phasorpy 0.2__cp313-cp313-macosx_11_0_arm64.whl → 0.3__cp313-cp313-macosx_11_0_arm64.whl

phasorpy/_phasorpy.pyx

@@ -68,7 +68,8 @@ def _phasor_from_signal(
     float_t[:, :, ::1] phasor,
     const signal_t[:, :, ::1] signal,
     const double[:, :, ::1] sincos,
-    const int num_threads
+    const bint normalize,
+    const int num_threads,
 ):
     """Return phasor coordinates from signal along middle axis.
 
@@ -97,6 +98,8 @@ def _phasor_from_signal(
         1. number samples
         2. cos and sin
 
+    normalize : bool
+        Normalize phasor coordinates.
     num_threads : int
         Number of OpenMP threads to use for parallelization.
 
@@ -145,14 +148,16 @@ def _phasor_from_signal(
                             dc = dc + sample
                             re = re + sample * sincos[h, k, 0]
                             im = im + sample * sincos[h, k, 1]
-                        if dc != 0.0:
-                            re = re / dc
-                            im = im / dc
-                            dc = dc /samples
-                        else:
-                            dc = 0.0
-                            re = NAN if re == 0.0 else re * INFINITY
-                            im = NAN if im == 0.0 else im * INFINITY
+                        if normalize:
+                            if dc != 0.0:
+                                # includes isnan(dc)
+                                re = re / dc
+                                im = im / dc
+                                dc = dc / samples
+                            else:
+                                # dc = 0.0
+                                re = NAN if re == 0.0 else re * INFINITY
+                                im = NAN if im == 0.0 else im * INFINITY
                         if h == 0:
                             mean[i, j] = <float_t> dc
                         real[h, i, j] = <float_t> re
@@ -173,14 +178,16 @@ def _phasor_from_signal(
                             dc = dc + sample
                             re = re + sample * sincos[h, k, 0]
                             im = im + sample * sincos[h, k, 1]
-                        if dc != 0.0:
-                            re = re / dc
-                            im = im / dc
-                            dc = dc /samples
-                        else:
-                            dc = 0.0
-                            re = NAN if re == 0.0 else re * INFINITY
-                            im = NAN if im == 0.0 else im * INFINITY
+                        if normalize:
+                            if dc != 0.0:
+                                # includes isnan(dc)
+                                re = re / dc
+                                im = im / dc
+                                dc = dc / samples
+                            else:
+                                # dc = 0.0
+                                re = NAN if re == 0.0 else re * INFINITY
+                                im = NAN if im == 0.0 else im * INFINITY
                         if h == 0:
                             mean[i, j] = <float_t> dc
                         real[h, i, j] = <float_t> re
@@ -201,14 +208,16 @@ def _phasor_from_signal(
                             dc += sample
                             re += sample * sincos[h, k, 0]
                             im += sample * sincos[h, k, 1]
-                        if dc != 0.0:
-                            re /= dc
-                            im /= dc
-                            dc /= samples
-                        else:
-                            dc = 0.0
-                            re = NAN if re == 0.0 else re * INFINITY
-                            im = NAN if im == 0.0 else im * INFINITY
+                        if normalize:
+                            if dc != 0.0:
+                                # includes isnan(dc)
+                                re /= dc
+                                im /= dc
+                                dc = dc / samples
+                            else:
+                                # dc = 0.0
+                                re = NAN if re == 0.0 else re * INFINITY
+                                im = NAN if im == 0.0 else im * INFINITY
                         if h == 0:
                             mean[i, j] = <float_t> dc
                         real[h, i, j] = <float_t> re
@@ -924,32 +933,41 @@ cdef (float_t, float_t) _phasor_at_harmonic(
 
 @cython.ufunc
 cdef (float_t, float_t) _phasor_multiply(
-    float_t real1,
-    float_t imag1,
+    float_t real,
+    float_t imag,
     float_t real2,
     float_t imag2,
 ) noexcept nogil:
-    """Return multiplication of two phasors."""
-    return real1 * real2 - imag1 * imag2, real1 * imag2 + imag1 * real2
+    """Return complex multiplication of two phasors."""
+    return (
+        real * real2 - imag * imag2,
+        real * imag2 + imag * real2
+    )
 
 
 @cython.ufunc
 cdef (float_t, float_t) _phasor_divide(
-    float_t real1,
-    float_t imag1,
+    float_t real,
+    float_t imag,
     float_t real2,
     float_t imag2,
 ) noexcept nogil:
-    """Return division of two phasors."""
+    """Return complex division of two phasors."""
     cdef:
-        float_t denom = real2 * real2 + imag2 * imag2
+        float_t divisor = real2 * real2 + imag2 * imag2
 
-    if isnan(denom) or denom == 0.0:
-        return <float_t> NAN, <float_t> NAN
+    if divisor != 0.0:
+        # includes isnan(divisor)
+        return (
+            (real * real2 + imag * imag2) / divisor,
+            (imag * real2 - real * imag2) / divisor
+        )
 
+    real = real * real2 + imag * imag2
+    imag = imag * real2 - real * imag2
     return (
-        (real1 * real2 + imag1 * imag2) / denom,
-        (imag1 * real2 - real1 * imag2) / denom
+        NAN if real == 0.0 else real * INFINITY,
+        NAN if imag == 0.0 else imag * INFINITY
     )
 
 

phasorpy/io.py

@@ -16,6 +16,7 @@ The ``phasorpy.io`` module provides functions to:
 - read time-resolved and hyperspectral image data and metadata (as relevant
   to phasor analysis) from many file formats used in bio-imaging:
 
+  - :py:func:`read_imspector_tiff` - ImSpector FLIM TIFF
   - :py:func:`read_lsm` - Zeiss LSM
   - :py:func:`read_ifli` - ISS IFLI
   - :py:func:`read_sdt` - Becker & Hickl SDT
@@ -123,6 +124,7 @@ __all__ = [
     'read_fbd',
     'read_flif',
     'read_ifli',
+    'read_imspector_tiff',
     # 'read_lif',
     'read_lsm',
     # 'read_nd2',
@@ -887,6 +889,146 @@ def read_lsm(
     return DataArray(data, **metadata)
 
 
+def read_imspector_tiff(
+    filename: str | PathLike[Any],
+    /,
+) -> DataArray:
+    """Return FLIM image stack and metadata from ImSpector TIFF file.
+
+    Parameters
+    ----------
+    filename : str or Path
+        Name of ImSpector FLIM TIFF file to read.
+
+    Returns
+    -------
+    xarray.DataArray
+        TCSPC image stack.
+        Usually, a 3-to-5-dimensional array of type ``uint16``.
+
+        - ``coords['H']``: times of histogram bins.
+        - ``attrs['frequency']``: repetition frequency in MHz.
+
+    Raises
+    ------
+    tifffile.TiffFileError
+        File is not a TIFF file.
+    ValueError
+        File is not an ImSpector FLIM TIFF file.
+
+    Examples
+    --------
+    >>> data = read_imspector_tiff(fetch('Embryo.tif'))
+    >>> data.values
+    array(...)
+    >>> data.dtype
+    dtype('uint16')
+    >>> data.shape
+    (56, 512, 512)
+    >>> data.dims
+    ('H', 'Y', 'X')
+    >>> data.coords['H'].data  # dtime bins
+    array(...)
+    >>> data.attrs['frequency']  # doctest: +NUMBER
+    80.109
+
+    """
+    from xml.etree import ElementTree
+
+    import tifffile
+
+    with tifffile.TiffFile(filename) as tif:
+        tags = tif.pages.first.tags
+        omexml = tags.valueof(270, '')
+        make = tags.valueof(271, '')
+
+        if (
+            make != 'ImSpector'
+            or not omexml.startswith('<?xml version')
+            or len(tif.series) != 1
+            or not tif.is_ome
+        ):
+            raise ValueError(f'{tif.filename} is not an ImSpector TIFF file')
+
+        series = tif.series[0]
+        ndim = series.ndim
+        axes = series.axes
+        shape = series.shape
+
+        if ndim < 3 or not axes.endswith('YX'):
+            raise ValueError(
+                f'{tif.filename} is not an ImSpector FLIM TIFF file'
+            )
+
+        data = series.asarray()
+
+    attrs: dict[str, Any] = {}
+    coords = {}
+    physical_size = {}
+
+    root = ElementTree.fromstring(omexml)
+    ns = {
+        '': 'http://www.openmicroscopy.org/Schemas/OME/2008-02',
+        'ca': 'http://www.openmicroscopy.org/Schemas/CA/2008-02',
+    }
+
+    description = root.find('.//Description', ns)
+    if (
+        description is not None
+        and description.text
+        and description.text != 'not_specified'
+    ):
+        attrs['description'] = description.text
+
+    pixels = root.find('.//Image/Pixels', ns)
+    assert pixels is not None
+    for ax in 'TZYX':
+        attrib = 'TimeIncrement' if ax == 'T' else f'PhysicalSize{ax}'
+        if ax not in axes or attrib not in pixels.attrib:
+            continue
+        size = float(pixels.attrib[attrib])
+        physical_size[ax] = size
+        coords[ax] = numpy.linspace(
+            0.0,
+            size,
+            shape[axes.index(ax)],
+            endpoint=False,
+            dtype=numpy.float64,
+        )
+
+    axes_labels = root.find('.//ca:CustomAttributes/AxesLabels', ns)
+    if (
+        axes_labels is None
+        or 'X' not in axes_labels.attrib
+        or 'TCSPC' not in axes_labels.attrib['X']
+        or 'FirstAxis' not in axes_labels.attrib
+        or 'SecondAxis' not in axes_labels.attrib
+    ):
+        raise ValueError(f'{tif.filename} is not an ImSpector FLIM TIFF file')
+
+    if axes_labels.attrib['FirstAxis'].endswith('TCSPC T'):
+        ax = axes[-3]
+        assert axes_labels.attrib['FirstAxis-Unit'] == 'ns'
+    elif axes_labels.attrib['SecondAxis'].endswith('TCSPC T') and ndim > 3:
+        ax = axes[-4]
+        assert axes_labels.attrib['SecondAxis-Unit'] == 'ns'
+    else:
+        raise ValueError(f'{tif.filename} is not an ImSpector FLIM TIFF file')
+    axes = axes.replace(ax, 'H')
+    coords['H'] = coords[ax]
+    del coords[ax]
+
+    attrs['frequency'] = float(
+        1000.0 / (shape[axes.index('H')] * physical_size[ax])
+    )
+
+    metadata = _metadata(axes, shape, filename, attrs=attrs, **coords)
+
+    from xarray import DataArray
+
+    return DataArray(data, **metadata)
+
+
 def read_ifli(
     filename: str | PathLike[Any],
     /,
@@ -942,8 +1084,8 @@ def read_ifli(
     (256, 256, 4, 3)
     >>> data.dims
     ('Y', 'X', 'F', 'S')
-    >>> data.coords['F'].data
-    array([8.033...])
+    >>> data.coords['F'].data  # doctest: +NUMBER
+    array([8.033e+07, 1.607e+08, 2.41e+08, 4.017e+08])
     >>> data.coords['S'].data
     array(['mean', 'real', 'imag'], dtype='<U4')
     >>> data.attrs
@@ -1035,8 +1177,8 @@ def read_sdt(
     ('Y', 'X', 'H')
     >>> data.coords['H'].data
     array(...)
-    >>> data.attrs['frequency']
-    79...
+    >>> data.attrs['frequency']  # doctest: +NUMBER
+    79.99
 
     """
     import sdtfile
@@ -1148,7 +1290,7 @@ def read_ptu(
     ('T', 'Y', 'X', 'C', 'H')
     >>> data.coords['H'].data
     array(...)
-    >>> data.attrs['frequency']
+    >>> data.attrs['frequency']  # doctest: +NUMBER
     78.02
 
     """
@@ -1221,8 +1363,8 @@ def read_flif(
     ('H', 'Y', 'X')
     >>> data.coords['H'].data
     array(...)
-    >>> data.attrs['frequency']
-    80.65...
+    >>> data.attrs['frequency']  # doctest: +NUMBER
+    80.65
 
     """
     import lfdfiles