def main(args):
iman = []
s3 = s3store(args.minio_address, args.minio_access_key,
args.minio_secret_key)
shutil.rmtree(args.ann_dir, ignore_errors=True)
for src in args.annotations:
destDir = args.ann_dir + '/' + src
s3.GetDir(args.srcbucket, src, destDir)
file_list = glob.glob(glob.escape(destDir) + '/*.' + args.image_type)
for imfile in file_list:
annFile = '{}{}'.format(
os.path.splitext(imfile)[0], args.annotation_decoration)
if (os.path.exists(imfile) and os.path.exists(annFile)):
iman.append({'im': imfile, 'an': annFile})
if (len(iman) < 1):
print('No files found {} Exiting'.format(args.annotations))
return
if not os.path.exists(args.record_dir):
os.makedirs(args.record_dir)
WriteRecords(args, iman)
print('Write to s3 {}/{}'.format(args.destbucket, args.setname))
s3.PutDir(args.destbucket, args.record_dir, args.setname)
shutil.rmtree(args.ann_dir, ignore_errors=True)
shutil.rmtree(args.record_dir, ignore_errors=True)
print('{} complete'.format(os.path.basename(__file__)))
def main(args):
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(
args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path'])
if not os.path.exists(args.path):
os.makedirs(args.path)
for url in cocourl:
outpath = '{}/{}'.format(args.path, os.path.basename(url))
if os.path.isfile(outpath):
print('{} exists. Skipping'.format(outpath))
else:
sysmsg = 'wget -O {} {} '.format(outpath, url)
print(sysmsg)
os.system(sysmsg)
sysmsg = 'unzip {} -d {}'.format(outpath, args.path)
print(sysmsg)
os.system(sysmsg)
os.remove(outpath) # Remove zip file once extracted
saved_name = '{}/{}'.format(s3def['sets']['dataset']['prefix'],
args.dataset)
print('Save model to {}/{}'.format(s3def['sets']['dataset']['bucket'],
saved_name))
if s3.PutDir(s3def['sets']['dataset']['bucket'], args.path, saved_name):
shutil.rmtree(args.path, ignore_errors=True)
url = s3.GetUrl(s3def['sets']['dataset']['bucket'], saved_name)
print("Complete. Results saved to {}".format(url))
def main(args):
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(
args.credentails))
return
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path'])
if not os.path.exists(args.record_dir):
os.makedirs(args.record_dir)
WriteRecords(s3def, s3, args)
def main(args):
print('Start Tensorflow to ONNX conversion')
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path']
)
trainingset = '{}/{}/'.format(s3def['sets']['trainingset']['prefix'] , args.trainingset)
print('Load training set {}/{} to {}'.format(s3def['sets']['trainingset']['bucket'],trainingset,args.trainingset_dir ))
s3.Mirror(s3def['sets']['trainingset']['bucket'], trainingset, args.trainingset_dir)
config = {
'descripiton': args.description,
'batch_size': args.batch_size,
'input_shape': [args.training_crop[0], args.training_crop[1], args.train_depth],
'learning_rate': args.learning_rate,
'weights': args.weights,
'channel_order': args.channel_order,
's3_address':s3def['address'],
's3_sets':s3def['sets'],
'initialmodel':args.initialmodel,
}
if args.initialmodel is None or len(args.initialmodel) == 0:
config['initialmodel'] = None
val_dataset = input_fn('val', args.trainingset_dir, config)
train_dataset = input_fn('train', args.trainingset_dir, config)
iterator = iter(train_dataset)
tempinitmodel = tempfile.TemporaryDirectory(prefix='initmodel', dir='.')
modelpath = tempinitmodel.name+'/'+config['initialmodel']
os.makedirs(modelpath)
file_count = 0
s3model=config['s3_sets']['model']['prefix']+'/'+config['initialmodel']
file_count = s3.GetDir(config['s3_sets']['model']['bucket'], s3model, modelpath)
FP = 'FP32'
num_calibration_steps = 20
def representative_dataset_gen():
for _ in range(num_calibration_steps):
# Get sample input data as a numpy array in a method of your choosing.
yield [input]
params = tf.experimental.tensorrt.ConversionParams(
precision_mode=FP,
# Set this to a large enough number so it can cache all the engines.
maximum_cached_engines=128)
converter = tf.experimental.tensorrt.Converter(input_saved_model_dir=modelpath, conversion_params=params)
converter.convert()
converter.build(input_fn=representative_dataset_gen) # Generate corresponding TRT engines
converter.save('./zzz') # Generated engines will be saved
'''print('Store {} to {}/{}'.format(onnx_filename, s3def['sets']['model']['bucket'],s3model))
if not s3.PutFile(s3def['sets']['model']['bucket'], onnx_filename, s3model):
print("s3.PutFile({},{},{} failed".format(s3def['sets']['model']['bucket'], onnx_filename, s3model))
obj_name = '{}/{}.onnx'.format(s3model, args.modelprefix)
objurl = s3.GetUrl(s3def['sets']['model']['bucket'], obj_name)'''
#print("Tensorflow to TRT complete. Results stored {}".format(objurl))
print("Tensorflow to TRT complete. Results stored")
def main(args):
print('Start training')
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path']
)
trainingset = '{}/{}/'.format(s3def['sets']['trainingset']['prefix'] , args.trainingset)
trainingsetdir = '{}/{}'.format(args.trainingsetdir,args.trainingset)
print('Load training set {}/{} to {}'.format(s3def['sets']['trainingset']['bucket'],trainingset,trainingsetdir ))
s3.Mirror(s3def['sets']['trainingset']['bucket'], trainingset, trainingsetdir)
if args.weights is not None and args.weights.lower() == 'none' or args.weights == '':
args.weights = None
trainingsetDescriptionFile = '{}/description.json'.format(trainingsetdir)
trainingsetDescription = json.load(open(trainingsetDescriptionFile))
config = {
'descripiton': args.description,
'batch_size': args.batch_size,
'traningset': trainingset,
'trainingset description': trainingsetDescription,
'input_shape': [args.training_crop[0], args.training_crop[1], args.train_depth],
'classScale': 0.001, # scale value for each product class
'augment_rotation' : 15., # Rotation in degrees
'augment_flip_x': False,
'augment_flip_y': True,
'augment_brightness':0.,
'augment_contrast': 0.,
'augment_shift_x': 0.1, # in fraction of image
'augment_shift_y': 0.1, # in fraction of image
'scale_min': 0.5, # in fraction of image
'scale_max': 2.0, # in fraction of image
'ignore_label': trainingsetDescription['classes']['ignore'],
'classes': trainingsetDescription['classes']['classes'],
'epochs': args.epochs,
'area_filter_min': 25,
'learning_rate': args.learning_rate,
'weights': args.weights,
'channel_order': args.channel_order,
'clean': args.clean,
's3_address':s3def['address'],
's3_sets':s3def['sets'],
'initialmodel':args.initialmodel,
'training_dir': args.training_dir,
'min':args.min,
'strategy': args.strategy,
'devices':args.devices,
}
if args.trainingset is None or len(args.trainingset) == 0:
config['trainingset'] = None
if args.initialmodel is None or len(args.initialmodel) == 0:
config['initialmodel'] = None
if args.training_dir is None or len(args.training_dir) == 0:
config['training_dir'] = tempfile.TemporaryDirectory(prefix='train', dir='.')
if args.clean:
shutil.rmtree(config['training_dir'], ignore_errors=True)
strategy = None
if(args.strategy == 'mirrored'):
strategy = tf.distribute.MirroredStrategy(devices=args.devices)
else:
device = "/gpu:0"
if args.devices is not None and len(args.devices) > 0:
device = args.devices[0]
strategy = tf.distribute.OneDeviceStrategy(device=device)
print('{} distribute with {} GPUs'.format(args.strategy,strategy.num_replicas_in_sync))
savedmodelpath = '{}/{}'.format(args.savedmodel, args.savedmodelname)
if not os.path.exists(savedmodelpath):
os.makedirs(savedmodelpath)
if not os.path.exists(config['training_dir']):
os.makedirs(config['training_dir'])
with strategy.scope(): # Apply training strategy
model = LoadModel(config, s3)
# Display model
model.summary()
train_dataset = input_fn('train', trainingsetdir, config)
val_dataset = input_fn('val', trainingsetdir, config)
#earlystop_callback = tf.keras.callbacks.EarlyStopping(monitor='loss', min_delta=1e-4, patience=3, verbose=0, mode='auto')
save_callback = tf.keras.callbacks.ModelCheckpoint(filepath=config['training_dir'], monitor='loss',verbose=0,save_weights_only=False,save_freq='epoch')
tensorboard_callback = tf.keras.callbacks.TensorBoard(log_dir=config['training_dir'], histogram_freq=100)
callbacks = [
save_callback,
tensorboard_callback
]
#file_writer = tf.summary.create_file_writer(config['training_dir'])
# Save plot of model model
# Failing with "AttributeError: 'dict' object has no attribute 'name'" when returning multiple outputs
#tf.keras.utils.plot_model(model, to_file='{}unet.png'.format(savedmodelpath), show_shapes=True)
train_images = config['batch_size'] # Guess training set if not provided
val_images = config['batch_size']
for dataset in trainingsetDescription['sets']:
if(dataset['name']=="train"):
train_images = dataset["length"]
if(dataset['name']=="val"):
val_images = dataset["length"]
steps_per_epoch=int(train_images/config['batch_size'])
validation_steps=int(val_images/config['batch_size']/config['epochs'])
if(args.min):
steps_per_epoch= min(args.min_steps, steps_per_epoch)
validation_steps=min(args.min_steps, validation_steps)
config['epochs'] = 1
if config['epochs'] > 0:
print("Fit model to data")
model_history = model.fit(train_dataset,
validation_data=val_dataset,
epochs=config['epochs'],
steps_per_epoch=steps_per_epoch,
validation_steps=validation_steps,
callbacks=callbacks)
history = model_history.history
if 'loss' in history:
loss = model_history.history['loss']
else:
loss = []
if 'val_loss' in history:
val_loss = model_history.history['val_loss']
else:
val_loss = []
model_description = {'config':config,
'results': history
}
graph_history(loss,val_loss,savedmodelpath)
else:
model_description = {'config':config,
}
print("Create saved model")
model.save(savedmodelpath, save_format='tf')
WriteDictJson(model_description, '{}/description.json'.format(savedmodelpath))
if args.saveonnx:
onnx_req = "python -m tf2onnx.convert --saved-model {0} --opset 10 --output {0}/model.onnx".format(savedmodelpath)
os.system(onnx_req)
# Make some predictions. In the interest of saving time, the number of epochs was kept small, but you may set this higher to achieve more accurate results.
WritePredictions(train_dataset, model, config, outpath=savedmodelpath, imgname='train_img')
WritePredictions(val_dataset, model, config, outpath=savedmodelpath, imgname='val_img')
# Kubeflow Pipeline results
results = model_description
WriteDictJson(results, '{}/results.json'.format(savedmodelpath))
saved_name = '{}/{}'.format(s3def['sets']['model']['prefix'] , args.savedmodelname)
print('Save model to {}/{}'.format(s3def['sets']['model']['bucket'],saved_name))
if s3.PutDir(s3def['sets']['model']['bucket'], savedmodelpath, saved_name):
shutil.rmtree(savedmodelpath, ignore_errors=True)
if args.clean or args.training_dir is None or len(args.training_dir) == 0:
shutil.rmtree(config['training_dir'], ignore_errors=True)
print("Segmentation training complete. Results saved to https://{}/minio/{}/{}".format(s3def['address'], s3def['sets']['model']['bucket'],saved_name))
def main(args):
print('Start test')
creds = ReadDictJson(args.credentails)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(args.credentails))
return False
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path']
)
trainingset = '{}/{}/'.format(s3def['sets']['trainingset']['prefix'] , args.trainingset)
print('Load training set {}/{} to {}'.format(s3def['sets']['trainingset']['bucket'],trainingset,args.trainingset_dir ))
s3.Mirror(s3def['sets']['trainingset']['bucket'], trainingset, args.trainingset_dir)
trainingsetDescriptionFile = '{}/description.json'.format(args.trainingset_dir)
trainingsetDescription = json.load(open(trainingsetDescriptionFile))
config = {
'name': args.name,
'description': args.description,
'initialmodel': args.model,
'trtmodel': args.trtmodel,
'batch_size': args.batch_size,
'trainingset description': trainingsetDescription,
'input_shape': [args.training_crop[0], args.training_crop[1], args.train_depth],
'classScale': 0.001, # scale value for each product class
'augment_rotation' : 5., # Rotation in degrees
'augment_flip_x': False,
'augment_flip_y': True,
'augment_brightness':0.,
'augment_contrast': 0.,
'augment_shift_x': 0.0, # in fraction of image
'augment_shift_y': 0.0, # in fraction of image
'scale_min': 0.75, # in fraction of image
'scale_max': 1.25, # in fraction of image
'ignore_label': trainingsetDescription['classes']['ignore'],
'classes': trainingsetDescription['classes']['classes'],
'epochs': 1,
'area_filter_min': 25,
'weights': None,
'channel_order': args.channel_order,
's3_address':s3def['address'],
's3_sets':s3def['sets'],
'training_dir': None, # used by LoadModel
'learning_rate': 1e-3, # used by LoadModel
'clean' : True,
'test_archive': trainingset,
'run_archive': '{}{}/'.format(trainingset, args.model),
'min':args.min,
}
trainingsetDescriptionFile = '{}/description.json'.format(args.trainingset_dir)
trainingsetDescription = json.load(open(trainingsetDescriptionFile))
strategy = None
if(args.strategy == 'mirrored'):
strategy = tf.distribute.MirroredStrategy(devices=args.devices)
else:
device = "/gpu:0"
if args.devices is not None and len(args.devices) > 0:
device = args.devices[0]
strategy = tf.distribute.OneDeviceStrategy(device=device)
modelobjname = '{}/{}/{}'.format(s3def['sets']['model']['prefix'], config['initialmodel'], config['trtmodel'])
modelfilename = '{}/{}/{}/{}'.format(args.test_dir, s3def['sets']['model']['prefix'], config['initialmodel'], config['trtmodel'])
print('Load trt model {}/{} to {}'.format(s3def['sets']['model']['bucket'], modelobjname, modelfilename))
s3.GetFile(s3def['sets']['model']['bucket'], modelobjname, modelfilename)
# Prepare datasets for similarity computation
objTypes = {}
for objType in trainingsetDescription['classes']['objects']:
if objType['trainId'] not in objTypes:
objTypes[objType['trainId']] = copy.deepcopy(objType)
# set name to category for objTypes and id to trainId
objTypes[objType['trainId']]['name'] = objType['category']
objTypes[objType['trainId']]['id'] = objType['trainId']
results = {'class similarity':{}, 'config':config, 'image':[]}
for objType in objTypes:
results['class similarity'][objType] = {'union':0, 'intersection':0}
with strategy.scope():
accuracy = tf.keras.metrics.Accuracy()
#train_dataset = input_fn('train', args.trainingset_dir, config)
val_dataset = input_fn('val', args.trainingset_dir, config)
trainingsetdesc = {}
validationsetdec = {}
for dataset in config['trainingset description']['sets']:
if dataset['name'] == 'val':
validationsetdec = dataset
if dataset['name'] == 'train':
trainingsetdesc = dataset
print("Begin inferences")
dtSum = 0.0
accuracySum = 0.0
total_confusion = None
iterator = iter(val_dataset)
numsteps = int(validationsetdec['length']/config['batch_size'])
step = 0
if(config['min']):
numsteps=min(args.min_steps, numsteps)
try:
f = open(modelfilename, "rb")
runtime = trt.Runtime(trt.Logger(trt.Logger.WARNING))
engine = runtime.deserialize_cuda_engine(f.read())
context = engine.create_execution_context()
target_dtype = np.float16 if args.fp16 else np.float32
dummy_input_batch = np.zeros((1, 480, 512, 3), dtype=np.float32)
output = np.empty([args.batch_size, config['input_shape'][0], config['input_shape'][1], config['classes']], dtype = np.float32)
# Allocate device memory
d_input = cuda.mem_alloc(1 * dummy_input_batch.nbytes)
d_output = cuda.mem_alloc(1 * output.nbytes)
bindings = [int(d_input), int(d_output)]
stream = cuda.Stream()
def predict(batch): # result gets copied into output
# Transfer input data to device
cuda.memcpy_htod_async(d_input, batch, stream)
# Execute model
context.execute_async_v2(bindings, stream.handle, None)
# Transfer predictions back
cuda.memcpy_dtoh_async(output, d_output, stream)
# Syncronize threads
stream.synchronize()
return output
if not os.path.exists(args.test_dir):
os.makedirs(args.test_dir)
output = predict(dummy_input_batch) # Run to load dependencies
tf.get_logger().setLevel('ERROR') # remove tf.cast warning from algorithm time
for i in tqdm(range(numsteps)):
step = i
image, annotation = iterator.get_next()
initial = datetime.now()
image_norm = tf.image.per_image_standardization(tf.cast(image, tf.float32))
logitstft = predict(image_norm.numpy())
segmentationtrt = np.argmax(logitstft, axis=-1).astype(np.uint8)
dt = (datetime.now()-initial).total_seconds()
dtSum += dt
imageTime = dt/config['batch_size']
for j in range(config['batch_size']):
img = tf.squeeze(image[j]).numpy().astype(np.uint8)
ann = tf.squeeze(annotation[j]).numpy().astype(np.uint8)
seg = tf.squeeze(segmentationtrt[j]).numpy().astype(np.uint8)
accuracy.update_state(ann,seg)
seg_accuracy = accuracy.result().numpy()
accuracySum += seg_accuracy
imagesimilarity, results['class similarity'], unique = jaccard(ann, seg, objTypes, results['class similarity'])
confusion = tf.math.confusion_matrix(ann.flatten(),seg.flatten(), config['classes']).numpy().astype(np.int64)
if total_confusion is None:
total_confusion = confusion
else:
total_confusion += confusion
if args.saveimg:
font = cv2.FONT_HERSHEY_SIMPLEX
iman = DrawFeatures(img, ann, config)
iman = cv2.putText(iman, 'Annotation',(10,25), font, 1,(255,255,255),1,cv2.LINE_AA)
imseg = DrawFeatures(img, seg, config)
imseg = cv2.putText(imseg, 'TensorRT',(10,25), font, 1,(255,255,255),1,cv2.LINE_AA)
im = cv2.hconcat([iman, imseg])
im_bgr = cv2.cvtColor(im, cv2.COLOR_RGB2BGR)
cv2.imwrite('{}/{}{:03d}{:03d}.png'.format(args.test_dir, 'segtrt', i, j), im_bgr)
results['image'].append({'dt':imageTime,'similarity':imagesimilarity, 'accuracy':seg_accuracy.astype(float), 'confusion':confusion.tolist()})
except Exception as e:
print("Error: test exception {} step {}".format(e, step))
numsteps = step
num_images = numsteps*config['batch_size']
if numsteps > 0:
num_images = numsteps*config['batch_size']
average_time = dtSum/num_images
average_accuracy = accuracySum/num_images
else:
num_images = 0
average_time = 0.0
average_accuracy = 0.0
sumIntersection = 0
sumUnion = 0
sumAccuracy = 0.0
dataset_similarity = {}
for key in results['class similarity']:
intersection = results['class similarity'][key]['intersection']
sumIntersection += intersection
union = results['class similarity'][key]['union']
sumUnion += union
class_similarity = similarity(intersection, union)
# convert to int from int64 for json.dumps
dataset_similarity[key] = {'intersection':int(intersection) ,'union':int(union) , 'similarity':class_similarity}
results['class similarity'] = dataset_similarity
total_similarity = similarity(sumIntersection, sumUnion)
now = datetime.now()
date_time = now.strftime("%m/%d/%Y, %H:%M:%S")
test_summary = {'date':date_time}
test_summary['name']=config['name']
test_summary['description']=config['description']
test_summary['model']=config['initialmodel']
test_summary['accuracy']=average_accuracy
test_summary['class_similarity']=dataset_similarity
test_summary['similarity']=total_similarity
test_summary['confusion']=total_confusion.tolist()
test_summary['images']=num_images
test_summary['image time']=average_time
test_summary['batch size']=config['batch_size']
test_summary['store address'] =s3def['address']
test_summary['test bucket'] = s3def['sets']['trainingset']['bucket']
test_summary['platform'] = platform.platform()
if args.saveresults:
test_summary['results'] = results
print ("Average time {}".format(average_time))
print ('Similarity: {}'.format(dataset_similarity))
# If there is a way to lock this object between read and write, it would prevent the possability of loosing data
training_data = s3.GetDict(s3def['sets']['trainingset']['bucket'], config['test_archive']+args.tests_json)
if training_data is None:
training_data = []
training_data.append(test_summary)
s3.PutDict(s3def['sets']['trainingset']['bucket'], config['test_archive']+args.tests_json, training_data)
test_url = s3.GetUrl(s3def['sets']['trainingset']['bucket'], config['test_archive']+args.tests_json)
print("Test results {}".format(test_url))
def main(args):
print('Platform: {}'.format(platform.platform()))
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(
args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path'])
config = {
'initialmodel': args.savedmodel,
's3_address': s3def['address'],
's3_sets': s3def['sets'],
'savedmodel': args.savedmodel,
'training_dir': None,
'clean': False,
'shape': (args.size_y, args.size_x, args.depth),
'training_dir': None,
}
using_tensorflow = True
using_tensorrt = True
modelpath = '{}/{}'.format(s3def['sets']['model']['prefix'],
config['savedmodel'])
savedmodelpath = '{}/{}'.format(args.work_path, config['savedmodel'])
onnxname = '{}/{}.onnx'.format(savedmodelpath, config['savedmodel'])
trtenginename = '{}/{}.trt'.format(savedmodelpath, config['savedmodel'])
if using_tensorflow:
import tensorflow
import keras2onnx
import onnx
print('Tensorflow: {}'.format(tensorflow.__version__))
model = LoadModel(config, s3)
onnx_model = keras2onnx.convert_keras(model, model.name)
if not s3.GetDir(s3def['sets']['model']['bucket'], modelpath,
savedmodelpath):
print('Failed to load model')
onnx.save_model(onnx_model, onnxname)
# Unload models to free memory for ONNX->TRT conversion
if using_tensorrt:
oscmd = 'trtexec --onnx={} --batch=1 --saveEngine={} --explicitBatch 2>&1'.format(
onnxname, trtenginename)
os.system(oscmd)
'''
trtenginename = '{}/{}.trt'.format(savedmodelpath, config['savedmodel'])
graph_def, inputs, outputs = tf_loader.from_saved_model(savedmodelpath, input_names=args.model_input_names, output_names=args.model_output_names)
print("inputs: {}".format(inputs))
print("outputs: {}".format(outputs))
with tensorflow.Graph().as_default() as tf_graph:
const_node_values = None
tensorflow.import_graph_def(graph_def, name='')
with tf_loader.tf_session(graph=tf_graph):
onnx_graph = process_tf_graph(tf_graph,
continue_on_error=args.continue_on_error,
target=args.target,
opset=args.opset,
custom_op_handlers={},
extra_opset=[],
shape_override=None,
input_names=inputs,
output_names=outputs,
inputs_as_nchw=args.inputs_as_nchw)
model_proto = onnx_graph.make_model(config['savedmodel'])
with open(onnxname, "wb") as f:
f.write(model_proto.SerializeToString())
#onnx_graph = optimizer.optimize_graph(onnx_graph)
TRT_LOGGER = trt.Logger(trt.Logger.WARNING)
trt_runtime = trt.Runtime(TRT_LOGGER)
EXPLICIT_BATCH = 1 << (int)(trt.NetworkDefinitionCreationFlag.EXPLICIT_BATCH) # https://docs.nvidia.com/deeplearning/tensorrt/developer-guide/index.html#import_onnx_python
with trt.Builder(TRT_LOGGER) as builder, builder.create_network(EXPLICIT_BATCH) as network, trt.OnnxParser(network, TRT_LOGGER) as parser:
#builder.max_workspace_size = (256 << 20)
with open(onnxname, 'rb') as model:
parser.parse(model.read())
#network.get_input(0).shape = [args.batch_size, args.image_size[0], args.image_size[1], args.image_depth]
engine = builder.build_cuda_engine(network)
buf = engine.serialize()
with open(trtenginename, 'wb') as f:
f.write(buf)
#builder.max_workspace_size = (256 << 20)
#parser.parse(model_proto.SerializeToString())
#network.get_input(0).shape = [args.batch_size, args.image_size[0], args.image_size[1], args.image_depth]
#engine = builder.build_cuda_engine(network)
#eng.save_engine(engine, trtenginename)
'''
s3.PutFile(s3def['sets']['model']['bucket'], onnxname, modelpath)
s3.PutFile(s3def['sets']['model']['bucket'], trtenginename, modelpath)
print("Conversion complete. Results saved to {}".format(trtenginename))
def main(args):
print('Start Tensorflow to ONNX conversion')
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(
args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path'])
config = {
'descripiton':
args.description,
'batch_size':
args.batch_size,
'input_shape':
[args.training_crop[0], args.training_crop[1], args.train_depth],
'learning_rate':
args.learning_rate,
'weights':
args.weights,
'channel_order':
args.channel_order,
's3_address':
s3def['address'],
's3_sets':
s3def['sets'],
'initialmodel':
args.initialmodel,
}
if args.initialmodel is None or len(args.initialmodel) == 0:
config['initialmodel'] = None
tempinitmodel = tempfile.TemporaryDirectory(prefix='initmodel', dir='.')
modelpath = tempinitmodel.name + '/' + config['initialmodel']
os.makedirs(modelpath)
file_count = 0
s3model = config['s3_sets']['model']['prefix'] + '/' + config[
'initialmodel']
file_count = s3.GetDir(config['s3_sets']['model']['bucket'], s3model,
modelpath)
onnx_filename = "{}/{}.onnx".format(modelpath, args.modelprefix)
onnx_req = "python -m tf2onnx.convert --saved-model {} --opset 10 --output {}".format(
modelpath, onnx_filename)
os.system(onnx_req)
# Fix ONNX size
'''
onnx_model = onnx.load(onnx_filename)
inputs = onnx_model.graph.input
for input in inputs:
dim1 = input.type.tensor_type.shape.dim[0]
dim1.dim_value = config['batch_size']
onnx.save_model(onnx_model, onnx_filename)
'''
print('Store {} to {}/{}'.format(onnx_filename,
s3def['sets']['model']['bucket'],
s3model))
if not s3.PutFile(s3def['sets']['model']['bucket'], onnx_filename,
s3model):
print("s3.PutFile({},{},{} failed".format(
s3def['sets']['model']['bucket'], onnx_filename, s3model))
obj_name = '{}/{}.onnx'.format(s3model, args.modelprefix)
objurl = s3.GetUrl(s3def['sets']['model']['bucket'], obj_name)
print("Tensorflow to ONNX complete. Results stored {}".format(objurl))
def main(args):
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(
args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path'])
trainingset = '{}/{}/'.format(s3def['sets']['trainingset']['prefix'],
args.trainingset)
print('Load training set {}/{} to {}'.format(
s3def['sets']['trainingset']['bucket'], trainingset,
args.trainingset_dir))
s3.Mirror(s3def['sets']['trainingset']['bucket'], trainingset,
args.trainingset_dir)
trainingsetDescriptionFile = '{}/description.json'.format(
args.trainingset_dir)
trainingsetDescription = json.load(open(trainingsetDescriptionFile))
config = {
'batch_size':
args.batch_size,
'trainingset':
args.trainingset,
'trainingset description':
trainingsetDescription,
'input_shape':
[args.training_crop[0], args.training_crop[1], args.train_depth],
'classScale':
0.001, # scale value for each product class
'augment_rotation':
5., # Rotation in degrees
'augment_flip_x':
False,
'augment_flip_y':
True,
'augment_brightness':
0.,
'augment_contrast':
0.,
'augment_shift_x':
0.0, # in fraction of image
'augment_shift_y':
0.0, # in fraction of image
'scale_min':
0.75, # in fraction of image
'scale_max':
1.25, # in fraction of image
'ignore_label':
trainingsetDescription['classes']['ignore'],
'classes':
trainingsetDescription['classes']['classes'],
'image_crops':
args.crops,
'epochs':
args.epochs,
'area_filter_min':
25,
'channel_order':
'channels_last',
's3_address':
s3def['address'],
's3_sets':
s3def['sets'],
'min':
args.min,
}
# ## Train the model
# Now, all that is left to do is to compile and train the model. The loss being used here is `losses.SparseCategoricalCrossentropy(from_logits=True)`. The reason to use this loss function is because the network is trying to assign each pixel a label, just like multi-class prediction. In the true segmentation mask, each pixel has either a {0,1,2}. The network here is outputting three channels. Essentially, each channel is trying to learn to predict a class, and `losses.SparseCategoricalCrossentropy(from_logits=True)` is the recommended loss for
# such a scenario. Using the output of the network, the label assigned to the pixel is the channel with the highest value. This is what the create_mask function is doing.
train_dataset = input_fn('train', args.trainingset_dir, config)
val_datast = input_fn('val', args.trainingset_dir, config)
outpath = 'test'
if not os.path.exists(outpath):
os.makedirs(outpath)
train_images = config['batch_size'] # Guess training set if not provided
val_images = config['batch_size']
for dataset in trainingsetDescription['sets']:
if (dataset['name'] == "train"):
train_images = dataset["length"]
if (dataset['name'] == "val"):
val_images = dataset["length"]
steps_per_epoch = int(train_images / config['batch_size'])
validation_steps = int(val_images / config['batch_size'])
if (args.min):
steps_per_epoch = min(args.min_steps, steps_per_epoch)
validation_steps = min(args.min_steps, validation_steps)
config['epochs'] = 1
try:
i = 0
j = 0
k = 0
iterator = iter(train_dataset)
for i in range(config['epochs']):
for j in range(steps_per_epoch):
image, mask = iterator.get_next()
for k in range(image.shape[0]):
img = tf.squeeze(image[k]).numpy().astype(np.uint8)
ann = tf.squeeze(mask[k]).numpy().astype(np.uint8)
img = cv.cvtColor(img, cv2.COLOR_RGB2BGR)
iman = DrawFeatures(img, ann, config)
inxstr = '{:02d}_{:04d}'.format(
i, config['batch_size'] * j + k)
cv2.imwrite('{}/train_iman{}.png'.format(outpath, inxstr),
iman)
except:
print("Write train_dataset failed epoch {} step {} image {}".format(
i, j, k))
try:
j = 0
k = 0
iterator = iter(val_datast)
for j in range(validation_steps):
image, mask = iterator.get_next()
for k in range(image.shape[0]):
img = tf.squeeze(image[k]).numpy().astype(np.uint8)
ann = tf.squeeze(mask[k]).numpy().astype(np.uint8)
iman = DrawFeatures(img, ann, config)
inxstr = '{:04d}'.format(config['batch_size'] * j + k)
cv2.imwrite('{}/val_iman{}.png'.format(outpath, inxstr), iman)
except:
print("Write val_datast failed step {} image {}".format(j, k))
#WriteImgAn(train_dataset, config, outpath=outpath)
#WriteImgAn(test_dataset, config, outpath=outpath)
print("Write complete. Results saved to {}".format(outpath))
def main(args):
failed = False
creds = {}
with open(args.credentails) as json_file:
creds = json.load(json_file)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(args.credentails))
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path']
)
workdir = '{}/{}'.format(args.workdir, args.savedmodelname)
inobj = '{}/{}/{}'.format(s3def['sets']['model']['prefix'],args.savedmodelname, args.onnxname)
objpath = '{}/{}'.format(s3def['sets']['model']['prefix'],args.savedmodelname)
infile = '{}/{}'.format(workdir, args.onnxname)
if not s3.GetFile(s3def['sets']['model']['bucket'], inobj, infile):
print('Failed to load {}/{} to {}'.format(s3def['sets']['model']['bucket'], inobj, infile ))
failed = True
return failed
onnx_model = onnx.load(infile)
inputs = onnx_model.graph.input
for input in inputs:
dim1 = input.type.tensor_type.shape.dim[0]
dim1.dim_value = args.batch_size
fixedfile = '{}/fixed-{}'.format(workdir, args.onnxname)
onnx.save_model(onnx_model, fixedfile)
targetname = args.targetname
params = ''
if args.fp16:
targetname += '-fp16'
params = '--fp16'
outfile = '{}/{}.trt'.format(workdir, targetname)
logfile = '{}/{}-trt.log'.format(workdir, targetname)
# USE_FP16 = True
# May need to shut down all kernels and restart before this - otherwise you might get cuDNN initialization errors:
#if USE_FP16:
# os.system("trtexec --onnx=resnet50_onnx_model.onnx --saveEngine=resnet_engine.trt --explicitBatch --fp16")
#else:
# os.system("trtexec --onnx=resnet50_onnx_model.onnx --saveEngine=resnet_engine.trt --explicitBatch")
# engine = build_engine(fixedfile)
succeeded = build_tensorrt_engine(fixedfile,
outfile,
precision_mode='fp16',
max_workspace_size=GB(1), # in bytes
max_batch_size=1,
min_timing_iterations=2,
avg_timing_iterations=2,
int8_calibrator=None)
if s3.PutFile(s3def['sets']['model']['bucket'], outfile, objpath):
shutil.rmtree(args.workdir, ignore_errors=True)
# trtcmd = "trtexec --onnx=/store/dmp/cl/store/mllib/model/2021-02-19-20-51-59-cocoseg/model.onnx --saveEngine=/store/dmp/cl/store/mllib/model/2021-02-19-20-51-59-cocoseg/model.trt --explicitBatch --workspace=4096 --verbose 2>&1 | tee trtexe.log"
print('onnx-trt complete return {}'.format(failed))
return failed
def main(args):
print('Start test')
creds = ReadDictJson(args.credentails)
if not creds:
print('Failed to load credentials file {}. Exiting'.format(
args.credentails))
return False
s3def = creds['s3'][0]
s3 = s3store(s3def['address'],
s3def['access key'],
s3def['secret key'],
tls=s3def['tls'],
cert_verify=s3def['cert_verify'],
cert_path=s3def['cert_path'])
trainingset = '{}/{}/'.format(s3def['sets']['trainingset']['prefix'],
args.trainingset)
print('Load training set {}/{} to {}'.format(
s3def['sets']['trainingset']['bucket'], trainingset,
args.trainingset_dir))
s3.Mirror(s3def['sets']['trainingset']['bucket'], trainingset,
args.trainingset_dir)
trainingsetDescriptionFile = '{}/description.json'.format(
args.trainingset_dir)
trainingsetDescription = json.load(open(trainingsetDescriptionFile))
config = {
'name':
args.name,
'description':
args.description,
'initialmodel':
args.model,
'onnxmodel':
args.onnxmodel,
'batch_size':
args.batch_size,
'trainingset description':
trainingsetDescription,
'input_shape':
[args.training_crop[0], args.training_crop[1], args.train_depth],
'classScale':
0.001, # scale value for each product class
'augment_rotation':
5., # Rotation in degrees
'augment_flip_x':
False,
'augment_flip_y':
True,
'augment_brightness':
0.,
'augment_contrast':
0.,
'augment_shift_x':
0.0, # in fraction of image
'augment_shift_y':
0.0, # in fraction of image
'scale_min':
0.75, # in fraction of image
'scale_max':
1.25, # in fraction of image
'ignore_label':
trainingsetDescription['classes']['ignore'],
'classes':
trainingsetDescription['classes']['classes'],
'epochs':
1,
'area_filter_min':
25,
'weights':
None,
'channel_order':
args.channel_order,
's3_address':
s3def['address'],
's3_sets':
s3def['sets'],
'training_dir':
None, # used by LoadModel
'learning_rate':
1e-3, # used by LoadModel
'clean':
True,
'test_archive':
trainingset,
'run_archive':
'{}{}/'.format(trainingset, args.model),
'min':
args.min,
}
trainingsetDescriptionFile = '{}/description.json'.format(
args.trainingset_dir)
trainingsetDescription = json.load(open(trainingsetDescriptionFile))
onnxobjname = '{}/{}/{}'.format(s3def['sets']['model']['prefix'],
config['initialmodel'],
config['onnxmodel'])
onnxfilename = '{}/{}/{}/{}'.format(args.test_dir,
s3def['sets']['model']['prefix'],
config['initialmodel'],
config['onnxmodel'])
print('Load onnx model {}/{} to {}'.format(
s3def['sets']['model']['bucket'], onnxobjname, onnxfilename))
s3.GetFile(s3def['sets']['model']['bucket'], onnxobjname, onnxfilename)
strategy = None
if (args.strategy == 'mirrored'):
strategy = tf.distribute.MirroredStrategy(devices=args.devices)
else:
device = "/gpu:0"
if args.devices is not None and len(args.devices) > 0:
device = args.devices[0]
strategy = tf.distribute.OneDeviceStrategy(device=device)
# Prepare datasets for similarity computation
objTypes = {}
for objType in trainingsetDescription['classes']['objects']:
if objType['trainId'] not in objTypes:
objTypes[objType['trainId']] = copy.deepcopy(objType)
# set name to category for objTypes and id to trainId
objTypes[objType['trainId']]['name'] = objType['category']
objTypes[objType['trainId']]['id'] = objType['trainId']
results = {'class similarity': {}, 'config': config, 'image': []}
for objType in objTypes:
results['class similarity'][objType] = {'union': 0, 'intersection': 0}
with strategy.scope(): # Apply training strategy
accuracy = tf.keras.metrics.Accuracy()
#train_dataset = input_fn('train', args.trainingset_dir, config)
val_dataset = input_fn('val', args.trainingset_dir, config)
trainingsetdesc = {}
validationsetdec = {}
for dataset in config['trainingset description']['sets']:
if dataset['name'] == 'val':
validationsetdec = dataset
if dataset['name'] == 'train':
trainingsetdesc = dataset
print("Begin inferences")
dtSum = 0.0
accuracySum = 0.0
total_confusion = None
iterator = iter(val_dataset)
numsteps = int(validationsetdec['length'] / config['batch_size'])
step = 0
if (config['min']):
numsteps = min(args.min_steps, numsteps)
try:
print('ONNX runtime devices {}'.format(rt.get_device()))
onnxsess = rt.InferenceSession(onnxfilename)
for i in tqdm(range(numsteps)):
step = i
image, annotation = iterator.get_next()
initial = datetime.now()
input_name = onnxsess.get_inputs()[0].name
predonnx = onnxsess.run(
None, {input_name: image.numpy().astype(np.float32)})
segmentationonnx = tf.argmax(predonnx[0], axis=-1)
dt = (datetime.now() - initial).total_seconds()
dtSum += dt
imageTime = dt / config['batch_size']
for j in range(config['batch_size']):
img = tf.squeeze(image[j]).numpy().astype(np.uint8)
ann = tf.squeeze(annotation[j]).numpy().astype(np.uint8)
seg = tf.squeeze(segmentationonnx[j]).numpy().astype(
np.uint8)
accuracy.update_state(ann, seg)
seg_accuracy = accuracy.result().numpy()
accuracySum += seg_accuracy
imagesimilarity, results[
'class similarity'], unique = jaccard(
ann, seg, objTypes, results['class similarity'])
confusion = tf.math.confusion_matrix(
ann.flatten(), seg.flatten(),
config['classes']).numpy().astype(np.int64)
if total_confusion is None:
total_confusion = confusion
else:
total_confusion += confusion
if args.saveimg:
font = cv2.FONT_HERSHEY_SIMPLEX
iman = DrawFeatures(img, ann, config)
iman = cv2.putText(iman, 'Annotation', (10, 25), font,
1, (255, 255, 255), 1, cv2.LINE_AA)
imseg = DrawFeatures(img, seg, config)
imseg = cv2.putText(imseg, 'TensorRT', (10, 25), font,
1, (255, 255, 255), 1, cv2.LINE_AA)
im = cv2.hconcat([iman, imseg])
im_bgr = cv2.cvtColor(im, cv2.COLOR_RGB2BGR)
cv2.imwrite(
'{}/{}{:03d}{:03d}.png'.format(
args.test_dir, 'segtrt', i, j), im_bgr)
results['image'].append({
'dt':
imageTime,
'similarity':
imagesimilarity,
'accuracy':
seg_accuracy.astype(float),
'confusion':
confusion.tolist()
})
except Exception as e:
print("Error: test exception {} step {}".format(e, step))
numsteps = step
num_images = numsteps * config['batch_size']
if numsteps > 0:
num_images = numsteps * config['batch_size']
average_time = dtSum / num_images
average_accuracy = accuracySum / num_images
else:
num_images = 0
average_time = 0.0
average_accuracy = 0.0
sumIntersection = 0
sumUnion = 0
sumAccuracy = 0.0
dataset_similarity = {}
for key in results['class similarity']:
intersection = results['class similarity'][key]['intersection']
sumIntersection += intersection
union = results['class similarity'][key]['union']
sumUnion += union
class_similarity = similarity(intersection, union)
# convert to int from int64 for json.dumps
dataset_similarity[key] = {
'intersection': int(intersection),
'union': int(union),
'similarity': class_similarity
}
results['class similarity'] = dataset_similarity
total_similarity = similarity(sumIntersection, sumUnion)
now = datetime.now()
date_time = now.strftime("%m/%d/%Y, %H:%M:%S")
test_summary = {'date': date_time}
test_summary['name'] = config['name']
test_summary['description'] = config['description']
test_summary['model'] = config['initialmodel']
test_summary['accuracy'] = average_accuracy
test_summary['class_similarity'] = dataset_similarity
test_summary['similarity'] = total_similarity
test_summary['confusion'] = total_confusion.tolist()
test_summary['images'] = num_images
test_summary['image time'] = average_time
test_summary['batch size'] = config['batch_size']
test_summary['store address'] = s3def['address']
test_summary['test bucket'] = s3def['sets']['trainingset']['bucket']
test_summary['platform'] = platform.platform()
if args.saveresults:
test_summary['results'] = results
print("Average time {}".format(average_time))
print('Similarity: {}'.format(dataset_similarity))
# If there is a way to lock this object between read and write, it would prevent the possability of loosing data
training_data = s3.GetDict(s3def['sets']['trainingset']['bucket'],
config['test_archive'] + args.tests_json)
if training_data is None:
training_data = []
training_data.append(test_summary)
s3.PutDict(s3def['sets']['trainingset']['bucket'],
config['test_archive'] + args.tests_json, training_data)
test_url = s3.GetUrl(s3def['sets']['trainingset']['bucket'],
config['test_archive'] + args.tests_json)
print("Test results {}".format(test_url))
