def main(args, sess):
## Search for slides
slide_list = sorted(glob.glob(os.path.join(args.slide_dir, '*.svs')))
print('Found {} slides'.format(len(slide_list)))
if args.shuffle:
np.random.shuffle(slide_list)
model = load_model(args.snapshot)
## Loop over found slides:
for src in slide_list[:5]:
ramdisk_path = transfer_to_ramdisk(
src, args.ramdisk) # never use the original src
svs = Slide(slide_path=ramdisk_path,
preprocess_fn=lambda x: (x / 255.).astype(np.float32),
process_mag=args.mag,
process_size=args.input_dim,
oversample_factor=1.5)
svs.initialize_output(name='prob', dim=args.n_classes, mode='full')
svs.initialize_output(name='rgb', dim=3, mode='full')
n_tiles = len(svs.tile_list)
prefetch = min(512, n_tiles)
# Get tensors for image an index
img, idx = get_img_idx(svs, args.batch_size, prefetch)
yhat_op = model(img)
batches = 0
while True:
try:
batches += 1
yhat, img_, idx_ = sess.run([yhat_op, img, idx])
yhat = vect_to_tile(yhat, args.input_dim)
svs.place_batch(yhat, idx_, 'prob', mode='full')
svs.place_batch(img_, idx_, 'rgb', mode='full')
if batches % 50 == 0:
print('batch {:04d}'.format(batches))
except tf.errors.OutOfRangeError:
print('Done')
break
svs.make_outputs(reference='prob')
prob_img = svs.output_imgs['prob']
rgb_img = svs.output_imgs['rgb'] * 255
color_img = colorize(rgb_img, prob_img)
basename = os.path.basename(src).replace('.svs', '')
dst = os.path.join(args.save_dir, '{}.npy'.format(basename))
np.save(dst, (prob_img * 255).astype(np.uint8))
dst = os.path.join(args.save_dir, '{}.jpg'.format(basename))
cv2.imwrite(dst, rgb_img[:, :, ::-1])
dst = os.path.join(args.save_dir, '{}_c.jpg'.format(basename))
cv2.imwrite(dst, color_img[:, :, ::-1])
os.remove(ramdisk_path)
def process_slide(slide_path, fg_path, model, sess, out_dir, process_mag,
process_size, oversample, batch_size, n_classes):
""" Process a slide
Args:
slide_path: str
absolute or relative path to svs formatted slide
fb_path: str
absolute or relative path to foreground png
model: tfmodels.SegmentationBasemodel object
model definition to use. Weights must be restored first,
i.e. call model.restore() before passing model
sess: tf.Session
out_dir: str
path to use for output
process_mag: int
Usually one of: 5, 10, 20, 40.
Other values may work but have not been tested
process_size: int
The input size required by model.
oversample: float. Usually in [1., 2.]
How much to oversample between tiles. Larger values
will increase processing time.
batch_size: int
The batch size for inference. If the batch size is too
large given the model and process_size, then OOM errors
will be raised
n_classes: int
The number of classes output by model.
i.e. shape(model.yhat) = (batch, h, w, n_classes)
"""
print('Working {}'.format(slide_path))
# print('Working {}'.format(fg_path))
# fgimg = cv2.imread(fg_path, 0)
# fgimg = cv2.morphologyEx(fgimg, cv2.MORPH_CLOSE,
# cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (7,7)))
svs = Slide(
slide_path=slide_path,
background_speed='all',
# background_image = fgimg,
preprocess_fn=preprocess_fn,
normalize_fn=lambda x: x,
process_mag=process_mag,
process_size=process_size,
oversample=oversample,
verbose=False,
)
svs.initialize_output('prob', dim=n_classes)
svs.initialize_output('rgb', dim=3)
PREFETCH = min(len(svs.place_list), 256)
def wrapped_fn(idx):
try:
coords = svs.tile_list[idx]
img = svs._read_tile(coords)
return img, idx
except:
return 0
def read_region_at_index(idx):
return tf.py_func(func=wrapped_fn,
inp=[idx],
Tout=[tf.float32, tf.int64],
stateful=False)
ds = tf.data.Dataset.from_generator(generator=svs.generate_index,
output_types=tf.int64)
ds = ds.map(read_region_at_index, num_parallel_calls=6)
ds = ds.prefetch(PREFETCH)
ds = ds.batch(batch_size)
iterator = ds.make_one_shot_iterator()
img, idx = iterator.get_next()
print('Processing {} tiles'.format(len(svs.tile_list)))
tstart = time.time()
n_processed = 0
while True:
try:
tile, idx_ = sess.run([img, idx])
output = model.inference(tile)
svs.place_batch(output, idx_, 'prob')
svs.place_batch(tile, idx_, 'rgb')
n_processed += BATCH_SIZE
if n_processed % PRINT_ITER == 0:
print('[{:06d}] elapsed time [{:3.3f}]'.format(
n_processed,
time.time() - tstart))
except tf.errors.OutOfRangeError:
print('Finished')
dt = time.time() - tstart
spt = dt / float(len(svs.tile_list))
fps = len(svs.tile_list) / dt
print('\nFinished. {:2.2f}min {:3.3f}s/tile\n'.format(
dt / 60., spt))
print('\t {:3.3f} fps\n'.format(fps))
svs.make_outputs()
prob_img = prob_output(svs)
rgb_img = rgb_output(svs)
break
except Exception as e:
print('Caught exception at tiles {}'.format(idx_))
# print(e.__doc__)
# print(e.message)
prob_img = None
rgb_img = None
break
svs.close()
return prob_img, rgb_img, fps
def main(args):
## Search for slides
# slide_list = sorted(glob.glob(os.path.join(args.slide_dir, '*.svs')))
slide_list = read_list(args.slide_list)
print('Found {} slides'.format(len(slide_list)))
if args.shuffle:
np.random.shuffle(slide_list)
encoder_args = get_encoder_args(args.encoder)
model = ClassifierEager(encoder_args=encoder_args,
deep_classifier=True,
n_classes=args.n_classes)
fake_data = tf.constant(
np.zeros((1, args.input_dim, args.input_dim, 3), dtype=np.float32))
yhat_ = model(fake_data)
model.load_weights(args.snapshot)
model.summary()
if not os.path.exists(args.save_dir):
# shutil.rmtree(args.save_dir)
os.makedirs(args.save_dir)
## Loop over found slides:
for src in slide_list:
basename = os.path.basename(src).replace('.svs', '')
dst = os.path.join(args.save_dir, '{}.npy'.format(basename))
if os.path.exists(dst):
print('{} exists. Skipping'.format(dst))
continue
ramdisk_path = transfer_to_ramdisk(
src, args.ramdisk) # never use the original src
try:
fgpth = os.path.join(args.fgdir, '{}_fg.png'.format(basename))
fgimg = cv2.imread(fgpth, 0)
fgimg = fill_fg(fgimg)
svs = Slide(slide_path=ramdisk_path,
preprocess_fn=lambda x: (x / 255.).astype(np.float32),
normalize_fn=lambda x: x,
background_speed='image',
background_image=fgimg,
process_mag=args.mag,
process_size=args.input_dim,
oversample_factor=1.1)
svs.initialize_output(name='prob', dim=args.n_classes, mode='full')
svs.initialize_output(name='rgb', dim=3, mode='full')
n_tiles = len(svs.tile_list)
prefetch = min(512, n_tiles)
# Get tensors for image an index
iterator = get_img_idx(svs, args.batch_size, prefetch)
batches = 0
for img_, idx_ in iterator:
batches += 1
yhat = model(img_, training=False)
yhat = yhat.numpy()
idx_ = idx_.numpy()
img_ = img_.numpy()
yhat = vect_to_tile(yhat, args.input_dim)
svs.place_batch(yhat, idx_, 'prob', mode='full')
svs.place_batch(img_, idx_, 'rgb', mode='full')
if batches % 50 == 0:
print('\tbatch {:04d}'.format(batches))
svs.make_outputs(reference='prob')
prob_img = svs.output_imgs['prob']
rgb_img = svs.output_imgs['rgb'] * 255
color_img = colorize(rgb_img, prob_img)
dst = os.path.join(args.save_dir, '{}.npy'.format(basename))
np.save(dst, (prob_img * 255).astype(np.uint8))
dst = os.path.join(args.save_dir, '{}.jpg'.format(basename))
cv2.imwrite(dst, rgb_img[:, :, ::-1])
dst = os.path.join(args.save_dir, '{}_c.jpg'.format(basename))
cv2.imwrite(dst, color_img[:, :, ::-1])
except Exception as e:
print(e)
finally:
try:
print('Closing SVS')
svs.close()
except:
print('No SVS to close')
os.remove(ramdisk_path)
def main(args):
## Search for slides
slide_list = sorted(glob.glob(os.path.join(args.slide_dir, '*.svs')))
print('Found {} slides'.format(len(slide_list)))
if args.shuffle:
np.random.shuffle(slide_list)
model = ClassifierEager(encoder_args=encoder_args,
n_classes=args.n_classes)
xdummy = tf.constant(
np.zeros((args.batch_size, args.input_dim, args.input_dim, 3),
dtype=np.float32))
yhat_op = model(xdummy, verbose=True)
model.load_weights(args.snapshot, by_name=True)
# model = tf.keras.models.load_model(args.snapshot, compile=False)
model.summary()
## Loop over found slides:
for src in slide_list:
basename = os.path.basename(src).replace('.svs', '')
dst = os.path.join(args.save_dir, '{}.npy'.format(basename))
if os.path.exists(dst):
print('{} exists. continuing'.format(dst))
continue
fgpth = os.path.join(args.fgdir, '{}_fg.png'.format(basename))
if os.path.exists(fgpth):
print('fg image found:', fgpth)
fgimg = cv2.imread(fgpth, 0)
speed = 'image'
else:
speed = 'fast'
fgimg = None
ramdisk_path = transfer_to_ramdisk(
src, args.ramdisk) # never use the original src
try:
svs = Slide(slide_path=ramdisk_path,
preprocess_fn=lambda x:
(reinhard(x) / 255.).astype(np.float32),
background_speed=speed,
background_image=fgimg,
process_mag=args.mag,
process_size=args.input_dim,
oversample_factor=1.75)
svs.initialize_output(name='prob', dim=args.n_classes, mode='full')
svs.initialize_output(name='rgb', dim=3, mode='full')
n_tiles = len(svs.tile_list)
prefetch = min(128, n_tiles)
print('Tiles:', n_tiles)
# Get tensors for image an index
# img, idx = get_img_idx(svs, args.batch_size, prefetch)
iterator = get_iterator(svs, args.batch_size, prefetch)
batches = 0
for img_, idx_ in iterator:
batches += 1
# img_, idx_ = next(iterator)
yhat = model(img_, training=False)
yhat = yhat.numpy()
idx_ = idx_.numpy()
yhat = vect_to_tile(yhat, args.input_dim)
svs.place_batch(yhat, idx_, 'prob', mode='full')
svs.place_batch(img_.numpy(), idx_, 'rgb', mode='full')
if batches % 50 == 0:
print('batch {:04d}'.format(batches))
print('Making outputs')
svs.make_outputs(reference='prob')
prob_img = svs.output_imgs['prob']
print('prob img', prob_img.shape)
rgb_img = svs.output_imgs['rgb'] * 255
print('rgb img', rgb_img.shape)
color_img = colorize(rgb_img, prob_img)
print('color img', color_img.shape)
dst = os.path.join(args.save_dir, '{}.npy'.format(basename))
np.save(dst, (prob_img * 255).astype(np.uint8))
dst = os.path.join(args.save_dir, '{}.jpg'.format(basename))
cv2.imwrite(dst, rgb_img[:, :, ::-1])
dst = os.path.join(args.save_dir, '{}_c.jpg'.format(basename))
cv2.imwrite(dst, color_img[:, :, ::-1])
svs.close()
svs = []
except Exception as e:
print(e)
finally:
print('Removing {}'.format(ramdisk_path))
os.remove(ramdisk_path)