def setReloadedData(self, uidx, path):
c = h5py.File(path)
agen = augments.Augments()
object_num = len(c['slideIdx'][:])
augment_object_num = agen.AUG_BATCH_SIZE * object_num
for idx in range(self.u_size):
if idx == uidx:
for i in range(object_num):
# init sample
init_sample = dict(id=0,
checkpoints=0,
f_idx=0,
aurl=0,
feature=0,
label=0,
iteration=0,
centX=0,
centY=0,
slideIdx=0,
slide=None)
# add feature
init_sample['id'] = c['db_id'][:][i, 0]
init_sample['checkpoints'] = c['checkpoints'][:][i, 0]
init_sample['aurl'] = c['augUrls'][:][i]
init_sample['slideIdx'] = c['slideIdx'][:][i, 0]
init_sample['slide'] = c['slides'][:][c['slideIdx'][:][i,
0]]
init_sample['centX'] = c['x_centroid'][:][i, 0]
init_sample['centY'] = c['y_centroid'][:][i, 0]
init_sample['f_idx'] = c['f_idx'][:][i, 0]
init_sample['feature'] = c['features'][:][i]
init_sample['label'] = 1 if c['labels'][:][i, 0] > 0 else 0
init_sample['iteration'] = c['sample_iter'][:][i, 0]
self.users[idx]['samples'].append(init_sample)
a_idx = 0
for i in range(object_num):
# init sample and augment
init_augment = dict(id=0,
checkpoints=0,
feature=0,
label=0)
a_featureSet = np.zeros(
(agen.AUG_BATCH_SIZE,
self.FEATURE_DIM)).astype(np.float32)
a_labelSet = np.zeros(
(agen.AUG_BATCH_SIZE, )).astype(np.uint8)
a_idSet = []
a_checkpointSet = []
if c['augments_labels'][:][a_idx, 0] > 0:
a_labelSet.fill(1)
for j in range(agen.AUG_BATCH_SIZE):
a_idSet.append(c['augments_db_id'][:][a_idx, 0])
a_checkpointSet.append(
c['augments_checkpoints'][:][a_idx, 0])
a_featureSet[j, :] = c['augments_features'][:][a_idx]
a_idx += 1
# add feature
init_augment['id'] = a_idSet
init_augment['checkpoints'] = a_checkpointSet
init_augment['feature'] = a_featureSet
init_augment['label'] = a_labelSet
self.users[idx]['augments'].append(init_augment)
def getData(self, users):
if self.reloaded == "true":
tag = self.uid[-3:]
fileName = self.classifier + "-" + tag + ".h5"
else:
fileName = self.classifier + ".h5"
data = {}
data['iterations'] = str(self.iteration)
data['filename'] = fileName
data['samples'] = []
sample_num = len(users['samples'])
features = np.zeros((sample_num, self.FEATURE_DIM), dtype=np.float32)
labels = np.zeros((sample_num, 1), dtype=np.int32)
db_id = np.zeros((sample_num, 1), dtype=np.int32)
checkpoints = np.zeros((sample_num, 1), dtype=np.int32)
f_idx = np.zeros((sample_num, 1), dtype=np.int32)
sample_iter = np.zeros((sample_num, 1), dtype=np.int32)
x_centroid = np.zeros((sample_num, 1), dtype=np.float32)
y_centroid = np.zeros((sample_num, 1), dtype=np.float32)
slideIdx = np.zeros((sample_num, 1), dtype=np.int32)
slides = []
class_names = []
augUrls = []
# add augments
agen = augments.Augments()
augments_num = agen.AUG_BATCH_SIZE * sample_num
augments_features = np.zeros((augments_num, self.FEATURE_DIM),
dtype=np.float32)
augments_labels = np.zeros((augments_num, 1), dtype=np.int32)
augments_db_id = np.zeros((augments_num, 1), dtype=np.int32)
augments_checkpoints = np.zeros((augments_num, 1), dtype=np.int32)
# set slides to unique
for sample in users['samples']:
slides.append(sample['slide'].encode("utf-8"))
slides = np.unique(slides)
sidx = 0
for sample in users['samples']:
sample_data = {}
sample_data['id'] = str(sample['id'])
sample_data['label'] = "1" if sample['label'] == 1 else "-1"
sample_data['iteration'] = str(sample['iteration'])
sample_data['aurl'] = sample['aurl']
data['samples'].append(sample_data)
# save file
features[sidx] = sample['feature']
labels[sidx] = 1 if sample['label'] == 1 else -1
db_id[sidx] = sample['id']
checkpoints[sidx] = sample['checkpoints']
f_idx[sidx] = sample['f_idx']
sample_iter[sidx] = sample['iteration']
x_centroid[sidx] = sample['centX']
y_centroid[sidx] = sample['centY']
for i in range(len(slides)):
if slides[i] == sample['slide'].encode("utf-8"):
slideIdx[sidx] = i
augUrls.append(sample['aurl'].encode("utf-8"))
sidx += 1
class_names.append(self.negclass.encode("utf-8"))
class_names.append(self.posclass.encode("utf-8"))
mean = np.reshape(np.mean(features[:], axis=0),
(self.FEATURE_DIM, 1)).astype(np.float32)
std_dev = np.reshape(np.std(features[:], axis=0),
(self.FEATURE_DIM, 1)).astype(np.float32)
aidx = 0
for sample in users['augments']:
# related to save file
for i in range(agen.AUG_BATCH_SIZE):
augments_features[aidx] = sample['feature'][i]
augments_labels[aidx] = 1 if sample['label'][i] == 1 else -1
augments_db_id[aidx] = sample['id'][i]
augments_checkpoints[aidx] = sample['checkpoints'][i]
aidx += 1
# write training file
out_train_file = self.traindir + fileName
output = h5py.File(out_train_file, 'w')
output.create_dataset('features', data=features)
output.create_dataset('labels', data=labels)
output.create_dataset('db_id', data=db_id)
output.create_dataset('checkpoints', data=checkpoints)
output.create_dataset('augments_features', data=augments_features)
output.create_dataset('augments_labels', data=augments_labels)
output.create_dataset('augments_db_id', data=augments_db_id)
output.create_dataset('augments_checkpoints',
data=augments_checkpoints)
output.create_dataset('sample_iter', data=sample_iter)
output.create_dataset('x_centroid', data=x_centroid)
output.create_dataset('y_centroid', data=y_centroid)
output.create_dataset('slideIdx', data=slideIdx)
output.create_dataset('slides', data=slides)
output.create_dataset('f_idx', data=f_idx)
output.create_dataset('class_names', data=class_names)
output.create_dataset('augUrls', data=augUrls)
output.create_dataset('mean', data=mean)
output.create_dataset('std_dev', data=std_dev)
output.close()
return data
def run():
# initialize VGG Model and PCA
iset = init.Init()
# initialize neural network model
model = networks.Network()
model.init_model()
# initialize global instance
uset = users.Users()
# store special features in memory
# dset_special = dataset.Dataset(set.PATH_TO_SPECIAL)
dset_special = None
print "Dataset Loaded."
# set normal features in memory to false
is_normal_loaded = True
tset_name = None
is_reloaded = False
m_checkpoints = 0
while True:
queue = db.lrange(set.REQUEST_QUEUE, set.REQUEST_START, set.REQUEST_END)
q_uid = None
# initialize local instance
select = selectonly.Select()
finalize = save.Save()
viewer = view.View()
retrain_v = retrainView.retrainView()
retrain_h = retrainHeatmap.retrainHeatmap()
heat = heatmap.Heatmap()
t_train = train.Train()
report_label = label.label()
report_count = count.count()
report_map = mapping.map()
for q in queue:
q = json.loads(q.decode("utf-8"))
q_uid = q["uid"]
target = q["target"]
session_uid = q["uid"]
dataSetPath = set.DATASET_DIR + q["dataset"]
pcaPath = set.DATASET_DIR + q["pca"]
# if specific features then set m_loaded to true
is_normal_loaded = False if dataSetPath == set.PATH_TO_SPECIAL else True
if target == "label":
report_label.setData(q)
if target == "count":
report_count.setData(q)
if target == "map":
report_map.setData(q)
if target == 'selectonly':
select.setData(q)
if target == 'save':
finalize.setData(q)
if target == 'view':
viewer.setData(q)
if target == 'retrainView':
retrain_v.setData(q)
if target == 'retrainHeatmap':
retrain_h.setData(q)
if target == 'heatmapAll':
heatmaps = q["viewJSONs"]
if target == 'heatmap':
heat.setData(q)
if target == 'train':
t_train.setData(q)
if target == 'reload':
t_path = set.TRAININGSET_DIR + q["trainingSetName"]
is_reloaded = True
if target == 'reviewSave':
q_samples = json.loads(q["samples"])
if q_uid is not None:
print target, " Session Start ....."
no_uid = True
uidx = 0
# find current user Index
for i in range(len(uset.users)):
if uset.users[i]['uid'] == session_uid:
uidx = i
no_uid = False
if no_uid:
# set users data
uset.addUser(session_uid)
if is_normal_loaded:
dset = dataset.Dataset(dataSetPath)
else:
dset = dset_special
PCA = joblib.load(pcaPath)
if target == 'selectonly':
uset.setIter(uidx, select.iter)
print "Predict Start ... "
t0 = time()
scores = model.predict_prob(dset.features)
t1 = time()
print "Predict took ", t1 - t0
# Find uncertain samples
data = select.getData(scores, dset.slideIdx, dset.slides, dset.x_centroid, dset.y_centroid)
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'view':
slide_idx = dset.getSlideIdx(viewer.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
print "Predict Start ... "
t0 = time()
predictions = model.predict(feature_set)
t1 = time()
print "Predict took ", t1 - t0
object_idx = load(
viewer.left, viewer.right, viewer.top, viewer.bottom, x_centroid_set.astype(np.float), y_centroid_set.astype(np.float)
)
data = {}
for i in object_idx:
data[str(x_centroid_set[i][0])+'_'+str(y_centroid_set[i][0])] = str(predictions[i])
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'heatmap':
slide_idx = dset.getSlideIdx(heat.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
print "Predict Start ... "
t0 = time()
if set.IS_HEATMAP == False:
scores = model.predict_prob(feature_set)
t1 = time()
print "Predict took ", t1 - t0
# set x and y maps
heat.setXandYmap()
# write heatmaps
heat.setHeatMap(x_centroid_set, y_centroid_set, scores)
# get heatmap data
data = heat.getData(0)
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'heatmapAll':
data = []
index = 0
t0 = time()
scores = model.predict_prob(dset.features)
t1 = time()
print "Predict took ", t1 - t0
for h in heatmaps:
h['uid'] = session_uid
heat.setData(h)
slide_idx = dset.getSlideIdx(heat.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
# feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
score_set = scores[data_idx: data_idx+object_num]
# set x and y maps
heat.setXandYmap()
# write heatmaps
heat.setHeatMap(x_centroid_set, y_centroid_set, score_set)
# get heatmap data
data_k = heat.getData(index)
data.append(data_k)
index += 1
# print data
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'reload':
# initialize augment
agen = augments.Augments()
# set user train samples
# uset.setReloadedData(uidx, t_path, dset.slides)
uset.setReloadedData(uidx, t_path)
sample_size = len(uset.users[uidx]['samples'])
m_checkpoints = uset.users[uidx]['samples'][sample_size-1]['checkpoints']
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
tset_path = t_path.split('/')[-1]
tset_name = tset_path.split('.')[0]
print "Training ... ", len(train_labels)
t0 = time()
model.train_model(train_features, train_labels, tset_name)
t1 = time()
print "Training took ", t1 - t0
data = {"success": 'pass'}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'label':
# initialize augment
agen = augments.Augments()
# set user train samples
uset.setReloadedData(uidx, report_label.trainSet)
sample_size = len(uset.users[uidx]['samples'])
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
print "Training ... ", len(train_labels)
t0 = time()
model.train_model(train_features, train_labels, report_label.classifier)
t1 = time()
print "Training took ", t1 - t0
slide_idx = dset.getSlideIdx(report_label.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
test_features = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
print "Testing Start ... "
t0 = time()
predicts = model.predict(test_features)
t1 = time()
print "Predict took ", t1 - t0
inputImageFile = '/datasets/tif/'+ report_label.slide + '.svs.dzi.tif'
bold = 512
bold_left = report_label.left - bold
bold_top = report_label.top - bold
bold_bottom = report_label.bottom + bold
bold_right = report_label.right + bold
bold_width = report_label.width + 2*bold
bold_height = report_label.height + 2*bold
ts = large_image.getTileSource(inputImageFile)
region = dict(
left=report_label.left, top=report_label.top,
width=report_label.width, height=report_label.height,
)
im_region = ts.getRegion(
region=region, format=large_image.tilesource.TILE_FORMAT_NUMPY
)[0]
mydb = mysql.connector.connect(
host=set.MYSQL_HOST,
user="******",
passwd="guest",
database="nuclei",
charset='utf8',
use_unicode=True
)
boundaryTablename = 'sregionboundaries'
runcursor = mydb.cursor()
query = 'SELECT centroid_x, centroid_y, boundary from ' + boundaryTablename + ' where slide="' + report_label.slide + \
'" AND centroid_x BETWEEN ' + str(report_label.left) + ' AND ' + str(report_label.right) + \
' AND centroid_y BETWEEN ' + str(report_label.top) + ' AND ' + str(report_label.bottom)
runcursor.execute(query)
boundarySet = runcursor.fetchall()
# find region index from hdf5
object_idx = load(
report_label.left, report_label.right, report_label.top, report_label.bottom, x_centroid_set.astype(np.float), y_centroid_set.astype(np.float)
)
# set an array for boundary points in a region to zero
im_bold = np.zeros((bold_height, bold_width), dtype=np.uint8)
for i in object_idx:
for j in range(len(boundarySet)):
x = int(boundarySet[j][0])
y = int(boundarySet[j][1])
boundaryPoints = []
if x == int(x_centroid_set[i, 0]) and y == int(y_centroid_set[i, 0]):
object = boundarySet[j][2].encode('utf-8').split(' ')
object_points = []
for p in range(len(object)-1):
intP = map(int, object[p].split(','))
intP[0] = intP[0] - report_label.left + bold
intP[1] = intP[1] - report_label.top + bold
object_points.append(intP)
boundaryPoints.append(np.asarray(object_points))
cv2.fillPoly(im_bold, boundaryPoints, 255 if predicts[i] > 0 else 128)
im_out = im_bold[bold:bold+report_label.height, bold:bold+report_label.width]
imsave(report_label.inFile, im_out)
runcursor.close()
mydb.close()
print ("label success ", report_label.inFile)
data = {"success": report_label.outFile}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
uset.users = []
uset.u_size = 0
model = networks.Network()
model.init_model()
print ("label done")
if target == 'count':
# initialize augment
agen = augments.Augments()
# set user train samples
uset.setReloadedData(uidx, report_count.trainSet)
sample_size = len(uset.users[uidx]['samples'])
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
print "Training ... ", len(train_labels)
t0 = time()
model.train_model(train_features, train_labels, report_count.classifier)
t1 = time()
print "Training took ", t1 - t0
print "Testing Start ... "
t0 = time()
predicts = model.predict(dset.features)
t1 = time()
print "Predict took ", t1 - t0
# find positive and negative numbers for each slide
pos_num = []
neg_num = []
for i in range(dset.n_slides):
if i == len(dset.dataIdx) - 1:
predict = predicts[dset.dataIdx[i, 0]:]
else:
predict = predicts[dset.dataIdx[i, 0]: dset.dataIdx[i+1, 0]]
pos = len(predict[predict>0])
neg = len(predict) - pos
pos_num.append(pos)
neg_num.append(neg)
print('>> Writing count file')
out_file = open(report_count.inFile, 'w')
out_file.write("Slide\t")
out_file.write("Predicted positive (superpixels)\t")
out_file.write("Predicted negative (superpixels)\t")
out_file.write("\n")
for i in range(len(dset.slides)):
out_file.write("%s\t" % dset.slides[i])
out_file.write("%d\t" % pos_num[i])
out_file.write("%d\t" % neg_num[i])
out_file.write("\n")
out_file.close()
print ("count success ", report_count.inFile)
data = {"success": report_count.outFile}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
uset.users = []
uset.u_size = 0
model = networks.Network()
model.init_model()
print ("count done")
if target == 'map':
# initialize augment
agen = augments.Augments()
# set user train samples
uset.setReloadedData(uidx, report_map.trainSet)
sample_size = len(uset.users[uidx]['samples'])
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
print "Training ... ", len(train_labels)
t0 = time()
model.train_model(train_features, train_labels, report_map.classifier)
t1 = time()
print "Training took ", t1 - t0
slide_idx = dset.getSlideIdx(report_map.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
test_features = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
print "Testing Start ... "
t0 = time()
predicts = model.predict(test_features)
t1 = time()
print "Predict took ", t1 - t0
output = h5py.File(report_map.inFile, 'w')
output.create_dataset('features', data=test_features)
output.create_dataset('predicts', data=predicts)
output.create_dataset('x_centroid', data=x_centroid_set)
output.create_dataset('y_centroid', data=y_centroid_set)
output.create_dataset('slides', data=[report_map.slide])
output.close()
print ("map success ", report_map.inFile)
data = {"success": report_map.outFile}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
uset.users = []
uset.u_size = 0
model = networks.Network()
model.init_model()
print ("map done")
if target == 'save':
data = finalize.getData(uset.users[uidx])
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'review':
data = {}
data['review'] = []
for sample in uset.users[uidx]['samples']:
sample_data = {}
sample_data['id'] = str(sample['id'])
sample_data['label'] = 1 if sample['label'] == 1 else -1
sample_data['iteration'] = int(sample['iteration'])
sample_data['slide'] = str(sample['slide'])
sample_data['centX'] = str(sample['centX'])
sample_data['centY'] = str(sample['centY'])
sample_data['boundary'] = ""
sample_data['maxX'] = 0
sample_data['maxY'] = 0
data['review'].append(sample_data)
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'train':
# increase checkpoint by 1
m_checkpoints += 1
# initialize augment
agen = augments.Augments()
uset.setIter(uidx, t_train.iter)
for sample in t_train.samples:
# init sample and augment
init_sample = dict(
id=0, f_idx=0, checkpoints=0,
aurl=None, feature=None, label=0,
iteration=0, centX=0, centY=0,
slideIdx=0, slide=None
)
init_augment = dict(
id=[], checkpoints=[], feature=[], label=[]
)
# check db_id in users samples
remove_idx = []
for u in range(len(uset.users[uidx]['samples'])):
if uset.users[uidx]['samples'][u]['id'] == sample['id']:
remove_idx.append(u)
for r in remove_idx:
uset.users[uidx]['samples'].pop(r)
uset.users[uidx]['augments'].pop(r)
# add feature
init_sample['id'] = sample['id']
init_sample['aurl'] = str(sample['aurl'])
init_sample['slide'] = str(sample['slide'])
slide_idx = dset.getSlideIdx(init_sample['slide'])
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
slideIdx_set = dset.getSlideIdxSet(data_idx, object_num)
c_idx = getIdx(
x_centroid_set.astype(np.float), y_centroid_set.astype(np.float), slideIdx_set.astype(np.int), np.float32(sample['centX']), np.float32(sample['centY']), slide_idx
)
f_idx = data_idx + c_idx
init_sample['f_idx'] = f_idx
init_sample['feature'] = feature_set[c_idx]
init_sample['label'] = 1 if sample['label'] == 1 else 0
init_sample['iteration'] = t_train.iter
init_sample['centX'] = sample['centX']
init_sample['centY'] = sample['centY']
init_sample['checkpoints'] = m_checkpoints
# add augment features
slide_idx = dset.getSlideIdx(init_sample['slide'])
slide_mean = dset.getWSI_Mean(slide_idx)
slide_std = dset.getWSI_Std(slide_idx)
a_imgs = agen.prepare_image(init_sample['aurl'], slide_mean, slide_std)
a_featureSet = iset.FC1_MODEL.predict(a_imgs)
a_featureSet = PCA.transform(a_featureSet)
a_labelSet = np.zeros((agen.AUG_BATCH_SIZE, )).astype(np.uint8)
a_idSet = []
a_checkpointSet = []
for i in range(agen.AUG_BATCH_SIZE):
a_idSet.append(init_sample['id'])
a_checkpointSet.append(init_sample['checkpoints'])
if init_sample['label'] > 0:
a_labelSet.fill(1)
init_augment['id'] = a_idSet
init_augment['feature'] = a_featureSet
init_augment['label'] = a_labelSet
init_augment['checkpoints'] = a_checkpointSet
uset.setAugmentData(uidx, init_augment)
uset.setTrainSampleData(uidx, init_sample)
sample_size = len(uset.users[uidx]['samples'])
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
# train_labels = to_categorical(train_labels, num_classes=2)
if tset_name is None:
tset_name = t_train.classifier
print "Training ... ", len(train_labels)
t0 = time()
model.train_model(train_features, train_labels, tset_name)
t1 = time()
print "Training took ", t1 - t0
data = {"success": 'pass'}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'retrainView':
m_checkpoints += 1
# initialize augment
agen = augments.Augments()
uset.setIter(uidx, retrain_v.iter)
print "Augment ... ", len(retrain_v.samples)
t0 = time()
for sample in retrain_v.samples:
# init sample and augment
init_sample = dict(
id=0, f_idx=0, checkpoints=0,
aurl=None, feature=None, label=0,
iteration=0, centX=0, centY=0,
slideIdx=0, slide=None
)
init_augment = dict(
id=[], checkpoints=[], feature=[], label=[]
)
# remove samples stored if it already exists
remove_idx = []
for u in range(len(uset.users[uidx]['samples'])):
if uset.users[uidx]['samples'][u]['id'] == sample['id']:
remove_idx.append(u)
for r in remove_idx:
uset.users[uidx]['samples'].pop(r)
uset.users[uidx]['augments'].pop(r)
# add feature
init_sample['id'] = sample['id']
init_sample['aurl'] = str(sample['aurl'])
init_sample['slide'] = str(sample['slide'])
slide_idx = dset.getSlideIdx(init_sample['slide'])
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
slideIdx_set = dset.getSlideIdxSet(data_idx, object_num)
c_idx = getIdx(
x_centroid_set.astype(np.float), y_centroid_set.astype(np.float), slideIdx_set.astype(np.int), np.float32(sample['centX']), np.float32(sample['centY']), slide_idx
)
f_idx = data_idx + c_idx
init_sample['f_idx'] = f_idx
init_sample['feature'] = feature_set[c_idx]
init_sample['label'] = 1 if sample['label'] == 1 else 0
init_sample['iteration'] = retrain_v.iter
init_sample['centX'] = sample['centX']
init_sample['centY'] = sample['centY']
init_sample['checkpoints'] = m_checkpoints
# add augment features
slide_idx = dset.getSlideIdx(init_sample['slide'])
slide_mean = dset.getWSI_Mean(slide_idx)
slide_std = dset.getWSI_Std(slide_idx)
a_imgs = agen.prepare_image(init_sample['aurl'], slide_mean, slide_std)
a_featureSet = iset.FC1_MODEL.predict(a_imgs)
a_featureSet = PCA.transform(a_featureSet)
a_labelSet = np.zeros((agen.AUG_BATCH_SIZE, )).astype(np.uint8)
a_idSet = []
a_checkpointSet = []
for i in range(agen.AUG_BATCH_SIZE):
a_idSet.append(init_sample['id'])
a_checkpointSet.append(init_sample['checkpoints'])
if init_sample['label'] > 0:
a_labelSet.fill(1)
init_augment['id'] = a_idSet
init_augment['feature'] = a_featureSet
init_augment['label'] = a_labelSet
init_augment['checkpoints'] = a_checkpointSet
uset.setAugmentData(uidx, init_augment)
uset.setTrainSampleData(uidx, init_sample)
t1 = time()
print "Augmentation took ", t1 - t0
sample_size = len(uset.users[uidx]['samples'])
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
# train_labels = to_categorical(train_labels, num_classes=2)
if tset_name is None:
tset_name = retrain_v.classifier
t0 = time()
model.train_model(train_features, train_labels, tset_name)
t1 = time()
print "Training took ", t1 - t0, " ", len(train_labels), "Samples"
slide_idx = dset.getSlideIdx(retrain_v.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
print "Testing Start ... "
t0 = time()
predictions = model.predict(feature_set)
t1 = time()
print "Predict took ", t1 - t0
object_idx = load(
retrain_v.left, retrain_v.right, retrain_v.top, retrain_v.bottom, x_centroid_set.astype(np.float), y_centroid_set.astype(np.float)
)
data = {}
for i in object_idx:
data[str(x_centroid_set[i][0])+'_'+str(y_centroid_set[i][0])] = str(predictions[i])
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'retrainHeatmap':
m_checkpoints += 1
# initialize augment
agen = augments.Augments()
uset.setIter(uidx, retrain_h.iter)
for sample in retrain_h.samples:
# init sample and augment
init_sample = dict(
id=0, f_idx=0, checkpoints=0,
aurl=None, feature=None, label=0,
iteration=0, centX=0, centY=0,
slideIdx=0, slide=None
)
init_augment = dict(
id=[], checkpoints=[], feature=[], label=[]
)
# remove samples stored if it already exists
remove_idx = []
for u in range(len(uset.users[uidx]['samples'])):
if uset.users[uidx]['samples'][u]['id'] == sample['id']:
remove_idx.append(u)
for r in remove_idx:
uset.users[uidx]['samples'].pop(r)
uset.users[uidx]['augments'].pop(r)
# add feature
init_sample['id'] = sample['id']
init_sample['aurl'] = str(sample['aurl'])
init_sample['slide'] = str(sample['slide'])
slide_idx = dset.getSlideIdx(init_sample['slide'])
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
slideIdx_set = dset.getSlideIdxSet(data_idx, object_num)
c_idx = getIdx(
x_centroid_set.astype(np.float), y_centroid_set.astype(np.float), slideIdx_set.astype(np.int), np.float32(sample['centX']), np.float32(sample['centY']), slide_idx
)
f_idx = data_idx + c_idx
init_sample['f_idx'] = f_idx
init_sample['feature'] = feature_set[c_idx]
init_sample['label'] = 1 if sample['label'] == 1 else 0
init_sample['iteration'] = retrain_h.iter
init_sample['centX'] = sample['centX']
init_sample['centY'] = sample['centY']
init_sample['checkpoints'] = m_checkpoints
# add augment features
slide_idx = dset.getSlideIdx(init_sample['slide'])
slide_mean = dset.getWSI_Mean(slide_idx)
slide_std = dset.getWSI_Std(slide_idx)
a_imgs = agen.prepare_image(init_sample['aurl'], slide_mean, slide_std)
a_featureSet = iset.FC1_MODEL.predict(a_imgs)
a_featureSet = PCA.transform(a_featureSet)
a_labelSet = np.zeros((agen.AUG_BATCH_SIZE, )).astype(np.uint8)
a_idSet = []
a_checkpointSet = []
for i in range(agen.AUG_BATCH_SIZE):
a_idSet.append(init_sample['id'])
a_checkpointSet.append(init_sample['checkpoints'])
if init_sample['label'] > 0:
a_labelSet.fill(1)
init_augment['id'] = a_idSet
init_augment['feature'] = a_featureSet
init_augment['label'] = a_labelSet
init_augment['checkpoints'] = a_checkpointSet
uset.setAugmentData(uidx, init_augment)
uset.setTrainSampleData(uidx, init_sample)
sample_size = len(uset.users[uidx]['samples'])
sample_batch_size = agen.AUG_BATCH_SIZE * sample_size
train_size = sample_size + sample_batch_size
train_features = np.zeros((train_size, set.FEATURE_DIM))
train_labels = np.zeros((train_size, ))
for i in range(sample_size):
train_features[i] = uset.users[uidx]['samples'][i]['feature']
train_labels[i] = uset.users[uidx]['samples'][i]['label']
train_features[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['feature']
train_labels[i+sample_size:i+sample_size+agen.AUG_BATCH_SIZE] = uset.users[uidx]['augments'][i]['label']
if tset_name is None:
tset_name = retrain_h.classifier
t0 = time()
model.train_model(train_features, train_labels, tset_name)
t1 = time()
print "Training took ", t1 - t0, " ", len(train_labels), "Samples"
slide_idx = dset.getSlideIdx(retrain_h.slide)
object_num = dset.getObjNum(slide_idx)
data_idx = dset.getDataIdx(slide_idx)
feature_set = dset.getFeatureSet(data_idx, object_num)
x_centroid_set = dset.getXcentroidSet(data_idx, object_num)
y_centroid_set = dset.getYcentroidSet(data_idx, object_num)
print "Testing Start ... "
t0 = time()
if set.IS_HEATMAP == False:
scores = model.predict_prob(feature_set)
t1 = time()
print "Predict took ", t1 - t0
# set x and y maps
retrain_h.setXandYmap()
# write heatmaps
retrain_h.setHeatMap(x_centroid_set, y_centroid_set, scores)
# get heatmap data
data = retrain_h.getData(0)
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'cancel':
uset.users = []
uset.u_size = 0
is_normal_loaded = True
tset_name = None
is_reloaded = False
m_checkpoints = 0
del select
del finalize
del viewer
del retrain_v
del retrain_h
del heat
del t_train
del report_label
model = networks.Network()
model.init_model()
# dset = dataset.Dataset(set.PATH_TO_SPECIAL)
data = {"success": 'pass'}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)
if target == 'reviewSave':
# modify labels if they are changed on review tab
for q_sample in q_samples:
for sample in uset.users[uidx]['samples']:
if sample['id'] == q_sample['id']:
sample['label'] = 1 if q_sample['label'] == 1 else 0
for sample in uset.users[uidx]['augments']:
if sample['id'][0] == q_sample['id']:
sample['label'][:] = 1 if q_sample['label'] == 1 else 0
data = {"success": 'pass'}
db.set(q_uid, json.dumps(data))
db.ltrim(set.REQUEST_QUEUE, len(q_uid), -1)