def create_tf_example(dcm_path, bboxes, patient_id=None, patients_detailed_info_dict={}):
dcm_data = pydicom.read_file(dcm_path)
if not patient_id:
patient_id = dcm_data.PatientName
image = dcm_data.pixel_array
pixel_spacing = np.array(dcm_data.PixelSpacing)
resize_factor = np.array([1.0, 1.0])
if FLAGS.resample:
requested_spacing = [FLAGS.pixel_scacing, FLAGS.pixel_spacing]
image, pixel_spacing, resize_factor = dicom_resample(dcm_data, requested_spacing)
height = image.shape[0]
width = image.shape[1]
encoded_image_data = encode_image_array_as_png_str(image)
image_format = b'png'
xmins = [resize_factor[0] * bbox.x / width for bbox in bboxes]
xmaxs = [resize_factor[0] * bbox.xmax() / width for bbox in bboxes]
ymins = [resize_factor[1] * bbox.y / height for bbox in bboxes]
ymaxs = [resize_factor[1] * bbox.ymax() / height for bbox in bboxes]
for coords in [xmins, ymins, xmaxs, ymaxs]:
assert(all([0.0 <= c and c <= 1.0 for c in coords]))
classes_text = [b'opacity' for bbox in bboxes]
classes = [1 for bbox in bboxes]
if len(patients_detailed_info_dict):
assert(patient_id in patients_detailed_info_dict)
decease_class = patients_detailed_info_dict.get(patient_id, (-1,'UNK'))[0]
decease_name = patients_detailed_info_dict.get(patient_id, (-1,'UNK'))[1]
tf_example = tf.train.Example(features=tf.train.Features(feature={
'image/height': dataset_util.int64_feature(height),
'image/width': dataset_util.int64_feature(width),
'image/filename': dataset_util.bytes_feature(bytes(dcm_path, encoding='utf-8')),
'image/source_id': dataset_util.bytes_feature(bytes(dcm_path, encoding='utf-8')),
'image/encoded': dataset_util.bytes_feature(encoded_image_data),
'image/format': dataset_util.bytes_feature(image_format),
'image/object/bbox/xmin': dataset_util.float_list_feature(xmins),
'image/object/bbox/xmax': dataset_util.float_list_feature(xmaxs),
'image/object/bbox/ymin': dataset_util.float_list_feature(ymins),
'image/object/bbox/ymax': dataset_util.float_list_feature(ymaxs),
'image/object/class/text': dataset_util.bytes_list_feature(classes_text),
'image/object/class/label': dataset_util.int64_list_feature(classes),
'image/pixel_spacing': dataset_util.float_list_feature(pixel_spacing),
'patient/id': dataset_util.bytes_feature(bytes(patient_id, encoding='utf-8')),
'patient/view_position': dataset_util.int64_feature({'AP':0, 'PA':1}.get(dcm_data.ViewPosition, -1)),
'patient/sex': dataset_util.int64_feature({'F':0, 'M':1}.get(dcm_data.PatientSex, -1)),
'patient/age': dataset_util.float_list_feature([float(dcm_data.PatientAge)]),
'patient/decease_class': dataset_util.int64_feature(decease_class),
'patient/decease_name': dataset_util.bytes_feature(bytes(decease_name, encoding='utf-8')),
}))
return tf_example
def visualize_detection_results(result_dict,
tag,
global_step,
categories,
summary_dir='',
export_dir='',
agnostic_mode=False,
show_groundtruth=False,
groundtruth_box_visualization_color='black',
min_score_thresh=.5,
max_num_predictions=20,
skip_scores=False,
skip_labels=False,
keep_image_id_for_visualization_export=False):
"""Visualizes detection results and writes visualizations to image summaries.
This function visualizes an image with its detected bounding boxes and writes
to image summaries which can be viewed on tensorboard. It optionally also
writes images to a directory. In the case of missing entry in the label map,
unknown class name in the visualization is shown as "N/A".
Args:
result_dict: a dictionary holding groundtruth and detection
data corresponding to each image being evaluated. The following keys
are required:
'original_image': a numpy array representing the image with shape
[1, height, width, 3] or [1, height, width, 1]
'detection_boxes': a numpy array of shape [N, 4]
'detection_scores': a numpy array of shape [N]
'detection_classes': a numpy array of shape [N]
The following keys are optional:
'groundtruth_boxes': a numpy array of shape [N, 4]
'groundtruth_keypoints': a numpy array of shape [N, num_keypoints, 2]
Detections are assumed to be provided in decreasing order of score and for
display, and we assume that scores are probabilities between 0 and 1.
tag: tensorboard tag (string) to associate with image.
global_step: global step at which the visualization are generated.
categories: a list of dictionaries representing all possible categories.
Each dict in this list has the following keys:
'id': (required) an integer id uniquely identifying this category
'name': (required) string representing category name
e.g., 'cat', 'dog', 'pizza'
'supercategory': (optional) string representing the supercategory
e.g., 'animal', 'vehicle', 'food', etc
summary_dir: the output directory to which the image summaries are written.
export_dir: the output directory to which images are written. If this is
empty (default), then images are not exported.
agnostic_mode: boolean (default: False) controlling whether to evaluate in
class-agnostic mode or not.
show_groundtruth: boolean (default: False) controlling whether to show
groundtruth boxes in addition to detected boxes
groundtruth_box_visualization_color: box color for visualizing groundtruth
boxes
min_score_thresh: minimum score threshold for a box to be visualized
max_num_predictions: maximum number of detections to visualize
skip_scores: whether to skip score when drawing a single detection
skip_labels: whether to skip label when drawing a single detection
keep_image_id_for_visualization_export: whether to keep image identifier in
filename when exported to export_dir
Raises:
ValueError: if result_dict does not contain the expected keys (i.e.,
'original_image', 'detection_boxes', 'detection_scores',
'detection_classes')
"""
detection_fields = fields.DetectionResultFields
input_fields = fields.InputDataFields
if not set([
input_fields.original_image,
detection_fields.detection_boxes,
detection_fields.detection_scores,
detection_fields.detection_classes,
]).issubset(set(result_dict.keys())):
raise ValueError('result_dict does not contain all expected keys.')
if show_groundtruth and input_fields.groundtruth_boxes not in result_dict:
raise ValueError('If show_groundtruth is enabled, result_dict must contain '
'groundtruth_boxes.')
logging.info('Creating detection visualizations.')
category_index = label_map_util.create_category_index(categories)
image = np.squeeze(result_dict[input_fields.original_image], axis=0)
if image.shape[2] == 1: # If one channel image, repeat in RGB.
image = np.tile(image, [1, 1, 3])
detection_boxes = result_dict[detection_fields.detection_boxes]
detection_scores = result_dict[detection_fields.detection_scores]
detection_classes = np.int32((result_dict[
detection_fields.detection_classes]))
detection_keypoints = result_dict.get(detection_fields.detection_keypoints)
detection_masks = result_dict.get(detection_fields.detection_masks)
detection_boundaries = result_dict.get(detection_fields.detection_boundaries)
# Plot groundtruth underneath detections
if show_groundtruth:
groundtruth_boxes = result_dict[input_fields.groundtruth_boxes]
groundtruth_keypoints = result_dict.get(input_fields.groundtruth_keypoints)
vis_utils.visualize_boxes_and_labels_on_image_array(
image=image,
boxes=groundtruth_boxes,
classes=None,
scores=None,
category_index=category_index,
keypoints=groundtruth_keypoints,
use_normalized_coordinates=False,
max_boxes_to_draw=None,
groundtruth_box_visualization_color=groundtruth_box_visualization_color)
vis_utils.visualize_boxes_and_labels_on_image_array(
image,
detection_boxes,
detection_classes,
detection_scores,
category_index,
instance_masks=detection_masks,
instance_boundaries=detection_boundaries,
keypoints=detection_keypoints,
use_normalized_coordinates=False,
max_boxes_to_draw=max_num_predictions,
min_score_thresh=min_score_thresh,
agnostic_mode=agnostic_mode,
skip_scores=skip_scores,
skip_labels=skip_labels)
if export_dir:
'''
if keep_image_id_for_visualization_export and result_dict[fields.
InputDataFields()
.key]:
export_path = os.path.join(export_dir, 'export-{}-{}.png'.format(
tag, result_dict[fields.InputDataFields().key]))
'''
'''
Modified key to filename
'''
if keep_image_id_for_visualization_export and result_dict[fields.
InputDataFields()
.key]:
# Debugging steps
#print(result_dict[fields.InputDataFields().key])
#print(type(export_dir))
export_path=os.path.join(export_dir,result_dict[fields.InputDataFields().key].decode("ASCII").split("/")[-1]+".png")
'''
export_path = os.path.join(export_dir, #result_dict[fields.InputDataFields().key].split("/")[-1])
'export-{}-{}.png'.format(
tag, result_dict[fields.InputDataFields().key]))
'''
else:
export_path = os.path.join(export_dir, 'export-{}.png'.format(tag))
print(export_path)
vis_utils.save_image_array_as_png(image, export_path)
summary = tf.Summary(value=[
tf.Summary.Value(
tag=tag,
image=tf.Summary.Image(
encoded_image_string=vis_utils.encode_image_array_as_png_str(
image)))
])
summary_writer = tf.summary.FileWriterCache.get(summary_dir)
summary_writer.add_summary(summary, global_step)
logging.info('Detection visualizations written to summary with tag %s.', tag)
def visualize_detection_results(result_dict,
tag,
global_step,
categories,
summary_dir='',
export_dir='',
agnostic_mode=False,
show_groundtruth=False,
min_score_thresh=.5,
max_num_predictions=20):
"""Visualizes detection results and writes visualizations to image summaries.
This function visualizes an image with its detected bounding boxes and writes
to image summaries which can be viewed on tensorboard. It optionally also
writes images to a directory. In the case of missing entry in the label map,
unknown class name in the visualization is shown as "N/A".
Args:
result_dict: a dictionary holding groundtruth and detection
data corresponding to each image being evaluated. The following keys
are required:
'original_image': a numpy array representing the image with shape
[1, height, width, 3]
'detection_boxes': a numpy array of shape [N, 4]
'detection_scores': a numpy array of shape [N]
'detection_classes': a numpy array of shape [N]
The following keys are optional:
'groundtruth_boxes': a numpy array of shape [N, 4]
'groundtruth_keypoints': a numpy array of shape [N, num_keypoints, 2]
Detections are assumed to be provided in decreasing order of score and for
display, and we assume that scores are probabilities between 0 and 1.
tag: tensorboard tag (string) to associate with image.
global_step: global step at which the visualization are generated.
categories: a list of dictionaries representing all possible categories.
Each dict in this list has the following keys:
'id': (required) an integer id uniquely identifying this category
'name': (required) string representing category name
e.g., 'cat', 'dog', 'pizza'
'supercategory': (optional) string representing the supercategory
e.g., 'animal', 'vehicle', 'food', etc
summary_dir: the output directory to which the image summaries are written.
export_dir: the output directory to which images are written. If this is
empty (default), then images are not exported.
agnostic_mode: boolean (default: False) controlling whether to evaluate in
class-agnostic mode or not.
show_groundtruth: boolean (default: False) controlling whether to show
groundtruth boxes in addition to detected boxes
min_score_thresh: minimum score threshold for a box to be visualized
max_num_predictions: maximum number of detections to visualize
Raises:
ValueError: if result_dict does not contain the expected keys (i.e.,
'original_image', 'detection_boxes', 'detection_scores',
'detection_classes')
"""
if not set([
'original_image', 'detection_boxes', 'detection_scores',
'detection_classes'
]).issubset(set(result_dict.keys())):
raise ValueError('result_dict does not contain all expected keys.')
if show_groundtruth and 'groundtruth_boxes' not in result_dict:
raise ValueError(
'If show_groundtruth is enabled, result_dict must contain '
'groundtruth_boxes.')
logging.info('Creating detection visualizations.')
category_index = label_map_util.create_category_index(categories)
image = np.squeeze(result_dict['original_image'], axis=0)
detection_boxes = result_dict['detection_boxes']
detection_scores = result_dict['detection_scores']
detection_classes = np.int32((result_dict['detection_classes']))
detection_keypoints = result_dict.get('detection_keypoints', None)
detection_masks = result_dict.get('detection_masks', None)
# Plot groundtruth underneath detections
if show_groundtruth:
groundtruth_boxes = result_dict['groundtruth_boxes']
groundtruth_keypoints = result_dict.get('groundtruth_keypoints', None)
vis_utils.visualize_boxes_and_labels_on_image_array(
image,
groundtruth_boxes,
None,
None,
category_index,
keypoints=groundtruth_keypoints,
use_normalized_coordinates=False,
max_boxes_to_draw=None)
vis_utils.visualize_boxes_and_labels_on_image_array(
image,
detection_boxes,
detection_classes,
detection_scores,
category_index,
instance_masks=detection_masks,
keypoints=detection_keypoints,
use_normalized_coordinates=False,
max_boxes_to_draw=max_num_predictions,
min_score_thresh=min_score_thresh,
agnostic_mode=agnostic_mode)
if export_dir:
export_path = os.path.join(export_dir, 'export-{}.png'.format(tag))
vis_utils.save_image_array_as_png(image, export_path)
summary = tf.Summary(value=[
tf.Summary.Value(
tag=tag,
image=tf.Summary.Image(
encoded_image_string=vis_utils.encode_image_array_as_png_str(
image)))
])
summary_writer = tf.summary.FileWriter(summary_dir)
summary_writer.add_summary(summary, global_step)
summary_writer.close()
logging.info('Detection visualizations written to summary with tag %s.',
tag)
def visualize_detection_results(result_dict,
tag,
global_step,
categories,
summary_dir='',
export_dir='',
agnostic_mode=False,
show_groundtruth=False,
groundtruth_box_visualization_color='black',
min_score_thresh=.5,
max_num_predictions=20,
skip_scores=False,
skip_labels=False,
keep_image_id_for_visualization_export=False):
"""Visualizes detection results and writes visualizations to image summaries.
This function visualizes an image with its detected bounding boxes and writes
to image summaries which can be viewed on tensorboard. It optionally also
writes images to a directory. In the case of missing entry in the label map,
unknown class name in the visualization is shown as "N/A".
Args:
result_dict: a dictionary holding groundtruth and detection
data corresponding to each image being evaluated. The following keys
are required:
'original_image': a numpy array representing the image with shape
[1, height, width, 3] or [1, height, width, 1]
'detection_boxes': a numpy array of shape [N, 4]
'detection_scores': a numpy array of shape [N]
'detection_classes': a numpy array of shape [N]
The following keys are optional:
'groundtruth_boxes': a numpy array of shape [N, 4]
'groundtruth_keypoints': a numpy array of shape [N, num_keypoints, 2]
Detections are assumed to be provided in decreasing order of score and for
display, and we assume that scores are probabilities between 0 and 1.
tag: tensorboard tag (string) to associate with image.
global_step: global step at which the visualization are generated.
categories: a list of dictionaries representing all possible categories.
Each dict in this list has the following keys:
'id': (required) an integer id uniquely identifying this category
'name': (required) string representing category name
e.g., 'cat', 'dog', 'pizza'
'supercategory': (optional) string representing the supercategory
e.g., 'animal', 'vehicle', 'food', etc
summary_dir: the output directory to which the image summaries are written.
export_dir: the output directory to which images are written. If this is
empty (default), then images are not exported.
agnostic_mode: boolean (default: False) controlling whether to evaluate in
class-agnostic mode or not.
show_groundtruth: boolean (default: False) controlling whether to show
groundtruth boxes in addition to detected boxes
groundtruth_box_visualization_color: box color for visualizing groundtruth
boxes
min_score_thresh: minimum score threshold for a box to be visualized
max_num_predictions: maximum number of detections to visualize
skip_scores: whether to skip score when drawing a single detection
skip_labels: whether to skip label when drawing a single detection
keep_image_id_for_visualization_export: whether to keep image identifier in
filename when exported to export_dir
Raises:
ValueError: if result_dict does not contain the expected keys (i.e.,
'original_image', 'detection_boxes', 'detection_scores',
'detection_classes')
"""
detection_fields = fields.DetectionResultFields
input_fields = fields.InputDataFields
if not set([
input_fields.original_image,
detection_fields.detection_boxes,
detection_fields.detection_scores,
detection_fields.detection_classes,
]).issubset(set(result_dict.keys())):
raise ValueError('result_dict does not contain all expected keys.')
if show_groundtruth and input_fields.groundtruth_boxes not in result_dict:
raise ValueError('If show_groundtruth is enabled, result_dict must contain '
'groundtruth_boxes.')
logging.info('Creating detection visualizations.')
category_index = label_map_util.create_category_index(categories)
image = np.squeeze(result_dict[input_fields.original_image], axis=0)
if image.shape[2] == 1: # If one channel image, repeat in RGB.
image = np.tile(image, [1, 1, 3])
detection_boxes = result_dict[detection_fields.detection_boxes]
detection_scores = result_dict[detection_fields.detection_scores]
detection_classes = np.int32((result_dict[
detection_fields.detection_classes]))
detection_keypoints = result_dict.get(detection_fields.detection_keypoints)
detection_masks = result_dict.get(detection_fields.detection_masks)
detection_boundaries = result_dict.get(detection_fields.detection_boundaries)
# Plot groundtruth underneath detections
if show_groundtruth:
groundtruth_boxes = result_dict[input_fields.groundtruth_boxes]
groundtruth_keypoints = result_dict.get(input_fields.groundtruth_keypoints)
vis_utils.visualize_boxes_and_labels_on_image_array(
image=image,
boxes=groundtruth_boxes,
classes=None,
scores=None,
category_index=category_index,
keypoints=groundtruth_keypoints,
use_normalized_coordinates=False,
max_boxes_to_draw=None,
groundtruth_box_visualization_color=groundtruth_box_visualization_color)
vis_utils.visualize_boxes_and_labels_on_image_array(
image,
detection_boxes,
detection_classes,
detection_scores,
category_index,
instance_masks=detection_masks,
instance_boundaries=detection_boundaries,
keypoints=detection_keypoints,
use_normalized_coordinates=False,
max_boxes_to_draw=max_num_predictions,
min_score_thresh=min_score_thresh,
agnostic_mode=agnostic_mode,
skip_scores=skip_scores,
skip_labels=skip_labels)
if export_dir:
if keep_image_id_for_visualization_export and result_dict[fields.
InputDataFields()
.key]:
export_path = os.path.join(export_dir, 'export-{}-{}.png'.format(
tag, result_dict[fields.InputDataFields().key]))
else:
export_path = os.path.join(export_dir, 'export-{}.png'.format(tag))
vis_utils.save_image_array_as_png(image, export_path)
summary = tf.Summary(value=[
tf.Summary.Value(
tag=tag,
image=tf.Summary.Image(
encoded_image_string=vis_utils.encode_image_array_as_png_str(
image)))
])
summary_writer = tf.summary.FileWriterCache.get(summary_dir)
summary_writer.add_summary(summary, global_step)
logging.info('Detection visualizations written to summary with tag %s.', tag)
