path: root/silx/math/colormap.pyx

# coding: utf-8
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# Copyright (c) 2018 European Synchrotron Radiation Facility
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"""This module provides :func:`cmap` which applies a colormap to a dataset.
"""

__authors__ = ["T. Vincent"]
__license__ = "MIT"
__date__ = "16/05/2018"


cimport cython
from cython.parallel import prange
cimport numpy as cnumpy
from libc.math cimport frexp, sqrt
from math_compatibility cimport asinh, isnan, isfinite, lrint, INFINITY, NAN

import logging
import numpy

__all__ = ['cmap']

_logger = logging.getLogger(__name__)


# Supported data types
ctypedef fused data_types:
    cnumpy.uint8_t
    cnumpy.int8_t
    cnumpy.uint16_t
    cnumpy.int16_t
    cnumpy.uint32_t
    cnumpy.int32_t
    cnumpy.uint64_t
    cnumpy.int64_t
    float
    double
    long double


# Data types using a LUT to apply the colormap
ctypedef fused lut_types:
    cnumpy.uint8_t
    cnumpy.int8_t
    cnumpy.uint16_t
    cnumpy.int16_t


# Data types using default colormap implementation
ctypedef fused default_types:
    cnumpy.uint32_t
    cnumpy.int32_t
    cnumpy.uint64_t
    cnumpy.int64_t
    float
    double
    long double


# Supported colors/output types
ctypedef fused image_types:
    cnumpy.uint8_t
    float


# Type of scale function
ctypedef double (*scale_function)(double) nogil


# Normalization


cdef double linear_scale(double value) nogil:
    """No-Op scaling function"""
    return value


cdef double asinh_scale(double value) nogil:
    """asinh scaling function

    Wraps asinh as it is defined as a macro for Windows support.
    """
    return asinh(value)


DEF LOG_LUT_SIZE = 4096
cdef double[::1] _log_lut
"""LUT used for fast log approximation"""

# Initialize log approximation LUT
_log_lut = numpy.log2(
    numpy.linspace(0.5, 1., LOG_LUT_SIZE + 1,
                   endpoint=True).astype(numpy.float64))
# index_lut can overflow of 1
_log_lut[LOG_LUT_SIZE] = _log_lut[LOG_LUT_SIZE - 1]


@cython.wraparound(False)
@cython.boundscheck(False)
@cython.nonecheck(False)
@cython.cdivision(True)
cdef double fast_log10(double value) nogil:
    """Return log10(value) fast approximation based on LUT"""
    cdef double result = NAN  # if value < 0.0 or value == NAN
    cdef int exponent, index_lut
    cdef double mantissa  # in [0.5, 1) unless value == 0 NaN or +/-inf

    if value <= 0.0 or not isfinite(value):
        if value == 0.0:
            result = - INFINITY
        elif value > 0.0:  # i.e., value = +INFINITY
            result = value  # i.e. +INFINITY
    else:
        mantissa = frexp(value, &exponent)
        index_lut = lrint(LOG_LUT_SIZE * 2 * (mantissa - 0.5))
        # 1/log2(10) = 0.30102999566398114
        result = 0.30102999566398114 * (<double> exponent +
                                        _log_lut[index_lut])
    return result


# Colormap

@cython.wraparound(False)
@cython.boundscheck(False)
@cython.nonecheck(False)
@cython.cdivision(True)
cdef image_types[:, ::1] compute_cmap(
           default_types[:] data,
           image_types[:, ::1] colors,
           double normalized_vmin,
           double normalized_vmax,
           image_types[::1] nan_color,
           scale_function scale_func):
    """Apply colormap to data.

    :param data: Input data
    :param colors: Colors look-up-table
    :param normalized_vmin: Normalized lower bound of the colormap range
    :param normalized_vmax: Normalized upper bound of the colormap range
    :param nan_color: Color to use for NaN value
    :param scale_func: The function to use to scale data
    :return: Data converted to colors
    """
    cdef image_types[:, ::1] output
    cdef double scale, value
    cdef int length, nb_channels, nb_colors
    cdef int channel, index, lut_index

    nb_colors = <int> colors.shape[0]
    nb_channels = <int> colors.shape[1]
    length = <int> data.size

    output = numpy.empty((length, nb_channels),
                         dtype=numpy.array(colors, copy=False).dtype)

    if normalized_vmin == normalized_vmax:
        scale = 0.
    else:
        scale = nb_colors / (normalized_vmax - normalized_vmin)

    with nogil:
        for index in prange(length):
            value = scale_func(<double> data[index])

            # Handle NaN
            if isnan(value):
                for channel in range(nb_channels):
                    output[index, channel] = nan_color[channel]
                continue

            if value <= normalized_vmin:
                lut_index = 0
            elif value >= normalized_vmax:
                lut_index = nb_colors - 1
            else:
                lut_index = <int>((value - normalized_vmin) * scale)
                # Index can overflow of 1
                if lut_index >= nb_colors:
                    lut_index = nb_colors - 1

            for channel in range(nb_channels):
                output[index, channel] = colors[lut_index, channel]

    return output

@cython.wraparound(False)
@cython.boundscheck(False)
@cython.nonecheck(False)
@cython.cdivision(True)
cdef image_types[:, ::1] compute_cmap_with_lut(
               lut_types[:] data,
               image_types[:, ::1] colors,
               double normalized_vmin,
               double normalized_vmax,
               image_types[::1] nan_color,
               scale_function scale_func):
    """Convert data to colors using look-up table to speed the process.

    Only supports data of types: uint8, uint16, int8, int16.

    :param data: Input data
    :param colors: Colors look-up-table
    :param normalized_vmin: Normalized lower bound of the colormap range
    :param normalized_vmax: Normalized upper bound of the colormap range
    :param nan_color: Color to use for NaN values
    :param scale_func: The function to use for scaling data
    :return: The generated image
    """
    cdef image_types[:, ::1] output
    cdef double[:] values
    cdef image_types[:, ::1] lut
    cdef int type_min, type_max
    cdef int nb_channels, length
    cdef int channel, index, lut_index

    length = <int> data.size
    nb_channels = <int> colors.shape[1]

    if lut_types is cnumpy.int8_t:
        type_min = -128
        type_max = 127
    elif lut_types is cnumpy.uint8_t:
        type_min = 0
        type_max = 255
    elif lut_types is cnumpy.int16_t:
        type_min = -32768
        type_max = 32767
    else:  # uint16_t
        type_min = 0
        type_max = 65535

    colors_dtype = numpy.array(colors).dtype

    values = numpy.arange(type_min, type_max + 1, dtype=numpy.float64)
    lut = compute_cmap(
        values, colors, normalized_vmin, normalized_vmax,
        nan_color, scale_func)

    output = numpy.empty((length, nb_channels), dtype=colors_dtype)

    with nogil:
        # Apply LUT
        for index in prange(length):
            lut_index = data[index] - type_min
            for channel in range(nb_channels):
                output[index, channel] = lut[lut_index, channel]

    return output


@cython.wraparound(False)
@cython.boundscheck(False)
@cython.nonecheck(False)
@cython.cdivision(True)
def _cmap(data_types[:] data,
          image_types[:, ::1] colors,
          str normalization,
          double vmin,
          double vmax,
          image_types[::1] nan_color):
    """Implementation of colormap.

    Use :func:`cmap`.

    :param data: Input data
    :param colors: Colors look-up-table
    :param normalization: Kind of scaling to apply on data
    :param vmin: Lower bound of the colormap range
    :param vmax: Upper bound of the colormap range
    :param nan_color: Color to use for NaN value.
    :return: The generated image
    """
    cdef double normalized_vmin, normalized_vmax
    cdef scale_function scale_func

    if normalization == 'linear':
        scale_func = linear_scale
    elif normalization == 'log':
        scale_func = fast_log10
    elif normalization == 'arcsinh':
        scale_func = asinh_scale
    elif normalization == 'sqrt':
        scale_func = sqrt
    else:
        raise ValueError('Unsupported normalization %s' % normalization)

    normalized_vmin = scale_func(vmin)
    normalized_vmax = scale_func(vmax)

    if not isfinite(normalized_vmin) or not isfinite(normalized_vmax):
        raise ValueError('Colormap range is not valid')

    # Proxy for calling the right implementation depending on data type
    if data_types in lut_types:  # Use LUT implementation
        output = compute_cmap_with_lut(
            data, colors, normalized_vmin, normalized_vmax,
            nan_color, scale_func)

    elif data_types in default_types:  # Use default implementation
        output = compute_cmap(
            data, colors, normalized_vmin, normalized_vmax,
            nan_color, scale_func)

    else:
        raise ValueError('Unsupported data type')

    return numpy.array(output, copy=False)


def cmap(data,
         colors,
         double vmin,
         double vmax,
         str normalization='linear',
         nan_color=None):
    """Convert data to colors with provided colors look-up table.

    :param numpy.ndarray data: The input data
    :param numpy.ndarray colors: Color look-up table as a 2D array.
       It MUST be of type uint8 or float32
    :param vmin: Data value to map to the beginning of colormap.
    :param vmax: Data value to map to the end of the colormap.
    :param str normalization: The normalization to apply:

        - 'linear' (default)
        - 'log'
        - 'arcsinh'
        - 'sqrt'

    :param nan_color: Color to use for NaN value.
        Default: A color with all channels set to 0
    :return: Array of colors. The shape of the
        returned array is that of data array + the last dimension of colors.
        The dtype of the returned array is that of the colors array.
    :rtype: numpy.ndarray
    """
    cdef int nb_channels

    # Make data a numpy array of native endian type (no need for contiguity)
    data = numpy.array(data, copy=False)
    native_endian_dtype = data.dtype.newbyteorder('N')
    if native_endian_dtype.kind == 'f' and native_endian_dtype.itemsize == 2:
        native_endian_dtype = "=f4"  # Use native float32 instead of float16
    data = numpy.array(data, copy=False, dtype=native_endian_dtype)

    # Make colors a contiguous array of native endian type
    colors = numpy.array(colors, copy=False)
    nb_channels = colors.shape[colors.ndim - 1]
    colors = numpy.ascontiguousarray(colors,
                                     dtype=colors.dtype.newbyteorder('N'))

    # Check nan_color
    if nan_color is None:
        nan_color = numpy.zeros((nb_channels,), dtype=colors.dtype)
    else:
        nan_color = numpy.ascontiguousarray(
            nan_color, dtype=colors.dtype).reshape(-1)
    assert nan_color.shape == (nb_channels,)

    image = _cmap(
        data.reshape(-1),
        colors.reshape(-1, nb_channels),
        normalization,
        vmin, vmax, nan_color)
    image.shape = data.shape + (nb_channels,)

    return image