def evaluate(object_folder):
test_images_list = os.path.join(object_folder, 'test_images_list.csv')
test_labels_list = os.path.join(object_folder, 'test_labels_list.csv')
test_image_filenames = KScsv.read_csv(test_images_list)
test_label_filenames = KScsv.read_csv(test_labels_list)
all_prediction = list()
all_label = list()
f1score_per_image = list()
all_score = list()
for i_image, (image_file, label_file) in enumerate(
zip(test_image_filenames, test_label_filenames)):
tick = time.time()
basename = os.path.basename(image_file[0])
basename = os.path.splitext(basename)[0]
image_file = os.path.join(object_folder, 'result', basename + '.mat')
# Read in result and label
mat_content = matlab.load(image_file)
score = mat_content['mask']
prediction = score > 0.5
prediction = prediction.astype('float')
label = KSimage.imread(label_file[0])
label = label.astype('float')
label = label / 255.0
label = label > 0.5
label = label.astype('float')
prediction = np.reshape(prediction, -1)
label = np.reshape(label, -1)
score = np.reshape(score, -1)
all_prediction.append(prediction)
all_label.append(label)
all_score.append(score)
f1score = metrics.f1_score(label, prediction, average='binary')
f1score_per_image.append(f1score)
duration = time.time() - tick
print('evaluate %d / %d (%.2f sec)' %
(i_image + 1, len(test_image_filenames), duration))
all_label = np.reshape(np.array(all_label), -1)
all_prediction = np.reshape(np.array(all_prediction), -1)
all_score = np.reshape(np.array(all_score), -1)
total_f1score = metrics.f1_score(all_label,
all_prediction,
average='binary')
avg_f1score = np.mean(f1score_per_image)
average_precision = metrics.average_precision_score(all_label,
all_score,
average='micro')
return total_f1score, avg_f1score, average_precision, f1score_per_image
def inputs2(object_folder, mode, flags, mat_contents):
if mode == 'train':
log_file_path = os.path.join(object_folder, 'train', 'train_log.csv')
else:
log_file_path = os.path.join(object_folder, 'val', 'val_log.csv')
log_list = KScsv.read_csv(log_file_path)
#key_list = ['HE', 'DAPI', 'weight']
key_list = list(
flags['dict_path'].keys())[:-1] # all items except last item: 'group'
allimageslist = []
for ind, key in enumerate(key_list):
image_dict = collections.defaultdict(list)
#label_dict = collections.defaultdict(list)
#weight_dict = collections.defaultdict(list)
for row in log_list:
image_dict[key].append(row[ind])
#label_dict['label'].append(row[1])
#weight_dict['weight'].append(row[2])
min_queue_examples = int(
len(image_dict[key[0]]) *
flags['min_fraction_of_examples_in_queue'])
print('Filling queue with %d images before starting to train. '
'This will take a few minutes.' % min_queue_examples)
# Create a queue that produces the filenames to read.
combine_image_dict = list()
#combine_label_dict = list()
#combine_weight_dict = list()
allimageslist.append(image_dict[key])
filename_queue = tf.train.slice_input_producer(allimageslist,
shuffle=True)
queue_dict = read_data(filename_queue, flags)
image, label, weight = process_image_and_label(image, label, weight,
mean_image,
variance_image, flags)
# Generate a batch of images and labels by building up a queue of examples.
image, label, weight = generate_batch(image,
label,
weight,
min_queue_examples,
int(flags['batch_size']),
shuffle=False,
flags=flags)
combine_image_dict.append(image)
combine_label_dict.append(label)
combine_weight_dict.append(weight)
out_image = tf.concat(combine_image_dict, 0)
out_label = tf.concat(combine_label_dict, 0)
out_weight = tf.concat(combine_weight_dict, 0)
return {'images': out_image, 'labels': out_label, 'weights': out_weight}
def main(argv):
he_log_file = argv[0]
he_dcis_segmentation_result_path = argv[1]
igpu = argv[2]
row_list = KScsv.read_csv(he_log_file)
main_he_dcis_segmentation.main(1, 'test_model', flags_he_dcis_segmentation,
row_list, he_dcis_segmentation_result_path, igpu)
def main(argv):
file_list = argv[0]
result_path = argv[1]
he_dcis_segmentation_result_path = argv[2]
igpu = argv[3]
row_list = KScsv.read_csv(file_list)
main_probe_detection.main(1, 'test_model', flags_probe_detection_green,
row_list, result_path,
he_dcis_segmentation_result_path, igpu)
def main(argv):
file_list = argv[0]
he_cell_segmentation_result_path = argv[1]
he_dcis_segmentation_result_path = argv[2]
igpu = argv[3]
row_list = KScsv.read_csv(file_list)
main_he_cell_segmentation.main(1, 'test_model', flags_he_cell_segmentation,
row_list, he_cell_segmentation_result_path,
he_dcis_segmentation_result_path, igpu)
def inputs(mean_image, variance_image, object_folder, mode, flags):
if mode == 'train':
log_file_path = os.path.join(object_folder, 'train', 'train_log.csv')
else:
log_file_path = os.path.join(object_folder, 'val', 'val_log.csv')
log_list = KScsv.read_csv(log_file_path)
image_dict = collections.defaultdict(list)
label_dict = collections.defaultdict(list)
for row in log_list:
for i_class in range(flags['n_classes']):
if int(row[2]) == i_class:
image_dict[i_class].append(row[0])
label_dict[i_class].append(int(row[2]))
min_queue_examples = int(
np.sum([len(image_dict[k]) for k in image_dict.keys()]) *
flags['min_fraction_of_examples_in_queue'])
print('Filling queue with %d images before starting to train. '
'This will take a few minutes.' % min_queue_examples)
# Create a queue that produces the filenames to read.
combine_image_dict = list()
combine_label_dict = list()
for i_class in range(flags['n_classes']):
filename_queue = tf.train.slice_input_producer(
[image_dict[i_class], label_dict[i_class]], shuffle=True)
image, label = read_data(filename_queue, flags)
image = tf.cast(image, tf.float32)
label = tf.cast(label, tf.float32)
image, label = process_image_and_label(image, label, mean_image,
variance_image, flags)
# Generate a batch of images and labels by building up a queue of examples.
image, label = generate_batch(image,
label,
min_queue_examples,
int(flags['batch_size'] /
flags['n_classes']),
shuffle=False,
flags=flags)
combine_image_dict.append(image)
combine_label_dict.append(label)
out_image = tf.concat(0, combine_image_dict)
out_label = tf.concat(0, combine_label_dict)
return {'images': out_image, 'labels': out_label}
def select_train_val_instances(nth_fold, method, flags):
"""
select_train_val_instances is used to balance the class instances found in the training and validation sets
param: nth_fold
param: method
return: void
"""
# check if log files exist
list_dir = os.listdir(os.path.join(flags['experiment_folder']))
if ('cv' + str(nth_fold) in list_dir) and ('perm' + str(nth_fold)
in list_dir):
raise ValueError('Dangerous! You have both cv and perm on the path.')
elif 'cv' + str(nth_fold) in list_dir:
object_folder = os.path.join(flags['experiment_folder'],
'cv' + str(nth_fold))
elif 'perm' + str(nth_fold) in list_dir:
object_folder = os.path.join(flags['experiment_folder'],
'perm' + str(nth_fold))
else:
raise ValueError('No cv or perm folder!')
train_log_file_path = os.path.join(object_folder, 'train', 'train_log.csv')
val_log_file_path = os.path.join(object_folder, 'val', 'val_log.csv')
if not os.path.isfile(train_log_file_path):
raise ValueError('no ' + train_log_file_path)
if not os.path.isfile(val_log_file_path):
raise ValueError('no ' + val_log_file_path)
# read csv
train_log = KScsv.read_csv(train_log_file_path)
val_log = KScsv.read_csv(val_log_file_path)
# count the number
if method == 'by_numbers':
train_log = select_instances.by_numbers(train_log)
val_log = select_instances.by_numbers(val_log)
KScsv.write_csv(train_log, train_log_file_path)
KScsv.write_csv(val_log, val_log_file_path)
else:
raise ValueError('no method ' + method + ' exists!')
def main(nth_fold, mode, flags, testdir):
"""
main trains, tests, or executes the model on the provided
data based on the specified preferences
param: nth_fold
param: mode
param: experiment_folder
param: image_ext
param: test_model
param: test_image_list
return: saves segmentation results to appropriate file/directory
"""
# check if cv or perm
list_dir = os.listdir(os.path.join(flags['experiment_folder']))
if ('cv' + str(nth_fold) in list_dir) and ('perm' + str(nth_fold)
in list_dir):
raise ValueError('Dangerous! You have both cv and perm on the path.')
elif 'cv' + str(nth_fold) in list_dir:
object_folder = os.path.join(flags['experiment_folder'],
'cv' + str(nth_fold))
elif 'perm' + str(nth_fold) in list_dir:
object_folder = os.path.join(flags['experiment_folder'],
'perm' + str(nth_fold))
else:
raise ValueError('No cv or perm folder!')
# Train model
if mode == 'train':
checkpoint_folder = os.path.join(object_folder, 'checkpoint')
network_stats_file_path = os.path.join(checkpoint_folder,
'network_stats.mat')
train_images_folder = os.path.join(object_folder, 'train', 'image')
if not os.path.isfile(network_stats_file_path):
list_images = glob.glob(
os.path.join(train_images_folder, '*' + flags['image_ext']))
print('calculating mean and variance image')
mean_image, variance_image = utils.calculate_mean_variance_image(
list_images)
routine.create_dir(checkpoint_folder)
matlab.save(network_stats_file_path, {
'mean_image': mean_image,
'variance_image': variance_image
})
tf_model_train.train(object_folder, flags)
# Test model on validation set
elif mode == 'test_model':
checkpointlist = glob.glob(
os.path.join(object_folder, 'checkpoint', 'model*meta'))
checkpointlist = [
file for file in checkpointlist if 'pretrain' not in file
]
temp = []
for filepath in checkpointlist:
basename = os.path.basename(filepath)
temp.append(int(float(basename.split('-')[-1].split('.')[0])))
temp = np.sort(temp)
model_path = os.path.join(
object_folder, 'checkpoint',
'model.ckpt-' + str(temp[flags['test_model']]))
print('use epoch %d : model %s' % (flags['test_model'], 'model.ckpt-' +
str(temp[flags['test_model']])))
test_images_list = flags['test_image_list']
filename_list = KScsv.read_csv(test_images_list)
tf_model_test.test(object_folder, model_path, filename_list, flags)
#Segment WSIs
elif mode == 'test_WSI':
checkpointlist = glob.glob(
os.path.join(object_folder, 'checkpoint', 'model*meta'))
checkpointlist = [
file for file in checkpointlist if 'pretrain' not in file
]
temp = []
for filepath in checkpointlist:
basename = os.path.basename(filepath)
temp.append(int(float(basename.split('-')[-1].split('.')[0])))
temp = np.sort(temp)
model_path = os.path.join(
object_folder, 'checkpoint',
'model.ckpt-' + str(temp[flags['test_model']]))
print('use epoch %d : model %s' % (flags['test_model'], 'model.ckpt-' +
str(temp[flags['test_model']])))
#should iterate over all subdirectories
paths = get_immediate_subdirectories(testdir)
list.sort(paths) #sort WSIs into ascending numerical order
#paths = paths[100:] #TODO: Enable based on which batch this code is running
print("TEST DIR: " + str(testdir))
for path in paths:
print(os.path.join(testdir, path))
if not os.path.isdir(
os.path.join(testdir, path + 'epiStromalSeg')
): #prevents this from being executed with exsiting directories
tf_model_test.testWSI(object_folder, model_path,
os.path.join(testdir, path), flags)
#TODO: uncomment to process only controls
#imageCSV = open(os.path.join('/data', 'avellal14', 'WSI_patches', 'BBD_NCC_Covariate_Outcome_KK_JH_modifiedWithPaths.csv'),'rb')
#reader = csv.reader(imageCSV)
#csvList = list(reader)
#patientId = path[:path.index('_')]
#caseControlList = next(subl for subl in csvList if patientId in subl)
#TODO: uncomment to process only cases
# if(caseControlList[1] == '1'): #only test the WSI if the image is indeed a case(1)
# tf_model_test.testWSI(object_folder, model_path, os.path.join(testdir,path), flags)
#Segment WSIs at patient level using data from CSV
elif mode == 'test_Case_Control':
checkpointlist = glob.glob(
os.path.join(object_folder, 'checkpoint', 'model*meta'))
checkpointlist = [
file for file in checkpointlist if 'pretrain' not in file
]
temp = []
for filepath in checkpointlist:
basename = os.path.basename(filepath)
temp.append(int(float(basename.split('-')[-1].split('.')[0])))
temp = np.sort(temp)
model_path = os.path.join(
object_folder, 'checkpoint',
'model.ckpt-' + str(temp[flags['test_model']]))
print('use epoch %d : model %s' % (flags['test_model'], 'model.ckpt-' +
str(temp[flags['test_model']])))
with open(
os.path.join('/home', 'avellal14', 'data', 'Adithya_BBD_NHS',
'NHS_BBD_CODE',
'casesAndMatchedControls224.csv')) as csvFile:
csvReader = csv.DictReader(csvFile)
for row in csvReader:
if (row['path'] == 'BBD_NCC_extractedat20x'
or row['path'] == 'BBD_NCC_extractedat20x_round2'):
testdir = os.path.join('/home', 'avellal14', 'data',
'Adithya_BBD_NHS', row['path'])
paths = get_subdirectories_by_patient(testdir, row['id'])
for path in paths:
print('CURRENT WSI BEING SEGMENTED',
os.path.join(testdir, path))
if not os.path.isdir(
os.path.join(testdir, path + '_cellSeg')
): #prevents this from being executed with exsiting directories
tf_model_test.testWSI(object_folder, model_path,
os.path.join(testdir, path),
flags)
def gen_train_val_data(nth_fold, flags):
"""
gen_train_val_data generates training and validation data for training the network. It builds
directories for train and test and extract patches according to the provided 'method', and it
maintains a log file containing the contents of all the data splits
param: nth_fold
param method: sliding_window
return: void
"""
########## check whether 'cv' or 'perm' exists and which one to use ##########
list_dir = os.listdir(os.path.join(flags['experiment_folder']))
if ('cv' + str(nth_fold) in list_dir) and ('perm' + str(nth_fold)
in list_dir):
raise ValueError('Dangerous! You have both cv and perm on the path.')
elif 'cv' + str(nth_fold) in list_dir:
object_folder = os.path.join(flags['experiment_folder'],
'cv' + str(nth_fold))
elif 'perm' + str(nth_fold) in list_dir:
object_folder = os.path.join(flags['experiment_folder'],
'perm' + str(nth_fold))
else:
raise ValueError('No cv or perm folder!')
########## create train and val paths ##########
path_dict = dict()
path_dict['train_folder'] = os.path.join(object_folder, 'train')
path_dict['val_folder'] = os.path.join(object_folder, 'val')
create_dir(path_dict['train_folder'])
create_dir(path_dict['val_folder'])
print("Gets to the beginning of an if statement")
########## extract patches and put in a designated directory ##########
if flags['gen_train_val_method'] == 'sliding_window':
key_list = ['image', 'groundtruth', 'weight']
for key in key_list:
path_dict['train_' + key + '_folder'] = os.path.join(
path_dict['train_folder'], key)
create_dir(path_dict['train_' + key + '_folder'])
path_dict['val_' + key + '_folder'] = os.path.join(
path_dict['val_folder'], key)
create_dir(path_dict['val_' + key + '_folder'])
list_dict = dict()
for key in key_list:
list_dict['train_' + key + '_list'] = KScsv.read_csv(
os.path.join(object_folder, 'train_' + key + '_list.csv'))
list_dict['val_' + key + '_list'] = KScsv.read_csv(
os.path.join(object_folder, 'val_' + key + '_list.csv'))
########## train ##########
for key in ['train', 'val']:
if not os.path.isfile(
os.path.join(path_dict[key + '_folder'],
key + '_log.csv')):
log_data = list()
for i_image in range(len(list_dict[key + '_image_list'])):
tic = time.time()
path_image = list_dict[key + '_image_list'][i_image][0]
path_groundtruth = list_dict[
key + '_groundtruth_list'][i_image][0]
path_weight = list_dict[key + '_weight_list'][i_image][0]
#Resize image, groundtruth, and weight from 10x input size to 2.5x (level at which network operates)
image = KSimage.imread(path_image)
image = KSimage.imresize(image, 0.25)
groundtruth = KSimage.imread(path_groundtruth)
groundtruth = KSimage.imresize(groundtruth, 0.25)
weight = KSimage.imread(path_weight)
weight = KSimage.imresize(weight, 0.25)
#make sure that groundtruth images have depth = 1
if (len(groundtruth.shape) > 2
and groundtruth.shape[2] > 1):
groundtruth = groundtruth[:, :, 1]
groundtruth[
groundtruth ==
3] = 2 #remove all intra-stromal epithelium labels and set them simply to stroma
groundtruth[
groundtruth ==
4] = 3 #fat label was originally 4 but is now changed to 3
dict_obj = {
'image': image,
'groundtruth': groundtruth,
'weight': weight
}
extractor = extract_patches.sliding_window(
dict_obj, flags['size_input_patch'],
flags['size_output_patch'], flags['stride'])
for j, (out_obj_dict, coord_dict) in enumerate(extractor):
images = out_obj_dict['image']
groundtruths = out_obj_dict['groundtruth']
weights = out_obj_dict['weight']
coord_images = coord_dict['image']
#############################################################
basename = os.path.basename(path_image)
basename = os.path.splitext(basename)[0]
image_name = os.path.join(
path_dict[key + '_image_folder'], basename +
'_idx' + str(j) + '_row' + str(coord_images[0]) +
'_col' + str(coord_images[1]) + flags['image_ext'])
label_name = os.path.join(
path_dict[key + '_groundtruth_folder'],
basename + '_idx' + str(j) + '_row' +
str(coord_images[0]) + '_col' +
str(coord_images[1]) + flags['groundtruth_ext'])
weight_name = os.path.join(
path_dict[key + '_weight_folder'],
basename + '_idx' + str(j) + '_row' +
str(coord_images[0]) + '_col' +
str(coord_images[1]) + flags['weight_ext'])
if not os.path.isfile(image_name):
KSimage.imwrite(images, image_name)
if not os.path.isfile(label_name):
KSimage.imwrite(groundtruths, label_name)
if not os.path.isfile(weight_name):
KSimage.imwrite(weights, weight_name)
log_data.append((image_name, label_name, weight_name))
print('finish processing %d image from %d images : %.2f' %
(i_image + 1, len(list_dict[key + '_image_list']),
time.time() - tic))
KScsv.write_csv(
log_data,
os.path.join(path_dict[key + '_folder'], key + '_log.csv'))
####################################################################################################################
else:
print(
"ONLY SLIDING WINDOW TRAINING IS SUPPORTED!!!! Training terminated."
)
return
def split_perm(obj_list, flags):
"""
split_perm splits data using permutation with stratification based on group label
param: images_list
param: labels_list
param: groups_list
param: num
param: test_percentage
param: val_percentage
return: void
"""
num = flags['num_split']
test_percentage = flags['test_percentage']
val_percentage = flags['val_percentage']
groups_label = list()
for file in obj_list['group']:
row = KScsv.read_csv(file)
groups_label.append(row[0][0])
groups_label = np.array(groups_label)
for key in obj_list.keys():
obj_list[key] = np.array(obj_list[key])
if test_percentage != 0:
skf = StratifiedShuffleSplit(n_splits=num,
test_size=test_percentage / 100.0)
for i_num, (train_idx, test_idx) in enumerate(
skf.split(obj_list['image'], groups_label)):
cv_folder = os.path.join(flags['experiment_folder'],
'perm' + str(i_num + 1))
create_dir(cv_folder)
test_obj_list_dict = dict()
train_obj_list_dict = dict()
for key in obj_list.keys():
test_obj_list_dict[key] = obj_list[key][test_idx]
train_obj_list_dict[key] = obj_list[key][train_idx]
train_groups_label = groups_label[train_idx]
sss = StratifiedShuffleSplit(n_splits=1,
test_size=val_percentage / 100.0)
for train_train_index, train_val_index in sss.split(
train_obj_list_dict['image'], train_groups_label):
train_train_obj_list_dict = dict()
train_val_obj_list_dict = dict()
for key in train_obj_list_dict.keys():
train_train_obj_list_dict[key] = train_obj_list_dict[key][
train_train_index]
train_val_obj_list_dict[key] = train_obj_list_dict[key][
train_val_index]
#################################################################
# test
for key in test_obj_list_dict.keys():
filename = os.path.join(cv_folder, 'test_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item] for item in test_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
#################################################################
# train
dict_path = flags['dict_path']
dict_ext = flags['dict_ext']
obj_list_dict = dict()
for key in dict_path.keys():
obj_list_dict[key] = glob.glob(
os.path.join(dict_path[key], '*' + dict_ext[key]))
temp_train_train_obj_list_dict = collections.defaultdict(list)
for name in train_train_obj_list_dict['image']:
basename = os.path.basename(name)
basename = os.path.splitext(basename)[0]
matching = sorted(
[s for s in obj_list_dict['image'] if basename in s])
for m in matching:
basename = os.path.basename(m)
basename = os.path.splitext(basename)[0]
basename_dict = dict()
for key in train_train_obj_list_dict.keys():
basename_dict[key] = os.path.join(
dict_path[key], basename + dict_ext[key])
if all(basename_dict[k] in obj_list_dict[k]
for k in basename_dict.keys()):
for key in train_train_obj_list_dict.keys():
temp_train_train_obj_list_dict[key].append(
basename_dict[key])
for key in train_train_obj_list_dict.keys():
train_train_obj_list_dict[key] = np.array(
temp_train_train_obj_list_dict[key])
filename = os.path.join(cv_folder,
'train_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item]
for item in train_train_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
#################################################################
# validation
dict_path = flags['dict_path']
dict_ext = flags['dict_ext']
obj_list_dict = dict()
for key in dict_path.keys():
obj_list_dict[key] = glob.glob(
os.path.join(dict_path[key], '*' + dict_ext[key]))
temp_train_val_obj_list_dict = collections.defaultdict(list)
for name in train_val_obj_list_dict['image']:
basename = os.path.basename(name)
basename = os.path.splitext(basename)[0]
matching = sorted(
[s for s in obj_list_dict['image'] if basename in s])
for m in matching:
basename = os.path.basename(m)
basename = os.path.splitext(basename)[0]
basename_dict = dict()
for key in train_val_obj_list_dict.keys():
basename_dict[key] = os.path.join(
dict_path[key], basename + dict_ext[key])
if all(basename_dict[k] in obj_list_dict[k]
for k in basename_dict.keys()):
for key in train_val_obj_list_dict.keys():
temp_train_val_obj_list_dict[key].append(
basename_dict[key])
for key in train_val_obj_list_dict.keys():
train_val_obj_list_dict[key] = np.array(
temp_train_val_obj_list_dict[key])
filename = os.path.join(cv_folder, 'val_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item]
for item in train_val_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
else:
for i_num in range(num):
cv_folder = os.path.join(flags['experiment_folder'],
'perm' + str(i_num + 1))
create_dir(cv_folder)
train_obj_list_dict = dict()
for key in obj_list.keys():
train_obj_list_dict[key] = obj_list[key]
train_groups_label = groups_label
sss = StratifiedShuffleSplit(n_splits=1,
test_size=val_percentage / 100.0)
for train_train_index, train_val_index in sss.split(
train_obj_list_dict['image'], train_groups_label):
train_train_obj_list_dict = dict()
train_val_obj_list_dict = dict()
for key in train_obj_list_dict.keys():
train_train_obj_list_dict[key] = train_obj_list_dict[key][
train_train_index]
train_val_obj_list_dict[key] = train_obj_list_dict[key][
train_val_index]
#################################################################
# train
dict_path = flags['dict_path']
dict_ext = flags['dict_ext']
obj_list_dict = dict()
for key in dict_path.keys():
obj_list_dict[key] = glob.glob(
os.path.join(dict_path[key], '*' + dict_ext[key]))
temp_train_train_obj_list_dict = collections.defaultdict(list)
for name in train_train_obj_list_dict['image']:
basename = os.path.basename(name)
basename = os.path.splitext(basename)[0]
matching = sorted(
[s for s in obj_list_dict['image'] if basename in s])
for m in matching:
basename = os.path.basename(m)
basename = os.path.splitext(basename)[0]
basename_dict = dict()
for key in train_train_obj_list_dict.keys():
basename_dict[key] = os.path.join(
dict_path[key], basename + dict_ext[key])
if all(basename_dict[k] in obj_list_dict[k]
for k in basename_dict.keys()):
for key in train_train_obj_list_dict.keys():
temp_train_train_obj_list_dict[key].append(
basename_dict[key])
for key in train_train_obj_list_dict.keys():
train_train_obj_list_dict[key] = np.array(
temp_train_train_obj_list_dict[key])
filename = os.path.join(cv_folder,
'train_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item]
for item in train_train_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
#################################################################
# validation
dict_path = flags['dict_path']
dict_ext = flags['dict_ext']
obj_list_dict = dict()
for key in dict_path.keys():
obj_list_dict[key] = glob.glob(
os.path.join(dict_path[key], '*' + dict_ext[key]))
temp_train_val_obj_list_dict = collections.defaultdict(list)
for name in train_val_obj_list_dict['image']:
basename = os.path.basename(name)
basename = os.path.splitext(basename)[0]
matching = sorted(
[s for s in obj_list_dict['image'] if basename in s])
for m in matching:
basename = os.path.basename(m)
basename = os.path.splitext(basename)[0]
basename_dict = dict()
for key in train_val_obj_list_dict.keys():
basename_dict[key] = os.path.join(
dict_path[key], basename + dict_ext[key])
if all(basename_dict[k] in obj_list_dict[k]
for k in basename_dict.keys()):
for key in train_val_obj_list_dict.keys():
temp_train_val_obj_list_dict[key].append(
basename_dict[key])
for key in train_val_obj_list_dict.keys():
train_val_obj_list_dict[key] = np.array(
temp_train_val_obj_list_dict[key])
filename = os.path.join(cv_folder, 'val_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item]
for item in train_val_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
def split_cv(obj_list, flags):
"""
split_cv splits data into train, validation, and test stratified by the group label
param: images_list
param: labels_list
param: groups_list
param: num
param: val_percentage
return: void
"""
num = flags['num_split']
val_percentage = flags['val_percentage']
groups_label = list()
for file in obj_list['group']:
row = KScsv.read_csv(file)
groups_label.append(row[0][0])
groups_label = np.array(groups_label)
for key in obj_list.keys():
obj_list[key] = np.array(obj_list[key])
skf = StratifiedKFold(n_splits=num)
for i_num, (train_idx, test_idx) in enumerate(
skf.split(obj_list['image'], groups_label)):
cv_folder = os.path.join(flags['experiment_folder'],
'cv' + str(i_num + 1))
create_dir(cv_folder)
test_obj_list_dict = dict()
train_obj_list_dict = dict()
for key in obj_list.keys():
test_obj_list_dict[key] = obj_list[key][test_idx]
train_obj_list_dict[key] = obj_list[key][train_idx]
train_groups_label = groups_label[train_idx]
sss = StratifiedShuffleSplit(n_splits=1,
test_size=val_percentage / 100.0)
for train_train_index, train_val_index in sss.split(
train_obj_list_dict['image'], train_groups_label):
train_train_obj_list_dict = dict()
train_val_obj_list_dict = dict()
for key in train_obj_list_dict.keys():
train_train_obj_list_dict[key] = train_obj_list_dict[key][
train_train_index]
train_val_obj_list_dict[key] = train_obj_list_dict[key][
train_val_index]
#################################################################
# test
for key in test_obj_list_dict.keys():
filename = os.path.join(cv_folder, 'test_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item] for item in test_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
#################################################################
# train
for key in train_train_obj_list_dict.keys():
filename = os.path.join(cv_folder, 'train_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item] for item in train_train_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
#################################################################
# validation
for key in train_val_obj_list_dict.keys():
filename = os.path.join(cv_folder, 'val_' + key + '_list.csv')
if not os.path.isfile(filename):
row_list = [[item] for item in train_val_obj_list_dict[key]]
KScsv.write_csv(row_list, filename)
def inputs(object_folder, mode, flags, mat_contents):
#keys = ['HE', 'DAPI', 'label']
key_list = list(flags['dict_path'].keys())
key_list.remove('group')
if mode == 'train':
log_file_path = os.path.join(object_folder, 'train', 'train_log.csv')
else:
log_file_path = os.path.join(object_folder, 'val', 'val_log.csv')
log_list = KScsv.read_csv(log_file_path)
#image_dict = collections.defaultdict(list)
#label_dict = collections.defaultdict(list)
#weight_dict = collections.defaultdict(list)
all_img_dict = {}
slice_input_list = []
for ind, key in enumerate(key_list):
key_img_list = []
#deal with mean, var img
mean_img = np.float32(mat_contents[key + '_mean'])
var_img = np.float32(mat_contents[key + '_var'])
if mean_img.ndim == 2:
mean_img = np.expand_dims(mean_img, axis=2)
if var_img.ndim == 2:
var_img = np.expand_dims(var_img, axis=2)
#mean_image = tf.constant(mean_img, name='mean_image')
#var_image = tf.constant(var_img, name='var_image')
for row in log_list:
key_img_list.append(row[ind])
slice_input_list.append(key_img_list)
min_queue_examples = int(
len(slice_input_list[0]) * flags['min_fraction_of_examples_in_queue'])
print('Filling queue with %d images before starting to train. '
'This will take a few minutes.' % min_queue_examples)
# Create a queue that produces the filenames to read.
combine_image_dict = list()
#fliename_queue- list of file names
filename_queue = tf.train.slice_input_producer(slice_input_list,
shuffle=True)
queue_dict, label_dict = read_data(filename_queue, flags)
processed_dict = process_image_and_label(queue_dict, mat_contents, flags)
# Generate a batch of images and labels by building up a queue of examples.
batch_list, label = generate_batch(processed_dict,
label_dict,
min_queue_examples,
int(flags['batch_size']),
shuffle=False,
flags=flags)
#create final combined dict
#combine_image_dict = collections.defaultdict(list)
#combine_label_dict = collections.defaultdict(list)
combine_image_dict = {}
combine_label_dict = {}
for ind, key in enumerate(key_list):
#combine_image_dict[key].append(batch_list[ind])
combine_image_dict[key] = batch_list[ind]
#combine_image_dict[key] = tf.concat(combine_image_dict[key],0)
combine_label_dict[key] = label
return combine_image_dict, combine_label_dict
def inputs(mean_image, variance_image, object_folder, mode, flags):
"""
inputs takes in either training or validation inputs, then performs aggressive data
augmentation and normalization using process_image_and_label and places them into
a mini_batch to be passed through the network
param: mean_image
param: variance_image
param: object_folder
param: mode
param: min_fraction_of_examples_in_queue
param: batch_size
return: image dict, label dict, weight dict
"""
if mode == 'train':
log_file_path = os.path.join(object_folder, 'train', 'train_log.csv')
else:
log_file_path = os.path.join(object_folder, 'val', 'val_log.csv')
log_list = KScsv.read_csv(log_file_path)
image_dict = collections.defaultdict(list)
label_dict = collections.defaultdict(list)
weight_dict = collections.defaultdict(list)
for row in log_list:
image_dict['image'].append(row[0])
label_dict['label'].append(row[1])
weight_dict['weight'].append(row[2])
min_queue_examples = int(
len(image_dict['image']) * flags['min_fraction_of_examples_in_queue'])
print('Filling queue with %d images before starting to train. '
'This will take a few minutes.' % min_queue_examples)
# Create a queue that produces the filenames to read.
combine_image_dict = list()
combine_label_dict = list()
combine_weight_dict = list()
filename_queue = tf.train.slice_input_producer(
[image_dict['image'], label_dict['label'], weight_dict['weight']],
shuffle=True)
image, label, weight = read_data(filename_queue, flags)
image = tf.cast(image, tf.float32)
label = tf.cast(label, tf.float32)
weight = tf.cast(weight, tf.float32)
image, label, weight = process_image_and_label(image, label, weight,
mean_image, variance_image,
flags)
# Generate a batch of images and labels by building up a queue of examples.
image, label, weight = generate_batch(image,
label,
weight,
min_queue_examples,
int(flags['batch_size']),
shuffle=False,
flags=flags)
combine_image_dict.append(image)
combine_label_dict.append(label)
combine_weight_dict.append(weight)
out_image = tf.concat(0, combine_image_dict)
out_label = tf.concat(0, combine_label_dict)
out_weight = tf.concat(0, combine_weight_dict)
return {'images': out_image, 'labels': out_label, 'weights': out_weight}
