phasorpy 0.4__cp313-cp313-win_arm64.whl → 0.6__cp313-cp313-win_arm64.whl

phasorpy/io/_leica.py

@@ -0,0 +1,329 @@
+"""Read Leica image file formats."""
+
+from __future__ import annotations
+
+__all__ = ['lifetime_from_lif', 'phasor_from_lif', 'signal_from_lif']
+
+from typing import TYPE_CHECKING
+
+from .._utils import xarray_metadata
+
+if TYPE_CHECKING:
+    from .._typing import Any, DataArray, Literal, NDArray, PathLike
+
+import numpy
+
+
+def phasor_from_lif(
+    filename: str | PathLike[Any],
+    /,
+    image: str | None = None,
+) -> tuple[NDArray[Any], NDArray[Any], NDArray[Any], dict[str, Any]]:
+    """Return phasor coordinates and metadata from Leica image file.
+
+    Leica image files may contain uncalibrated phasor coordinate images and
+    metadata from the analysis of FLIM measurements.
+
+    Parameters
+    ----------
+    filename : str or Path
+        Name of Leica image file to read.
+    image : str, optional
+        Name of parent image containing phasor coordinates.
+
+    Returns
+    -------
+    mean : ndarray
+        Average intensity image.
+    real : ndarray
+        Image of real component of phasor coordinates.
+    imag : ndarray
+        Image of imaginary component of phasor coordinates.
+    attrs : dict
+        Select metadata:
+
+        - ``'dims'`` (tuple of str):
+          :ref:`Axes codes <axes>` for `mean` image dimensions.
+        - ``'frequency'`` (float):
+          Fundamental frequency of time-resolved phasor coordinates in MHz.
+          May not be present in all files.
+        - ``'flim_rawdata'`` (dict):
+          Settings from SingleMoleculeDetection/RawData XML element.
+        - ``'flim_phasor_channels'`` (list of dict):
+          Settings from SingleMoleculeDetection/.../PhasorData/Channels XML
+          elements.
+
+    Raises
+    ------
+    liffile.LifFileError
+        File is not a Leica image file.
+    ValueError
+        File or `image` do not contain phasor coordinates and metadata.
+
+    Notes
+    -----
+    The implementation is based on the
+    `liffile <https://github.com/cgohlke/liffile/>`__ library.
+
+    Examples
+    --------
+    >>> mean, real, imag, attrs = phasor_from_lif(fetch('FLIM_testdata.lif'))
+    >>> real.shape
+    (1024, 1024)
+    >>> attrs['dims']
+    ('Y', 'X')
+    >>> attrs['frequency']
+    19.505
+
+    """
+    # TODO: read harmonic from XML if possible
+    # TODO: get calibration settings from XML metadata, lifetime, or
+    #   phasor plot images
+    import liffile
+
+    image = '' if image is None else f'.*{image}.*/'
+    samples = 1
+
+    with liffile.LifFile(filename) as lif:
+        try:
+            im = lif.images[image + 'Phasor Intensity$']
+            dims = im.dims
+            coords = im.coords
+            # meta = image.attrs
+            mean = im.asarray().astype(numpy.float32)
+            real = lif.images[image + 'Phasor Real$'].asarray()
+            imag = lif.images[image + 'Phasor Imaginary$'].asarray()
+            # mask = lif.images[image + 'Phasor Mask$'].asarray()
+        except Exception as exc:
+            raise ValueError(
+                f'{lif.filename!r} does not contain Phasor images'
+            ) from exc
+
+        attrs: dict[str, Any] = {'dims': dims, 'coords': coords}
+        flim = im.parent_image
+        if flim is not None and isinstance(flim, liffile.LifFlimImage):
+            xml = flim.parent.xml_element
+            frequency = xml.find('.//Dataset/RawData/LaserPulseFrequency')
+            if frequency is not None and frequency.text is not None:
+                attrs['frequency'] = float(frequency.text) * 1e-6
+                clock_period = xml.find('.//Dataset/RawData/ClockPeriod')
+                if clock_period is not None and clock_period.text is not None:
+                    tmp = float(clock_period.text) * float(frequency.text)
+                    samples = int(round(1.0 / tmp))
+                    attrs['samples'] = samples
+            channels = []
+            for channel in xml.findall(
+                './/Dataset/FlimData/PhasorData/Channels'
+            ):
+                ch = liffile.xml2dict(channel)['Channels']
+                ch.pop('PhasorPlotShapes', None)
+                channels.append(ch)
+            attrs['flim_phasor_channels'] = channels
+            attrs['flim_rawdata'] = flim.attrs.get('RawData', {})
+
+    if samples > 1:
+        mean /= samples
+    return (
+        mean,
+        real.astype(numpy.float32),
+        imag.astype(numpy.float32),
+        attrs,
+    )
+
+
+def lifetime_from_lif(
+    filename: str | PathLike[Any],
+    /,
+    image: str | None = None,
+) -> tuple[NDArray[Any], NDArray[Any], NDArray[Any], dict[str, Any]]:
+    """Return lifetime image and metadata from Leica image file.
+
+    Leica image files may contain fluorescence lifetime images and metadata
+    from the analysis of FLIM measurements.
+
+    Parameters
+    ----------
+    filename : str or Path
+        Name of Leica image file to read.
+    image : str, optional
+        Name of parent image containing lifetime image.
+
+    Returns
+    -------
+    lifetime : ndarray
+        Fluorescence lifetime image in ns.
+    intensity : ndarray
+        Fluorescence intensity image.
+    stddev : ndarray
+        Standard deviation of fluorescence lifetimes in ns.
+    attrs : dict
+        Select metadata:
+
+        - ``'dims'`` (tuple of str):
+          :ref:`Axes codes <axes>` for `intensity` image dimensions.
+        - ``'frequency'`` (float):
+          Fundamental frequency of lifetimes in MHz.
+          May not be present in all files.
+        - ``'samples'`` (int):
+          Number of bins in TCSPC histogram. May not be present in all files.
+        - ``'flim_rawdata'`` (dict):
+          Settings from SingleMoleculeDetection/RawData XML element.
+
+    Raises
+    ------
+    liffile.LifFileError
+        File is not a Leica image file.
+    ValueError
+        File or `image` does not contain lifetime coordinates and metadata.
+
+    Notes
+    -----
+    The implementation is based on the
+    `liffile <https://github.com/cgohlke/liffile/>`__ library.
+
+    Examples
+    --------
+    >>> lifetime, intensity, stddev, attrs = lifetime_from_lif(
+    ...     fetch('FLIM_testdata.lif')
+    ... )
+    >>> lifetime.shape
+    (1024, 1024)
+    >>> attrs['dims']
+    ('Y', 'X')
+    >>> attrs['frequency']
+    19.505
+
+    """
+    import liffile
+
+    image = '' if image is None else f'.*{image}.*/'
+
+    with liffile.LifFile(filename) as lif:
+        try:
+            im = lif.images[image + 'Intensity$']
+            dims = im.dims
+            coords = im.coords
+            # meta = im.attrs
+            intensity = im.asarray()
+            lifetime = lif.images[image + 'Fast Flim$'].asarray()
+            stddev = lif.images[image + 'Standard Deviation$'].asarray()
+        except Exception as exc:
+            raise ValueError(
+                f'{lif.filename!r} does not contain lifetime images'
+            ) from exc
+
+        attrs: dict[str, Any] = {'dims': dims, 'coords': coords}
+        flim = im.parent_image
+        if flim is not None and isinstance(flim, liffile.LifFlimImage):
+            xml = flim.parent.xml_element
+            frequency = xml.find('.//Dataset/RawData/LaserPulseFrequency')
+            if frequency is not None and frequency.text is not None:
+                attrs['frequency'] = float(frequency.text) * 1e-6
+                clock_period = xml.find('.//Dataset/RawData/ClockPeriod')
+                if clock_period is not None and clock_period.text is not None:
+                    tmp = float(clock_period.text) * float(frequency.text)
+                    samples = int(round(1.0 / tmp))
+                    attrs['samples'] = samples
+            attrs['flim_rawdata'] = flim.attrs.get('RawData', {})
+
+    return (
+        lifetime.astype(numpy.float32),
+        intensity.astype(numpy.float32),
+        stddev.astype(numpy.float32),
+        attrs,
+    )
+
+
+def signal_from_lif(
+    filename: str | PathLike[Any],
+    /,
+    *,
+    image: int | str | None = None,
+    dim: Literal['λ', 'Λ'] | str = 'λ',
+) -> DataArray:
+    """Return hyperspectral image and metadata from Leica image file.
+
+    Leica image files may contain hyperspectral images and metadata from laser
+    scanning microscopy measurements.
+
+    Parameters
+    ----------
+    filename : str or Path
+        Name of Leica image file to read.
+    image : str or int, optional
+        Index or regex pattern of image to return.
+        By default, return the first image containing hyperspectral data.
+    dim : str or None
+        Character code of hyperspectral dimension.
+        Either ``'λ'`` for emission (default) or ``'Λ'`` for excitation.
+
+    Returns
+    -------
+    xarray.DataArray
+        Hyperspectral image data.
+
+        - ``coords['C']``: wavelengths in nm.
+        - ``coords['T']``: time coordinates in s, if any.
+
+    Raises
+    ------
+    liffile.LifFileError
+        File is not a Leica image file.
+    ValueError
+        File is not a Leica image file or does not contain hyperspectral image.
+
+    Notes
+    -----
+    The implementation is based on the
+    `liffile <https://github.com/cgohlke/liffile/>`__ library.
+
+    Reading of TCSPC histograms from FLIM measurements is not supported
+    because the compression scheme is patent-pending.
+
+    Examples
+    --------
+    >>> signal = signal_from_lif('ScanModesExamples.lif')  # doctest: +SKIP
+    >>> signal.values  # doctest: +SKIP
+    array(...)
+    >>> signal.shape  # doctest: +SKIP
+    (9, 128, 128)
+    >>> signal.dims  # doctest: +SKIP
+    ('C', 'Y', 'X')
+    >>> signal.coords['C'].data  # doctest: +SKIP
+    array([560, 580, 600, ..., 680, 700, 720])
+
+    """
+    import liffile
+
+    with liffile.LifFile(filename) as lif:
+        if image is None:
+            # find image with excitation or emission dimension
+            for im in lif.images:
+                if dim in im.dims:
+                    break
+            else:
+                raise ValueError(
+                    f'{lif.filename!r} does not contain hyperspectral image'
+                )
+        else:
+            im = lif.images[image]
+
+        if dim not in im.dims or im.sizes[dim] < 4:
+            raise ValueError(f'{im!r} does not contain spectral dimension')
+        if 'C' in im.dims:
+            raise ValueError(
+                'hyperspectral image must not contain channel axis'
+            )
+
+        data = im.asarray()
+        coords: dict[str, Any] = {
+            ('C' if k == dim else k): (v * 1e9 if k == dim else v)
+            for (k, v) in im.coords.items()
+        }
+        dims = tuple(('C' if d == dim else d) for d in im.dims)
+
+        metadata = xarray_metadata(dims, im.shape, filename, **coords)
+
+    from xarray import DataArray
+
+    return DataArray(data, **metadata)