Inspect and visualize data loading and pre-processing code.
import os
import sys
import itertools
import math
import logging
import json
import re
import random
from collections import OrderedDict
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import matplotlib.lines as lines
from matplotlib.patches import Polygon
# Root directory of the project
ROOT_DIR = os.path.abspath("../../")
# Import Mask RCNN
sys.path.append(ROOT_DIR) # To find local version of the library
from mrcnn import utils
from mrcnn import visualize
from mrcnn.visualize import display_images
import mrcnn.model as modellib
from mrcnn.model import log
%matplotlib inline
Using TensorFlow backend.
Run one of the code blocks below to import and load the configurations to use.
# Run one of the code blocks
# Shapes toy dataset
# import shapes
# config = shapes.ShapesConfig()
# MS COCO Dataset
import coco
config = coco.CocoConfig()
COCO_DIR = "path to COCO dataset" # TODO: enter value here
# Load dataset
if config.NAME == 'shapes':
dataset = shapes.ShapesDataset()
dataset.load_shapes(500, config.IMAGE_SHAPE[0], config.IMAGE_SHAPE[1])
elif config.NAME == "coco":
dataset = coco.CocoDataset()
dataset.load_coco(COCO_DIR, "train")
# Must call before using the dataset
dataset.prepare()
print("Image Count: {}".format(len(dataset.image_ids)))
print("Class Count: {}".format(dataset.num_classes))
for i, info in enumerate(dataset.class_info):
print("{:3}. {:50}".format(i, info['name']))
loading annotations into memory... Done (t=11.93s) creating index... index created! Image Count: 82081 Class Count: 81 0. BG 1. person 2. bicycle 3. car 4. motorcycle 5. airplane 6. bus 7. train 8. truck 9. boat 10. traffic light 11. fire hydrant 12. stop sign 13. parking meter 14. bench 15. bird 16. cat 17. dog 18. horse 19. sheep 20. cow 21. elephant 22. bear 23. zebra 24. giraffe 25. backpack 26. umbrella 27. handbag 28. tie 29. suitcase 30. frisbee 31. skis 32. snowboard 33. sports ball 34. kite 35. baseball bat 36. baseball glove 37. skateboard 38. surfboard 39. tennis racket 40. bottle 41. wine glass 42. cup 43. fork 44. knife 45. spoon 46. bowl 47. banana 48. apple 49. sandwich 50. orange 51. broccoli 52. carrot 53. hot dog 54. pizza 55. donut 56. cake 57. chair 58. couch 59. potted plant 60. bed 61. dining table 62. toilet 63. tv 64. laptop 65. mouse 66. remote 67. keyboard 68. cell phone 69. microwave 70. oven 71. toaster 72. sink 73. refrigerator 74. book 75. clock 76. vase 77. scissors 78. teddy bear 79. hair drier 80. toothbrush
Load and display images and masks.
# Load and display random samples
image_ids = np.random.choice(dataset.image_ids, 4)
for image_id in image_ids:
image = dataset.load_image(image_id)
mask, class_ids = dataset.load_mask(image_id)
visualize.display_top_masks(image, mask, class_ids, dataset.class_names)
Rather than using bounding box coordinates provided by the source datasets, we compute the bounding boxes from masks instead. This allows us to handle bounding boxes consistently regardless of the source dataset, and it also makes it easier to resize, rotate, or crop images because we simply generate the bounding boxes from the updates masks rather than computing bounding box transformation for each type of image transformation.
# Load random image and mask.
image_id = random.choice(dataset.image_ids)
image = dataset.load_image(image_id)
mask, class_ids = dataset.load_mask(image_id)
# Compute Bounding box
bbox = utils.extract_bboxes(mask)
# Display image and additional stats
print("image_id ", image_id, dataset.image_reference(image_id))
log("image", image)
log("mask", mask)
log("class_ids", class_ids)
log("bbox", bbox)
# Display image and instances
visualize.display_instances(image, bbox, mask, class_ids, dataset.class_names)
image_id 74886 http://cocodataset.org/#explore?id=118535 image shape: (375, 500, 3) min: 0.00000 max: 255.00000 mask shape: (375, 500, 5) min: 0.00000 max: 1.00000 class_ids shape: (5,) min: 1.00000 max: 35.00000 bbox shape: (5, 4) min: 1.00000 max: 329.00000
To support multiple images per batch, images are resized to one size (1024x1024). Aspect ratio is preserved, though. If an image is not square, then zero padding is added at the top/bottom or right/left.
# Load random image and mask.
image_id = np.random.choice(dataset.image_ids, 1)[0]
image = dataset.load_image(image_id)
mask, class_ids = dataset.load_mask(image_id)
original_shape = image.shape
# Resize
image, window, scale, padding, _ = utils.resize_image(
image,
min_dim=config.IMAGE_MIN_DIM,
max_dim=config.IMAGE_MAX_DIM,
mode=config.IMAGE_RESIZE_MODE)
mask = utils.resize_mask(mask, scale, padding)
# Compute Bounding box
bbox = utils.extract_bboxes(mask)
# Display image and additional stats
print("image_id: ", image_id, dataset.image_reference(image_id))
print("Original shape: ", original_shape)
log("image", image)
log("mask", mask)
log("class_ids", class_ids)
log("bbox", bbox)
# Display image and instances
visualize.display_instances(image, bbox, mask, class_ids, dataset.class_names)
/usr/local/lib/python3.5/dist-packages/scipy/ndimage/interpolation.py:600: UserWarning: From scipy 0.13.0, the output shape of zoom() is calculated with round() instead of int() - for these inputs the size of the returned array has changed. "the returned array has changed.", UserWarning)
image_id: 6480 http://cocodataset.org/#explore?id=402563 Original shape: (476, 640, 3) image shape: (1024, 1024, 3) min: 0.00000 max: 255.00000 mask shape: (1024, 1024, 32) min: 0.00000 max: 1.00000 class_ids shape: (32,) min: 1.00000 max: 77.00000 bbox shape: (32, 4) min: 1.00000 max: 991.00000
Instance binary masks can get large when training with high resolution images. For example, if training with 1024x1024 image then the mask of a single instance requires 1MB of memory (Numpy uses bytes for boolean values). If an image has 100 instances then that's 100MB for the masks alone.
To improve training speed, we optimize masks by:
To visualize the effect of mask resizing, and to verify the code correctness, we visualize some examples.
image_id = np.random.choice(dataset.image_ids, 1)[0]
image, image_meta, class_ids, bbox, mask = modellib.load_image_gt(
dataset, config, image_id, use_mini_mask=False)
log("image", image)
log("image_meta", image_meta)
log("class_ids", class_ids)
log("bbox", bbox)
log("mask", mask)
display_images([image]+[mask[:,:,i] for i in range(min(mask.shape[-1], 7))])
image shape: (1024, 1024, 3) min: 0.00000 max: 255.00000 image_meta shape: (89,) min: 0.00000 max: 23221.00000 bbox shape: (1, 5) min: 62.00000 max: 578.00000 mask shape: (1024, 1024, 1) min: 0.00000 max: 1.00000
visualize.display_instances(image, bbox, mask, class_ids, dataset.class_names)
# Add augmentation and mask resizing.
image, image_meta, class_ids, bbox, mask = modellib.load_image_gt(
dataset, config, image_id, augment=True, use_mini_mask=True)
log("mask", mask)
display_images([image]+[mask[:,:,i] for i in range(min(mask.shape[-1], 7))])
mask shape: (56, 56, 1) min: 0.00000 max: 1.00000
mask = utils.expand_mask(bbox, mask, image.shape)
visualize.display_instances(image, bbox, mask, class_ids, dataset.class_names)
The order of anchors is important. Use the same order in training and prediction phases. And it must match the order of the convolution execution.
For an FPN network, the anchors must be ordered in a way that makes it easy to match anchors to the output of the convolution layers that predict anchor scores and shifts.
Anchor Stride: In the FPN architecture, feature maps at the first few layers are high resolution. For example, if the input image is 1024x1024 then the feature map of the first layer is 256x256, which generates about 200K anchors (256x256x3). These anchors are 32x32 pixels and their stride relative to image pixels is 4 pixels, so there is a lot of overlap. We can reduce the load significantly if we generate anchors for every other cell in the feature map. A stride of 2 will cut the number of anchors by 4, for example.
In this implementation we use an anchor stride of 2, which is different from the paper.
# Generate Anchors
backbone_shapes = modellib.compute_backbone_shapes(config, config.IMAGE_SHAPE)
anchors = utils.generate_pyramid_anchors(config.RPN_ANCHOR_SCALES,
config.RPN_ANCHOR_RATIOS,
backbone_shapes,
config.BACKBONE_STRIDES,
config.RPN_ANCHOR_STRIDE)
# Print summary of anchors
num_levels = len(backbone_shapes)
anchors_per_cell = len(config.RPN_ANCHOR_RATIOS)
print("Count: ", anchors.shape[0])
print("Scales: ", config.RPN_ANCHOR_SCALES)
print("ratios: ", config.RPN_ANCHOR_RATIOS)
print("Anchors per Cell: ", anchors_per_cell)
print("Levels: ", num_levels)
anchors_per_level = []
for l in range(num_levels):
num_cells = backbone_shapes[l][0] * backbone_shapes[l][1]
anchors_per_level.append(anchors_per_cell * num_cells // config.RPN_ANCHOR_STRIDE**2)
print("Anchors in Level {}: {}".format(l, anchors_per_level[l]))
Count: 65472 Scales: (32, 64, 128, 256, 512) ratios: [0.5, 1, 2] Anchors per Cell: 3 Levels: 5 Anchors in Level 0: 49152 Anchors in Level 1: 12288 Anchors in Level 2: 3072 Anchors in Level 3: 768 Anchors in Level 4: 192
Visualize anchors of one cell at the center of the feature map of a specific level.
## Visualize anchors of one cell at the center of the feature map of a specific level
# Load and draw random image
image_id = np.random.choice(dataset.image_ids, 1)[0]
image, image_meta, _, _, _ = modellib.load_image_gt(dataset, config, image_id)
fig, ax = plt.subplots(1, figsize=(10, 10))
ax.imshow(image)
levels = len(backbone_shapes)
for level in range(levels):
colors = visualize.random_colors(levels)
# Compute the index of the anchors at the center of the image
level_start = sum(anchors_per_level[:level]) # sum of anchors of previous levels
level_anchors = anchors[level_start:level_start+anchors_per_level[level]]
print("Level {}. Anchors: {:6} Feature map Shape: {}".format(level, level_anchors.shape[0],
backbone_shapes[level]))
center_cell = backbone_shapes[level] // 2
center_cell_index = (center_cell[0] * backbone_shapes[level][1] + center_cell[1])
level_center = center_cell_index * anchors_per_cell
center_anchor = anchors_per_cell * (
(center_cell[0] * backbone_shapes[level][1] / config.RPN_ANCHOR_STRIDE**2) \
+ center_cell[1] / config.RPN_ANCHOR_STRIDE)
level_center = int(center_anchor)
# Draw anchors. Brightness show the order in the array, dark to bright.
for i, rect in enumerate(level_anchors[level_center:level_center+anchors_per_cell]):
y1, x1, y2, x2 = rect
p = patches.Rectangle((x1, y1), x2-x1, y2-y1, linewidth=2, facecolor='none',
edgecolor=(i+1)*np.array(colors[level]) / anchors_per_cell)
ax.add_patch(p)
/usr/local/lib/python3.5/dist-packages/scipy/ndimage/interpolation.py:600: UserWarning: From scipy 0.13.0, the output shape of zoom() is calculated with round() instead of int() - for these inputs the size of the returned array has changed. "the returned array has changed.", UserWarning)
Level 0. Anchors: 49152 Feature map Shape: [256 256] Level 1. Anchors: 12288 Feature map Shape: [128 128] Level 2. Anchors: 3072 Feature map Shape: [64 64] Level 3. Anchors: 768 Feature map Shape: [32 32] Level 4. Anchors: 192 Feature map Shape: [16 16]
# Create data generator
random_rois = 2000
g = modellib.data_generator(
dataset, config, shuffle=True, random_rois=random_rois,
batch_size=4,
detection_targets=True)
# Uncomment to run the generator through a lot of images
# to catch rare errors
# for i in range(1000):
# print(i)
# _, _ = next(g)
# Get Next Image
if random_rois:
[normalized_images, image_meta, rpn_match, rpn_bbox, gt_class_ids, gt_boxes, gt_masks, rpn_rois, rois], \
[mrcnn_class_ids, mrcnn_bbox, mrcnn_mask] = next(g)
log("rois", rois)
log("mrcnn_class_ids", mrcnn_class_ids)
log("mrcnn_bbox", mrcnn_bbox)
log("mrcnn_mask", mrcnn_mask)
else:
[normalized_images, image_meta, rpn_match, rpn_bbox, gt_boxes, gt_masks], _ = next(g)
log("gt_class_ids", gt_class_ids)
log("gt_boxes", gt_boxes)
log("gt_masks", gt_masks)
log("rpn_match", rpn_match, )
log("rpn_bbox", rpn_bbox)
image_id = modellib.parse_image_meta(image_meta)["image_id"][0]
print("image_id: ", image_id, dataset.image_reference(image_id))
# Remove the last dim in mrcnn_class_ids. It's only added
# to satisfy Keras restriction on target shape.
mrcnn_class_ids = mrcnn_class_ids[:,:,0]
/usr/local/lib/python3.5/dist-packages/scipy/ndimage/interpolation.py:600: UserWarning: From scipy 0.13.0, the output shape of zoom() is calculated with round() instead of int() - for these inputs the size of the returned array has changed. "the returned array has changed.", UserWarning)
rois shape: (4, 128, 4) min: 0.00000 max: 1023.00000 mrcnn_class_ids shape: (4, 128, 1) min: 0.00000 max: 67.00000 mrcnn_bbox shape: (4, 128, 81, 5) min: -3.58824 max: 3.45455 mrcnn_mask shape: (4, 128, 28, 28, 81) min: 0.00000 max: 1.00000 gt_boxes shape: (4, 100, 5) min: 0.00000 max: 1024.00000 gt_masks shape: (4, 56, 56, 100) min: 0.00000 max: 1.00000 rpn_match shape: (4, 65472, 1) min: -1.00000 max: 1.00000 rpn_bbox shape: (4, 256, 4) min: -4.60969 max: 1.76777 image_id: 2937 http://cocodataset.org/#explore?id=135453
b = 0
# Restore original image (reverse normalization)
sample_image = modellib.unmold_image(normalized_images[b], config)
# Compute anchor shifts.
indices = np.where(rpn_match[b] == 1)[0]
refined_anchors = utils.apply_box_deltas(anchors[indices], rpn_bbox[b, :len(indices)] * config.RPN_BBOX_STD_DEV)
log("anchors", anchors)
log("refined_anchors", refined_anchors)
# Get list of positive anchors
positive_anchor_ids = np.where(rpn_match[b] == 1)[0]
print("Positive anchors: {}".format(len(positive_anchor_ids)))
negative_anchor_ids = np.where(rpn_match[b] == -1)[0]
print("Negative anchors: {}".format(len(negative_anchor_ids)))
neutral_anchor_ids = np.where(rpn_match[b] == 0)[0]
print("Neutral anchors: {}".format(len(neutral_anchor_ids)))
# ROI breakdown by class
for c, n in zip(dataset.class_names, np.bincount(mrcnn_class_ids[b].flatten())):
if n:
print("{:23}: {}".format(c[:20], n))
# Show positive anchors
visualize.draw_boxes(sample_image, boxes=anchors[positive_anchor_ids],
refined_boxes=refined_anchors)
anchors shape: (65472, 4) min: -362.03867 max: 1258.03867 refined_anchors shape: (4, 4) min: 112.99997 max: 912.00000 Positive anchors: 4 Negative anchors: 252 Neutral anchors: 65216 BG : 90 chair : 6 bed : 30 remote : 2
# Show negative anchors
visualize.draw_boxes(sample_image, boxes=anchors[negative_anchor_ids])
# Show neutral anchors. They don't contribute to training.
visualize.draw_boxes(sample_image, boxes=anchors[np.random.choice(neutral_anchor_ids, 100)])
if random_rois:
# Class aware bboxes
bbox_specific = mrcnn_bbox[b, np.arange(mrcnn_bbox.shape[1]), mrcnn_class_ids[b], :]
# Refined ROIs
refined_rois = utils.apply_box_deltas(rois[b].astype(np.float32), bbox_specific[:,:4] * config.BBOX_STD_DEV)
# Class aware masks
mask_specific = mrcnn_mask[b, np.arange(mrcnn_mask.shape[1]), :, :, mrcnn_class_ids[b]]
visualize.draw_rois(sample_image, rois[b], refined_rois, mask_specific, mrcnn_class_ids[b], dataset.class_names)
# Any repeated ROIs?
rows = np.ascontiguousarray(rois[b]).view(np.dtype((np.void, rois.dtype.itemsize * rois.shape[-1])))
_, idx = np.unique(rows, return_index=True)
print("Unique ROIs: {} out of {}".format(len(idx), rois.shape[1]))
Positive ROIs: 38 Negative ROIs: 90 Positive Ratio: 0.30 Unique ROIs: 128 out of 128
if random_rois:
# Dispalay ROIs and corresponding masks and bounding boxes
ids = random.sample(range(rois.shape[1]), 8)
images = []
titles = []
for i in ids:
image = visualize.draw_box(sample_image.copy(), rois[b,i,:4].astype(np.int32), [255, 0, 0])
image = visualize.draw_box(image, refined_rois[i].astype(np.int64), [0, 255, 0])
images.append(image)
titles.append("ROI {}".format(i))
images.append(mask_specific[i] * 255)
titles.append(dataset.class_names[mrcnn_class_ids[b,i]][:20])
display_images(images, titles, cols=4, cmap="Blues", interpolation="none")
# Check ratio of positive ROIs in a set of images.
if random_rois:
limit = 10
temp_g = modellib.data_generator(
dataset, config, shuffle=True, random_rois=10000,
batch_size=1, detection_targets=True)
total = 0
for i in range(limit):
_, [ids, _, _] = next(temp_g)
positive_rois = np.sum(ids[0] > 0)
total += positive_rois
print("{:5} {:5.2f}".format(positive_rois, positive_rois/ids.shape[1]))
print("Average percent: {:.2f}".format(total/(limit*ids.shape[1])))
42 0.33 42 0.33
/usr/local/lib/python3.5/dist-packages/scipy/ndimage/interpolation.py:600: UserWarning: From scipy 0.13.0, the output shape of zoom() is calculated with round() instead of int() - for these inputs the size of the returned array has changed. "the returned array has changed.", UserWarning)
42 0.33 42 0.33 42 0.33 42 0.33 42 0.33 42 0.33 42 0.33 42 0.33 Average percent: 0.33