Python numpy.logical_not() Examples

def test_class(self):
        """Tests container behavior."""
        model = kproxy_supercell.TDProxy(self.model_krhf, "hf", [self.k, 1, 1], density_fitting_hf)
        model.nroots = self.td_model_krhf.nroots
        assert not model.fast
        model.kernel()
        testing.assert_allclose(model.e, self.td_model_krhf.e, atol=1e-5)
        # Test real
        testing.assert_allclose(model.e.imag, 0, atol=1e-8)

        nocc = nvirt = 4
        testing.assert_equal(model.xy.shape, (len(model.e), 2, self.k, self.k, nocc, nvirt))

        # Test only non-degenerate roots
        d = abs(model.e[1:] - model.e[:-1]) < 1e-8
        d = numpy.logical_or(numpy.concatenate(([False], d)), numpy.concatenate((d, [False])))
        d = numpy.logical_not(d)
        assert_vectors_close(self.td_model_krhf.xy[d], model.xy[d], atol=1e-5) 

def find_outliers_upper_tail(mu):

    # remove values that are nan
    I = np.where(np.logical_and(np.logical_not(np.isnan(mu)), np.logical_not(np.isinf(mu))))[0]
    mu = mu[I]

    # calculate mean and sigma
    mean, sigma = mu.mean(), mu.std()

    # calculate the deviation in terms of sigma
    deviation = (mu - mean) / sigma

    # 2 * sigma is considered as an outlier
    S = I[np.where(deviation >= 2)[0]]

    if len(S) == 0 and deviation.max() > 1:
        S = I[[np.argmax(mu)]]

    return S if len(S) > 0 else None 

def test_subsample_selection(self):
    # Test random sampling when only some examples can be sampled:
    # 100 samples, 20 positives, 10 positives cannot be sampled
    numpy_labels = np.arange(100)
    numpy_indicator = numpy_labels < 90
    indicator = tf.constant(numpy_indicator)
    numpy_labels = (numpy_labels - 80) >= 0

    labels = tf.constant(numpy_labels)

    sampler = (balanced_positive_negative_sampler.
               BalancedPositiveNegativeSampler())
    is_sampled = sampler.subsample(indicator, 64, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 64)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 10)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 54)
      self.assertAllEqual(is_sampled, np.logical_and(is_sampled,
                                                     numpy_indicator)) 

def test_subsample_all_examples(self):
    numpy_labels = np.random.permutation(300)
    indicator = tf.constant(np.ones(300) == 1)
    numpy_labels = (numpy_labels - 200) > 0

    labels = tf.constant(numpy_labels)

    sampler = (balanced_positive_negative_sampler.
               BalancedPositiveNegativeSampler())
    is_sampled = sampler.subsample(indicator, 64, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 64)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 32)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 32) 

def _get_result_map(self, mask):
        """Processing mask data"""

        # mask.shape[0]: row, mask.shape[1]: column
        result_map = np.zeros((mask.shape[1], mask.shape[0], self.nb_classes))
        # 0 (background pixel), 128 (face area pixel) or 255 (hair area pixel).
        skin = (mask == 128)
        hair = (mask == 255)

        if self.nb_classes == 2:
            # hair = (mask > 128)
            background = np.logical_not(hair)
            result_map[:, :, 0] = np.where(background, 1, 0)
            result_map[:, :, 1] = np.where(hair, 1, 0)
        elif self.nb_classes == 3:
            background = np.logical_not(hair + skin)
            result_map[:, :, 0] = np.where(background, 1, 0)
            result_map[:, :, 1] = np.where(skin, 1, 0)
            result_map[:, :, 2] = np.where(hair, 1, 0)
        else:
            raise Exception("error...")

        return result_map 

def test_2d_with_missing(self):
        # Test cov on 2D variable w/ missing value
        x = self.data
        x[-1] = masked
        x = x.reshape(3, 4)
        valid = np.logical_not(getmaskarray(x)).astype(int)
        frac = np.dot(valid, valid.T)
        xf = (x - x.mean(1)[:, None]).filled(0)
        assert_almost_equal(cov(x),
                            np.cov(xf) * (x.shape[1] - 1) / (frac - 1.))
        assert_almost_equal(cov(x, bias=True),
                            np.cov(xf, bias=True) * x.shape[1] / frac)
        frac = np.dot(valid.T, valid)
        xf = (x - x.mean(0)).filled(0)
        assert_almost_equal(cov(x, rowvar=False),
                            (np.cov(xf, rowvar=False) *
                             (x.shape[0] - 1) / (frac - 1.)))
        assert_almost_equal(cov(x, rowvar=False, bias=True),
                            (np.cov(xf, rowvar=False, bias=True) *
                             x.shape[0] / frac)) 

def test_subsample_all_examples_dynamic(self):
    numpy_labels = np.random.permutation(300)
    indicator = tf.constant(np.ones(300) == 1)
    numpy_labels = (numpy_labels - 200) > 0

    labels = tf.constant(numpy_labels)

    sampler = (
        balanced_positive_negative_sampler.BalancedPositiveNegativeSampler())
    is_sampled = sampler.subsample(indicator, 64, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 64)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 32)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 32) 

def test_object_logical(self):
        a = np.array([3, None, True, False, "test", ""], dtype=object)
        assert_equal(np.logical_or(a, None),
                        np.array([x or None for x in a], dtype=object))
        assert_equal(np.logical_or(a, True),
                        np.array([x or True for x in a], dtype=object))
        assert_equal(np.logical_or(a, 12),
                        np.array([x or 12 for x in a], dtype=object))
        assert_equal(np.logical_or(a, "blah"),
                        np.array([x or "blah" for x in a], dtype=object))

        assert_equal(np.logical_and(a, None),
                        np.array([x and None for x in a], dtype=object))
        assert_equal(np.logical_and(a, True),
                        np.array([x and True for x in a], dtype=object))
        assert_equal(np.logical_and(a, 12),
                        np.array([x and 12 for x in a], dtype=object))
        assert_equal(np.logical_and(a, "blah"),
                        np.array([x and "blah" for x in a], dtype=object))

        assert_equal(np.logical_not(a),
                        np.array([not x for x in a], dtype=object))

        assert_equal(np.logical_or.reduce(a), 3)
        assert_equal(np.logical_and.reduce(a), None) 

def test_subsample_selection(self):
    # Test random sampling when only some examples can be sampled:
    # 100 samples, 20 positives, 10 positives cannot be sampled
    numpy_labels = np.arange(100)
    numpy_indicator = numpy_labels < 90
    indicator = tf.constant(numpy_indicator)
    numpy_labels = (numpy_labels - 80) >= 0

    labels = tf.constant(numpy_labels)

    sampler = (balanced_positive_negative_sampler.
               BalancedPositiveNegativeSampler())
    is_sampled = sampler.subsample(indicator, 64, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 64)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 10)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 54)
      self.assertAllEqual(is_sampled, np.logical_and(is_sampled,
                                                     numpy_indicator)) 

def test_subsample_all_examples(self):
    numpy_labels = np.random.permutation(300)
    indicator = tf.constant(np.ones(300) == 1)
    numpy_labels = (numpy_labels - 200) > 0

    labels = tf.constant(numpy_labels)

    sampler = (balanced_positive_negative_sampler.
               BalancedPositiveNegativeSampler())
    is_sampled = sampler.subsample(indicator, 64, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 64)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 32)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 32) 

def test_subsample_selection_no_batch_size(self):
    # Test random sampling when only some examples can be sampled:
    # 1000 samples, 6 positives (5 can be sampled).
    numpy_labels = np.arange(1000)
    numpy_indicator = numpy_labels < 999
    indicator = tf.constant(numpy_indicator)
    numpy_labels = (numpy_labels - 994) >= 0

    labels = tf.constant(numpy_labels)

    sampler = (balanced_positive_negative_sampler.
               BalancedPositiveNegativeSampler(0.01))
    is_sampled = sampler.subsample(indicator, None, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 500)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 5)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 495)
      self.assertAllEqual(is_sampled, np.logical_and(is_sampled,
                                                     numpy_indicator)) 

def test_subsample_selection_larger_batch_size_static(self):
    # Test random sampling when total number of examples that can be sampled are
    # less than batch size:
    # 100 samples, 50 positives, 40 positives cannot be sampled, batch size 64.
    # It should still return 64 samples, with 4 of them that couldn't have been
    # sampled.
    numpy_labels = np.arange(100)
    numpy_indicator = numpy_labels < 60
    indicator = np.array(numpy_indicator, np.bool)
    numpy_labels = (numpy_labels - 50) >= 0

    labels = np.array(numpy_labels, np.bool)

    def graph_fn(indicator, labels):
      sampler = (
          balanced_positive_negative_sampler.BalancedPositiveNegativeSampler(
              is_static=True))
      return sampler.subsample(indicator, 64, labels)

    is_sampled = self.execute(graph_fn, [indicator, labels])
    self.assertTrue(sum(is_sampled) == 64)
    self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) >= 10)
    self.assertTrue(
        sum(np.logical_and(np.logical_not(numpy_labels), is_sampled)) >= 50)
    self.assertTrue(sum(np.logical_and(is_sampled, numpy_indicator)) == 60) 

def color_pcl(pcl, K, im, color_axis=0, as_int=True, invalid_color=[0,0,0]):
  uvd = K @ pcl.T
  uvd /= uvd[2]
  uvd = np.round(uvd).astype(np.int32)
  mask = np.logical_and(uvd[0] >= 0, uvd[1] >= 0)
  color = np.empty((pcl.shape[0], 3), dtype=im.dtype)
  if color_axis == 0:
    mask = np.logical_and(mask, uvd[0] < im.shape[2])
    mask = np.logical_and(mask, uvd[1] < im.shape[1])
    uvd = uvd[:,mask]
    color[mask,:] = im[:,uvd[1],uvd[0]].T
  elif color_axis == 2:
    mask = np.logical_and(mask, uvd[0] < im.shape[1])
    mask = np.logical_and(mask, uvd[1] < im.shape[0])
    uvd = uvd[:,mask]
    color[mask,:] = im[uvd[1],uvd[0], :]
  else:
    raise Exception('invalid color_axis')
  color[np.logical_not(mask),:3] = invalid_color
  if as_int:
    color = (255.0 * color).astype(np.int32)
  return color 

def number_of_changes(self, percent):
        """
        The 'point of change' algorithm for each pixel,
        vectorized using numpy array operations
        Returns a 1D array
        """

        image_shape = self.shape
        j = np.ones(self.size, dtype=int)
        l = np.ones(self.size, dtype=int)
        result = np.zeros(self.size, dtype=np.float32)
        for repeat in range(1, self.k):
            # Numpy array indexing black magic to obtain an image mask
            # indicating if there is change at this (l, j) time point
            change_mask = (1 - self.K[l, j, np.arange(self.size)]) < percent

            # Where there is change
            l[change_mask] += j[change_mask]
            j[change_mask] = 1
            result[change_mask] += 1

            # Where there is no change
            j[np.logical_not(change_mask)] += 1

        return result 

def test_subsample_selection_static(self):
    # Test random sampling when only some examples can be sampled:
    # 100 samples, 20 positives, 10 positives cannot be sampled.
    numpy_labels = np.arange(100)
    numpy_indicator = numpy_labels < 90
    indicator = np.array(numpy_indicator, np.bool)
    numpy_labels = (numpy_labels - 80) >= 0

    labels = np.array(numpy_labels, np.bool)

    def graph_fn(indicator, labels):
      sampler = (
          balanced_positive_negative_sampler.BalancedPositiveNegativeSampler(
              is_static=True))
      return sampler.subsample(indicator, 64, labels)

    is_sampled = self.execute(graph_fn, [indicator, labels])
    self.assertTrue(sum(is_sampled) == 64)
    self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 10)
    self.assertTrue(sum(np.logical_and(
        np.logical_not(numpy_labels), is_sampled)) == 54)
    self.assertAllEqual(is_sampled, np.logical_and(is_sampled, numpy_indicator)) 

def test_subsample_selection_dynamic(self):
    # Test random sampling when only some examples can be sampled:
    # 100 samples, 20 positives, 10 positives cannot be sampled
    numpy_labels = np.arange(100)
    numpy_indicator = numpy_labels < 90
    indicator = tf.constant(numpy_indicator)
    numpy_labels = (numpy_labels - 80) >= 0

    labels = tf.constant(numpy_labels)

    sampler = (
        balanced_positive_negative_sampler.BalancedPositiveNegativeSampler())
    is_sampled = sampler.subsample(indicator, 64, labels)
    with self.test_session() as sess:
      is_sampled = sess.run(is_sampled)
      self.assertTrue(sum(is_sampled) == 64)
      self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 10)
      self.assertTrue(sum(np.logical_and(
          np.logical_not(numpy_labels), is_sampled)) == 54)
      self.assertAllEqual(is_sampled, np.logical_and(is_sampled,
                                                     numpy_indicator)) 

def _node_regr(self, configs, wf):
        """ 
        Return true if a given configuration is within nodal_cutoff 
        of the node 
        Also return the regularization polynomial if true, 
        f = a * r ** 2 + b * r ** 4 + c * r ** 3
        """
        ne = configs.configs.shape[1]
        d2 = 0.0
        for e in range(ne):
            d2 += np.sum(wf.gradient(e, configs.electron(e)) ** 2, axis=0)
        r = 1.0 / d2
        mask = r < self.nodal_cutoff ** 2

        c = 7.0 / (self.nodal_cutoff ** 6)
        b = -15.0 / (self.nodal_cutoff ** 4)
        a = 9.0 / (self.nodal_cutoff ** 2)

        f = a * r + b * r ** 2 + c * r ** 3
        f[np.logical_not(mask)] = 1.0

        return mask, f 

def _node_regr(self, configs, wf):
        """ 
        Return true if a given configuration is within nodal_cutoff 
        of the node 
        Also return the regularization polynomial if true, 
        f = a * r ** 2 + b * r ** 4 + c * r ** 3
        """
        ne = configs.configs.shape[1]
        d2 = 0.0
        for e in range(ne):
            d2 += np.sum(wf.gradient(e, configs.electron(e)) ** 2, axis=0)
        r = 1.0 / d2
        mask = r < self.nodal_cutoff ** 2

        c = 7.0 / (self.nodal_cutoff ** 6)
        b = -15.0 / (self.nodal_cutoff ** 4)
        a = 9.0 / (self.nodal_cutoff ** 2)

        f = a * r + b * r ** 2 + c * r ** 3
        f[np.logical_not(mask)] = 1.0

        return mask, f 

def test_subsample_all_examples_static(self):
    numpy_labels = np.random.permutation(300)
    indicator = np.array(np.ones(300) == 1, np.bool)
    numpy_labels = (numpy_labels - 200) > 0

    labels = np.array(numpy_labels, np.bool)

    def graph_fn(indicator, labels):
      sampler = (
          balanced_positive_negative_sampler.BalancedPositiveNegativeSampler(
              is_static=True))
      return sampler.subsample(indicator, 64, labels)

    is_sampled = self.execute(graph_fn, [indicator, labels])
    self.assertTrue(sum(is_sampled) == 64)
    self.assertTrue(sum(np.logical_and(numpy_labels, is_sampled)) == 32)
    self.assertTrue(sum(np.logical_and(
        np.logical_not(numpy_labels), is_sampled)) == 32) 

def iterate_eos_scores(new_scores, eos_idx, existing_cases = None, beam_width=None)->Tuple[Sequence, Sequence, Sequence]:
    """
    Return the indices and scores corresponding to the eos word.
    Meaning of returned values is the same as for iterate_best_score
    """
    nb_cases, v_size = new_scores.shape
    num_cases = np.arange(nb_cases, dtype=np.int32)
    scores = -cuda.to_cpu(new_scores[:, eos_idx])
    if existing_cases is not None:
        need_to_return = np.logical_not(np.isin(num_cases, existing_cases))
        num_cases = num_cases[need_to_return]
        scores = scores[need_to_return]

    idx_in_cases = np.full(num_cases.shape[0], eos_idx, dtype=np.int32)

    if beam_width is not None:
        if beam_width < len(scores):
            idx_to_keep = np.argpartition(scores, beam_width)[:beam_width]
            scores = scores[idx_to_keep]
            num_cases = num_cases[idx_to_keep]
            idx_in_cases = idx_in_cases[idx_to_keep]

    return num_cases, idx_in_cases, scores 

def add_patch(self, labels, predicted, weights,
                coord=None, volname=None, patches=None):
    """Evaluates single-object segmentation quality."""

    predicted = mask.crop_and_pad(predicted, (0, 0, 0), self._eval_shape)
    weights = mask.crop_and_pad(weights, (0, 0, 0), self._eval_shape)
    labels = mask.crop_and_pad(labels, (0, 0, 0), self._eval_shape)
    loss, = self.sess.run([self.eval_loss], {self.eval_labels: labels,
                                             self.eval_preds: predicted})
    self.loss += loss
    self.total_voxels += labels.size
    self.masked_voxels += np.sum(weights == 0.0)

    pred_mask = predicted >= self.eval_threshold
    true_mask = labels > 0.5
    pred_bg = np.logical_not(pred_mask)
    true_bg = np.logical_not(true_mask)

    self.tp += np.sum(pred_mask & true_mask)
    self.fp += np.sum(pred_mask & true_bg)
    self.fn += np.sum(pred_bg & true_mask)
    self.tn += np.sum(pred_bg & true_bg)
    self.num_patches += 1

    predicted = expit(predicted)
    self.images_xy.append(self.slice_image(labels, predicted, weights, 0))
    self.images_xz.append(self.slice_image(labels, predicted, weights, 1))
    self.images_yz.append(self.slice_image(labels, predicted, weights, 2)) 

def _keep_possible_multi_couplings(self, lat_ijkl, lat_ijkl_shifted, u_ijkl):
        """Filter possible couplings from :meth:`possible_multi_couplings`"""
        return np.all(
            np.logical_or(
                lat_ijkl_shifted == lat_ijkl,  # not accross the boundary
                np.logical_not(self.bc)),  # direction has PBC
            axis=(1, 2)) 

def calculate_accuracy(threshold, dist, actual_issame):
    predict_issame = np.less(dist, threshold)
    tp = np.sum(np.logical_and(predict_issame, actual_issame))
    fp = np.sum(np.logical_and(predict_issame, np.logical_not(actual_issame)))
    tn = np.sum(np.logical_and(np.logical_not(predict_issame), np.logical_not(actual_issame)))
    fn = np.sum(np.logical_and(np.logical_not(predict_issame), actual_issame))
  
    tpr = 0 if (tp+fn==0) else float(tp) / float(tp+fn)
    fpr = 0 if (fp+tn==0) else float(fp) / float(fp+tn)
    acc = float(tp+tn)/dist.size
    return tpr, fpr, acc 

def information_gain(y, mask, func=entropy):
    s1 = np.sum(mask)
    s2 = mask.size - s1
    if (s1 == 0 | s2 == 0): return 0
    return func(y) - s1 / float(s1 + s2) * func(y[mask]) - s2 / float(s1 + s2) * func(y[np.logical_not(mask)]) 

def color_map(im_, cmap='viridis', vmin=None, vmax=None):
  cm = plt.get_cmap(cmap)
  im = im_.copy()
  if vmin is None:
    vmin = np.nanmin(im)
  if vmax is None:
    vmax = np.nanmax(im)
  mask = np.logical_not(np.isfinite(im))
  im[mask] = vmin
  im = (im.clip(vmin, vmax) - vmin) / (vmax - vmin)
  im = cm(im)
  im = im[...,:3]
  for c in range(3):
    im[mask, c] = 1
  return im 

def evaluate_voxel_prediction(preds, gt, thresh):
    preds_occupy = preds[:, 1, :, :] >= thresh
    diff = np.sum(np.logical_xor(preds_occupy, gt[:, 1, :, :]))
    intersection = np.sum(np.logical_and(preds_occupy, gt[:, 1, :, :]))
    union = np.sum(np.logical_or(preds_occupy, gt[:, 1, :, :]))
    num_fp = np.sum(np.logical_and(preds_occupy, gt[:, 0, :, :]))  # false positive
    num_fn = np.sum(np.logical_and(np.logical_not(preds_occupy), gt[:, 1, :, :]))  # false negative
    return np.array([diff, intersection, union, num_fp, num_fn]) 

def compute_tp_fp(ref_descriptors, query_descriptors,
                  gt_matches, *arg, **kwarg):
    indices = retrieval(ref_descriptors, query_descriptors, *arg, **kwarg)
    tp = gt_matches[np.expand_dims(np.arange(len(indices)), axis=1), indices]
    fp = np.logical_not(tp)
    tp_cum = np.cumsum(tp, axis=1)
    fp_cum = np.cumsum(fp, axis=1)
    valid = np.any(gt_matches, axis=1)
    return tp_cum, fp_cum, valid 

def calculate_val_far(threshold, dist, actual_issame):
    predict_issame = np.less(dist, threshold)
    true_accept = np.sum(np.logical_and(predict_issame, actual_issame))
    false_accept = np.sum(np.logical_and(predict_issame, np.logical_not(actual_issame)))
    n_same = np.sum(actual_issame)
    n_diff = np.sum(np.logical_not(actual_issame))
    val = float(true_accept) / float(n_same)
    far = float(false_accept) / float(n_diff)
    return val, far 

def calculate_accuracy(threshold, dist, actual_issame):
    predict_issame = np.less(dist, threshold)
    tp = np.sum(np.logical_and(predict_issame, actual_issame))
    fp = np.sum(np.logical_and(predict_issame, np.logical_not(actual_issame)))
    tn = np.sum(np.logical_and(np.logical_not(predict_issame), np.logical_not(actual_issame)))
    fn = np.sum(np.logical_and(np.logical_not(predict_issame), actual_issame))
  
    tpr = 0 if (tp+fn==0) else float(tp) / float(tp+fn)
    fpr = 0 if (fp+tn==0) else float(fp) / float(fp+tn)
    acc = float(tp+tn)/dist.size
    return tpr, fpr, acc 

def calculate_val_far(threshold, dist, actual_issame):
    predict_issame = np.less(dist, threshold)
    true_accept = np.sum(np.logical_and(predict_issame, actual_issame))
    false_accept = np.sum(np.logical_and(predict_issame, np.logical_not(actual_issame)))
    n_same = np.sum(actual_issame)
    n_diff = np.sum(np.logical_not(actual_issame))
    val = float(true_accept) / float(n_same)
    far = float(false_accept) / float(n_diff)
    return val, far