phasorpy._phasorpy#

Note

This module and its functions are not part of the public interface. They are intended to facilitate the development of the PhasorPy library.

Cython implementation of low-level functions for the PhasorPy library.

phasorpy._phasorpy._flimlabs_mean(mean, data, channel=-1)#

Return mean intensity image from FLIM LABS JSON intensity data.

phasorpy._phasorpy._flimlabs_signal(signal, data, channel=-1)#

Return TCSPC histogram image from FLIM LABS JSON intensity data.

phasorpy._phasorpy._gaussian_signal(signal, mean, stdev)#

Return normal distribution, wrapped around at borders.

Parameters:

  • signal (memoryview of float32 or float64) – Writable buffer where calculated signal samples are stored.

  • mean (float) – Mean of normal distribution.

  • stdev (float) – Standard deviation of normal distribution.

phasorpy._phasorpy._median_filter_2d(image, filtered_image, kernel_size, repeat=1, num_threads=1)#

Apply 2D median filter ignoring NaN.

phasorpy._phasorpy._nearest_neighbor_2d(indices, x0, y0, x1, y1, distance_max, num_threads)#

Find nearest neighbors in 2D.

For each point in the first set of arrays (x0, y0) find the nearest point in the second set of arrays (x1, y1) and store the index of the nearest point in the second array in the indices array. If any coordinates are NaN, or the distance to the nearest point is larger than distance_max, the index is set to -1.

phasorpy._phasorpy._phasor_from_lifetime(phasor, frequency, lifetime, fraction, unit_conversion, preexponential)#

Calculate phasor coordinates from lifetime components.

Parameters:

  • phasor (3D memoryview of float32 or float64) –

    Writable buffer of three dimensions where calculated phasor coordinates are stored:

    1. real and imaginary components

    2. frequencies

    3. lifetimes or fractions

  • frequency (2D memoryview of float64) – One-dimensional sequence of laser-pulse or modulation frequencies.

  • lifetime (2D memoryview of float64) –

    Buffer of two dimensions:

    1. lifetimes

    2. components of lifetimes

  • fraction (2D memoryview of float64) –

    Buffer of two dimensions:

    1. fractions

    2. fractions of lifetime components

  • unit_conversion (float) – Product of frequency and lifetime units’ prefix factors. 1e-3 for MHz and ns. 1.0 for Hz and s.

  • preexponential (bool) – If true, fractions are pre-exponential amplitudes, else fractional intensities.

phasorpy._phasorpy._phasor_from_signal(phasor, signal, sincos, normalize, num_threads)#

Return phasor coordinates from signal along middle axis.

Parameters:

  • phasor (3D memoryview of float32 or float64) –

    Writable buffer of three dimensions where calculated phasor coordinates are stored:

    1. mean, real, and imaginary components

    2. lower dimensions flat

    3. upper dimensions flat

  • signal (3D memoryview of float32 or float64) –

    Buffer of three dimensions containing signal:

    1. lower dimensions flat

    2. dimension over which to compute FFT, number samples

    3. upper dimensions flat

  • sincos (3D memoryview of float64) –

    Buffer of three dimensions containing sine and cosine terms to be multiplied with signal:

    1. number harmonics

    2. number samples

    3. cos and sin

  • normalize (bool) – Normalize phasor coordinates.

  • num_threads (int) – Number of OpenMP threads to use for parallelization.

Notes

This implementation requires contiguous input arrays.

phasorpy._phasorpy._phasor_from_signal_vector(phasor, signal, sincos, num_threads)#

Calculate phasor coordinate vectors from signal along last axis.

Parameters:

  • phasor (2D memoryview of float32 or float64) –

    Writable buffer of two dimensions where calculated phasor vectors are stored:

    1. other dimensions flat

    2. real and imaginary components

  • signal (2D memoryview of float32 or float64) –

    Buffer of two dimensions containing signal:

    1. other dimensions flat

    2. dimension over which to compute FFT, number samples

  • sincos (3D memoryview of float64) –

    Buffer of three dimensions containing sine and cosine terms to be multiplied with signal:

    1. number harmonics

    2. number samples

    3. cos and sin

  • num_threads (int) – Number of OpenMP threads to use for parallelization.

Notes

This implementation requires contiguous input arrays.

phasorpy._phasorpy._signal_denoise_vector(denoised, integrated, signal, spectral_vector, sigma, vmin, num_threads)#

Calculate denoised signal from spectral_vector.