".*"
) -> Iterable[Polygon]:
    """Parse polygon annotations from ASAP XML file.

    Args:
        name: Regex pattern to match annotation names.
        part_of_group: Regex pattern to match annotation groups.

    Returns:
        An iterable of shapely Polygon objects.
    """
    for annotation in self._get_filtered_annotations(name, part_of_group):
        if annotation.attrib["Type"] in ["Polygon", "Spline"]:
            yield Polygon(self._extract_coordinates(annotation))