def test_load_volume():
path = "../datasets/original/train/ct/volume-0.nii"
vol_np = utils.load_volume(path)
# Type
msg = "Problem in utils.load_volume: Return type is {} and should be {}."
assert isinstance(vol_np, np.ndarray), msg.format(type(vol_np), np.ndarray)
def view_volume(self, idx, focus):
"""
Function to view one or multiple volumes simultaniously.
Arguments
--------
idx : int
Index of volume to view. Assumes there exists
"""
## Get volumes list based on path and index.
assert isinstance(idx, int), "idx must be an integer."
assert focus in self._focus_options, f"focus must be among: {self._focus_options}."
paths = self.get_paths(idx, focus)
volslist = [load_volume(p) for p in paths.values()]
names = list(paths.keys())
self._remove_keymap_conflicts({'j', 'k', 's'})
fig, ax = plt.subplots(ncols=len(volslist))
for i in range(len(volslist)):
print(volslist[i].shape)
ax[i].volume = volslist[i]
ax[i].index = volslist[i].shape[0] // 2
ax[i].imshow(volslist[i][ax[i].index], cmap='magma')
ax[i].set_title(names[i])
fig.canvas.mpl_connect('key_press_event', self._process_key)
plt.subplots_adjust(hspace=0.1, wspace=0.1)
plt.show()
def main():
args = parse_args()
vol = load_volume(args.input, stop=args.depth, ext='.bmp')
with h5py.File('downsampled_histogram.h5', 'r') as f:
hist = f['hist'][:]
hist = np.cumsum(hist)
vol = np.floor(255 * hist[vol])
vol[vol > 255] = 255
vol[vol < 0] = 0
vol = vol.astype(np.uint8)
if not os.path.isdir(args.output):
os.makedirs(args.output)
sums, counts = summate(integral_image(vol), np.asarray(args.window))
for t in np.arange(0, 1, 0.01):
seg = threshold_bradley_nd(vol,
t=t,
s=np.asarray(args.window),
sums=sums,
counts=counts)
dirname = os.path.join(args.output, '{0:.2f}'.format(t))
save_imgs(seg * 255, dirname)
def test_store():
path1 = "../datasets/preprocessed_2d/train/slices/slice_00001.npy"
path2 = "../datasets/preprocessed_2d/train/slices/slice_00002.npy"
slice1 = torch.tensor(np.load(path1)).unsqueeze(dim=0)
slice2 = torch.tensor(np.load(path2)).unsqueeze(dim=0)
batch1 = torch.cat([slice1, slice2], dim=0)
path1 = "../datasets/original/train/ct/volume-0.nii"
path2 = "../datasets/original/train/ct/volume-1.nii"
vol1 = torch.tensor(utils.load_volume(path1))[None, 0:20]
vol2 = torch.tensor(utils.load_volume(path2))[None, 0:20]
batch2 = torch.cat([vol1, vol2], dim=0)
dst = "deleteme/"
if not os.path.exists(dst):
os.mkdir(dst)
utils.store(batch1, dst, format='npy')
utils.store(batch1, dst, format='nii')
utils.store(batch2, dst, format='npy')
utils.store(batch2, dst, format='nii')
shutil.rmtree(dst)
def main():
args = parse_args()
start = time.time()
print("Loading image volume")
vol = load_volume(args.input)
if args.show:
plt.imshow(vol[0], cmap='Greys_r')
plt.show()
print("Prepping threshold subvolume shape")
if len(args.shape) < len(vol.shape):
shape = list(vol.shape[:len(vol.shape) - len(args.shape)])
shape.extend(args.shape)
else:
shape = args.shape
if len(args.step) < len(shape):
step = list(vol.shape[:len(vol.shape) - len(args.step)])
step.extend(args.step)
else:
step = args.step
print("Thresholding subvolumes")
step = args.step
thresh = np.zeros(vol.shape)
for i in range(0, vol.shape[0], step[0] if step else vol.shape[0]):
endi = i + shape[0] if i + shape[0] < vol.shape[0] else vol.shape[0]
for j in range(0, vol.shape[1], step[1] if step else vol.shape[1]):
endj = j + shape[1] if j + shape[1] < vol.shape[1] else vol.shape[1]
for k in range(0, vol.shape[2], step[2] if step else vol.shape[2]):
endk = k + shape[2] if k + shape[2] < vol.shape[
2] else vol.shape[2]
subvol = np.copy(vol[i:endi, j:endj, k:endk])
subvol = threshold_bradley_nd(subvol,
s=(4, shape[1], shape[2]),
t=args.threshold)
subvol = np.abs(1 - subvol) if np.max(subvol) > 0 else subvol
subvol = binary_opening(subvol)
subvol = binary_fill_holes(subvol)
subvol[subvol > 0] = 1
thresh[i:endi, j:endj, k:endk] += subvol
if args.show:
plt.imshow(thresh[0], cmap='Greys_r')
plt.show()
thresh[thresh > 0] = 255
print("Saving segmentation")
save_imgs(thresh, args.output)
print("Running Time: {}s".format(time.time() - start))
def __getitem__(self, idx):
"""
Returns
-------
sample : dict
'vol': torch.tensor of input volumetric image
'lab': torch.tensor of input volumetric image
idx : int
Index of image as stored in files.
"""
vol = load_volume(os.path.join(self.volpath, self.volnames[idx]))
vol = vol[None, ...]
lab = load_volume(os.path.join(self.labpath, self.labnames[idx]))
vol = torch.tensor(vol, dtype=torch.float32)
lab = torch.tensor(lab, dtype=torch.float32)
sample = {'vol': vol, 'lab': lab}
if self.transform:
self.transform(sample)
return sample
def calculate_metrics(prediction_volume,
gt_path,
classification_threshold=0.5):
"""helper function for metric calculation"""
if gt_path is not None:
logging.info(
"calculating performance metrics against test dataset {}".format(
str(gt_path)))
ground_truth = load_volume(gt_path)
metrics = PerformanceMetrics(
y_true=ground_truth,
y_pred=prediction_volume[:, :, :, 0],
thr=classification_threshold,
)
performance_metrics_dict = metrics.measure_dict
else:
performance_metrics_dict = None
return performance_metrics_dict
def main():
args = parse_args()
images = args.input
vol = load_volume(images, ext='.bmp')
with h5py.File('downsampled_histogram.h5', 'r') as f:
hist = f['hist'][:]
hist = np.cumsum(hist)
vol = np.floor(255 * hist[vol])
vol[vol > 255] = 255
vol[vol < 0] = 0
vol = vol.astype(np.uint8)
sel = ndi.generate_binary_structure(3, 1)
sel[0] = 0
sel[2] = 0
subject = os.path.basename(args.input)
print(subject)
params = {}
if args.recover_parameters:
# try:
with open(args.parameter_file, 'r') as f:
params = json.load(f)
t_iris = params[subject]['t_iris']
t_pupil = params[subject]['t_pupil']
window_iris = tuple(params[subject]['window_iris'])
window_pupil = tuple(params[subject]['window_pupil'])
# except KeyError:
# pass
if args.t_iris is not None:
t_iris = args.t_iris
if args.t_pupil is not None:
t_pupil = args.t_pupil
if args.window_iris is not None:
window_iris = tuple(args.window_iris)
if args.window_pupil is not None:
window_pupil = tuple(args.window_pupil)
depth = args.depth
radius = int(min(vol.shape[1], vol.shape[2]) / 4)
if args.save_iris:
iris_seg = np.zeros(vol.shape, dtype=np.uint8)
if args.save_pupil:
pupil_seg = np.zeros(vol.shape, dtype=np.uint8)
seg = np.zeros(vol.shape, dtype=np.uint8)
sums, counts = None, None
for i in range(0, vol.shape[0], depth):
subvol = np.copy(vol[i:i + depth])
orig_shape = subvol.shape
if subvol.shape[0] < depth:
subvol = np.concatenate([
subvol,
np.repeat(subvol[-1].reshape(1, subvol.shape[1],
subvol.shape[2]),
depth - subvol.shape[0],
axis=0)
],
axis=0)
if all([
window_iris[j] == window_pupil[j]
for j in range(len(window_iris))
]):
sums, counts = summate(integral_image(subvol),
np.asarray(window_iris))
# Iris Segmentation
iris = 1.0 - threshold_bradley_nd(
subvol, t=t_iris, s=window_iris, sums=sums, counts=counts)
iris = ndi.binary_fill_holes(iris, structure=sel)
# Pupil Segmentation
pupil = 1.0 - threshold_bradley_nd(
subvol, t=t_pupil, s=window_pupil, sums=sums, counts=counts)
pupil = ndi.binary_fill_holes(pupil, structure=sel)
pupil = ndi.binary_erosion(pupil, structure=sel)
pupil = ndi.binary_dilation(pupil, structure=sel)
pupil = ndi.binary_dilation(pupil, structure=sel).astype(np.uint8)
pupil_collapsed = (np.sum(pupil, axis=0) > 1).astype(np.uint8)
pupil_collapsed = remove_small_objects(label(pupil_collapsed),
min_size=200).astype(np.uint8)
circle_mask = np.zeros(pupil_collapsed.shape, dtype=np.uint8)
try:
objs = regionprops(label(pupil_collapsed),
intensity_image=np.mean(subvol, axis=0).astype(
np.uint8))
for obj in objs:
if obj.convex_area > 1000 and obj.solidity < 0.5 or np.sum(
obj.inertia_tensor_eigvals) == 0:
pupil_collapsed[obj.coords[:, 0], obj.coords[:, 1]] = 0
pupil_idx = np.argmax([
o.area * np.abs(o.orientation) * o.solidity /
(o.eccentricity + 1e-7) /
(o.inertia_tensor_eigvals[0] - o.inertia_tensor_eigvals[1])
for o in objs
])
pupil_obj = objs[pupil_idx]
circle_coords = circle(pupil_obj.centroid[0],
pupil_obj.centroid[1],
radius,
shape=pupil_collapsed.shape)
circle_mask[circle_coords] = 1
except (ValueError, IndexError):
pass
pupil = np.logical_and(
pupil,
np.repeat(pupil_collapsed.reshape((1, ) + pupil_collapsed.shape),
pupil.shape[0],
axis=0))
# Final Segmentation
final = np.logical_xor(iris, pupil).astype(np.uint8)
final = ndi.binary_dilation(final, structure=sel)
final[:, circle_mask == 0] = 0
# Save it
seg[i:i + depth] = final[:orig_shape[0]]
if args.save_iris:
iris_seg[i:i + depth] += iris[:orig_shape[0]]
if args.save_pupil:
pupil_seg[i:i + depth] += pupil[:orig_shape[0]]
seg[:, np.sum(seg, axis=0) < 20] = 0
seg = ndi.binary_erosion(seg, structure=sel)
seg = ndi.binary_erosion(seg, structure=sel).astype(np.uint8)
outdir = os.path.join(args.output, subject)
if not os.path.isdir(outdir):
os.makedirs(outdir)
seg[seg.nonzero()] = 255
save_imgs(seg, outdir, prefix=subject)
if args.save_iris:
outdir = os.path.join(args.output, 'iris', subject)
if not os.path.isdir(outdir):
os.makedirs(outdir)
iris_seg[iris_seg.nonzero()] = 255
save_imgs(iris_seg, outdir)
if args.save_pupil:
outdir = os.path.join(args.output, 'pupil', subject)
if not os.path.isdir(outdir):
os.makedirs(outdir)
pupil_seg[pupil_seg.nonzero()] = 255
save_imgs(pupil_seg, outdir)
shutil.copy(args.parameter_file, args.parameter_file + '.bak')
with open(args.parameter_file, 'w') as f:
params[subject] = {
't_iris': t_iris,
't_pupil': t_pupil,
'window_iris': window_iris,
'window_pupil': window_pupil,
}
json.dump(params, f)
def main():
parser = ArgumentParser()
parser.add_argument(
"-i",
"--img",
action="store",
type=str,
dest="img_path_str",
default="test_frames.tif",
help="Input images path",
)
parser.add_argument(
"-o",
"--output",
action="store",
type=str,
dest="out_path_str",
default="out",
help="Output path",
)
parser.add_argument(
"-m",
"--model",
action="store",
type=str,
dest="model_path_str",
default="out/model.hdf5",
help="Model location",
)
parser.add_argument(
"-g",
"--groundtruth",
action="store",
type=str,
dest="gt_path_str",
default=None,
help="Ground truth path, optional",
)
parser.add_argument(
"--thr",
action="store",
type=float,
dest="threshold",
default=0.5,
help="Threshold for crisp performance metrics evaluation, optional",
)
parser.add_argument(
"-b",
"--batch_size",
action="store",
type=int,
dest="batch_size",
default=60,
help="Batch size",
)
parser.add_argument(
"-t",
"--temp",
action="store",
type=str,
dest="tmp_path_str",
default="tmp",
help="temp directory path, optional",
)
parser.add_argument(
"--descriptorpath",
action="store",
type=str,
dest="descriptor_path",
help="RunDescriptor file path",
)
parser.add_argument("--notes",
action="store",
type=str,
dest="notes",
help="Notes for RunDescriptor")
# Loading args from file
parser.add_argument("--file", type=open, action=LoadArgsFromFile)
# Option parsing
args = parser.parse_args()
# Path definitions
model_path = Path(args.model_path_str)
img_path = Path(args.img_path_str)
out_path = Path(args.out_path_str)
tmp_path = Path(args.tmp_path_str)
gt_path = Path(args.gt_path_str) if args.gt_path_str is not None else None
# Output directories
out_path.mkdir(exist_ok=True, parents=True)
if args.descriptor_path is not None:
descriptor_path = Path(args.descriptor_path)
else:
descriptor_path = out_path
# Logs directory
logs_path = out_path.joinpath("logs")
logs_path.mkdir(exist_ok=True, parents=True)
logfile_path = logs_path.joinpath("logging_log.log")
fh = logging.FileHandler(str(logfile_path))
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
# Custom metrics
custom_objects = {
"jaccard_index": jaccard_index,
"dice_coefficient": dice_coefficient
}
keras_model = load_model(str(model_path), custom_objects=custom_objects)
# Data loading
in_volume = load_volume(img_path, expand_dims=False)
# Prediction and Reconstruction
predictions = TiledPredictor(input_volume=in_volume,
batch_size=args.batch_size,
tmp_path=tmp_path,
num_rotations=0,
model=keras_model)
# Saving results
save_volume(
volume=predictions.out_volume[:, :, :, 0],
out_path=out_path,
filename=img_path.stem,
)
# Calculating performances on test dataset
performance_metrics_dict = calculate_metrics(
predictions.out_volume,
gt_path=gt_path,
classification_threshold=args.threshold)
# Run descriptor output
RunDescriptor(
descriptor_dir_path=descriptor_path,
entry_type="predict",
model_type="2d",
model_path=model_path,
log_dir_path=logs_path,
input_data_path=img_path,
script_options=vars(args),
git_repo=git.Repo(".."),
notes=args.notes,
predictions_path=out_path,
ground_truth_path=gt_path,
performance_metrics_dict=performance_metrics_dict,
)
