def main(args):
## Read in the slides
slides = []
with open(args.slides, 'r') as f:
for line in f:
lstrip = line.strip()
if os.path.exists(lstrip):
slides.append(lstrip)
else:
print(lstrip)
print('Working with {} slides'.format(len(slides)))
## Initialize the dataset; store the metadata file
with open(args.meta_file, 'r') as f:
lines = [line for line in f]
## Read in the labels
attrs = ['case_id', 'stage_str', 'stage_code']
labels = read_labels(args.labels, attrs)
print('Working with labels:', len(labels))
## Create the dataset
meta_string = ''.join(lines)
if not os.path.exists(args.data_h5):
create_dataset(args.data_h5, meta_string)
else:
print('HDF5 {} already exists'.format(args.data_h5))
## Load the dataset
mildataset = MILDataset(args.data_h5, meta_string)
# slides = [s for s in slides if s not in mildataset.data_group_names]
for i, src in enumerate(slides):
print('\n[\t{}/{}\t]'.format(i, len(slides)))
print('File {:04d} {} --> {}'.format(i, src, args.ramdisk))
basename = os.path.splitext(os.path.basename(src))[0]
try:
lab = labels[basename]
print(basename, lab)
if lab[-1] > 1:
print('Skipping unused labels')
continue
except Exception as e:
print('basename {} no labels.'.format(basename))
traceback.print_tb(e.__traceback__)
rdsrc = cpramdisk(src, args.ramdisk)
try:
slide = Slide(rdsrc, args)
tile_stack = stack_tiles(slide, args)
mildataset.new_dataset(basename, tile_stack, attrs, lab)
except Exception as e:
print('Breaking')
traceback.print_tb(e.__traceback__)
finally:
print('Removing {}'.format(rdsrc))
os.remove(rdsrc)
def main(args):
with open(args.lst, 'r') as f:
srclist = [x.strip() for x in f]
for src in srclist:
dst = repext(src, args.suffix)
if os.path.exists(dst):
print('Exists', src, '-->', dst)
continue
# Loading data from ramdisk incurs a one-time copy cost
rdsrc = cpramdisk(src, args.ramdisk)
print('File:', rdsrc)
try:
slide = Slide(src, args)
slide.initialize_output('wsi',
3,
mode='full',
compute_fn=compute_fn)
ret = slide.compute('wsi', args)
print('Saving {} --> {}'.format(ret.shape, dst))
cv2.imwrite(dst, ret)
except Exception as e:
traceback.print_tb(e.__traceback__)
finally:
print('Removing {}'.format(rdsrc))
os.remove(rdsrc)
def main(args):
# Define a compute_fn that should do three things:
# 1. define an iterator over the slide's tiles
# 2. compute an output with given model parameter
# 3.
if args.iter_type == 'python':
def compute_fn(slide, args, model=None):
print('Slide with {}'.format(len(slide.tile_list)))
it_factory = PythonIterator(slide, args)
for k, (img, idx) in enumerate(it_factory.yield_batch()):
prob = model(img)
if k % 50 == 0:
print('Batch #{:04d} idx:{} img:{} prob:{}'.format(
k, idx.shape, img.shape, prob.shape))
slide.place_batch(prob, idx, 'prob', mode='tile')
ret = slide.output_imgs['prob']
return ret
# Tensorflow multithreaded queue-based iterator (in eager mode)
elif args.iter_type == 'tf':
def compute_fn(slide, args, model=None):
assert tf.executing_eagerly()
print('Slide with {}'.format(len(slide.tile_list)))
# In eager mode, we return a tf.contrib.eager.Iterator
eager_iterator = TensorflowIterator(slide, args).make_iterator()
# The iterator can be used directly. Ququeing and multithreading
# are handled in the backend by the tf.data.Dataset ops
features, indices = [], []
for k, (img, idx) in enumerate(eager_iterator):
# img = tf.expand_dims(img, axis=0)
features.append(
model.encode_bag(img, training=False, return_z=True))
indices.append(idx.numpy())
img, idx = img.numpy(), idx.numpy()
if k % 50 == 0:
print('Batch #{:04d}\t{}'.format(k, img.shape))
features = tf.concat(features, axis=0)
z_att, att = model.mil_attention(features,
training=False,
return_raw_att=True)
att = np.squeeze(att)
indices = np.concatenate(indices)
slide.place_batch(att, indices, 'att', mode='tile')
ret = slide.output_imgs['att']
return ret
# Set up the model first
encoder_args = get_encoder_args(args.encoder)
model = MilkEager(encoder_args=encoder_args,
mil_type=args.mil,
deep_classifier=args.deep_classifier,
batch_size=args.batchsize,
temperature=args.temperature,
heads=args.heads)
x = tf.zeros((1, 1, args.process_size, args.process_size, 3))
_ = model(x, verbose=True, head='all', training=True)
model.load_weights(args.snapshot, by_name=True)
# keras Model subclass
model.summary()
# Read list of inputs
with open(args.slides, 'r') as f:
slides = [x.strip() for x in f]
# Loop over slides
for src in slides:
# Dirty substitution of the file extension give us the
# destination. Do this first so we can just skip the slide
# if this destination already exists.
# Set the --suffix option to reflect the model / type of processed output
dst = repext(src, args.suffix)
# Loading data from ramdisk incurs a one-time copy cost
rdsrc = cpramdisk(src, args.ramdisk)
print('File:', rdsrc)
# Wrapped inside of a try-except-finally.
# We want to make sure the slide gets cleaned from
# memory in case there's an error or stop signal in the
# middle of processing.
try:
# Initialze the side from our temporary path, with
# the arguments passed in from command-line.
# This returns an svsutils.Slide object
slide = Slide(rdsrc, args)
# This step will eventually be included in slide creation
# with some default compute_fn's provided by svsutils
# For now, do it case-by-case, and use the compute_fn
# that we defined just above.
slide.initialize_output('att',
args.n_classes,
mode='tile',
compute_fn=compute_fn)
# Call the compute function to compute this output.
# Again, this may change to something like...
# slide.compute_all
# which would loop over all the defined output types.
ret = slide.compute('att', args, model=model)
print('{} --> {}'.format(ret.shape, dst))
np.save(dst, ret[:, :, ::-1])
except Exception as e:
print(e)
traceback.print_tb(e.__traceback__)
finally:
print('Removing {}'.format(rdsrc))
os.remove(rdsrc)
def main(args):
# Define a compute_fn that should do three things:
# 1. define an iterator over the slide's tiles
# 2. compute an output with a given model / arguments
# 3. return a reconstructed slide
def compute_fn(slide, args, model=None, n_dropout=10 ):
assert tf.executing_eagerly()
print('Slide with {}'.format(len(slide.tile_list)))
# In eager mode, we return a tf.contrib.eager.Iterator
eager_iterator = TensorflowIterator(slide, args).make_iterator()
# The iterator can be used directly. Ququeing and multithreading
# are handled in the backend by the tf.data.Dataset ops
features, indices = [], []
for k, (img, idx) in enumerate(eager_iterator):
# img = tf.expand_dims(img, axis=0)
features.append( model.encode_bag(img, training=False, return_z=True) )
indices.append(idx.numpy())
img, idx = img.numpy(), idx.numpy()
if k % 50 == 0:
print('Batch #{:04d}\t{}'.format(k, img.shape))
features = tf.concat(features, axis=0)
## Sample-dropout
# features = features.numpy()
# print(features.shape)
# n_instances = features.shape[0]
# att = np.zeros(n_instances)
# n_choice = int(n_instances * 0.7)
# all_heads = list(range(args.heads))
# for j in range(n_dropout):
# idx = np.random.choice(range(n_instances), n_choice, replace=False)
# print(idx)
# fdrop = features[idx, :]
z_att, att = model.mil_attention(features,
training=False,
return_raw_att=True)
# att[idx] += np.squeeze(attdrop)
yhat_multihead = model.apply_classifier(z_att, heads=all_heads,
training=False)
print('yhat mean {}'.format(np.mean(yhat_multihead, axis=0)))
indices = np.concatenate(indices)
att = np.squeeze(att)
slide.place_batch(att, indices, 'att', mode='tile')
ret = slide.output_imgs['att']
print('Got attention image: {}'.format(ret.shape))
return ret, features.numpy()
## Begin main script:
# Set up the model first
encoder_args = get_encoder_args(args.encoder)
model = MilkEager(encoder_args=encoder_args,
mil_type=args.mil,
deep_classifier=args.deep_classifier,
batch_size=args.batchsize,
temperature=args.temperature,
heads = args.heads)
x = tf.zeros((1, 1, args.process_size,
args.process_size, 3))
all_heads = [0,1,2,3,4,5,6,7,8,9]
_ = model(x, verbose=True, heads=all_heads, training=True)
model.load_weights(args.snapshot, by_name=True)
# keras Model subclass
model.summary()
# Read list of inputs
with open(args.slides, 'r') as f:
slides = [x.strip() for x in f]
# Loop over slides
for src in slides:
# Dirty substitution of the file extension give us the
# destination. Do this first so we can just skip the slide
# if this destination already exists.
# Set the --suffix option to reflect the model / type of processed output
dst = repext(src, args.suffix)
featdst = repext(src, args.suffix+'.feat.npy')
# Loading data from ramdisk incurs a one-time copy cost
rdsrc = cpramdisk(src, args.ramdisk)
print('\n\nFile:', rdsrc)
# Wrapped inside of a try-except-finally.
# We want to make sure the slide gets cleaned from
# memory in case there's an error or stop signal in the
# middle of processing.
try:
# Initialze the side from our temporary path, with
# the arguments passed in from command-line.
# This returns an svsutils.Slide object
slide = Slide(rdsrc, args)
# This step will eventually be included in slide creation
# with some default compute_fn's provided by svsutils
# For now, do it case-by-case, and use the compute_fn
# that we defined just above.
slide.initialize_output('att', args.n_classes, mode='tile',
compute_fn=compute_fn)
# Call the compute function to compute this output.
# Again, this may change to something like...
# slide.compute_all
# which would loop over all the defined output types.
ret, features = slide.compute('att', args, model=model)
print('{} --> {}'.format(ret.shape, dst))
print('{} --> {}'.format(features.shape, featdst))
np.save(dst, ret)
np.save(featdst, features)
except Exception as e:
print(e)
traceback.print_tb(e.__traceback__)
finally:
print('Removing {}'.format(rdsrc))
os.remove(rdsrc)
def main(args, sess):
# Define a compute_fn that should do three things:
# 1. define an iterator over the slide's tiles
# 2. compute an output with given model parameter
# 3. asseble / gather the output
#
# compute_fn - function can define part of a computation
# graph in eager mode -- possibly in graph mode.
# We should completely reset the graph each call then
# I still don't know how nodes are actually represented in memory
# or if keeping them around has a real cost.
def compute_fn(slide, args, sess=None):
# assert tf.executing_eagerly()
print('\n\nSlide with {}'.format(len(slide.tile_list)))
# I'm not sure if spinning up new ops every time is bad.
# In this example the iterator is separate from the
# infernce function, it can also be set up with the two
# connected to skip the feed_dict
tf_iterator = TensorflowIterator(slide, args).make_iterator()
img_op, idx_op = tf_iterator.get_next()
# prob_op = model(img_op)
# sess.run(tf.global_variables_initializer())
# The iterator can be used directly. Ququeing and multithreading
# are handled in the backend by the tf.data.Dataset ops
# for k, (img, idx) in enumerate(eager_iterator):
k, nk = 0, 0
while True:
try:
img, idx = sess.run([
img_op,
idx_op,
])
prob = model.inference(img)
nk += img.shape[0]
slide.place_batch(prob, idx, 'prob', mode='full', clobber=True)
k += 1
if k % 50 == 0:
prstr = 'Batch #{:04d} idx:{} img:{} ({:2.2f}-{:2.2f}) prob:{} T {} \
'.format(k, idx.shape, img.shape, img.min(), img.max(), prob.shape,
nk)
print(prstr)
if args.verbose:
print('More info: ')
print('img: ', img.dtype, img.min(), img.max(),
img.mean())
pmax = np.argmax(prob, axis=-1).ravel()
for u in range(args.n_classes):
count_u = (pmax == u).sum()
print('- class {:02d} : {}'.format(u, count_u))
except tf.errors.OutOfRangeError:
print('Finished.')
print('Total: {}'.format(nk))
break
except Exception as e:
print(e)
traceback.print_tb(e.__traceback__)
break
# We've exited the loop. Clean up the iterator
del tf_iterator, idx_op, img_op
# slide.make_outputs()
slide.make_outputs()
ret = slide.output_imgs['prob']
return ret
# Set up the model first
model = gg.get_model(args.model, sess, args.process_size, args.n_classes)
# NOTE big time wasted because you have to initialize,
# THEN run the restore op to replace the already-created weights
sess.run(tf.global_variables_initializer())
model.restore(args.snapshot)
# Read list of inputs
with open(args.slides, 'r') as f:
slides = [x.strip() for x in f]
# Loop over slides; Record times
nslides = len(slides)
successes, ntiles, total_time, fpss = [], [], [], []
for i, src in enumerate(slides):
# Dirty substitution of the file extension give us the
# destination. Do this first so we can just skip the slide
# if this destination already exists.
# Set the --suffix option to reflect the model / type of processed output
dst = repext(src, args.suffix)
if os.path.exists(dst):
print('{} Exists.'.format(dst))
continue
# Loading data from ramdisk incurs a one-time copy cost
rdsrc = cpramdisk(src, args.ramdisk)
# Wrapped inside of a try-except-finally.
# We want to make sure the slide gets cleaned from
# memory in case there's an error or stop signal in the
# middle of processing.
try:
# Initialze the side from our temporary path, with
# the arguments passed in from command-line.
# This returns an svsutils.Slide object
print('\n\n-------------------------------')
print('File:', rdsrc, '{:04d} / {:04d}'.format(i, nslides))
t0 = time.time()
slide = Slide(rdsrc, args)
# This step will eventually be included in slide creation
# with some default compute_fn's provided by svsutils
# For now, do it case-by-case, and use the compute_fn
# that we defined just above.
# TODO pull the expected output size from the model.. ?
# support common model types - keras, tfmodels, tfhub..
slide.initialize_output('prob',
args.n_classes,
mode='full',
compute_fn=compute_fn)
# Call the compute function to compute this output.
# Again, this may change to something like...
# slide.compute_all
# which would loop over all the defined output types.
ret = slide.compute('prob', args, sess=sess)
print('{} --> {}'.format(ret.shape, dst))
ret = (ret * 255).astype(np.uint8)
np.save(dst, ret)
# If it finishes, record some stats
tend = time.time()
deltat = tend - t0
fps = len(slide.tile_list) / float(deltat)
successes.append(rdsrc)
ntiles.append(len(slide.tile_list))
total_time.append(deltat)
fpss.append(fps)
except Exception as e:
print(e)
traceback.print_tb(e.__traceback__)
finally:
print('Removing {}'.format(rdsrc))
os.remove(rdsrc)
try:
print('Cleaning slide object')
slide.close()
del slide
except:
print('No slide object not found to clean up ?')
write_times(args.timefile, successes, ntiles, total_time, fpss)
def main(args, sess):
# Define a compute_fn that should do three things:
# 1. define an iterator over the slide's tiles
# 2. compute an output with given model parameter
# 3.
# def compute_fn(slide, args, model=None):
# print('Slide with {}'.format(len(slide.tile_list)))
# it_factory = PythonIterator(slide, args)
# for k, (img, idx) in enumerate(it_factory.yield_batch()):
# prob = model.predict_on_batch(img)
# if k % 50 == 0:
# print('Batch #{:04d} idx:{} img:{} prob:{} \
# '.format(k, idx.shape, img.shape, prob.shape))
# slide.place_batch(prob, idx, 'prob', mode='tile')
# ret = slide.output_imgs['prob']
# return ret
# Tensorflow multithreaded queue-based iterator (in eager mode)
# elif args.iter_type == 'tf':
def compute_fn(slide, args, sess=None, img_pl=None, prob_op=None):
# assert tf.executing_eagerly()
print('\n\nSlide with {}'.format(len(slide.tile_list)))
# I'm not sure if spinning up new ops every time is bad.
tf_iterator = TensorflowIterator(slide, args).make_iterator()
img_op, idx_op = tf_iterator.get_next()
# prob_op = model(img_op)
# sess.run(tf.global_variables_initializer())
# The iterator can be used directly. Ququeing and multithreading
# are handled in the backend by the tf.data.Dataset ops
# for k, (img, idx) in enumerate(eager_iterator):
k, nk = 0, 0
while True:
try:
img, idx = sess.run([
img_op,
idx_op,
])
prob = sess.run(prob_op, {img_pl: img})
nk += img.shape[0]
if k % 50 == 0:
print('Batch #{:04d} idx:{} img:{} ({}) prob:{} T {} \
'.format(k, idx.shape, img.max(), img.shape, prob.shape, nk))
slide.place_batch(prob, idx, 'prob', mode='tile')
k += 1
except tf.errors.OutOfRangeError:
print('Finished.')
print('Total: {}'.format(nk))
break
finally:
ret = slide.output_imgs['prob']
return ret
# Set up the model first
# Set up a placeholder for the input
img_pl = tf.placeholder(tf.float32,
(None, args.process_size, args.process_size, 3))
model = load_model(args.snapshot)
prob_op = model(img_pl)
sess.run(tf.global_variables_initializer())
# Read list of inputs
with open(args.slides, 'r') as f:
slides = [x.strip() for x in f]
# Loop over slides
for src in slides:
# Dirty substitution of the file extension give us the
# destination. Do this first so we can just skip the slide
# if this destination already exists.
# Set the --suffix option to reflect the model / type of processed output
dst = repext(src, args.suffix)
# Loading data from ramdisk incurs a one-time copy cost
rdsrc = cpramdisk(src, args.ramdisk)
print('File:', rdsrc)
# Wrapped inside of a try-except-finally.
# We want to make sure the slide gets cleaned from
# memory in case there's an error or stop signal in the
# middle of processing.
try:
# Initialze the side from our temporary path, with
# the arguments passed in from command-line.
# This returns an svsutils.Slide object
print('\n\n-------------------------------')
slide = Slide(rdsrc, args)
# This step will eventually be included in slide creation
# with some default compute_fn's provided by svsutils
# For now, do it case-by-case, and use the compute_fn
# that we defined just above.
slide.initialize_output('prob',
4,
mode='tile',
compute_fn=compute_fn)
# Call the compute function to compute this output.
# Again, this may change to something like...
# slide.compute_all
# which would loop over all the defined output types.
ret = slide.compute('prob',
args,
sess=sess,
img_pl=img_pl,
prob_op=prob_op)
print('{} --> {}'.format(ret.shape, dst))
np.save(dst, ret)
except Exception as e:
print(e)
traceback.print_tb(e.__traceback__)
finally:
print('Removing {}'.format(rdsrc))
os.remove(rdsrc)