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""" |
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Mask R-CNN |
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Common utility functions and classes. |
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Copyright (c) 2017 Matterport, Inc. |
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Licensed under the MIT License (see LICENSE for details) |
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Written by Waleed Abdulla |
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""" |
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import sys |
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import os |
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import math |
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import random |
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import numpy as np |
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import tensorflow as tf |
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import scipy.misc |
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import skimage.color |
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import skimage.io |
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import urllib.request |
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import shutil |
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COCO_MODEL_URL = "https://github.com/matterport/Mask_RCNN/releases/download/v2.0/mask_rcnn_coco.h5" |
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def extract_bboxes(mask): |
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"""Compute bounding boxes from masks. |
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mask: [height, width, num_instances]. Mask pixels are either 1 or 0. |
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Returns: bbox array [num_instances, (y1, x1, y2, x2)]. |
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""" |
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boxes = np.zeros([mask.shape[-1], 4], dtype=np.int32) |
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for i in range(mask.shape[-1]): |
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m = mask[:, :, i] |
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horizontal_indicies = np.where(np.any(m, axis=0))[0] |
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vertical_indicies = np.where(np.any(m, axis=1))[0] |
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if horizontal_indicies.shape[0]: |
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x1, x2 = horizontal_indicies[[0, -1]] |
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y1, y2 = vertical_indicies[[0, -1]] |
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x2 += 1 |
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y2 += 1 |
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else: |
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x1, x2, y1, y2 = 0, 0, 0, 0 |
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boxes[i] = np.array([y1, x1, y2, x2]) |
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return boxes.astype(np.int32) |
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def compute_iou(box, boxes, box_area, boxes_area): |
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"""Calculates IoU of the given box with the array of the given boxes. |
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box: 1D vector [y1, x1, y2, x2] |
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boxes: [boxes_count, (y1, x1, y2, x2)] |
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box_area: float. the area of 'box' |
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boxes_area: array of length boxes_count. |
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Note: the areas are passed in rather than calculated here for |
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efficency. Calculate once in the caller to avoid duplicate work. |
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""" |
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y1 = np.maximum(box[0], boxes[:, 0]) |
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y2 = np.minimum(box[2], boxes[:, 2]) |
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x1 = np.maximum(box[1], boxes[:, 1]) |
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x2 = np.minimum(box[3], boxes[:, 3]) |
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intersection = np.maximum(x2 - x1, 0) * np.maximum(y2 - y1, 0) |
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union = box_area + boxes_area[:] - intersection[:] |
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iou = intersection / union |
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return iou |
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def compute_overlaps(boxes1, boxes2): |
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"""Computes IoU overlaps between two sets of boxes. |
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boxes1, boxes2: [N, (y1, x1, y2, x2)]. |
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For better performance, pass the largest set first and the smaller second. |
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""" |
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area1 = (boxes1[:, 2] - boxes1[:, 0]) * (boxes1[:, 3] - boxes1[:, 1]) |
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area2 = (boxes2[:, 2] - boxes2[:, 0]) * (boxes2[:, 3] - boxes2[:, 1]) |
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overlaps = np.zeros((boxes1.shape[0], boxes2.shape[0])) |
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for i in range(overlaps.shape[1]): |
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box2 = boxes2[i] |
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overlaps[:, i] = compute_iou(box2, boxes1, area2[i], area1) |
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return overlaps |
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def compute_overlaps_masks(masks1, masks2): |
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'''Computes IoU overlaps between two sets of masks. |
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masks1, masks2: [Height, Width, instances] |
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''' |
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masks1 = np.reshape(masks1 > .5, (-1, masks1.shape[-1])).astype(np.float32) |
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masks2 = np.reshape(masks2 > .5, (-1, masks2.shape[-1])).astype(np.float32) |
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area1 = np.sum(masks1, axis=0) |
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area2 = np.sum(masks2, axis=0) |
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intersections = np.dot(masks1.T, masks2) |
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union = area1[:, None] + area2[None, :] - intersections |
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overlaps = intersections / union |
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return overlaps |
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def non_max_suppression(boxes, scores, threshold): |
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"""Performs non-maximum supression and returns indicies of kept boxes. |
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boxes: [N, (y1, x1, y2, x2)]. Notice that (y2, x2) lays outside the box. |
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scores: 1-D array of box scores. |
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threshold: Float. IoU threshold to use for filtering. |
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""" |
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assert boxes.shape[0] > 0 |
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if boxes.dtype.kind != "f": |
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boxes = boxes.astype(np.float32) |
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y1 = boxes[:, 0] |
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x1 = boxes[:, 1] |
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y2 = boxes[:, 2] |
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x2 = boxes[:, 3] |
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area = (y2 - y1) * (x2 - x1) |
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ixs = scores.argsort()[::-1] |
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pick = [] |
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while len(ixs) > 0: |
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i = ixs[0] |
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pick.append(i) |
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iou = compute_iou(boxes[i], boxes[ixs[1:]], area[i], area[ixs[1:]]) |
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remove_ixs = np.where(iou > threshold)[0] + 1 |
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ixs = np.delete(ixs, remove_ixs) |
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ixs = np.delete(ixs, 0) |
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return np.array(pick, dtype=np.int32) |
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def apply_box_deltas(boxes, deltas): |
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"""Applies the given deltas to the given boxes. |
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boxes: [N, (y1, x1, y2, x2)]. Note that (y2, x2) is outside the box. |
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deltas: [N, (dy, dx, log(dh), log(dw))] |
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""" |
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boxes = boxes.astype(np.float32) |
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height = boxes[:, 2] - boxes[:, 0] |
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width = boxes[:, 3] - boxes[:, 1] |
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center_y = boxes[:, 0] + 0.5 * height |
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center_x = boxes[:, 1] + 0.5 * width |
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center_y += deltas[:, 0] * height |
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center_x += deltas[:, 1] * width |
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height *= np.exp(deltas[:, 2]) |
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width *= np.exp(deltas[:, 3]) |
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y1 = center_y - 0.5 * height |
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x1 = center_x - 0.5 * width |
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y2 = y1 + height |
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x2 = x1 + width |
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return np.stack([y1, x1, y2, x2], axis=1) |
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def box_refinement_graph(box, gt_box): |
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"""Compute refinement needed to transform box to gt_box. |
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box and gt_box are [N, (y1, x1, y2, x2)] |
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""" |
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box = tf.cast(box, tf.float32) |
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gt_box = tf.cast(gt_box, tf.float32) |
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height = box[:, 2] - box[:, 0] |
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width = box[:, 3] - box[:, 1] |
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center_y = box[:, 0] + 0.5 * height |
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center_x = box[:, 1] + 0.5 * width |
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gt_height = gt_box[:, 2] - gt_box[:, 0] |
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gt_width = gt_box[:, 3] - gt_box[:, 1] |
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gt_center_y = gt_box[:, 0] + 0.5 * gt_height |
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gt_center_x = gt_box[:, 1] + 0.5 * gt_width |
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dy = (gt_center_y - center_y) / height |
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dx = (gt_center_x - center_x) / width |
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dh = tf.log(gt_height / height) |
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dw = tf.log(gt_width / width) |
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result = tf.stack([dy, dx, dh, dw], axis=1) |
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return result |
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def box_refinement(box, gt_box): |
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"""Compute refinement needed to transform box to gt_box. |
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box and gt_box are [N, (y1, x1, y2, x2)]. (y2, x2) is |
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assumed to be outside the box. |
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""" |
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box = box.astype(np.float32) |
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gt_box = gt_box.astype(np.float32) |
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height = box[:, 2] - box[:, 0] |
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width = box[:, 3] - box[:, 1] |
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center_y = box[:, 0] + 0.5 * height |
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center_x = box[:, 1] + 0.5 * width |
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gt_height = gt_box[:, 2] - gt_box[:, 0] |
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gt_width = gt_box[:, 3] - gt_box[:, 1] |
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gt_center_y = gt_box[:, 0] + 0.5 * gt_height |
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gt_center_x = gt_box[:, 1] + 0.5 * gt_width |
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dy = (gt_center_y - center_y) / height |
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dx = (gt_center_x - center_x) / width |
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dh = np.log(gt_height / height) |
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dw = np.log(gt_width / width) |
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return np.stack([dy, dx, dh, dw], axis=1) |
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class Dataset(object): |
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"""The base class for dataset classes. |
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To use it, create a new class that adds functions specific to the dataset |
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you want to use. For example: |
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class CatsAndDogsDataset(Dataset): |
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def load_cats_and_dogs(self): |
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... |
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def load_mask(self, image_id): |
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... |
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def image_reference(self, image_id): |
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... |
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See COCODataset and ShapesDataset as examples. |
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""" |
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def __init__(self, class_map=None): |
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self._image_ids = [] |
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self.image_info = [] |
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self.class_info = [{"source": "", "id": 0, "name": "BG"}] |
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self.source_class_ids = {} |
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def add_class(self, source, class_id, class_name): |
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assert "." not in source, "Source name cannot contain a dot" |
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for info in self.class_info: |
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if info['source'] == source and info["id"] == class_id: |
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return |
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self.class_info.append({ |
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"source": source, |
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"id": class_id, |
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"name": class_name, |
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}) |
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def add_image(self, source, image_id, path, **kwargs): |
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image_info = { |
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"id": image_id, |
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"source": source, |
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"path": path, |
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} |
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image_info.update(kwargs) |
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self.image_info.append(image_info) |
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def image_reference(self, image_id): |
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"""Return a link to the image in its source Website or details about |
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the image that help looking it up or debugging it. |
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Override for your dataset, but pass to this function |
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if you encounter images not in your dataset. |
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""" |
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return "" |
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def prepare(self, class_map=None): |
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"""Prepares the Dataset class for use. |
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TODO: class map is not supported yet. When done, it should handle mapping |
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classes from different datasets to the same class ID. |
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""" |
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def clean_name(name): |
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"""Returns a shorter version of object names for cleaner display.""" |
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return ",".join(name.split(",")[:1]) |
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self.num_classes = len(self.class_info) |
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self.class_ids = np.arange(self.num_classes) |
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self.class_names = [clean_name(c["name"]) for c in self.class_info] |
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self.num_images = len(self.image_info) |
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self._image_ids = np.arange(self.num_images) |
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self.class_from_source_map = {"{}.{}".format(info['source'], info['id']): id |
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for info, id in zip(self.class_info, self.class_ids)} |
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self.sources = list(set([i['source'] for i in self.class_info])) |
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self.source_class_ids = {} |
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for source in self.sources: |
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self.source_class_ids[source] = [] |
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for i, info in enumerate(self.class_info): |
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if i == 0 or source == info['source']: |
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self.source_class_ids[source].append(i) |
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def map_source_class_id(self, source_class_id): |
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"""Takes a source class ID and returns the int class ID assigned to it. |
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For example: |
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dataset.map_source_class_id("coco.12") -> 23 |
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""" |
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return self.class_from_source_map[source_class_id] |
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def get_source_class_id(self, class_id, source): |
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"""Map an internal class ID to the corresponding class ID in the source dataset.""" |
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info = self.class_info[class_id] |
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assert info['source'] == source |
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return info['id'] |
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def append_data(self, class_info, image_info): |
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self.external_to_class_id = {} |
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for i, c in enumerate(self.class_info): |
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for ds, id in c["map"]: |
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self.external_to_class_id[ds + str(id)] = i |
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self.external_to_image_id = {} |
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for i, info in enumerate(self.image_info): |
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self.external_to_image_id[info["ds"] + str(info["id"])] = i |
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@property |
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def image_ids(self): |
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return self._image_ids |
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def source_image_link(self, image_id): |
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"""Returns the path or URL to the image. |
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Override this to return a URL to the image if it's availble online for easy |
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debugging. |
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""" |
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return self.image_info[image_id]["path"] |
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def load_image(self, image_id): |
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"""Load the specified image and return a [H,W,3] Numpy array. |
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""" |
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image = skimage.io.imread(self.image_info[image_id]['path']) |
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if image.ndim != 3: |
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image = skimage.color.gray2rgb(image) |
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return image |
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def load_mask(self, image_id): |
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"""Load instance masks for the given image. |
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Different datasets use different ways to store masks. Override this |
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method to load instance masks and return them in the form of am |
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array of binary masks of shape [height, width, instances]. |
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Returns: |
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masks: A bool array of shape [height, width, instance count] with |
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a binary mask per instance. |
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class_ids: a 1D array of class IDs of the instance masks. |
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""" |
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mask = np.empty([0, 0, 0]) |
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class_ids = np.empty([0], np.int32) |
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return mask, class_ids |
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def resize_image(image, min_dim=None, max_dim=None, padding=False): |
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""" |
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Resizes an image keeping the aspect ratio. |
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min_dim: if provided, resizes the image such that it's smaller |
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dimension == min_dim |
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max_dim: if provided, ensures that the image longest side doesn't |
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exceed this value. |
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padding: If true, pads image with zeros so it's size is max_dim x max_dim |
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Returns: |
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image: the resized image |
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window: (y1, x1, y2, x2). If max_dim is provided, padding might |
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be inserted in the returned image. If so, this window is the |
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coordinates of the image part of the full image (excluding |
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the padding). The x2, y2 pixels are not included. |
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scale: The scale factor used to resize the image |
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padding: Padding added to the image [(top, bottom), (left, right), (0, 0)] |
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""" |
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h, w = image.shape[:2] |
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window = (0, 0, h, w) |
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scale = 1 |
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if min_dim: |
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scale = max(1, min_dim / min(h, w)) |
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if max_dim: |
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image_max = max(h, w) |
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if round(image_max * scale) > max_dim: |
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scale = max_dim / image_max |
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if scale != 1: |
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image = scipy.misc.imresize( |
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image, (round(h * scale), round(w * scale))) |
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if padding: |
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h, w = image.shape[:2] |
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top_pad = (max_dim - h) // 2 |
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bottom_pad = max_dim - h - top_pad |
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left_pad = (max_dim - w) // 2 |
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right_pad = max_dim - w - left_pad |
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padding = [(top_pad, bottom_pad), (left_pad, right_pad), (0, 0)] |
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image = np.pad(image, padding, mode='constant', constant_values=0) |
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window = (top_pad, left_pad, h + top_pad, w + left_pad) |
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return image, window, scale, padding |
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def resize_mask(mask, scale, padding): |
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"""Resizes a mask using the given scale and padding. |
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Typically, you get the scale and padding from resize_image() to |
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ensure both, the image and the mask, are resized consistently. |
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scale: mask scaling factor |
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padding: Padding to add to the mask in the form |
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[(top, bottom), (left, right), (0, 0)] |
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""" |
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h, w = mask.shape[:2] |
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mask = scipy.ndimage.zoom(mask, zoom=[scale, scale, 1], order=0) |
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mask = np.pad(mask, padding, mode='constant', constant_values=0) |
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return mask |
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def minimize_mask(bbox, mask, mini_shape): |
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"""Resize masks to a smaller version to cut memory load. |
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Mini-masks can then resized back to image scale using expand_masks() |
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See inspect_data.ipynb notebook for more details. |
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""" |
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mini_mask = np.zeros(mini_shape + (mask.shape[-1],), dtype=bool) |
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for i in range(mask.shape[-1]): |
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m = mask[:, :, i] |
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y1, x1, y2, x2 = bbox[i][:4] |
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m = m[y1:y2, x1:x2] |
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if m.size == 0: |
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raise Exception("Invalid bounding box with area of zero") |
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m = scipy.misc.imresize(m.astype(float), mini_shape, interp='bilinear') |
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mini_mask[:, :, i] = np.where(m >= 128, 1, 0) |
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return mini_mask |
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def expand_mask(bbox, mini_mask, image_shape): |
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"""Resizes mini masks back to image size. Reverses the change |
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of minimize_mask(). |
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See inspect_data.ipynb notebook for more details. |
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""" |
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mask = np.zeros(image_shape[:2] + (mini_mask.shape[-1],), dtype=bool) |
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for i in range(mask.shape[-1]): |
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m = mini_mask[:, :, i] |
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y1, x1, y2, x2 = bbox[i][:4] |
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h = y2 - y1 |
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w = x2 - x1 |
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m = scipy.misc.imresize(m.astype(float), (h, w), interp='bilinear') |
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mask[y1:y2, x1:x2, i] = np.where(m >= 128, 1, 0) |
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return mask |
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def mold_mask(mask, config): |
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pass |
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def unmold_mask(mask, bbox, image_shape): |
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"""Converts a mask generated by the neural network into a format similar |
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to it's original shape. |
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mask: [height, width] of type float. A small, typically 28x28 mask. |
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bbox: [y1, x1, y2, x2]. The box to fit the mask in. |
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Returns a binary mask with the same size as the original image. |
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""" |
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threshold = 0.5 |
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y1, x1, y2, x2 = bbox |
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mask = scipy.misc.imresize( |
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mask, (y2 - y1, x2 - x1), interp='bilinear').astype(np.float32) / 255.0 |
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mask = np.where(mask >= threshold, 1, 0).astype(np.uint8) |
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full_mask = np.zeros(image_shape[:2], dtype=np.uint8) |
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full_mask[y1:y2, x1:x2] = mask |
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return full_mask |
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def generate_anchors(scales, ratios, shape, feature_stride, anchor_stride): |
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""" |
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scales: 1D array of anchor sizes in pixels. Example: [32, 64, 128] |
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ratios: 1D array of anchor ratios of width/height. Example: [0.5, 1, 2] |
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shape: [height, width] spatial shape of the feature map over which |
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to generate anchors. |
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feature_stride: Stride of the feature map relative to the image in pixels. |
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anchor_stride: Stride of anchors on the feature map. For example, if the |
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value is 2 then generate anchors for every other feature map pixel. |
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""" |
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scales, ratios = np.meshgrid(np.array(scales), np.array(ratios)) |
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scales = scales.flatten() |
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ratios = ratios.flatten() |
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heights = scales / np.sqrt(ratios) |
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widths = scales * np.sqrt(ratios) |
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shifts_y = np.arange(0, shape[0], anchor_stride) * feature_stride |
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shifts_x = np.arange(0, shape[1], anchor_stride) * feature_stride |
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shifts_x, shifts_y = np.meshgrid(shifts_x, shifts_y) |
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box_widths, box_centers_x = np.meshgrid(widths, shifts_x) |
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box_heights, box_centers_y = np.meshgrid(heights, shifts_y) |
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box_centers = np.stack( |
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[box_centers_y, box_centers_x], axis=2).reshape([-1, 2]) |
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box_sizes = np.stack([box_heights, box_widths], axis=2).reshape([-1, 2]) |
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|
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boxes = np.concatenate([box_centers - 0.5 * box_sizes, |
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box_centers + 0.5 * box_sizes], axis=1) |
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return boxes |
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|
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def generate_pyramid_anchors(scales, ratios, feature_shapes, feature_strides, |
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anchor_stride): |
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"""Generate anchors at different levels of a feature pyramid. Each scale |
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is associated with a level of the pyramid, but each ratio is used in |
|
all levels of the pyramid. |
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|
|
Returns: |
|
anchors: [N, (y1, x1, y2, x2)]. All generated anchors in one array. Sorted |
|
with the same order of the given scales. So, anchors of scale[0] come |
|
first, then anchors of scale[1], and so on. |
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""" |
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|
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|
|
anchors = [] |
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for i in range(len(scales)): |
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anchors.append(generate_anchors(scales[i], ratios, feature_shapes[i], |
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feature_strides[i], anchor_stride)) |
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return np.concatenate(anchors, axis=0) |
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|
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def trim_zeros(x): |
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"""It's common to have tensors larger than the available data and |
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pad with zeros. This function removes rows that are all zeros. |
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|
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x: [rows, columns]. |
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""" |
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assert len(x.shape) == 2 |
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return x[~np.all(x == 0, axis=1)] |
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|
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def compute_ap(gt_boxes, gt_class_ids, gt_masks, |
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pred_boxes, pred_class_ids, pred_scores, pred_masks, |
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iou_threshold=0.5): |
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"""Compute Average Precision at a set IoU threshold (default 0.5). |
|
|
|
Returns: |
|
mAP: Mean Average Precision |
|
precisions: List of precisions at different class score thresholds. |
|
recalls: List of recall values at different class score thresholds. |
|
overlaps: [pred_boxes, gt_boxes] IoU overlaps. |
|
""" |
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|
|
|
|
gt_boxes = trim_zeros(gt_boxes) |
|
gt_masks = gt_masks[..., :gt_boxes.shape[0]] |
|
pred_boxes = trim_zeros(pred_boxes) |
|
pred_scores = pred_scores[:pred_boxes.shape[0]] |
|
indices = np.argsort(pred_scores)[::-1] |
|
pred_boxes = pred_boxes[indices] |
|
pred_class_ids = pred_class_ids[indices] |
|
pred_scores = pred_scores[indices] |
|
pred_masks = pred_masks[..., indices] |
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|
|
|
|
overlaps = compute_overlaps_masks(pred_masks, gt_masks) |
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|
|
|
|
match_count = 0 |
|
pred_match = np.zeros([pred_boxes.shape[0]]) |
|
gt_match = np.zeros([gt_boxes.shape[0]]) |
|
for i in range(len(pred_boxes)): |
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|
|
sorted_ixs = np.argsort(overlaps[i])[::-1] |
|
for j in sorted_ixs: |
|
|
|
if gt_match[j] == 1: |
|
continue |
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|
|
iou = overlaps[i, j] |
|
if iou < iou_threshold: |
|
break |
|
|
|
if pred_class_ids[i] == gt_class_ids[j]: |
|
match_count += 1 |
|
gt_match[j] = 1 |
|
pred_match[i] = 1 |
|
break |
|
|
|
|
|
precisions = np.cumsum(pred_match) / (np.arange(len(pred_match)) + 1) |
|
recalls = np.cumsum(pred_match).astype(np.float32) / len(gt_match) |
|
|
|
|
|
precisions = np.concatenate([[0], precisions, [0]]) |
|
recalls = np.concatenate([[0], recalls, [1]]) |
|
|
|
|
|
|
|
|
|
for i in range(len(precisions) - 2, -1, -1): |
|
precisions[i] = np.maximum(precisions[i], precisions[i + 1]) |
|
|
|
|
|
indices = np.where(recalls[:-1] != recalls[1:])[0] + 1 |
|
mAP = np.sum((recalls[indices] - recalls[indices - 1]) * |
|
precisions[indices]) |
|
|
|
return mAP, precisions, recalls, overlaps |
|
|
|
|
|
def compute_recall(pred_boxes, gt_boxes, iou): |
|
"""Compute the recall at the given IoU threshold. It's an indication |
|
of how many GT boxes were found by the given prediction boxes. |
|
|
|
pred_boxes: [N, (y1, x1, y2, x2)] in image coordinates |
|
gt_boxes: [N, (y1, x1, y2, x2)] in image coordinates |
|
""" |
|
|
|
overlaps = compute_overlaps(pred_boxes, gt_boxes) |
|
iou_max = np.max(overlaps, axis=1) |
|
iou_argmax = np.argmax(overlaps, axis=1) |
|
positive_ids = np.where(iou_max >= iou)[0] |
|
matched_gt_boxes = iou_argmax[positive_ids] |
|
|
|
recall = len(set(matched_gt_boxes)) / gt_boxes.shape[0] |
|
return recall, positive_ids |
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|
|
def batch_slice(inputs, graph_fn, batch_size, names=None): |
|
"""Splits inputs into slices and feeds each slice to a copy of the given |
|
computation graph and then combines the results. It allows you to run a |
|
graph on a batch of inputs even if the graph is written to support one |
|
instance only. |
|
|
|
inputs: list of tensors. All must have the same first dimension length |
|
graph_fn: A function that returns a TF tensor that's part of a graph. |
|
batch_size: number of slices to divide the data into. |
|
names: If provided, assigns names to the resulting tensors. |
|
""" |
|
if not isinstance(inputs, list): |
|
inputs = [inputs] |
|
|
|
outputs = [] |
|
for i in range(batch_size): |
|
inputs_slice = [x[i] for x in inputs] |
|
output_slice = graph_fn(*inputs_slice) |
|
if not isinstance(output_slice, (tuple, list)): |
|
output_slice = [output_slice] |
|
outputs.append(output_slice) |
|
|
|
|
|
|
|
outputs = list(zip(*outputs)) |
|
|
|
if names is None: |
|
names = [None] * len(outputs) |
|
|
|
result = [tf.stack(o, axis=0, name=n) |
|
for o, n in zip(outputs, names)] |
|
if len(result) == 1: |
|
result = result[0] |
|
|
|
return result |
|
|
|
|
|
def download_trained_weights(coco_model_path, verbose=1): |
|
"""Download COCO trained weights from Releases. |
|
|
|
coco_model_path: local path of COCO trained weights |
|
""" |
|
if verbose > 0: |
|
print("Downloading pretrained model to " + coco_model_path + " ...") |
|
with urllib.request.urlopen(COCO_MODEL_URL) as resp, open(coco_model_path, 'wb') as out: |
|
shutil.copyfileobj(resp, out) |
|
if verbose > 0: |
|
print("... done downloading pretrained model!") |
|
|
|
|
|
def resize_image_with_scale(h1, w1, h2_max, w2_max): |
|
"""resize image with scale and which fits in rectangle h2_max x w2_max""" |
|
if h1 == w1: return h2_max, h2_max |
|
elif h1 < w1: return int(h1/(w1/w2_max)), int(w2_max) |
|
else: return int(h2_max), int(w1/(h1/h2_max)) |
|
|