Python morphology.label方法代码示例

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def compute_fp_loss(probs_log, blob_dict, reduction='sum'):
    if blob_dict["n_fp"] == 0:
        return 0.

    blobs = blob_dict["blobs"]

    
    loss = 0.
    n_fp = 0.
    for b in blob_dict["blobList"]:
        if b["n_points"] != 0:
            continue

        T = np.ones(blobs.shape[-2:])
        T[blobs[b["class"]] == b["label"]] = 0

        loss += F.nll_loss(probs_log, torch.LongTensor(T).to(device=probs_log.device)[None],
                                   ignore_index=1, reduction='mean')
        n_fp += 1

    if reduction == 'mean':
        loss = loss / max(n_fp, 1)

    return loss 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def get_blobs(logits, roi_mask=None):
    n, k, _, _ = logits.shape
    pred_mask = logits.max(1)[1].squeeze().cpu().numpy()
    
    h, w = pred_mask.shape
    blobs = np.zeros((k - 1, h, w), int)

    for category_id in np.unique(pred_mask):
        if category_id == 0:
            continue
        blobs[category_id - 1] = morph.label(pred_mask == category_id)

    if roi_mask is not None:
        blobs = (blobs * roi_mask[None]).astype(int)

    return blobs 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def _heatmap_to_rects(self, grid_pred, bb_img):
        """Convert a heatmap to rectangles / bounding box candidates."""
        grid_pred = np.squeeze(grid_pred) # (1, H, W) => (H, W)

        # remove low activations
        grid_thresh = grid_pred >= self.heatmap_activation_threshold

        # find connected components
        grid_labeled, num_labels = morphology.label(
            grid_thresh, background=0, connectivity=1, return_num=True
        )

        # for each connected components,
        # - draw a bounding box around it,
        # - shrink the bounding box to optimal size
        # - estimate a score/confidence value
        bbs = []
        for label in range(1, num_labels+1):
            (yy, xx) = np.nonzero(grid_labeled == label)
            min_y, max_y = np.min(yy), np.max(yy)
            min_x, max_x = np.min(xx), np.max(xx)
            rect = RectangleOnImage(x1=min_x, x2=max_x+1, y1=min_y, y2=max_y+1, shape=grid_labeled)
            activation = self._rect_to_score(rect, grid_pred)
            rect_shrunk, activation_shrunk = self._shrink(grid_pred, rect)
            rect_rs_shrunk = rect_shrunk.on(bb_img)
            bbs.append((rect_rs_shrunk, activation_shrunk))

        return bbs 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def multi_rle_encode(img):
    labels = label(img[:, :, 0])
    return [rle_encode(labels==k) for k in np.unique(labels[labels>0])]


# ref: https://www.kaggle.com/paulorzp/run-length-encode-and-decode 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def make_train_char_db(ori_img_dir):
    import pandas as pd
    import h5py
    """
    均分四份，制作训练集
    :param ori_img_dir: 原始的图像的目录
    :return:
    """
    even_split_train_path = os.path.join(os.getcwd(), 'evensplit_train_im')
    if not os.path.exists(even_split_train_path):
        os.makedirs(even_split_train_path)

    train_imgs = os.listdir(ori_img_dir)
    letters = list('02345678abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ')
    answer_data = pd.read_table(os.path.join(os.getcwd(), 'lvy_ans.txt'), sep=':', names=['Index', 'Answer'])
    # 保存数据
    img = np.zeros((len(train_imgs)*4, 1, 35, 35), dtype=np.uint8)
    label = np.zeros((len(train_imgs)*4), dtype=np.uint32)
    index = 0
    for train_img in train_imgs:
        ori_train_img = os.path.join(ori_img_dir, train_img)
        binary_train_img = binary_img(ori_train_img)  # 二值化之后的图像
        dingge_train_img = ding_ge(binary_train_img)  # 顶格之后的图像

        # 均分成四份
        step_train = dingge_train_img.shape[1] / float(4)
        start_train = [j for j in np.arange(0, dingge_train_img.shape[1], step_train).tolist()]
        for p, k in enumerate(start_train):
            print train_img + '_' + str((p+1))
            split_train_img = dingge_train_img[:, k:k + step_train]
            small_img = ding_ge(split_train_img)
            split_train_resize_img = cv2.resize(small_img, (35, 35))
            img[index, 0, :, :] = split_train_resize_img
            label[index] = letters.index(answer_data['Answer'][int(train_img.split('.')[0])-1][p])
            index += 1
            cv2.imwrite(os.path.join(even_split_train_path,
                                     train_img.split('.')[0] + '_' + str(p+1) + '.png'), split_train_resize_img*255)
    f = h5py.File(os.path.join(os.getcwd(), 'train_chars_data.h5'), 'w')
    f.create_dataset('img', data=img)
    f.create_dataset('label', data=label)
    f.close() 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def skeleton_transform_volume(label):
    vol_distance = np.zeros_like(label, dtype=np.float32)
    vol_skeleton = np.zeros_like(label, dtype=np.uint8)
    for i in range(label.shape[0]):
        label_img = label[i].copy()
        distance, skeleton = skeleton_transform(label_img)
        vol_distance[i] = distance
        vol_skeleton[i] = skeleton

    return vol_distance, vol_skeleton 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def postprocess_prediction(seg):
    # basically look for connected components and choose the largest one, delete everything else
    print("running postprocessing... ")
    mask = seg != 0
    lbls = label(mask, 8)
    lbls_sizes = [np.sum(lbls == i) for i in np.unique(lbls)]
    largest_region = np.argmax(lbls_sizes[1:]) + 1
    seg[lbls != largest_region] = 0
    return seg 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def postprocess_prediction(seg):
    # basically look for connected components and choose the largest one, delete everything else
    mask = seg != 0
    lbls = label(mask, 8)
    lbls_sizes = [np.sum(lbls==i) for i in np.unique(lbls)]
    largest_region = np.argmax(lbls_sizes[1:]) + 1
    seg[lbls != largest_region]=0
    return seg 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def hard_dice(y_pred, y_true, n_classes):
    # y_true must be label map, not one hot encoding
    y_true = T.flatten(y_true)
    y_pred = T.argmax(y_pred, axis=1)

    dice = T.zeros(n_classes)

    for i in range(n_classes):
        i_val = T.constant(i)
        y_true_i = T.eq(y_true, i_val)
        y_pred_i = T.eq(y_pred, i_val)
        dice = T.set_subtensor(dice[i], (T.constant(2.) * T.sum(y_true_i * y_pred_i) + T.constant(1e-7)) /
                               (T.sum(y_true_i) + T.sum(y_pred_i) + T.constant(1e-7)))
    return dice 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def prob_to_rles(x, cutoff=0.5):
    lab_img = label(x > cutoff)
    for i in range(1, lab_img.max() + 1):
        yield rle_encoding(lab_img == i) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def __call__(self, **data_dict):
        data = data_dict.get(self.key)
        for b in range(data.shape[0]):
            if np.random.uniform() < self.p_per_sample:
                for c in self.channel_idx:
                    if np.random.uniform() < self.p_per_label:
                        workon = np.copy(data[b, c])
                        num_voxels = np.prod(workon.shape, dtype=np.uint64)
                        lab, num_comp = label(workon, return_num=True)
                        if num_comp > 0:
                            component_ids = []
                            component_sizes = []
                            for i in range(1, num_comp + 1):
                                component_ids.append(i)
                                component_sizes.append(np.sum(lab == i))
                            component_ids = [i for i, j in zip(component_ids, component_sizes) if j < num_voxels*self.dont_do_if_covers_more_than_X_percent]
                            #_ = component_ids.pop(np.argmax(component_sizes))
                            #else:
                            #    component_ids = list(range(1, num_comp + 1))
                            if len(component_ids) > 0:
                                random_component = np.random.choice(component_ids)
                                data[b, c][lab == random_component] = 0
                                if np.random.uniform() < self.fill_with_other_class_p:
                                    other_ch = [i for i in self.channel_idx if i != c]
                                    if len(other_ch) > 0:
                                        other_class = np.random.choice(other_ch)
                                        data[b, other_class][lab == random_component] = 1
        data_dict[self.key] = data
        return data_dict 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def _check_if_all_in_one_region(seg, regions):
        res = OrderedDict()
        for r in regions:
            new_seg = np.zeros(seg.shape)
            for c in r:
                new_seg[seg == c] = 1
            labelmap, numlabels = label(new_seg, return_num=True)
            if numlabels != 1:
                res[tuple(r)] = False
            else:
                res[tuple(r)] = True
        return res 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def _collect_class_and_region_sizes(seg, all_classes, vol_per_voxel):
        volume_per_class = OrderedDict()
        region_volume_per_class = OrderedDict()
        for c in all_classes:
            region_volume_per_class[c] = []
            volume_per_class[c] = np.sum(seg == c) * vol_per_voxel
            labelmap, numregions = label(seg == c, return_num=True)
            for l in range(1, numregions + 1):
                region_volume_per_class[c].append(np.sum(labelmap == l) * vol_per_voxel)
        return volume_per_class, region_volume_per_class 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def split_label_clusters(self, neighbors=4):
        """ Expand the set of labels by looking at each connected component in
        the labels.  Assign each component a new label number, and copy its old
        intensity value to its new label. This typically expands the number of
        labels from ~30 to ~3000, so you should only really do it on the last
        iteration. """

        if self.params.logging:
            prev_r_s = self.decomposition.get_r_s()

        rows, cols = self.input.shape[0:2]
        labels = self.decomposition.get_labels()
        intensities = self.decomposition.intensities
        chromaticities = self.decomposition.chromaticities

        # split labels
        new_labels = morphology.label(labels, neighbors=neighbors)

        # map labels
        self.decomposition.labels_nz = new_labels[self.input.mask_nz]

        # map intensities
        _, indices = np.unique(new_labels.ravel(), return_index=True)
        new_to_old = labels.ravel()[indices]
        new_to_old = new_to_old[new_to_old != -1]
        self.decomposition.intensities = intensities[new_to_old]
        self.decomposition.chromaticities = chromaticities[new_to_old]

        if self.params.logging:
            print ('split_label_clusters: %s --> %s' % (
                   intensities.shape[0], self.decomposition.intensities.shape[0]))

        self.remove_unused_intensities()

        if self.params.logging:
            np.testing.assert_equal(self.decomposition.get_r_s(), prev_r_s)
            assert (self.decomposition.chromaticities.shape[0] ==
                    self.decomposition.intensities.shape[0]) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import label [as 别名]
def postprocess(preds, config):
    assert preds.shape[2]==5
    ldelta = delta(preds[:,:,1:])
    #ldelta = delta0(preds[:,:,5:])
    connected = np.all(ldelta>config.GRADIENT_THRES, 2)
    base = connected * (preds[:,:,0]>config.MASK_THRES)
    
    wall = np.sum(np.abs(preds[:,:,1:]),axis = -1)   
    base_label = label(base) 
    vals, counts = np.unique(base_label[base_label>0], return_counts=True)
    for val in vals[(counts<config.CLIP_AREA_LOW)]:
        base_label[base_label==val]=0
    vals = vals[(counts>=config.CLIP_AREA_LOW)]

    for val in vals:
        
        label_mask = base_label == val   
        if np.sum(label_mask)==0:
            continue
        label_mask = remove_small_holes(label_mask)
        label_mask = basin(label_mask, wall)
        label_mask = remove_small_holes(label_mask)

        '''
        label_bdr = label_mask^binary_erosion(label_mask)
        min_wall = np.min(wall[label_mask])
        ave_bdr_wall = np.mean(wall[label_bdr])
        if ave_bdr_wall < min_wall + config.WALL_DEPTH:
            label_mask = 0
        '''
        base_label[label_mask] = val

    vals, counts = np.unique(base_label[base_label>0], return_counts=True)
    for val in vals[(counts<config.CLIP_AREA_LOW)]:
        base_label[base_label==val]=0        
    return base_label