__init__.py

# Copyright (C) 2015 Simon Biggs

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version (the "AGPL-3.0+").

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License and the additional terms for more
# details.

# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.

# ADDITIONAL TERMS are also included as allowed by Section 7 of the GNU
# Affrero General Public License. These aditional terms are Sections 1, 5,
# 6, 7, 8, and 9 from the Apache License, Version 2.0 (the "Apache-2.0")
# where all references to the definition "License" are instead defined to
# mean the AGPL-3.0+.

# You should have received a copy of the Apache-2.0 along with this
# program. If not, see <http://www.apache.org/licenses/LICENSE-2.0>.

"""[DEPRECATED] Use `pymedphys.gamma` instead. See
https://pymedphys.com/en/latest/user/gamma.html

Compare two dose grids with the gamma index.

This module is a python implementation of the gamma index.
It computes 1, 2, or 3 dimensional gamma with arbitrary gird sizes while
interpolating on the fly.
This module makes use of some of the ideas presented within
<http://dx.doi.org/10.1118/1.2721657>.

It needs to be noted that this code base has not yet undergone sufficient
independent validation.
"""



import numpy as np
from scipy.interpolate import RegularGridInterpolator
from multiprocessing import Process, Queue

import warnings

WARNING_STRING = (
    'The `npgamma` module is deprecated. It contains known bugs. '
    'The bugfixes for these are within the `pymedphys.gamma` module. '
    'See https://pymedphys.com/en/latest/user/gamma.html for how to use '
    'the module that has superseded `npgamma`.'
)


warnings.warn(WARNING_STRING, UserWarning)


def _run_input_checks(
        coords_reference, dose_reference,
        coords_evaluation, dose_evaluation):
    """Check user inputs."""
    if (
            not isinstance(coords_evaluation, tuple) or
            not isinstance(coords_reference, tuple)):
        if (
                isinstance(coords_evaluation, np.ndarray) and
                isinstance(coords_reference, np.ndarray)):
            if (
                    len(np.shape(coords_evaluation)) == 1 and
                    len(np.shape(coords_reference)) == 1):

                coords_evaluation = (coords_evaluation,)
                coords_reference = (coords_reference,)

            else:
                raise Exception(
                    "Can only use numpy arrays as input for one dimensional "
                    "gamma."
                    )
        else:
            raise Exception(
                "Input coordinates must be inputted as a tuple, for "
                "one dimension input is (x,), for two dimensions, (x, y),  "
                "for three dimensions input is (x, y, z).")

    reference_coords_shape = tuple([len(item) for item in coords_reference])
    if reference_coords_shape != np.shape(dose_reference):
        raise Exception(
            "Length of items in coords_reference does not match the shape of "
            "dose_reference")

    evaluation_coords_shape = tuple([len(item) for item in coords_evaluation])
    if evaluation_coords_shape != np.shape(dose_evaluation):
        raise Exception(
            "Length of items in coords_evaluation does not match the shape of "
            "dose_evaluation")

    if not (len(np.shape(dose_evaluation)) ==
            len(np.shape(dose_reference)) ==
            len(coords_evaluation) ==
            len(coords_reference)):
        raise Exception(
            "The dimensions of the input data do not match")

    return coords_reference, coords_evaluation


def _calculate_coordinates_kernel(
        distance, num_dimensions, distance_step_size):
    """Determine the coodinate shifts required.

    Coordinate shifts are determined to check the reference dose for a
    given distance, dimension, and step size
    """
    if num_dimensions == 1:
        if distance == 0:
            x_coords = np.array([0])
        else:
            x_coords = np.array([distance, -distance])

        return (x_coords,)

    elif num_dimensions == 2:
        amount_to_check = np.floor(
            2 * np.pi * distance / distance_step_size) + 2
        theta = np.linspace(0, 2*np.pi, amount_to_check + 1)[:-1:]
        x_coords = distance * np.cos(theta)
        y_coords = distance * np.sin(theta)

        return (x_coords, y_coords)

    elif num_dimensions == 3:
        number_of_rows = np.floor(
            np.pi * distance / distance_step_size) + 2
        elevation = np.linspace(0, np.pi, number_of_rows)
        row_radii = distance * np.sin(elevation)
        row_circumference = 2 * np.pi * row_radii
        amount_in_row = np.floor(
            row_circumference / distance_step_size) + 2

        x_coords = []
        y_coords = []
        z_coords = []
        for i, phi in enumerate(elevation):
            azimuth = np.linspace(0, 2*np.pi, amount_in_row[i] + 1)[:-1:]
            x_coords.append(distance * np.sin(phi) * np.cos(azimuth))
            y_coords.append(distance * np.sin(phi) * np.sin(azimuth))
            z_coords.append(distance * np.cos(phi) * np.ones_like(azimuth))

        return (
            np.hstack(x_coords), np.hstack(y_coords), np.hstack(z_coords))

    else:
        raise Exception("No valid dimension")


def _calculate_min_dose_difference(
        num_dimensions, mesh_coords_evaluation, to_be_checked,
        reference_interpolation, dose_evaluation,
        coordinates_at_distance_kernel):
    """Determine the minimum dose difference.

    Calculated for a given distance from each evaluation point.
    """
    coordinates_at_distance = []
    for i in range(num_dimensions):
        coordinates_at_distance.append(np.array(
            mesh_coords_evaluation[i][to_be_checked][None, :] +
            coordinates_at_distance_kernel[i][:, None])[:, :, None])

    all_points = np.concatenate(coordinates_at_distance, axis=2)

    dose_difference = np.array([
        reference_interpolation(points) -
        dose_evaluation[to_be_checked] for
        points in all_points
    ])
    min_dose_difference = np.min(np.abs(dose_difference), axis=0)

    return min_dose_difference


def _calculate_min_dose_difference_by_slice(
        max_concurrent_calc_points,
        num_dimensions, mesh_coords_evaluation, to_be_checked,
        reference_interpolation, dose_evaluation,
        coordinates_at_distance_kernel, **kwargs):
    """Determine minimum dose differences.

    Calculation is made with the evaluation set divided into slices. This
    enables less RAM usage.
    """
    all_checks = np.where(to_be_checked)
    min_dose_difference = (np.nan * np.ones_like(all_checks[0]))

    num_slices = np.floor(
        len(coordinates_at_distance_kernel[0]) *
        len(all_checks[0]) / max_concurrent_calc_points) + 1

    index = np.arange(len(all_checks[0]))
    np.random.shuffle(index)
    sliced = np.array_split(index, num_slices)

    for current_slice in sliced:
        current_to_be_checked = np.zeros_like(to_be_checked).astype(bool)
        current_to_be_checked[[
            item[current_slice] for
            item in all_checks]] = True

        assert np.all(to_be_checked[current_to_be_checked])

        min_dose_difference[np.sort(current_slice)] = (
            _calculate_min_dose_difference(
                num_dimensions, mesh_coords_evaluation, current_to_be_checked,
                reference_interpolation, dose_evaluation,
                coordinates_at_distance_kernel))

    assert np.all(np.invert(np.isnan(min_dose_difference)))

    return min_dose_difference


def _calculation_loop(**kwargs):
    """Iteratively calculates gamma at increasing distances."""
    dose_valid = kwargs['dose_evaluation'] >= kwargs['lower_dose_cutoff']
    gamma_valid = np.ones_like(kwargs['dose_evaluation']).astype(bool)
    running_gamma = np.inf * np.ones_like(kwargs['dose_evaluation'])
    distance = 0

    while True:
        to_be_checked = (
            dose_valid & gamma_valid)

        coordinates_at_distance_kernel = _calculate_coordinates_kernel(
            distance, kwargs['num_dimensions'], kwargs['distance_step_size'])
        min_dose_difference = _calculate_min_dose_difference_by_slice(
            to_be_checked=to_be_checked,
            coordinates_at_distance_kernel=coordinates_at_distance_kernel,
            **kwargs)

        gamma_at_distance = np.sqrt(
            min_dose_difference ** 2 / kwargs['dose_threshold'] ** 2 +
            distance ** 2 / kwargs['distance_threshold'] ** 2)

        running_gamma[to_be_checked] = np.min(
            np.vstack((
                gamma_at_distance, running_gamma[to_be_checked]
            )), axis=0)

        gamma_valid = running_gamma > distance / kwargs['distance_threshold']

        distance += kwargs['distance_step_size']

        if (
                (np.sum(to_be_checked) == 0) |
                (distance > kwargs['maximum_test_distance'])):
            break

    return running_gamma


def _new_thread(kwargs, output, thread_index, gamma_store):
    gamma_store[thread_index] = _calculation_loop(**kwargs)
    output.put(gamma_store)


def calc_gamma(coords_reference, dose_reference,
               coords_evaluation, dose_evaluation,
               distance_threshold, dose_threshold,
               lower_dose_cutoff=0, distance_step_size=None,
               maximum_test_distance=np.inf,
               max_concurrent_calc_points=np.inf,
               num_threads=1):
    """[DEPRECATED] Use `pymedphys.gamma` instead. See
    https://pymedphys.com/en/latest/user/gamma.html

    Compare two dose grids with the gamma index.

    Args:
        coords_reference (tuple): The reference coordinates.
        dose_reference (np.array): The reference dose grid.
        coords_evaluation (tuple): The evaluation coordinates.
        dose_evaluation (np.array): The evaluation dose grid.
        distance_threshold (float): The gamma distance threshold. Units must
            match of the coordinates given.
        dose_threshold (float): An absolute dose threshold.
            If you wish to use 3% of maximum reference dose input
            np.max(dose_reference) * 0.03 here.
        lower_dose_cutoff (:obj:`float`, optional): The lower dose cutoff below
            which gamma will not be calculated.
        distance_step_size (:obj:`float`, optional): The step size to use in
            within the reference grid interpolation. Defaults to a tenth of the
            distance threshold as recommended within
            <http://dx.doi.org/10.1118/1.2721657>.
        maximum_test_distance (:obj:`float`, optional): The distance beyond
            which searching will stop. Defaults to np.inf. To speed up
            calculation it is recommended that this parameter is set to
            something reasonable such as 2*distance_threshold

    Returns:
        gamma (np.array): The array of gamma values the same shape as that
            given by the evaluation coordinates and dose.
    """
    warnings.warn(WARNING_STRING, UserWarning)

    coords_reference, coords_evaluation = _run_input_checks(
        coords_reference, dose_reference,
        coords_evaluation, dose_evaluation)

    if distance_step_size is None:
        distance_step_size = distance_threshold / 10

    reference_interpolation = RegularGridInterpolator(
        coords_reference, np.array(dose_reference),
        bounds_error=False, fill_value=np.inf
    )

    dose_evaluation = np.array(dose_evaluation)
    dose_evaluation_flat = np.ravel(dose_evaluation)

    mesh_coords_evaluation = np.meshgrid(*coords_evaluation, indexing='ij')
    coords_evaluation_flat = [
        np.ravel(item)
        for item in mesh_coords_evaluation]

    evaluation_index = np.arange(len(dose_evaluation_flat))
    np.random.shuffle(evaluation_index)
    thread_indicies = np.array_split(evaluation_index, num_threads)

    output = Queue()

    kwargs = {
        "coords_reference": coords_reference,
        "num_dimensions": len(coords_evaluation),
        "reference_interpolation": reference_interpolation,
        "lower_dose_cutoff": lower_dose_cutoff,
        "distance_threshold": distance_threshold,
        "dose_threshold": dose_threshold,
        "distance_step_size": distance_step_size,
        "max_concurrent_calc_points": max_concurrent_calc_points / num_threads,
        "maximum_test_distance": maximum_test_distance}

    for thread_index in thread_indicies:
        thread_index.sort()
        thread_dose_evaluation = dose_evaluation_flat[thread_index]
        thread_coords_evaluation = [
            coords[thread_index]
            for coords in coords_evaluation_flat]
        kwargs['dose_evaluation'] = thread_dose_evaluation
        kwargs['mesh_coords_evaluation'] = thread_coords_evaluation

        Process(
            target=_new_thread,
            args=(
                kwargs, output, thread_index,
                np.nan * np.ones_like(dose_evaluation_flat))).start()

    gamma_flat = np.nan * np.ones_like(dose_evaluation_flat)

    for i in range(num_threads):
        result = output.get()
        thread_reference = np.invert(np.isnan(result))
        gamma_flat[thread_reference] = result[thread_reference]

    assert np.all(np.invert(np.isnan(gamma_flat)))

    gamma_flat[np.isinf(gamma_flat)] = np.nan
    gamma = np.reshape(gamma_flat, np.shape(dose_evaluation))

    return gamma