# Sample points
sampleIds = get_random_points(model, SAMPLE_RATE)
progressPoints = [int(len(sampleIds) / 10 * (k + 1)) for k in range(10)
] # just to get some progress meter action
# Go through each sample, create features and label for that sample
for j, sID in enumerate(sampleIds):
if j in progressPoints: # print out some progress
print("About {} percent of {} sample points processed.".format(
(progressPoints.index(j) + 1) * 10, len(sampleIds)))
if PATCH_METHOD == "order":
samplePatch = create_patch(model, modelGraph, idArray, invIdArray,
sID, ORDER)
elif PATCH_METHOD == "size":
samplePatch = create_patch_optimised(model, modelGraph, idArray,
invIdArray, sID, PATCH_SIZE)
sampleFeatures = get_features(model, samplePatch, FEATURES,
PCA_COMPONENTS, sID)
sampleLabel = mapScalars.GetValue(sID)
if PCA_COMPONENTS != None:
sampleFeatures = sampleFeatures.flatten()
features.append(sampleFeatures)
labels.append(sampleLabel)
if j in progressPoints:
print(os.path.join(mapLocation, mapFilename))
print("Got feature {}, labelled {} for this".format(
sampleFeatures, sampleLabel))
if PCA_COMPONENTS != None:
print(sampleFeatures.shape)
scalars.SetNumberOfValues(model.GetNumberOfPoints())
# For example, set all scalars to 1
for i in range(model.GetNumberOfPoints()):
scalars.SetValue(i, 1)
# Make some patches at the landmarks, of a certain size
for landmarkSize in range(21):
# landmarkSize = 16
landmarkPatches = []
st = time.time()
# Iterative way
for i in landmarkIds:
landmarkPatches.append(
create_patch_optimised(model, modelGraph, idArray, invIdArray, i,
landmarkSize))
# Parallel way
# Parallel(n_jobs=2)(delayed(create_patch)(model, modelGraph, idArray, invIdArray, i, landmarkSize) for i in landmarkIds)
t = time.time() - st
print("Generated {} landmark patches of size {} in {} seconds.".format(
len(landmarkIds), landmarkSize, t))
print("Average patch generation time: {} seconds.".format(
t / len(landmarkIds)))
print(model.GetNumberOfPoints())
# Paint the patches
for patch in landmarkPatches:
for point in patch:
subBones = ["Patella", "Tibia", "Femur", ""]
subBone = subBones[1]
# Check to see if it exists
subBoneFilename = meshFilename.split(
".")[0] + subBone + "." + meshFilename.split(".")[1]
open(subBoneFilename, 'r')
# Load the mesh model and generate graph
model = read_mesh(subBoneFilename)
modelGraph, idArray, invIdArray = generate_graph(model)
for size in [
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20
]:
i = 1000
st = time.time()
patch = create_patch_optimised(model, modelGraph, idArray, invIdArray, i,
size)
t = time.time() - st
print(
"Took {} seconds to create dijkstra patch of size {}, with {} vertices"
.format(t, size, len(patch)))
# Iterative way
# for i in landmarkIds:
# landmarkPatches.append(create_patch(model, modelGraph, idArray, invIdArray, i, landmarkSize))
# Parallel way
# Parallel(n_jobs=2)(delayed(create_patch)(model, modelGraph, idArray, invIdArray, i, landmarkSize) for i in landmarkIds)