def collect_image_paths(data_dir):
image_keys = [
structure.BrainImageTypes.T1w, structure.BrainImageTypes.GroundTruth
]
class MyFilePathGenerator(futil.FilePathGenerator):
@staticmethod
def get_full_file_path(id_: str, root_dir: str, file_key,
file_extension: str) -> str:
if file_key == structure.BrainImageTypes.T1w:
file_name = 'T1native'
elif file_key == structure.BrainImageTypes.GroundTruth:
file_name = 'labels_native'
else:
raise ValueError('Unknown key')
return os.path.join(root_dir, file_name + file_extension)
dir_filter = futil.DataDirectoryFilter()
# todo: create an instance of futil.FileSystemDataCrawler and pass the correpsonding arguments
crawler = futil.FileSystemDataCrawler('../data/exercise/', image_keys,
MyFilePathGenerator(), dir_filter,
'.nii.gz') # todo: modify here
return crawler
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str,
data_test_dir: str):
"""Brain tissue segmentation using decision forests.
The main routine executes the medical image analysis pipeline:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params = {
'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True
}
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1]
for img in images]).squeeze()
#warnings.warn('Random forest parameters not properly set.')
forest = sk_ensemble.RandomForestClassifier(
max_features=images[0].feature_matrix[0].shape[1],
n_estimators=10,
max_depth=10)
start_time = timeit.default_timer()
forest.fit(data_train, labels_train)
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# create a result directory with timestamp
t = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
result_dir = os.path.join(result_dir, t)
os.makedirs(result_dir, exist_ok=True)
print('-' * 5, 'Testing...')
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_test_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
# load images for testing and pre-process
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
images_prediction = []
images_probabilities = []
for img in images_test:
print('-' * 10, 'Testing', img.id_)
start_time = timeit.default_timer()
predictions = forest.predict(img.feature_matrix[0])
probabilities = forest.predict_proba(img.feature_matrix[0])
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# convert prediction and probabilities back to SimpleITK images
image_prediction = conversion.NumpySimpleITKImageBridge.convert(
predictions.astype(np.uint8), img.image_properties)
image_probabilities = conversion.NumpySimpleITKImageBridge.convert(
probabilities, img.image_properties)
# evaluate segmentation without post-processing
evaluator.evaluate(image_prediction,
img.images[structure.BrainImageTypes.GroundTruth],
img.id_)
images_prediction.append(image_prediction)
images_probabilities.append(image_probabilities)
# post-process segmentation and evaluate with post-processing
post_process_params = {'simple_post': True}
images_post_processed = putil.post_process_batch(images_test,
images_prediction,
images_probabilities,
post_process_params,
multi_process=False)
for i, img in enumerate(images_test):
evaluator.evaluate(images_post_processed[i],
img.images[structure.BrainImageTypes.GroundTruth],
img.id_ + '-PP')
# save results
sitk.WriteImage(
images_prediction[i],
os.path.join(result_dir, images_test[i].id_ + '_SEG.mha'), True)
sitk.WriteImage(
images_post_processed[i],
os.path.join(result_dir, images_test[i].id_ + '_SEG-PP.mha'), True)
# use two writers to report the results
os.makedirs(
result_dir,
exist_ok=True) # generate result directory, if it does not exists
result_file = os.path.join(result_dir, 'results.csv')
writer.CSVWriter(result_file).write(evaluator.results)
print('\nSubject-wise results...')
writer.ConsoleWriter().write(evaluator.results)
# report also mean and standard deviation among all subjects
result_summary_file = os.path.join(result_dir, 'results_summary.csv')
functions = {'MEAN': np.mean, 'STD': np.std}
writer.CSVStatisticsWriter(result_summary_file,
functions=functions).write(evaluator.results)
print('\nAggregated statistic results...')
writer.ConsoleStatisticsWriter(functions=functions).write(
evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str, data_test_dir: str):
"""Brain tissue segmentation using decision forests.
The main routine executes the medical image analysis pipeline:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir,
LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params = {'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True}
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data, pre_process_params, multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1] for img in images]).squeeze()
warnings.warn('Random forest parameters not properly set.')
# visualization(images)
print(np.shape(images[0].feature_matrix[0]))
dfs= []
aggregated_results = []
print('-' * 5, 'Testing...')
crawler = futil.FileSystemDataCrawler(data_test_dir,
LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data, pre_process_params, multi_process=False)
for num_estimator in [10]:
forest = sk_ensemble.RandomForestClassifier(max_features=images[0].feature_matrix[0].shape[1],
n_estimators=num_estimator,
max_depth=10)
start_time = timeit.default_timer()
forest.fit(data_train, labels_train)
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# create a result directory with timestamp
t = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
result_dir = os.path.join(result_dir, t)
os.makedirs(result_dir, exist_ok=True)
print('-' * 5, 'Testing...')
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the training image directories
# crawler = futil.FileSystemDataCrawler(data_test_dir,
# LOADING_KEYS,
# futil.BrainImageFilePathGenerator(),
# futil.DataDirectoryFilter())
# load images for testing and pre-process
# data_test = np.concatenate([img.feature_matrix[0] for img in images_test])
# labels_test = np.concatenate([img.feature_matrix[1] for img in images_test]).squeeze()
# ax = plt.gca()
# rfc_disp = plot_roc_curve(forest, data_test, labels_test, ax=ax, alpha=0.8)
# svc_disp.plot(ax=ax, alpha=0.8)
# disp = plot_confusion_matrix(forest, data_test, labels_test, normalize='true')
# plt.show()
# y = label_binarize(labels_test, classes=[0, 1, 2 , 3, 4 , 5])
# n_classes = y.shape[1]
images_prediction = []
images_probabilities = []
for img in images_test:
print('-' * 10, 'Testing', img.id_)
start_time = timeit.default_timer()
predictions = forest.predict(img.feature_matrix[0])
probabilities = forest.predict_proba(img.feature_matrix[0])
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# convert prediction and probabilities back to SimpleITK images
image_prediction = conversion.NumpySimpleITKImageBridge.convert(predictions.astype(np.uint8),
img.image_properties)
image_probabilities = conversion.NumpySimpleITKImageBridge.convert(probabilities, img.image_properties)
# evaluate segmentation without post-processing
evaluator.evaluate(image_prediction, img.images[structure.BrainImageTypes.GroundTruth], img.id_)
images_prediction.append(image_prediction)
images_probabilities.append(image_probabilities)
results=evaluator.results
labels = sorted({result.label for result in results})
metrics = sorted({result.metric for result in results})
# functions = {'MEAN': np.mean, 'STD': np.std}
functions = {'MEAN': np.mean}
for label in labels:
for metric in metrics:
# search for results
values = [r.value for r in results if r.label == label and r.metric == metric]
for fn_id, fn in functions.items():
aggregated_results.append(
[num_estimator,
label,
metric,
float(fn(values))])
# for result in aggregated_results:
# # print([result.label, result.metric, result.id_, result.value])
# print(result)
# writer.ConsoleStatisticsWriter(functions=functions).write(evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
df=pd.DataFrame(aggregated_results, columns=['n_estimators', 'label', 'metric', 'value'])
return df
xdf = df[df.label == 'WhiteMatter']
del xdf['label']
# new_df=df[df.label=='GreyMatter']
# del new_df['label']
# new_df.set_index('n_estimators', inplace=True)
# fig, ax = plt.subplots(figsize=(15, 7))
# new_df.groupby(['metric']).plot(ax=ax)
# print(new_df)
# plt.show()
plt.figure(2)
# pd.crosstab(index=[df['Name'], df['Date']], columns=new_df['metric'])
my_df = pd.pivot_table(df,index=['label'], columns='metric', values='value')
my_df.plot()
print(my_df)
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str,
data_test_dir: str, tmp_result_dir: str):
"""Brain tissue segmentation using decision forests.
Section of the original main routine. Executes post processing part of the medical image analysis pipeline:
Must be done separately in advance:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
Is carried out in this section of the pipeline
- Loading of temporary data
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
# print('-' * 5, 'Training...')
#
# # crawl the training image directories
# crawler = futil.FileSystemDataCrawler(data_train_dir,
# LOADING_KEYS,
# futil.BrainImageFilePathGenerator(),
# futil.DataDirectoryFilter())
pre_process_params = {
'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True
}
# create a result directory with timestamp
t = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
result_dir = os.path.join(result_dir, t)
os.makedirs(result_dir, exist_ok=True)
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the test image directories
crawler = futil.FileSystemDataCrawler(data_test_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
# load necessary data to perform post processing
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
# load the prediction of the test images (segmented image
images_prediction, images_probabilities = putil.load_prediction_images(
images_test, tmp_result_dir, '2020-10-30-18-31-15')
# evaluate images without post-processing
for i, img in enumerate(images_test):
evaluator.evaluate(images_prediction[i],
img.images[structure.BrainImageTypes.GroundTruth],
img.id_)
# post-process segmentation and evaluate with post-processing
post_process_params = {
'simple_post': True,
'variance': 1.0,
'preserve_background': False
}
images_post_processed = putil.post_process_batch(images_test,
images_prediction,
images_probabilities,
post_process_params,
multi_process=False)
for i, img in enumerate(images_test):
evaluator.evaluate(images_post_processed[i],
img.images[structure.BrainImageTypes.GroundTruth],
img.id_ + '-PP')
# save results
sitk.WriteImage(
images_prediction[i],
os.path.join(result_dir, images_test[i].id_ + '_SEG.mha'), True)
sitk.WriteImage(
images_post_processed[i],
os.path.join(result_dir, images_test[i].id_ + '_SEG-PP.mha'), True)
# use two writers to report the results
os.makedirs(
result_dir,
exist_ok=True) # generate result directory, if it does not exists
result_file = os.path.join(result_dir, 'results.csv')
writer.CSVWriter(result_file).write(evaluator.results)
print('\nSubject-wise results...')
writer.ConsoleWriter().write(evaluator.results)
# report also mean and standard deviation among all subjects
result_summary_file = os.path.join(result_dir, 'results_summary.csv')
functions = {'MEAN': np.mean, 'STD': np.std}
writer.CSVStatisticsWriter(result_summary_file,
functions=functions).write(evaluator.results)
print('\nAggregated statistic results...')
writer.ConsoleStatisticsWriter(functions=functions).write(
evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str,
data_test_dir: str):
"""Brain tissue segmentation using decision forests.
The main routine executes the medical image analysis pipeline:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params = {
'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True
}
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1]
for img in images]).squeeze()
warnings.warn('Random forest parameters not properly set.')
# visualization(images)
print(np.shape(images[0].feature_matrix[0]))
forest = sk_ensemble.RandomForestClassifier(
max_features=images[0].feature_matrix[0].shape[1],
n_estimators=10,
max_depth=10)
start_time = timeit.default_timer()
# forest.fit(data_train, labels_train)
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# create a result directory with timestamp
t = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
result_dir = os.path.join(result_dir, t)
os.makedirs(result_dir, exist_ok=True)
print('-' * 5, 'Testing...')
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_test_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
# load images for testing and pre-process
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
data_test = np.concatenate([img.feature_matrix[0] for img in images_test])
labels_test = np.concatenate(
[img.feature_matrix[1] for img in images_test]).squeeze()
random_state = np.random.RandomState(0)
# ax = plt.gca()
# rfc_disp = plot_roc_curve(forest, data_test, labels_test, ax=ax, alpha=0.8)
# svc_disp.plot(ax=ax, alpha=0.8)
# disp = plot_confusion_matrix(forest, data_test, labels_test, normalize='true')
# plt.show()
X = np.concatenate((data_train, data_test))
y = np.concatenate((labels_train, labels_test))
y = label_binarize(y, classes=[0, 1, 2, 3, 4, 5])
n_classes = y.shape[1]
n_samples, n_features = X.shape
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=.5,
random_state=0)
# classifier = OneVsRestClassifier(svm.SVC(kernel='linear', probability=True,
# random_state=random_state))
classifier = OneVsRestClassifier(
sk_ensemble.RandomForestClassifier(
max_features=images[0].feature_matrix[0].shape[1],
n_estimators=10,
max_depth=5))
y_score = classifier.fit(X_train, y_train).predict(X_test)
# Compute ROC curve and ROC area for each class
fpr = dict()
tpr = dict()
roc_auc = dict()
for i in range(n_classes):
fpr[i], tpr[i], _ = roc_curve(y_test[:, i], y_score[:, i])
roc_auc[i] = auc(fpr[i], tpr[i])
# Compute micro-average ROC curve and ROC area
fpr["micro"], tpr["micro"], _ = roc_curve(y_test.ravel(), y_score.ravel())
roc_auc["micro"] = auc(fpr["micro"], tpr["micro"])
# First aggregate all false positive rates
all_fpr = np.unique(np.concatenate([fpr[i] for i in range(n_classes)]))
# Then interpolate all ROC curves at this points
mean_tpr = np.zeros_like(all_fpr)
for i in range(n_classes):
mean_tpr += interp(all_fpr, fpr[i], tpr[i])
# Finally average it and compute AUC
mean_tpr /= n_classes
fpr["macro"] = all_fpr
tpr["macro"] = mean_tpr
roc_auc["macro"] = auc(fpr["macro"], tpr["macro"])
plt.figure()
lw = 2
plt.plot(fpr[2],
tpr[2],
color='darkorange',
lw=lw,
label='ROC curve (area = %0.2f)' % roc_auc[2])
plt.plot([0, 1], [0, 1], color='navy', lw=lw, linestyle='--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Receiver operating characteristic example')
plt.legend(loc="lower right")
plt.show()
# Plot all ROC curves
plt.figure()
plt.plot(fpr["micro"],
tpr["micro"],
label='micro-average ROC curve (area = {0:0.2f})'
''.format(roc_auc["micro"]),
color='deeppink',
linestyle=':',
linewidth=4)
plt.plot(fpr["macro"],
tpr["macro"],
label='macro-average ROC curve (area = {0:0.2f})'
''.format(roc_auc["macro"]),
color='navy',
linestyle=':',
linewidth=4)
colors = cycle(['aqua', 'darkorange', 'cornflowerblue'])
for i, color in zip(range(n_classes), colors):
plt.plot(fpr[i],
tpr[i],
color=color,
lw=lw,
label='ROC curve of class {0} (area = {1:0.2f})'
''.format(i, roc_auc[i]))
plt.plot([0, 1], [0, 1], 'k--', lw=lw)
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title(
'Some extension of Receiver operating characteristic to multi-class')
plt.legend(loc="lower right")
plt.show()
#
# images_prediction = []
# images_probabilities = []
#
#
# for img in images_test:
# print('-' * 10, 'Testing', img.id_)
#
#
# start_time = timeit.default_timer()
# predictions = forest.predict(img.feature_matrix[0])
# probabilities = forest.predict_proba(img.feature_matrix[0])
# print(' Time elapsed:', timeit.default_timer() - start_time, 's')
#
# # convert prediction and probabilities back to SimpleITK images
# image_prediction = conversion.NumpySimpleITKImageBridge.convert(predictions.astype(np.uint8),
# img.image_properties)
# image_probabilities = conversion.NumpySimpleITKImageBridge.convert(probabilities, img.image_properties)
#
# # evaluate segmentation without post-processing
# evaluator.evaluate(image_prediction, img.images[structure.BrainImageTypes.GroundTruth], img.id_)
#
# images_prediction.append(image_prediction)
# images_probabilities.append(image_probabilities)
#
#
#
#
# # post-process segmentation and evaluate with post-processing
# post_process_params = {'simple_post': True}
# images_post_processed = putil.post_process_batch(images_test, images_prediction, images_probabilities,
# post_process_params, multi_process=True)
#
# for i, img in enumerate(images_test):
# evaluator.evaluate(images_post_processed[i], img.images[structure.BrainImageTypes.GroundTruth],
# img.id_ + '-PP')
#
# # save results
# sitk.WriteImage(images_prediction[i], os.path.join(result_dir, images_test[i].id_ + '_SEG.mha'), True)
# sitk.WriteImage(images_post_processed[i], os.path.join(result_dir, images_test[i].id_ + '_SEG-PP.mha'), True)
#
# # use two writers to report the results
# os.makedirs(result_dir, exist_ok=True) # generate result directory, if it does not exists
# result_file = os.path.join(result_dir, 'results.csv')
# writer.CSVWriter(result_file).write(evaluator.results)
#
# print('\nSubject-wise results...')
# writer.ConsoleWriter().write(evaluator.results)
#
# # report also mean and standard deviation among all subjects
# result_summary_file = os.path.join(result_dir, 'results_summary.csv')
# functions = {'MEAN': np.mean, 'STD': np.std}
# writer.CSVStatisticsWriter(result_summary_file, functions=functions).write(evaluator.results)
# print('\nAggregated statistic results...')
# writer.ConsoleStatisticsWriter(functions=functions).write(evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str,
data_test_dir: str):
"""Brain tissue segmentation using decision forests.
Section of the original main routine. Executes pre-processing and prediction part of the medical image
analysis pipeline and and saves the temporary data:
Is carried out in this section of the pipeline
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Save prediction data
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params = {
'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True
}
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1]
for img in images]).squeeze()
warnings.warn('Random forest parameters not properly set.')
forest = sk_ensemble.RandomForestClassifier(
max_features=images[0].feature_matrix[0].shape[1],
n_estimators=10,
max_depth=10)
start_time = timeit.default_timer()
forest.fit(data_train, labels_train)
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# create a result directory with timestamp
t = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
result_dir = os.path.join(result_dir, t)
os.makedirs(result_dir, exist_ok=True)
print('-' * 5, 'Testing...')
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_test_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
# load images for testing and pre-process
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
images_prediction = []
images_probabilities = []
for img in images_test:
print('-' * 10, 'Testing', img.id_)
start_time = timeit.default_timer()
predictions = forest.predict(img.feature_matrix[0])
probabilities = forest.predict_proba(img.feature_matrix[0])
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# convert prediction and probabilities back to SimpleITK images
image_prediction = conversion.NumpySimpleITKImageBridge.convert(
predictions.astype(np.uint8), img.image_properties)
image_probabilities = conversion.NumpySimpleITKImageBridge.convert(
probabilities, img.image_properties)
# evaluate segmentation without post-processing
evaluator.evaluate(image_prediction,
img.images[structure.BrainImageTypes.GroundTruth],
img.id_)
images_prediction.append(image_prediction)
images_probabilities.append(image_probabilities)
# save all data used for post processing
for i, img in enumerate(images_test):
sitk.WriteImage(
images_prediction[i],
os.path.join(result_dir, images_test[i].id_ + '_SEG.mha'), True)
sitk.WriteImage(
images_probabilities[i],
os.path.join(result_dir, images_test[i].id_ + '_PROB.mha'), True)
evaluator.clear()
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str,
data_test_dir: str):
"""Brain tissue segmentation using decision forests.
Section of the original main routine. Executes gird search of the probabilistic keyhole filling method parameters:
Must be done separately in advance:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
Is carried out in this section of the pipeline
- Loading of temporary data
- Grid search of PKF parameter of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params = {
'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True
}
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1]
for img in images]).squeeze()
#warnings.warn('Random forest parameters not properly set.')
forest = sk_ensemble.RandomForestClassifier(
max_features=images[0].feature_matrix[0].shape[1],
n_estimators=20,
max_depth=85)
start_time = timeit.default_timer()
forest.fit(data_train, labels_train)
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# create a result directory with timestamp
t = datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S')
result_dir = os.path.join(result_dir, t)
os.makedirs(result_dir, exist_ok=True)
print('-' * 5, 'Testing...')
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_test_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
# load images for testing and pre-process
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
images_prediction = []
images_probabilities = []
for img in images_test:
print('-' * 10, 'Testing', img.id_)
start_time = timeit.default_timer()
predictions = forest.predict(img.feature_matrix[0])
probabilities = forest.predict_proba(img.feature_matrix[0])
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# convert prediction and probabilities back to SimpleITK images
image_prediction = conversion.NumpySimpleITKImageBridge.convert(
predictions.astype(np.uint8), img.image_properties)
image_probabilities = conversion.NumpySimpleITKImageBridge.convert(
probabilities, img.image_properties)
# evaluate segmentation without post-processing
evaluator.evaluate(image_prediction,
img.images[structure.BrainImageTypes.GroundTruth],
img.id_)
images_prediction.append(image_prediction)
images_probabilities.append(image_probabilities)
# save results without post-processing
name = 'no_PP'
sub_dir = os.path.join(result_dir, name)
os.makedirs(sub_dir, exist_ok=True)
for i, img in enumerate(images_test):
sitk.WriteImage(images_prediction[i],
os.path.join(sub_dir, images_test[i].id_ + '_SEG.mha'),
True)
result_file = os.path.join(sub_dir, 'results.csv')
writer.CSVWriter(result_file).write(evaluator.results)
# report also mean and standard deviation among all subjects
result_summary_file = os.path.join(sub_dir, 'results_summary.csv')
functions = {'MEAN': np.mean, 'STD': np.std}
writer.CSVStatisticsWriter(result_summary_file,
functions=functions).write(evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
# define paramter for grid search
post_process_param_list = []
variance = np.arange(1, 2)
preserve_background = np.asarray([False])
#
# # define paramter for grid search
# post_process_param_list = []
# variance = np.arange(0.5, 4.0, 0.5)
# preserve_background = np.asarray([False, True])
for bg in preserve_background:
for var in variance:
post_process_param_list.append({
'simple_post': bool(True),
'variance': float(var),
'preserve_background': bool(bg)
})
# execute post processing with definde parameters
for post_process_params in post_process_param_list:
# create sub-directory for results
name = 'PP-V-'+ str(post_process_params.get('variance')).replace('.','_') +\
'-BG-' + str(post_process_params.get('preserve_background'))
sub_dir = os.path.join(result_dir, name)
os.makedirs(sub_dir, exist_ok=True)
#write the used parameter into a text file and store it in the result folder
completeName = os.path.join(sub_dir, "parameter.txt")
file1 = open(completeName, "w+")
json.dump(post_process_params, file1)
file1.close()
# post-process segmentation and evaluate with post-processing
images_post_processed = putil.post_process_batch(images_test,
images_prediction,
images_probabilities,
post_process_params,
multi_process=False)
for i, img in enumerate(images_test):
evaluator.evaluate(
images_post_processed[i],
img.images[structure.BrainImageTypes.GroundTruth],
img.id_ + '-PP')
# save results
sitk.WriteImage(
images_post_processed[i],
os.path.join(sub_dir, images_test[i].id_ + '_SEG-PP.mha'),
True)
# save all results in csv file
result_file = os.path.join(sub_dir, 'results.csv')
writer.CSVWriter(result_file).write(evaluator.results)
print('\nSubject-wise results...')
writer.ConsoleWriter().write(evaluator.results)
# report also mean and standard deviation among all subjects
result_summary_file = os.path.join(sub_dir, 'results_summary.csv')
functions = {'MEAN': np.mean, 'STD': np.std}
writer.CSVStatisticsWriter(
result_summary_file, functions=functions).write(evaluator.results)
print('\nAggregated statistic results...')
writer.ConsoleStatisticsWriter(functions=functions).write(
evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str,
data_test_dir: str):
"""Brain tissue segmentation using decision forests.
The main routine executes the medical image analysis pipeline:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir, LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
pre_process_params = {
'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'coordinates_feature': True,
'intensity_feature': True,
'gradient_intensity_feature': True
}
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data,
pre_process_params,
multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1]
for img in images]).squeeze()
warnings.warn('Random forest parameters not properly set.')
# visualization(images)
print(np.shape(images[0].feature_matrix[0]))
error_rate = []
for num_estimators in range(1, 10):
forest = sk_ensemble.RandomForestClassifier(
max_features=images[0].feature_matrix[0].shape[1],
n_estimators=num_estimators,
max_depth=10,
oob_score=True)
# start_time = timeit.default_timer()
forest.fit(data_train, labels_train)
oob_error = 1 - forest.oob_score_
print(forest.oob_score_)
error_rate += [oob_error]
plt.plot(range(1, 10), error_rate)
plt.show()
def main(result_dir: str, data_atlas_dir: str, data_train_dir: str, data_test_dir: str, parameters_file: str):
"""Brain tissue segmentation using decision forests.
The main routine executes the medical image analysis pipeline:
- Image loading
- Registration
- Pre-processing
- Feature extraction
- Decision forest classifier model building
- Segmentation using the decision forest classifier model on unseen images
- Post-processing of the segmentation
- Evaluation of the segmentation
"""
start_main = timeit.default_timer()
# load atlas images
putil.load_atlas_images(data_atlas_dir)
print('-' * 5, 'Training...')
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_train_dir,
LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
fof_parameters = {'10Percentile': True,
'90Percentile': True,
'Energy': True,
'Entropy': True,
'InterquartileRange': True,
'Kurtosis': True,
'Maximum': True,
'MeanAbsoluteDeviation': True,
'Mean': True,
'Median': True,
'Minimum': True,
'Range': True,
'RobustMeanAbsoluteDeviation': True,
'RootMeanSquared': True,
'Skewness': True,
'TotalEnergy': True,
'Uniformity': True,
'Variance': True}
glcm_parameters = {'Autocorrelation': True,
'ClusterProminence': True,
'ClusterShade': True,
'ClusterTendency': True,
'Contrast': True,
'Correlation': True,
'DifferenceAverage': True,
'DifferenceEntropy': True,
'DifferenceVariance': True,
'Id': True,
'Idm': True,
'Idmn': True,
'Idn': True,
'Imc1': True,
'Imc2': True,
'InverseVariance': True,
'JointAverage': True,
'JointEnergy': True,
'JointEntropy': True,
'MCC': True,
'MaximumProbability': True,
'SumAverage': True,
'SumEntropy': True,
'SumSquares': True}
pre_process_params = {'skullstrip_pre': True,
'normalization_pre': True,
'registration_pre': True,
'save_features': False,
'coordinates_feature': True,
'intensity_feature': False,
'gradient_intensity_feature': False,
'first_order_feature': False,
'first_order_feature_parameters': fof_parameters,
'HOG_feature': False,
'GLCM_features': False,
'GLCM_features_parameters': glcm_parameters,
'n_estimators': 50,
'max_depth': 60,
'experiment_name': 'default'
}
parameters = json.load(open(parameters_file, 'r'))
if bool(parameters):
pre_process_params = parameters
# load images for training and pre-process
images = putil.pre_process_batch(crawler.data, pre_process_params, multi_process=False)
# generate feature matrix and label vector
data_train = np.concatenate([img.feature_matrix[0] for img in images])
labels_train = np.concatenate([img.feature_matrix[1] for img in images]).squeeze()
np.nan_to_num(data_train, copy=False)
# warnings.warn('Random forest parameters not properly set.')
forest = sk_ensemble.RandomForestClassifier(max_features=images[0].feature_matrix[0].shape[1],
n_estimators=pre_process_params['n_estimators'], # 100
max_depth=pre_process_params['max_depth']) # 10
# Debugging
nan_data_idx = np.argwhere(np.isnan(data_train))
np.savez('data_train.npz', data_train)
np.save('data_nan.npy', nan_data_idx)
start_time = timeit.default_timer()
forest.fit(data_train, labels_train)
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# create a result directory with timestamp
result_dir = os.path.join(result_dir, pre_process_params['experiment_name'])
os.makedirs(result_dir, exist_ok=True)
print('-' * 5, 'Testing...')
# initialize evaluator
evaluator = putil.init_evaluator()
# crawl the training image directories
crawler = futil.FileSystemDataCrawler(data_test_dir,
LOADING_KEYS,
futil.BrainImageFilePathGenerator(),
futil.DataDirectoryFilter())
# load images for testing and pre-process
pre_process_params['training'] = False
images_test = putil.pre_process_batch(crawler.data, pre_process_params, multi_process=False)
images_prediction = []
images_probabilities = []
for img in images_test:
print('-' * 10, 'Testing', img.id_)
start_time = timeit.default_timer()
predictions = forest.predict(np.nan_to_num(img.feature_matrix[0],copy=False))
probabilities = forest.predict_proba(np.nan_to_num(img.feature_matrix[0],copy=False))
print(' Time elapsed:', timeit.default_timer() - start_time, 's')
# convert prediction and probabilities back to SimpleITK images
image_prediction = conversion.NumpySimpleITKImageBridge.convert(predictions.astype(np.uint8),
img.image_properties)
image_probabilities = conversion.NumpySimpleITKImageBridge.convert(probabilities, img.image_properties)
# evaluate segmentation without post-processing
evaluator.evaluate(image_prediction, img.images[structure.BrainImageTypes.GroundTruth], img.id_)
images_prediction.append(image_prediction)
images_probabilities.append(image_probabilities)
# post-process segmentation and evaluate with post-processing
post_process_params = {'simple_post': True}
images_post_processed = putil.post_process_batch(images_test, images_prediction, images_probabilities,
post_process_params, multi_process=False)
for i, img in enumerate(images_test):
evaluator.evaluate(images_post_processed[i], img.images[structure.BrainImageTypes.GroundTruth],
img.id_ + '-PP')
# save results
sitk.WriteImage(images_prediction[i], os.path.join(result_dir, images_test[i].id_ + '_SEG.mha'), True)
sitk.WriteImage(images_post_processed[i], os.path.join(result_dir, images_test[i].id_ + '_SEG-PP.mha'), True)
# use two writers to report the results
os.makedirs(result_dir, exist_ok=True) # generate result directory, if it does not exists
result_file = os.path.join(result_dir, 'results.csv')
writer.CSVWriter(result_file).write(evaluator.results)
print('\nSubject-wise results...')
writer.ConsoleWriter().write(evaluator.results)
# report also mean and standard deviation among all subjects
result_summary_file = os.path.join(result_dir, 'results_summary.csv')
functions = {'MEAN': np.mean, 'STD': np.std}
writer.CSVStatisticsWriter(result_summary_file, functions=functions).write(evaluator.results)
print('\nAggregated statistic results...')
writer.ConsoleStatisticsWriter(functions=functions).write(evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
end_main = timeit.default_timer()
main_time = end_main - start_main
# writing information on a txt file
reporter.feature_writer(result_dir, pre_process_params, main_time, 'feature_report')
