# Copyright (c) 2021-2025 The University of Texas Southwestern Medical Center. # All rights reserved. # Redistribution and use in source and binary forms, with or without # modification, are permitted for academic and research use only (subject to the # limitations in the disclaimer below) provided that the following conditions are met: # * Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and/or other materials provided with the distribution. # * Neither the name of the copyright holders nor the names of its # contributors may be used to endorse or promote products derived from this # software without specific prior written permission. # NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY # THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A # PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR # CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, # EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, # PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR # BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER # IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import math import numpy as np def im_circ(r=1, N=128): X, Y = np.meshgrid(range(-N // 2, N // 2), range(-N // 2, N // 2)) return (X * X + Y * Y) < r * r def test_has_tissue(): from navigate.model.analysis.boundary_detect import has_tissue for _ in range(100): N = 2 ** np.random.randint(5, 9) r = np.random.randint(math.ceil(0.2 * N), int(0.4 * N)) ds = np.random.randint(1, 6) print(N, r, ds) im = im_circ(r, N) * 1001 mu, sig = 100 * np.random.rand() + 1, 10 * np.random.rand() + 1 print(mu, sig) offsets = [None, np.ones((N, N)) * mu] variances = [None, np.ones((N, N)) * sig] for off, var in zip(offsets, variances): assert has_tissue(im, 0, 0, N, off, var) and not has_tissue( im, 0, 0, N // 2 - r, off, var ) def test_find_tissue_boundary_2d(): from skimage.transform import downscale_local_mean from navigate.model.analysis.boundary_detect import find_tissue_boundary_2d for _ in range(100): N = 2 ** np.random.randint(5, 9) r = np.random.randint(1, int(0.4 * N)) ds = np.random.randint(1, 6) print(N, r, ds) im = im_circ(r, N) b = find_tissue_boundary_2d(im, ds) b = np.vstack([x for x in b if x is not None]) idx_x, idx_y = np.where(downscale_local_mean(im, (ds, ds))) iixy = (np.unique(idx_x)[:, None] == idx_x[None, :]) * idx_y low, high = idx_y[np.argmax(iixy != 0, 1)], np.max(iixy, 1) np.testing.assert_equal(b, np.vstack([low, high]).T) def test_binary_detect(): from navigate.model.analysis.boundary_detect import ( find_tissue_boundary_2d, binary_detect, ) for _ in range(100): N = 2 ** np.random.randint(5, 9) r = np.random.randint(1, int(0.4 * N)) ds = np.random.randint(1, 6) print(N, r, ds) im = im_circ(r, N) b = find_tissue_boundary_2d(im, ds) assert binary_detect(im * 1001, b, ds) == b def test_map_boundary(): from navigate.model.analysis.boundary_detect import map_boundary assert map_boundary([[1, 2]]) == [(0, 1), (0, 2)] assert map_boundary([None, [1, 2]]) == [(1, 1), (1, 2)] assert map_boundary([None, [1, 2], None]) == [(1, 1), (1, 2)]