def save_images(self, directory: str,
pairs: List[Tuple[List[str], List[lt.LabeledTensor]]]):
filenames = list(itertools.chain(*[p[0] for p in pairs]))
image_lts = list(itertools.chain(*[p[1] for p in pairs]))
images = self.eval(image_lts)
path = os.path.join(os.environ['TEST_TMPDIR'], directory)
if not gfile.Exists(path):
gfile.MkDir(path)
for f, i in zip(filenames, images):
util.write_image(os.path.join(path, f), i)
def infer(
gitapp: controller.GetInputTargetAndPredictedParameters,
restore_directory: str,
output_directory: str,
extract_patch_size: int,
stitch_stride: int,
infer_size: int,
channel_whitelist: Optional[List[str]],
simplify_error_panels: bool,
):
"""Runs inference on an image.
Args:
gitapp: GetInputTargetAndPredictedParameters.
restore_directory: Where to restore the model from.
output_directory: Where to write the generated images.
extract_patch_size: The size of input to the model.
stitch_stride: The stride size when running model inference.
Equivalently, the output size of the model.
infer_size: The number of simultaneous inferences to perform in the
row and column dimensions.
For example, if this is 8, inference will be performed in 8 x 8 blocks
for a batch size of 64.
channel_whitelist: If provided, only images for the given channels will
be produced.
This can be used to create simpler error panels.
simplify_error_panels: Whether to create simplified error panels.
Raises:
ValueError: If
1) The DataParameters don't contain a ReadPNGsParameters.
2) The images must be larger than the input to the network.
3) The graph must not contain queues.
"""
rpp = gitapp.dp.io_parameters
if not isinstance(rpp, data_provider.ReadPNGsParameters):
raise ValueError(
'Data provider must contain a ReadPNGsParameter, but was: %r',
gitapp.dp)
original_crop_size = rpp.crop_size
image_num_rows, image_num_columns = util.image_size(rpp.directory)
logging.info('Uncropped image size is %d x %d', image_num_rows,
image_num_columns)
image_num_rows = min(image_num_rows, original_crop_size)
if image_num_rows < extract_patch_size:
raise ValueError(
'Image is too small for inference to be performed: %d vs %d',
image_num_rows, extract_patch_size)
image_num_columns = min(image_num_columns, original_crop_size)
if image_num_columns < extract_patch_size:
raise ValueError(
'Image is too small for inference to be performed: %d vs %d',
image_num_columns, extract_patch_size)
logging.info('After cropping, input image size is (%d, %d)', image_num_rows,
image_num_columns)
num_row_inferences = (image_num_rows - extract_patch_size) // (
stitch_stride * infer_size)
num_column_inferences = (image_num_columns - extract_patch_size) // (
stitch_stride * infer_size)
logging.info('Running %d x %d inferences', num_row_inferences,
num_column_inferences)
num_output_rows = (num_row_inferences * infer_size * stitch_stride)
num_output_columns = (num_column_inferences * infer_size * stitch_stride)
logging.info('Output image size is (%d, %d)', num_output_rows,
num_output_columns)
g = tf.Graph()
with g.as_default():
row_start = tf.placeholder(dtype=np.int32, shape=[])
column_start = tf.placeholder(dtype=np.int32, shape=[])
# Replace the parameters with a new set, which will cause the network to
# run inference in just a local region.
gitapp = gitapp._replace(
dp=gitapp.dp._replace(
io_parameters=rpp._replace(
row_start=row_start,
column_start=column_start,
crop_size=(infer_size - 1) * stitch_stride + extract_patch_size,
)))
visualization_lts = controller.setup_stitch(gitapp)
def get_statistics(tensor):
rc = lt.ReshapeCoder(list(tensor.axes.keys())[:-1], ['batch'])
return rc.decode(ops.distribution_statistics(rc.encode(tensor)))
visualize_input_lt = visualization_lts['input']
visualize_predict_input_lt = get_statistics(
visualization_lts['predict_input'])
visualize_target_lt = visualization_lts['target']
visualize_predict_target_lt = get_statistics(
visualization_lts['predict_target'])
input_lt = lt.LabeledTensor(
tf.placeholder(
dtype=np.float32,
shape=[
1, num_output_rows, num_output_columns,
len(gitapp.dp.input_z_values), 1, 2
]),
axes=[
'batch',
'row',
'column',
('z', gitapp.dp.input_z_values),
('channel', ['TRANSMISSION']),
('mask', [False, True]),
])
predict_input_lt = lt.LabeledTensor(
tf.placeholder(
dtype=np.float32,
shape=[
1,
num_output_rows,
num_output_columns,
len(gitapp.dp.input_z_values),
1,
len(visualize_predict_input_lt.axes['statistic']),
]),
axes=[
'batch',
'row',
'column',
('z', gitapp.dp.input_z_values),
('channel', ['TRANSMISSION']),
visualize_predict_input_lt.axes['statistic'],
])
input_error_panel_lt = visualize.error_panel_from_statistics(
input_lt, predict_input_lt, simplify_error_panels)
target_lt = lt.LabeledTensor(
tf.placeholder(
dtype=np.float32,
shape=[
1, num_output_rows, num_output_columns,
len(gitapp.dp.target_z_values),
len(gitapp.dp.target_channel_values) + 1, 2
]),
axes=[
'batch',
'row',
'column',
('z', gitapp.dp.target_z_values),
('channel', gitapp.dp.target_channel_values + ['NEURITE_CONFOCAL']),
('mask', [False, True]),
])
predict_target_lt = lt.LabeledTensor(
tf.placeholder(
dtype=np.float32,
shape=[
1,
num_output_rows,
num_output_columns,
len(gitapp.dp.target_z_values),
len(gitapp.dp.target_channel_values) + 1,
len(visualize_predict_target_lt.axes['statistic']),
]),
axes=[
'batch',
'row',
'column',
('z', gitapp.dp.target_z_values),
('channel', gitapp.dp.target_channel_values + ['NEURITE_CONFOCAL']),
visualize_predict_target_lt.axes['statistic'],
])
logging.info('input_lt: %r', input_lt)
logging.info('predict_input_lt: %r', predict_input_lt)
logging.info('target_lt: %r', target_lt)
logging.info('predict_target_lt: %r', predict_target_lt)
def select_channels(tensor):
if channel_whitelist is not None:
return lt.select(tensor, {'channel': channel_whitelist})
else:
return tensor
target_error_panel_lt = visualize.error_panel_from_statistics(
select_channels(target_lt), select_channels(predict_target_lt),
simplify_error_panels)
# There shouldn't be any queues in this configuration.
queue_runners = g.get_collection(tf.GraphKeys.QUEUE_RUNNERS)
if queue_runners:
raise ValueError('Graph must not have queues, but had: %r', queue_runners)
logging.info('Attempting to find restore checkpoint in %s',
restore_directory)
init_fn = util.restore_model(
restore_directory, restore_logits=True, restore_global_step=True)
with tf.Session() as sess:
logging.info('Generating images')
init_fn(sess)
input_rows = []
predict_input_rows = []
target_rows = []
predict_target_rows = []
for infer_row in range(num_row_inferences):
input_row = []
predict_input_row = []
target_row = []
predict_target_row = []
for infer_column in range(num_column_inferences):
rs = infer_row * infer_size * stitch_stride
cs = infer_column * infer_size * stitch_stride
logging.info('Running inference at offset: (%d, %d)', rs, cs)
[inpt, predict_input, target, predict_target] = sess.run(
[
visualize_input_lt,
visualize_predict_input_lt,
visualize_target_lt,
visualize_predict_target_lt,
],
feed_dict={
row_start: rs,
column_start: cs
})
input_row.append(inpt)
predict_input_row.append(predict_input)
target_row.append(target)
predict_target_row.append(predict_target)
input_rows.append(np.concatenate(input_row, axis=2))
predict_input_rows.append(np.concatenate(predict_input_row, axis=2))
target_rows.append(np.concatenate(target_row, axis=2))
predict_target_rows.append(np.concatenate(predict_target_row, axis=2))
logging.info('Stitching')
stitched_input = np.concatenate(input_rows, axis=1)
stitched_predict_input = np.concatenate(predict_input_rows, axis=1)
stitched_target = np.concatenate(target_rows, axis=1)
stitched_predict_target = np.concatenate(predict_target_rows, axis=1)
logging.info('Creating error panels')
import pickle
f = open('/home/ubuntu/resinfer.pk','wb')
#pickle.dump()
d = {'input_lt':stitched_input, 'predict_input_lt':stitched_predict_input,
'target_lt':stitched_target,'predict_target_lt':stitched_predict_target}
pickle.dump(d,f)
[input_error_panel, target_error_panel, global_step] = sess.run(
[
input_error_panel_lt, target_error_panel_lt,
tf.train.get_global_step()
],
feed_dict={
input_lt: stitched_input,
predict_input_lt: stitched_predict_input,
target_lt: stitched_target,
predict_target_lt: stitched_predict_target,
})
output_directory = os.path.join(output_directory, '%.8d' % global_step)
if not gfile.Exists(output_directory):
gfile.MakeDirs(output_directory)
util.write_image(
os.path.join(output_directory, 'input_error_panel.png'),
input_error_panel[0, :, :, :])
util.write_image(
os.path.join(output_directory, 'target_error_panel.png'),
target_error_panel[0, :, :, :])
logging.info('Done generating images')