# -*- coding: utf-8 -*- import pyqtgraph as pg import numpy as np import sys from copy import deepcopy from collections import OrderedDict from numpy.testing import assert_array_almost_equal, assert_almost_equal import pytest np.random.seed(12345) def testSolve3D(): p1 = np.array([[0,0,0,1], [1,0,0,1], [0,1,0,1], [0,0,1,1]], dtype=float) # transform points through random matrix tr = np.random.normal(size=(4, 4)) tr[3] = (0,0,0,1) p2 = np.dot(tr, p1.T).T[:,:3] # solve to see if we can recover the transformation matrix. tr2 = pg.solve3DTransform(p1, p2) assert_array_almost_equal(tr[:3], tr2[:3]) def test_interpolateArray_order0(): check_interpolateArray(order=0) def test_interpolateArray_order1(): check_interpolateArray(order=1) def check_interpolateArray(order): def interpolateArray(data, x): result = pg.interpolateArray(data, x, order=order) assert result.shape == x.shape[:-1] + data.shape[x.shape[-1]:] return result data = np.array([[ 1., 2., 4. ], [ 10., 20., 40. ], [ 100., 200., 400.]]) # test various x shapes interpolateArray(data, np.ones((1,))) interpolateArray(data, np.ones((2,))) interpolateArray(data, np.ones((1, 1))) interpolateArray(data, np.ones((1, 2))) interpolateArray(data, np.ones((5, 1))) interpolateArray(data, np.ones((5, 2))) interpolateArray(data, np.ones((5, 5, 1))) interpolateArray(data, np.ones((5, 5, 2))) with pytest.raises(TypeError): interpolateArray(data, np.ones((3,))) with pytest.raises(TypeError): interpolateArray(data, np.ones((1, 3,))) with pytest.raises(TypeError): interpolateArray(data, np.ones((5, 5, 3,))) x = np.array([[ 0.3, 0.6], [ 1. , 1. ], [ 0.501, 1. ], # NOTE: testing at exactly 0.5 can yield different results from map_coordinates [ 0.501, 2.501], # due to differences in rounding [ 10. , 10. ]]) result = interpolateArray(data, x) # make sure results match ndimage.map_coordinates import scipy.ndimage spresult = scipy.ndimage.map_coordinates(data, x.T, order=order) #spresult = np.array([ 5.92, 20. , 11. , 0. , 0. ]) # generated with the above line assert_array_almost_equal(result, spresult) # test mapping when x.shape[-1] < data.ndim x = np.array([[ 0.3, 0], [ 0.3, 1], [ 0.3, 2]]) r1 = interpolateArray(data, x) x = np.array([0.3]) # should broadcast across axis 1 r2 = interpolateArray(data, x) assert_array_almost_equal(r1, r2) # test mapping 2D array of locations x = np.array([[[0.501, 0.501], [0.501, 1.0], [0.501, 1.501]], [[1.501, 0.501], [1.501, 1.0], [1.501, 1.501]]]) r1 = interpolateArray(data, x) r2 = scipy.ndimage.map_coordinates(data, x.transpose(2,0,1), order=order) #r2 = np.array([[ 8.25, 11. , 16.5 ], # generated with the above line #[ 82.5 , 110. , 165. ]]) assert_array_almost_equal(r1, r2) def test_subArray(): a = np.array([0, 0, 111, 112, 113, 0, 121, 122, 123, 0, 0, 0, 211, 212, 213, 0, 221, 222, 223, 0, 0, 0, 0]) b = pg.subArray(a, offset=2, shape=(2,2,3), stride=(10,4,1)) c = np.array([[[111,112,113], [121,122,123]], [[211,212,213], [221,222,223]]]) assert np.all(b == c) # operate over first axis; broadcast over the rest aa = np.vstack([a, a/100.]).T cc = np.empty(c.shape + (2,)) cc[..., 0] = c cc[..., 1] = c / 100. bb = pg.subArray(aa, offset=2, shape=(2,2,3), stride=(10,4,1)) assert np.all(bb == cc) def test_subArray(): a = np.array([0, 0, 111, 112, 113, 0, 121, 122, 123, 0, 0, 0, 211, 212, 213, 0, 221, 222, 223, 0, 0, 0, 0]) b = pg.subArray(a, offset=2, shape=(2,2,3), stride=(10,4,1)) c = np.array([[[111,112,113], [121,122,123]], [[211,212,213], [221,222,223]]]) assert np.all(b == c) # operate over first axis; broadcast over the rest aa = np.vstack([a, a/100.]).T cc = np.empty(c.shape + (2,)) cc[..., 0] = c cc[..., 1] = c / 100. bb = pg.subArray(aa, offset=2, shape=(2,2,3), stride=(10,4,1)) assert np.all(bb == cc) def test_rescaleData(): dtypes = map(np.dtype, ('ubyte', 'uint16', 'byte', 'int16', 'int', 'float')) for dtype1 in dtypes: for dtype2 in dtypes: data = (np.random.random(size=10) * 2**32 - 2**31).astype(dtype1) for scale, offset in [(10, 0), (10., 0.), (1, -50), (0.2, 0.5), (0.001, 0)]: if dtype2.kind in 'iu': lim = np.iinfo(dtype2) lim = lim.min, lim.max else: lim = (-np.inf, np.inf) s1 = np.clip(float(scale) * (data-float(offset)), *lim).astype(dtype2) s2 = pg.rescaleData(data, scale, offset, dtype2) assert s1.dtype == s2.dtype if dtype2.kind in 'iu': assert np.all(s1 == s2) else: assert np.allclose(s1, s2) def test_makeARGB(): # Many parameters to test here: # * data dtype (ubyte, uint16, float, others) # * data ndim (2 or 3) # * levels (None, 1D, or 2D) # * lut dtype # * lut size # * lut ndim (1 or 2) # * useRGBA argument # Need to check that all input values map to the correct output values, especially # at and beyond the edges of the level range. def checkArrays(a, b): # because py.test output is difficult to read for arrays if not np.all(a == b): comp = [] for i in range(a.shape[0]): if a.shape[1] > 1: comp.append('[') for j in range(a.shape[1]): m = a[i,j] == b[i,j] comp.append('%d,%d %s %s %s%s' % (i, j, str(a[i,j]).ljust(15), str(b[i,j]).ljust(15), m, ' ********' if not np.all(m) else '')) if a.shape[1] > 1: comp.append(']') raise Exception("arrays do not match:\n%s" % '\n'.join(comp)) def checkImage(img, check, alpha, alphaCheck): assert img.dtype == np.ubyte assert alpha is alphaCheck if alpha is False: checkArrays(img[..., 3], 255) if np.isscalar(check) or check.ndim == 3: checkArrays(img[..., :3], check) elif check.ndim == 2: checkArrays(img[..., :3], check[..., np.newaxis]) elif check.ndim == 1: checkArrays(img[..., :3], check[..., np.newaxis, np.newaxis]) else: raise Exception('invalid check array ndim') # uint8 data tests im1 = np.arange(256).astype('ubyte').reshape(256, 1) im2, alpha = pg.makeARGB(im1, levels=(0, 255)) checkImage(im2, im1, alpha, False) im3, alpha = pg.makeARGB(im1, levels=(0.0, 255.0)) checkImage(im3, im1, alpha, False) im4, alpha = pg.makeARGB(im1, levels=(255, 0)) checkImage(im4, 255-im1, alpha, False) im5, alpha = pg.makeARGB(np.concatenate([im1]*3, axis=1), levels=[(0, 255), (0.0, 255.0), (255, 0)]) checkImage(im5, np.concatenate([im1, im1, 255-im1], axis=1), alpha, False) im2, alpha = pg.makeARGB(im1, levels=(128,383)) checkImage(im2[:128], 0, alpha, False) checkImage(im2[128:], im1[:128], alpha, False) # uint8 data + uint8 LUT lut = np.arange(256)[::-1].astype(np.uint8) im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, lut, alpha, False) # lut larger than maxint lut = np.arange(511).astype(np.uint8) im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, lut[::2], alpha, False) # lut smaller than maxint lut = np.arange(128).astype(np.uint8) im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, np.linspace(0, 127.5, 256, dtype='ubyte'), alpha, False) # lut + levels lut = np.arange(256)[::-1].astype(np.uint8) im2, alpha = pg.makeARGB(im1, lut=lut, levels=[-128, 384]) checkImage(im2, np.linspace(191.5, 64.5, 256, dtype='ubyte'), alpha, False) im2, alpha = pg.makeARGB(im1, lut=lut, levels=[64, 192]) checkImage(im2, np.clip(np.linspace(384.5, -127.5, 256), 0, 255).astype('ubyte'), alpha, False) # uint8 data + uint16 LUT lut = np.arange(4096)[::-1].astype(np.uint16) // 16 im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, np.arange(256)[::-1].astype('ubyte'), alpha, False) # uint8 data + float LUT lut = np.linspace(10., 137., 256) im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, lut.astype('ubyte'), alpha, False) # uint8 data + 2D LUT lut = np.zeros((256, 3), dtype='ubyte') lut[:,0] = np.arange(256) lut[:,1] = np.arange(256)[::-1] lut[:,2] = 7 im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, lut[:,None,::-1], alpha, False) # check useRGBA im2, alpha = pg.makeARGB(im1, lut=lut, useRGBA=True) checkImage(im2, lut[:,None,:], alpha, False) # uint16 data tests im1 = np.arange(0, 2**16, 256).astype('uint16')[:, None] im2, alpha = pg.makeARGB(im1, levels=(512, 2**16)) checkImage(im2, np.clip(np.linspace(-2, 253, 256), 0, 255).astype('ubyte'), alpha, False) lut = (np.arange(512, 2**16)[::-1] // 256).astype('ubyte') im2, alpha = pg.makeARGB(im1, lut=lut, levels=(512, 2**16-256)) checkImage(im2, np.clip(np.linspace(257, 2, 256), 0, 255).astype('ubyte'), alpha, False) lut = np.zeros(2**16, dtype='ubyte') lut[1000:1256] = np.arange(256) lut[1256:] = 255 im1 = np.arange(1000, 1256).astype('uint16')[:, None] im2, alpha = pg.makeARGB(im1, lut=lut) checkImage(im2, np.arange(256).astype('ubyte'), alpha, False) # float data tests im1 = np.linspace(1.0, 17.0, 256)[:, None] im2, alpha = pg.makeARGB(im1, levels=(5.0, 13.0)) checkImage(im2, np.clip(np.linspace(-128, 383, 256), 0, 255).astype('ubyte'), alpha, False) lut = (np.arange(1280)[::-1] // 10).astype('ubyte') im2, alpha = pg.makeARGB(im1, lut=lut, levels=(1, 17)) checkImage(im2, np.linspace(127.5, 0, 256).astype('ubyte'), alpha, False) # nans in image # 2d input image, one pixel is nan im1 = np.ones((10, 12)) im1[3, 5] = np.nan im2, alpha = pg.makeARGB(im1, levels=(0, 1)) assert alpha assert im2[3, 5, 3] == 0 # nan pixel is transparent assert im2[0, 0, 3] == 255 # doesn't affect other pixels # 3d RGB input image, any color channel of a pixel is nan im1 = np.ones((10, 12, 3)) im1[3, 5, 1] = np.nan im2, alpha = pg.makeARGB(im1, levels=(0, 1)) assert alpha assert im2[3, 5, 3] == 0 # nan pixel is transparent assert im2[0, 0, 3] == 255 # doesn't affect other pixels # 3d RGBA input image, any color channel of a pixel is nan im1 = np.ones((10, 12, 4)) im1[3, 5, 1] = np.nan im2, alpha = pg.makeARGB(im1, levels=(0, 1), useRGBA=True) assert alpha assert im2[3, 5, 3] == 0 # nan pixel is transparent # test sanity checks class AssertExc(object): def __init__(self, exc=Exception): self.exc = exc def __enter__(self): return self def __exit__(self, *args): assert args[0] is self.exc, "Should have raised %s (got %s)" % (self.exc, args[0]) return True with AssertExc(TypeError): # invalid image shape pg.makeARGB(np.zeros((2,), dtype='float')) with AssertExc(TypeError): # invalid image shape pg.makeARGB(np.zeros((2,2,7), dtype='float')) with AssertExc(): # float images require levels arg pg.makeARGB(np.zeros((2,2), dtype='float')) with AssertExc(): # bad levels arg pg.makeARGB(np.zeros((2,2), dtype='float'), levels=[1]) with AssertExc(): # bad levels arg pg.makeARGB(np.zeros((2,2), dtype='float'), levels=[1,2,3]) with AssertExc(): # can't mix 3-channel levels and LUT pg.makeARGB(np.zeros((2,2)), lut=np.zeros((10,3), dtype='ubyte'), levels=[(0,1)]*3) with AssertExc(): # multichannel levels must have same number of channels as image pg.makeARGB(np.zeros((2,2,3), dtype='float'), levels=[(1,2)]*4) with AssertExc(): # 3d levels not allowed pg.makeARGB(np.zeros((2,2,3), dtype='float'), levels=np.zeros([3, 2, 2])) def test_eq(): eq = pg.functions.eq zeros = [0, 0.0, np.float(0), np.int(0)] if sys.version[0] < '3': zeros.append(long(0)) for i,x in enumerate(zeros): for y in zeros[i:]: assert eq(x, y) assert eq(y, x) assert eq(np.nan, np.nan) # test class NotEq(object): def __eq__(self, x): return False noteq = NotEq() assert eq(noteq, noteq) # passes because they are the same object assert not eq(noteq, NotEq()) # Should be able to test for equivalence even if the test raises certain # exceptions class NoEq(object): def __init__(self, err): self.err = err def __eq__(self, x): raise self.err noeq1 = NoEq(AttributeError()) noeq2 = NoEq(ValueError()) noeq3 = NoEq(Exception()) assert eq(noeq1, noeq1) assert not eq(noeq1, noeq2) assert not eq(noeq2, noeq1) with pytest.raises(Exception): eq(noeq3, noeq2) # test array equivalence # note that numpy has a weird behavior here--np.all() always returns True # if one of the arrays has size=0; eq() will only return True if both arrays # have the same shape. a1 = np.zeros((10, 20)).astype('float') a2 = a1 + 1 a3 = a2.astype('int') a4 = np.empty((0, 20)) assert not eq(a1, a2) # same shape/dtype, different values assert not eq(a1, a3) # same shape, different dtype and values assert not eq(a1, a4) # different shape (note: np.all gives True if one array has size 0) assert not eq(a2, a3) # same values, but different dtype assert not eq(a2, a4) # different shape assert not eq(a3, a4) # different shape and dtype assert eq(a4, a4.copy()) assert not eq(a4, a4.T) # test containers assert not eq({'a': 1}, {'a': 1, 'b': 2}) assert not eq({'a': 1}, {'a': 2}) d1 = {'x': 1, 'y': np.nan, 3: ['a', np.nan, a3, 7, 2.3], 4: a4} d2 = deepcopy(d1) assert eq(d1, d2) d1_ordered = OrderedDict(d1) d2_ordered = deepcopy(d1_ordered) assert eq(d1_ordered, d2_ordered) assert not eq(d1_ordered, d2) items = list(d1.items()) assert not eq(OrderedDict(items), OrderedDict(reversed(items))) assert not eq([1,2,3], [1,2,3,4]) l1 = [d1, np.inf, -np.inf, np.nan] l2 = deepcopy(l1) t1 = tuple(l1) t2 = tuple(l2) assert eq(l1, l2) assert eq(t1, t2) assert eq(set(range(10)), set(range(10))) assert not eq(set(range(10)), set(range(9))) @pytest.mark.parametrize("s,suffix,expected", [ # usual cases ("100 uV", "V", ("100", "u", "V")), ("100 µV", "V", ("100", "µ", "V")), ("4.2 nV", None, ("4.2", "n", "V")), ("1.2 m", "m", ("1.2", "", "m")), ("1.2 m", None, ("1.2", "", "m")), ("5.0e9", None, ("5.0e9", "", "")), ("2 units", "units", ("2", "", "units")), # siPrefix with explicit empty suffix ("1.2 m", "", ("1.2", "m", "")), ("5.0e-9 M", "", ("5.0e-9", "M", "")), # weirder cases that should return the reasonable thing ("4.2 nV", "nV", ("4.2", "", "nV")), ("4.2 nV", "", ("4.2", "n", "")), ("1.2 j", "", ("1.2", "", "")), ("1.2 j", None, ("1.2", "", "j")), # expected error cases ("100 uV", "v", ValueError), ]) def test_siParse(s, suffix, expected): if isinstance(expected, tuple): assert pg.siParse(s, suffix=suffix) == expected else: with pytest.raises(expected): pg.siParse(s, suffix=suffix)