def main(args, conf):
## DIY dataset
tr_dataset = AudioDataset(conf, data)
cv_dataset = AudioDataset(conf, data)
## DIY dataloader
batch_size = conf.get("batch_size", 33)
nun_workers = conf.get("num_workers", 5)
tr_loader = AudioDataLoader(tr_dataset,
batch_size=batch_size,
num_workers=nun_workers)
cv_loader = AudioDataLoader(cv_dataset,
batch_size=batch_size,
num_workers=nun_workers)
loader_dict = {'tr_loader': tr_loader, 'cv_loader': cv_loader}
## DIY model
model = SegNet(conf)
print(model)
model.cuda()
optimizier = get_optim(model, conf)
# solver
solver = Solver(conf, loader_dict, model, optimizier)
solver.train()
def getModel(args):
if args.arch == 'UNet':
model = Unet(3, 1).to(device)
if args.arch == 'resnet34_unet':
model = resnet34_unet(1, pretrained=False).to(device)
if args.arch == 'unet++':
args.deepsupervision = True
model = NestedUNet(args, 3, 1).to(device)
if args.arch == 'Attention_UNet':
model = AttU_Net(3, 1).to(device)
if args.arch == 'segnet':
model = SegNet(3, 1).to(device)
if args.arch == 'r2unet':
model = R2U_Net(3, 1).to(device)
# if args.arch == 'fcn32s':
# model = get_fcn32s(1).to(device)
if args.arch == 'myChannelUnet':
model = myChannelUnet(3, 1).to(device)
if args.arch == 'fcn8s':
assert args.dataset != 'esophagus', "fcn8s模型不能用于数据集esophagus，因为esophagus数据集为80x80，经过5次的2倍降采样后剩下2.5x2.5，分辨率不能为小数，建议把数据集resize成更高的分辨率再用于fcn"
model = get_fcn8s(1).to(device)
if args.arch == 'cenet':
from cenet import CE_Net_
model = CE_Net_().to(device)
return model
def train_model(training_loader):
global epoch_list
global learning_rate_list
if train_from_last_model:
model = load_model()
learning_rate_list, epoch_list = load_info()
print("Load the exist model and continue")
else:
model = SegNet(input_channel,output_channel).cuda()
print("Train a new model")
optimizer = torch.optim.Adam(model.parameters(), lr=LEARNING_RATE)
for epoch in range(NUM_EPOCHS):
t_start = time.time()
# i = 0
count_batch = 0 #count loss
loss_sum = 0
epoch_list.append(epoch+1)
# x_axis_list = [] #graph
# y_axis_list = [] #graph
# tqdm.write('epoch = {}'.format(epoch+1))
for i, batch in enumerate(tqdm(training_loader)):
# load data
input_tensor = Variable(batch['camera_5']).cuda()
target_tensor = Variable(batch['fg_mask']).cuda()
predicted_tensor, softmaxed_tensor = model(input_tensor)
criterion = torch.nn.CrossEntropyLoss().cuda()
#criterion = nn.BCEWithLogitsLoss().cuda()
optimizer.zero_grad()
loss = criterion(predicted_tensor, target_tensor)
#print('loss = {}'.format(loss))
loss.backward()
optimizer.step()
loss_sum += loss
count_batch += 1
torch.cuda.empty_cache()
# tqdm().clear()
average_loss = loss_sum / count_batch
learning_rate_list.append(float(average_loss))
tqdm.write('{} epoch: loss = {}'.format(epoch+1,average_loss))
plot_learning_curve(len(epoch_list))
save_model(model)
save_info()
return model
def __init__(self, fusion, bottleneck, fusion_activ, segnet_models=None, num_classes=3, decoders="multi", pretrained_last_layer=False, late_dilation=1, branches=2, viz=False):
super(FusionNet, self).__init__()
self.fusion = False
self.viz = viz
fusion_module = {
"ssma": SSMA,
"custom": SSMACustom
}
if segnet_models is None:
segnet_models = [SegNet(num_classes=num_classes) for i in range(branches)]
else:
branches = len(segnet_models)
if len(segnet_models) > 1:
self.encoder_mod1 = segnet_models[0].encoders
# self.encoder_mod1.res_n50_enc.layer3[2].dropout = False
self.encoder_mod2 = segnet_models[1].encoders
# self.encoder_mod2.res_n50_enc.layer3[2].dropout = False
# self.ssma_s1 = SSMA(24, 6)
# self.ssma_s2 = SSMA(24, 6)
if branches == 3:
self.encoder_mod3 = segnet_models[2].encoders
else:
self.encoder_mod3 = None
self.ssma_res = fusion_module[fusion](
segnet_models[0].filter_config[-1],
bottleneck=bottleneck,
branches=branches,
fusion_activ=fusion_activ)
self.decoder_mod1 = segnet_models[0].decoders
if decoders == "multi" or decoders == "late":
self.decoder_mod2 = segnet_models[1].decoders
if branches == 3:
self.decoder_mod3 = segnet_models[2].decoders
else:
self.decoder_mod3 = None
self.classifier = fusion_module[fusion](
segnet_models[0].filter_config[0],
bottleneck=bottleneck,
out=num_classes,
branches=branches,
late_dilation=late_dilation,
fusion_activ=fusion_activ)
if fusion=="custom" and pretrained_last_layer:
self.classifier.final_conv = segnet_models[0].classifier
elif decoders == "single":
self.decoder_mod2 = None
self.classifier = segnet_models[0].classifier
self.fusion = decoders
else:
self.encoder_mod1 = segnet_models[0].encoders
self.decoder_mod1 = segnet_models[0].decoders
self.classifier = segnet_models[0].classifier
def __init__(self):
self.bridge = CvBridge()
self.img_height = 0
self.img_width = 0
self.blueColor = (255, 0, 0)
self.thickness = 2
self.fontScale = 0.7
self.font = cv2.FONT_HERSHEY_SIMPLEX
self.get_pixel_depth = rospy.ServiceProxy('get_depth', GetDepth)
self.fx = 1.93 #focal length of Intel D435i camera in mm
self.mm_pix = 0.003 # width of a pixel is .003 mm
self.img_center = (640, 360) #center of the image plane is (640, 360)
self.factor_scale = 1.509 #ratio between color matrix dims and depth matrix dims
self.segNet = SegNet()
with open('./ssd_coco_labels.txt', 'r') as f:
self.classes = f.read().splitlines()
def create():
'''
Creates the segmentation neural network
'''
return SegNet(SEGNET_IMAGE_DIMS, 2)
def __init__(self, conf, viz=False, save=False, test_set=None, test_checkpoint = None, test_max=None, model_only=False, num_classes = None, modalities=None, dataset_seq=None, nopredict=False, **kwargs):
super().__init__()
pl.seed_everything(RANDOM_SEED)
self.save_hyperparameters(conf)
if modalities is not None:
self.hparams.modalities = modalities
self.hparams.modalities = self.hparams.modalities.split(",")
logger.warning(f"params {self.hparams}")
init_channels = len(self.hparams.modalities) if self.hparams.init_channels is None else self.hparams.init_channels
self.model = SegNet(
num_classes=self.hparams.num_classes if num_classes is None else num_classes,
n_init_features=init_channels,
depthwise_conv=self.hparams.depthwise_conv
)
if not model_only:
self.save = save
logger.info(f"Save {self.save}")
self.viz = viz
self.hparams.resize = (480, 240)
self.hparams.masking = True
self.hparams.normalize = False
self.hparams.lwmap_range = tuple([float(i) for i in self.hparams.lwmap_range.split(",")])
self.test_checkpoint = test_checkpoint
self.test_max = test_max
self.test_set = test_set if test_set is not None else "test"
self.dataset_seq = dataset_seq
self.nopredict = nopredict
self.datasets = {
"freiburg": FreiburgDataLoader,
"freiburgthermal": FreiburgThermalDataLoader,
"cityscapes": CityscapesDataLoader,
"kitti": KittiDataLoader,
"own": OwnDataLoader,
"thermalvoc": ThermalVOCDataLoader,
"synthia": SynthiaDataLoader,
"kaistped": KAISTPedestrianDataLoader,
"kaistpedann": KAISTPedestrianAnnDataLoader,
"multispectralseg": MIRMultispectral,
"lostfound": LostFoundDataLoader,
"freiburgraw": FreiburgForestRawDataLoader,
"cityscapesraw": CityscapesRawDataLoader,
"rugd": RUGDDataLoader,
"wilddash": WildDashDataLoader
}
if self.hparams.orig_dataset is None and self.hparams.mode in ["affordances", "objects"]:
self.hparams.orig_dataset = self.hparams.dataset
if not (self.hparams.dataset == "combo"):
self.orig_dataset = self.get_dataset(name=self.hparams.orig_dataset, set=self.test_set)
else:
if self.hparams.dataset_combo is None:
self.hparams.dataset_combo = "freiburg,cityscapes,thermalvoc,synthia,kitti,multispectralseg,freiburgthermal,lostfound"
self.hparams.dataset_combo = self.hparams.dataset_combo.split(",")
self.orig_dataset = self.get_dataset_combo(set=self.test_set)
if self.hparams.loss in ["sord","compare"]:
self.hparams.ranks = [int(r) for r in self.hparams.ranks.split(",")]
else:
self.hparams.ranks = [1,2,3]
self.train_set, self.val_set, self.test_set = self.get_dataset_splits(normalize=self.hparams.normalize)
self.hparams.train_set, self.hparams.val_set, self.hparams.test_set = \
len(self.train_set.dataset), len(self.val_set.dataset), len(self.test_set.dataset)
self.update_settings()
def load_model():
segnet_save_path = os.path.join(model_dir,'segnet_model.pth')
# model = torch.load(segnet_save_path)
model = SegNet(input_channel,output_channel).cuda()
model.load_state_dict(torch.load(segnet_save_path))
return model
class ImageInfo():
def __init__(self):
self.bridge = CvBridge()
self.img_height = 0
self.img_width = 0
self.blueColor = (255, 0, 0)
self.thickness = 2
self.fontScale = 0.7
self.font = cv2.FONT_HERSHEY_SIMPLEX
self.get_pixel_depth = rospy.ServiceProxy('get_depth', GetDepth)
self.fx = 1.93 #focal length of Intel D435i camera in mm
self.mm_pix = 0.003 # width of a pixel is .003 mm
self.img_center = (640, 360) #center of the image plane is (640, 360)
self.factor_scale = 1.509 #ratio between color matrix dims and depth matrix dims
self.segNet = SegNet()
with open('./ssd_coco_labels.txt', 'r') as f:
self.classes = f.read().splitlines()
def deproject_cam_coords(self, obj_center, depth):
u_pixel = obj_center[0]
v_pixel = obj_center[1]
x_plane = self.mm_pix * (u_pixel - self.img_center[0])
y_plane = self.mm_pix * (self.img_center[1] - v_pixel)
#calc y coord
y_coord = (depth * y_plane) / math.sqrt(y_plane**2 +
(x_plane**2 + self.fx**2))
#calc x coord
if (y_coord == 0):
x_coord = depth * (x_plane / math.sqrt(x_plane**2 + self.fx**2))
else:
x_coord = y_coord * (x_plane / y_plane)
#calc z coord
if (x_coord == 0 and y_coord == 0):
z_coord = depth
elif (x_coord == 0):
z_coord = math.sqrt(depth**2 - y_coord**2)
elif (y_coord == 0):
z_coord = math.sqrt(depth**2 - x_coord**2)
else:
z_coord = x_coord * (self.fx / x_plane)
arr = [x_coord, y_coord, z_coord]
print(arr)
#return [x_coord, y_coord, z_coord]
def getDepthFromNeighborPixels(self, center):
radius = 5
depthsArr = []
#center query
center_x_scaled = int(center[0] / self.factor_scale)
center_y_scaled = int(center[1] / self.factor_scale)
center_req = GetDepthRequest(center_x_scaled, center_y_scaled)
center_depth = self.get_pixel_depth(center_req) #in mm
depthsArr.append(center_depth.depth)
#north point query
if (center[1] >= radius):
north_x_scaled = int(center[0] / self.factor_scale)
north_y_scaled = int((center[1] - radius) / self.factor_scale)
north_req = GetDepthRequest(north_x_scaled, north_y_scaled)
north_depth = self.get_pixel_depth(north_req) #in mm
depthsArr.append(north_depth.depth)
#east point query
if (center[0] + radius < 1280):
east_x_scaled = int((center[0] + radius) / self.factor_scale)
east_y_scaled = int(center[1] / self.factor_scale)
east_req = GetDepthRequest(east_x_scaled, east_y_scaled)
east_depth = self.get_pixel_depth(east_req) #in mm
depthsArr.append(east_depth.depth)
#south point query
if (center[1] + radius < 720):
south_x_scaled = int(center[0] / self.factor_scale)
south_y_scaled = int((center[1] + radius) / self.factor_scale)
south_req = GetDepthRequest(south_x_scaled, south_y_scaled)
south_depth = self.get_pixel_depth(south_req) #in mm
depthsArr.append(south_depth.depth)
#west point query
if (center[0] >= radius):
west_x_scaled = int((center[0] - radius) / self.factor_scale)
west_y_scaled = int(center[1] / self.factor_scale)
west_req = GetDepthRequest(west_x_scaled, west_y_scaled)
west_depth = self.get_pixel_depth(west_req) #in mm
depthsArr.append(west_depth.depth)
depthsArr = np.array(depthsArr)
return np.median(depthsArr)
def drawBoundingBox(self, img, detection):
#unpack detection object to get info about bounding box
classID = detection.ClassID
conf = detection.Confidence
center = detection.Center
width = int(detection.Width)
height = int(detection.Height)
#get top left coords and box label
topLeft_x = int(center[0] - (width / 2))
topLeft_y = int(center[1] - (height / 2))
box_label = '{}:{}'.format(self.classes[classID], round(conf, 2))
#only display bounding box, depths, and 3D coords if object is PERSON
if (classID == 62):
# Query segnet class for centroid.
crop = img[topLeft_y:topLeft_y + height,
topLeft_x:topLeft_x + width, :]
mask, crop_centroid = self.segNet.getCentroid(crop, classID)
img_centroid = (topLeft_x + crop_centroid[0],
topLeft_y + crop_centroid[1]
) # add coords to top left of bounding box
# Get depth of centroid by sampling neighboring pixels and deproject into 3D camera coords
depth = self.getDepthFromNeighborPixels(img_centroid)
#self.deproject_cam_coords(img_centroid, depth)
depthLabel = '{}m'.format(depth / 1000.0)
# Render important information.
cv2.rectangle(img, (topLeft_x, topLeft_y),
(topLeft_x + width, topLeft_y + height),
self.blueColor, self.thickness) #draw bounding box
cv2.putText(img, box_label, (topLeft_x, topLeft_y + 20), self.font,
self.fontScale, self.blueColor,
self.thickness) #draw class: conf
cv2.putText(img, depthLabel, (topLeft_x, topLeft_y + 40),
self.font, self.fontScale, self.blueColor,
self.thickness) #draw depth in meters
cv2.circle(img, (int(img_centroid[0]), int(img_centroid[1])), 5,
(0, 255, 0), -1) #draw centroid within bounding box
return img
def callback(self, msg):
height = msg.height
width = msg.width
np_image_bgr = self.bridge.imgmsg_to_cv2(msg)
np_image_rgb = cv2.cvtColor(np_image_bgr, cv2.COLOR_BGR2RGB)
cuda_img = jetson.utils.cudaFromNumpy(np_image_rgb)
detections = net.Detect(cuda_img)
jetson.utils.cudaDeviceSynchronize()
for detection in detections:
if (detection.ClassID != 62):
continue
np_image_rgb = self.drawBoundingBox(np_image_rgb, detection)
cv2.imshow('CV2 Capture', np_image_rgb)
keyPress = cv2.waitKey(1)
def main(_run, _config, world_size, rank, init_method, datadir, outdir_suffix,
batch_size, num_workers, outdir, lr, wd, num_epochs, nsamples):
cudnn.benchmark = True
device = torch.device('cuda:0') # device is set by CUDA_VISIBLE_DEVICES
torch.cuda.set_device(device)
# rank 0 creates experiment observer
is_master = rank == 0
# rank joins process group
print('rank', rank, 'init_method', init_method)
dist.init_process_group('nccl',
rank=rank,
world_size=world_size,
init_method=init_method)
# actual training stuff
train = make_loader(
pt.join(datadir, '') if datadir else None,
batch_size,
device,
world_size,
rank,
num_workers,
# this the parameter based on which augmentation is applied to the data
gpu_augmentation=False,
image_rng=None,
nsamples=nsamples)
print('\n experiment name ', exp)
# outdir stuff
if outdir is None:
outdir = pt.join(ROOT, '../exp/', outdir_suffix)
model = Net(batch_size=batch_size)
model = model.to(device)
model = nn.parallel.DistributedDataParallel(model, device_ids=[device])
optimizer, policy = make_policy(num_epochs, model, lr, 0.9, wd)
# loss for autoencoder
loss = L1Loss(output_key='output', target_key='target_image').to(device)
trainer = Trainer(model,
optimizer,
loss,
rank,
MSELossMetric(),
policy,
None,
train,
None,
outdir,
snapshot_interval=4 if is_master else None,
quiet=True if not is_master else False)
print('\n Number of epochs are: ', num_epochs)
start = datetime.now()
with train:
trainer.train(num_epochs, start_epoch=0)
print("Training complete in: " + str(datetime.now() - start))
def transfer_pretrained_weighted():
model = SegNet()
corresp_name = {
'features.0.weight': 'vgg16_block1.0.weight',
'features.0.bias': 'vgg16_block1.0.bias',
'features.1.weight': 'vgg16_block1.1.weight',
'features.1.bias': 'vgg16_block1.1.bias',
'features.1.running_mean': 'vgg16_block1.1.running_mean',
'features.1.running_var': 'vgg16_block1.1.running_var',
'features.3.weight': 'vgg16_block1.3.weight',
'features.3.bias': 'vgg16_block1.3.bias',
'features.4.weight': 'vgg16_block1.4.weight',
'features.4.bias': 'vgg16_block1.4.bias',
'features.4.running_mean': 'vgg16_block1.4.running_mean',
'features.4.running_var': 'vgg16_block1.4.running_var',
'features.7.weight': 'vgg16_block2.0.weight',
'features.7.bias': 'vgg16_block2.0.bias',
'features.8.weight': 'vgg16_block2.1.weight',
'features.8.bias': 'vgg16_block2.1.bias',
'features.8.running_mean': 'vgg16_block2.1.running_mean',
'features.8.running_var': 'vgg16_block2.1.running_var',
'features.10.weight': 'vgg16_block2.3.weight',
'features.10.bias': 'vgg16_block2.3.bias',
'features.11.weight': 'vgg16_block2.4.weight',
'features.11.bias': 'vgg16_block2.4.bias',
'features.11.running_mean': 'vgg16_block2.4.running_mean',
'features.11.running_var': 'vgg16_block2.4.running_var',
'features.14.weight': 'vgg16_block3.0.weight',
'features.14.bias': 'vgg16_block3.0.bias',
'features.15.weight': 'vgg16_block3.1.weight',
'features.15.bias': 'vgg16_block3.1.bias',
'features.15.running_mean': 'vgg16_block3.1.running_mean',
'features.15.running_var': 'vgg16_block3.1.running_var',
'features.17.weight': 'vgg16_block3.3.weight',
'features.17.bias': 'vgg16_block3.3.bias',
'features.18.weight': 'vgg16_block3.4.weight',
'features.18.bias': 'vgg16_block3.4.bias',
'features.18.running_mean': 'vgg16_block3.4.running_mean',
'features.18.running_var': 'vgg16_block3.4.running_var',
'features.20.weight': 'vgg16_block3.6.weight',
'features.20.bias': 'vgg16_block3.6.bias',
'features.21.weight': 'vgg16_block3.7.weight',
'features.21.bias': 'vgg16_block3.7.bias',
'features.21.running_mean': 'vgg16_block3.7.running_mean',
'features.21.running_var': 'vgg16_block3.7.running_var',
'features.24.weight': 'vgg16_block4.0.weight',
'features.24.bias': 'vgg16_block4.0.bias',
'features.25.weight': 'vgg16_block4.1.weight',
'features.25.bias': 'vgg16_block4.1.bias',
'features.25.running_mean': 'vgg16_block4.1.running_mean',
'features.25.running_var': 'vgg16_block4.1.running_var',
'features.27.weight': 'vgg16_block4.3.weight',
'features.27.bias': 'vgg16_block4.3.bias',
'features.28.weight': 'vgg16_block4.4.weight',
'features.28.bias': 'vgg16_block4.4.bias',
'features.28.running_mean': 'vgg16_block4.4.running_mean',
'features.28.running_var': 'vgg16_block4.4.running_var',
'features.30.weight': 'vgg16_block4.6.weight',
'features.30.bias': 'vgg16_block4.6.bias',
'features.31.weight': 'vgg16_block4.7.weight',
'features.31.bias': 'vgg16_block4.7.bias',
'features.31.running_mean': 'vgg16_block4.7.running_mean',
'features.31.running_var': 'vgg16_block4.7.running_var',
'features.34.weight': 'vgg16_block5.0.weight',
'features.34.bias': 'vgg16_block5.0.bias',
'features.35.weight': 'vgg16_block5.1.weight',
'features.35.bias': 'vgg16_block5.1.bias',
'features.35.running_mean': 'vgg16_block5.1.running_mean',
'features.35.running_var': 'vgg16_block5.1.running_var',
'features.37.weight': 'vgg16_block5.3.weight',
'features.37.bias': 'vgg16_block5.3.bias',
'features.38.weight': 'vgg16_block5.4.weight',
'features.38.bias': 'vgg16_block5.4.bias',
'features.38.running_mean': 'vgg16_block5.4.running_mean',
'features.38.running_var': 'vgg16_block5.4.running_var',
'features.40.weight': 'vgg16_block5.6.weight',
'features.40.bias': 'vgg16_block5.6.bias',
'features.41.weight': 'vgg16_block5.7.weight',
'features.41.bias': 'vgg16_block5.7.bias',
'features.41.running_mean': 'vgg16_block5.7.running_mean',
'features.41.running_var': 'vgg16_block5.7.running_var',
}
s_dict = model.state_dict()
pretrained_dict = torch.load(
'vgg16_bn-6c64b313.pth'
) # you have to download pretrained model weight pth
for name in pretrained_dict:
if name not in corresp_name:
continue
s_dict[corresp_name[name]] = pretrained_dict[name]
model.load_state_dict(s_dict)
torch.save(model.state_dict(), 'transfer-vgg16-for11classes.pth')
#print(i1.shape,i2.shape, i_12.shape)
i_12_w = self.link(i_12)
b,c,h,w = i_12_w.shape
i_12_w = i_12_w.view(b,self.branches,int(c/self.branches),h,w)
#print(i_12_w.shape)
i_12_w = self.sm(i_12_w)
#print(i_12_w.shape)
#x_12 = torch.sum(i_12_w, dim=1)
x_12 = torch.unbind(i_12_w, dim=1)
#print(i1.shape, x_12[0].shape)
#print(i1.long()[0][0][0][:5], i2.long()[0][0][0][:5])
fused = m_lst[0] * x_12[0]
for f in range(1,self.branches):
fused += (m_lst[f] * x_12[f])
#print(fused.long()[0][0][0][:5])
if self.final:
fused = self.final_conv(fused)
return fused
if __name__ == "__main__":
segnet = SegNet(num_classes=3)
encoder = segnet.encoders
#print(encoder)
fusion = FusionNet( encoders=[encoder], decoder=segnet.decoders, classifier=segnet.classifier)
print(fusion)
print(SSMA(features=512, bottleneck=3))
train_dataset,
batch_size=hparams.batch_size,
shuffle=True,
num_workers=hparams.num_workers,
pin_memory=True,
drop_last=True,
)
test_loader = DataLoader(
test_dataset,
batch_size=hparams.batch_size,
shuffle=False,
num_workers=hparams.num_workers,
pin_memory=True,
)
model = SegNet(11, 3, drop_rate=0.2)
writer.add_graph(model, torch.zeros(1, 3, 360, 480))
model = model.to(device)
cls_w = class_weights(train_dataset).astype(np.float32)
cls_w = torch.from_numpy(cls_w[:-1])
criterion = nn.CrossEntropyLoss(reduction="mean",
ignore_index=11,
weight=cls_w).to(device)
# optimizer = optim.Adam(
optimizer = optim.SGD(
model.parameters(),
lr=float(hparams.init_lr),
weight_decay=float(hparams.weight_decay),
momentum=0.9,
)
def train(train_run=(True, True), restore=False, epoch=0):
disc_train_run, segm_train_run = train_run
train_run = disc_train_run or segm_train_run
if not train_run:
FLAGS.batch_size = 1
FLAGS.num_epochs = 1
timestr = time.strftime("TRAIN/%d_%b_%Y_%H_%M",
time.localtime()) if train_run else time.strftime(
"TEST/%d_%b_%Y_%H_%M", time.localtime())
timestr = timestr + "_EPOCH_%d" % epoch
# Location to log to.
split = 'TRAIN' if train_run else 'TEST'
filestr = FLAGS.run_dir + "tensorlogs/" + timestr + '/'
ft.directoryFixer(filestr + 'patches/')
print("Running from: " + filestr)
tf.reset_default_graph()
discriminator = DiscNet(disc_train_run, restore, timestr, split)
tf.reset_default_graph()
segmenter = SegNet(segm_train_run, restore, timestr)
# Starts the input generator
print("\rSTARTING INPUT GENERATION THREADS...")
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=discriminator.sess,
coord=coord)
print("STARTING TRAINING...")
step = 0
full_pats = 0
epoch = 0
disc_losses = []
segm_losses = []
sum_cmat = np.zeros((FLAGS.num_classes, FLAGS.num_classes))
game_1 = []
game_2 = []
game_3 = []
game_4 = []
ssim = []
psnr = []
rers = []
maes = []
mses = []
try:
while not coord.should_stop():
# Run the network and write summaries
start = timeit.default_timer()
try:
orig_img, orig_lab, ids, img_pat, lab_pat, disc_log, count, disc_loss = discriminator.run(
)
disc_losses.append(disc_loss)
except IndexError:
break
# Epoch done.
if FLAGS.cell_selection or (FLAGS.positive_training and train_run):
img_pat = np.reshape(
img_pat, (-1, FLAGS.patch_size, FLAGS.patch_size, 3))
lab_pat = np.reshape(
lab_pat, (-1, FLAGS.patch_size, FLAGS.patch_size, 1))
disc_log = np.squeeze(disc_log)
else:
img_pat = np.reshape(orig_img, (-1, FLAGS.imgH, FLAGS.imgW, 3))
lab_pat = np.reshape(orig_lab, (-1, FLAGS.imgH, FLAGS.imgW, 1))
disc_log = np.ones((FLAGS.batch_size))
# Do some processing, create new array with only patches we need.
new_imgs = []
new_labs = []
for x in range(len(disc_log)):
if (disc_log[x] == 1):
new_imgs.append(img_pat[x])
new_labs.append(lab_pat[x])
new_imgs = np.array(new_imgs)
new_labs = np.array(new_labs)
imgs_labs_losses = []
if (np.sum(disc_log) > 0):
seg_log, seg_loss, per_pat_loss, cmat = segmenter.run(
new_imgs, new_labs, count)
segm_losses.append(seg_loss)
sum_cmat += cmat
# Train on the worst 1/2 images twice.
if train_run:
im_loss = zip(new_imgs, new_labs, per_pat_loss)
[
imgs_labs_losses.append(im_lab_loss)
for im_lab_loss in im_loss
]
# Do some more processing, weave the resultant patches into an array
# of the resultant logit map
y = 0
stop = timeit.default_timer()
print('\rTime: ', stop - start, end='')
if not train_run:
full_pats = np.zeros(shape=lab_pat.shape, dtype=np.float32)
for x in range(len(disc_log)):
if (disc_log[x] == 1):
full_pats[x] = seg_log[y]
y += 1
orig_img = np.squeeze(orig_img).astype('uint8')
orig_lab = np.squeeze(orig_lab)
result = np.squeeze(patches_to_image(full_pats))
with h5py.File(filestr + '%s_log.png' % ids, 'w') as hf:
hf['density'] = np.squeeze(orig_lab)
with h5py.File(filestr + '%s_ann.png' % ids, 'w') as hf:
hf['density'] = np.squeeze(result)
# Before we colorize the result, we want to run the GAME metrics
game_1.append(util.cpu_GAME(orig_lab, result, 1))
game_2.append(util.cpu_GAME(orig_lab, result, 2))
game_3.append(util.cpu_GAME(orig_lab, result, 3))
game_4.append(util.cpu_GAME(orig_lab, result, 4))
ssim.append(util.cpu_psnr(orig_lab, result))
psnr.append(util.cpu_ssim(orig_lab, result))
rers.append(
np.abs(np.sum(orig_lab) - np.sum(result)) /
np.sum(orig_lab))
maes.append(np.abs(np.sum(orig_lab) - np.sum(result)))
mses.append((np.sum(orig_lab) - np.sum(result))**2)
result = util.cpu_colorize(result)
orig_lab = util.cpu_colorize(np.squeeze(orig_lab))
img = Image.fromarray(result)
img.save(filestr + '%d_log.png' % step)
img = Image.fromarray(orig_img)
img.save(filestr + '%d_img.png' % step)
img = Image.fromarray(orig_lab)
img.save(filestr + '%d_lab.png' % step)
for x in range(new_imgs.shape[0]):
img = Image.fromarray(
np.squeeze(new_imgs[x]).astype(np.uint8))
img.save(filestr + 'patches/' + '%d_%d_img_pat.png' %
(step, x))
img = Image.fromarray(
np.squeeze(util.cpu_colorize(new_labs[x])))
img.save(filestr + 'patches/' + '%d_%d_lab_pat.png' %
(step, x))
img = Image.fromarray(
np.squeeze(util.cpu_colorize(seg_log[x])))
img.save(filestr + 'patches/' + '%d_%d_log_pat.png' %
(step, x))
step += 1
# Train on bad patches over again.
if segm_train_run:
imgs_labs_losses.sort(key=lambda tup: tup[2])
iterval = 0
while len(imgs_labs_losses) > 1:
iterval += 1
imgs_labs_losses = imgs_labs_losses[len(imgs_labs_losses) //
2:]
generator.perturb(imgs_labs_losses)
new_imgs = []
new_labs = []
[(new_imgs.append(new_img), new_labs.append(new_lab))
for new_img, new_lab, _ in imgs_labs_losses]
# Run through 10 patches at a time as a batch.
for x in range(len(new_imgs) // 10 + 1):
print('\rTRAINING ON HARD EXAMPLES %d/%d ITER %d' %
(x, len(new_imgs) // 10 + 1, iterval),
end='')
_ = segmenter.run(new_imgs[x * 10:(x + 1) * 10],
new_labs[x * 10:(x + 1) * 10], 0, False)
print('\rDONE TRAINING HARD EXAMPLES')
except KeyboardInterrupt:
pass
finally:
if train_run:
discriminator.save()
segmenter.save()
else:
print("GAME 1,2,3,4")
print("Game 1, ", np.mean(game_1))
print("Game 2, ", np.mean(game_2))
print("Game 3, ", np.mean(game_3))
print("Game 4, ", np.mean(game_4))
print("SSIM, ", np.mean(ssim))
print("PSNR, ", np.mean(psnr))
print("Rel_Err, ", np.mean(rers))
print("MAE, ", np.mean(maes))
print("MSE, ", np.mean(mses))
coord.request_stop()
coord.join(threads)
np.save(filestr + "data.dat", sum_cmat)
discriminator.close()
segmenter.close()
return np.mean(disc_losses), np.mean(segm_losses)
def main():
global args, best_prec1
args = parser.parse_args()
# Check if the save directory exists or not
if not os.path.exists(args.save_dir):
os.makedirs(args.save_dir)
model = SegNet(3, 3)
#model.features = torch.nn.DataParallel(model.features)
if use_gpu:
model.cuda()
# Optionally resume from a checkpoint
if args.resume:
if os.path.isfile(args.resume):
print("=> loading checkpoint '{}'".format(args.resume))
checkpoint = torch.load(args.resume)
args.start_epoch = checkpoint['epoch']
best_prec1 = checkpoint['best_prec1']
model.load_state_dict(checkpoint['state_dict'])
#optimizer.load_state_dict(checkpoint['optimizer'])
print("=> loaded checkpoint '{}' (epoch {})".format(
args.evaluate, checkpoint['epoch']))
else:
print("=> no checkpoint found at '{}'".format(args.resume))
cudnn.benchmark = True
# data_transforms = {
# 'train': transforms.Compose([
# transforms.Scale(256),
# transforms.RandomSizedCrop(224),
# transforms.RandomHorizontalFlip(),
# transforms.ToTensor(),
# transforms.Normalize([0.485,0.456,0.406],[0.229,0.224,0.225]),
# ]),
# 'val': transforms.Compose([
# transforms.Scale(256),
# transforms.CenterCrop(224),
# transforms.RandomHorizontalFlip(),
# transforms.ToTensor(),
# transforms.Normalize([0.485,0.456,0.406],[0.229,0.224,0.225]),
# ]),
# }
data_transforms = {
'train':
transforms.Compose([
transforms.Scale((224, 224)),
transforms.ToTensor(),
]),
'val':
transforms.Compose([
transforms.Scale((224, 224)),
transforms.ToTensor(),
]),
}
data_dir = '/media/salman/DATA/NUST/MS RIME/Thesis/MICCAI Dataset/miccai_all_images'
image_datasets = {
x: miccaiDataset(os.path.join(data_dir, x), data_transforms[x])
for x in ['train', 'val']
}
dataloaders = {
x: torch.utils.data.DataLoader(image_datasets[x],
batch_size=args.batch_size,
shuffle=True,
num_workers=args.workers)
for x in ['train', 'val']
}
dataset_sizes = {x: len(image_datasets[x]) for x in ['train', 'val']}
# Define loss function (criterion) and optimizer
criterion = nn.MSELoss().cuda()
if args.half:
model.half()
criterion.half()
#optimizer = torch.optim.SGD(model.parameters(), args.lr,
# momentum=args.momentum,
# weight_decay=args.weight_decay)
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
if args.evaluate:
validate(dataloaders['val'], model, criterion)
return
for epoch in range(args.start_epoch, args.epochs):
#adjust_learning_rate(optimizer, epoch)
# Train for one epoch
train(dataloaders['train'], model, criterion, optimizer, epoch)
# Evaulate on validation set
prec1 = validate(dataloaders['val'], model, criterion)
prec1 = prec1.cpu().data.numpy()
# Remember best prec1 and save checkpoint
print(prec1)
print(best_prec1)
is_best = prec1 < best_prec1
best_prec1 = min(prec1, best_prec1)
save_checkpoint(
{
'epoch': epoch + 1,
'state_dict': model.state_dict(),
'best_prec1': best_prec1,
#'optimizer': optimizer.state_dict(),
},
is_best,
filename=os.path.join(args.save_dir,
'checkpoint_{}.tar'.format(epoch)))
from torch import nn
from camvid_dataset import CamVidDataset
from segnet import SegNet
import time
import matplotlib.pyplot as plt
import argparse
parse = argparse.ArgumentParser()
parse.add_argument('--mode', choices=['train', 'val', 'test'])
parse.add_argument('--batch_size', '-b', type=int, default=16)
parse.add_argument('--resume', type=bool, default=False)
parse.add_argument('--epochs', type=int, default=33)
args = parse.parse_args()
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
model = SegNet()
if args.mode == 'train':
model.load_state_dict(torch.load('transfer-vgg16-for11classes.pth'))
else:
model.load_state_dict(torch.load('segnet_weight_11classes.pth'))
if torch.cuda.device_count() > 1:
print("Let's use", torch.cuda.device_count(), "GPUs!")
model = nn.DataParallel(model)
model.to(device)
def train(epochs):
model.train()
train_dataset = CamVidDataset(phase='train')
train_loader = DataLoader(train_dataset,
def handler(context):
# Dataset
dataset_alias = context.datasets
train_dataset_id = dataset_alias['train']
val_dataset_id = dataset_alias['val']
trainset = SegmentationDatasetFromAPI(train_dataset_id,
transform=SegNetAugmentation(MEANS))
valset = SegmentationDatasetFromAPI(val_dataset_id,
transform=SegNetAugmentation(
MEANS, False))
class_weight = calc_weight(
SegmentationDatasetFromAPI(train_dataset_id,
transform=SegNetAugmentation(MEANS, False)))
class_weight = class_weight.to(device)
trainloader = torch.utils.data.DataLoader(trainset,
batch_size=BATCHSIZE,
shuffle=True,
num_workers=0)
valloader = torch.utils.data.DataLoader(valset,
batch_size=BATCHSIZE,
shuffle=False,
num_workers=0)
# Model
net = SegNet(3, n_class=len(camvid_label_names))
net = net.to(device)
# Optimizer
#criterion = PixelwiseSoftmaxClassifier(weight=class_weight)
criterion = torch.nn.CrossEntropyLoss(weight=class_weight, ignore_index=-1)
optimizer = optim.SGD(net.parameters(),
lr=lr,
momentum=0.9,
weight_decay=5e-4)
scheduler = lr_scheduler.MultiStepLR(optimizer,
milestones=[150, 250],
gamma=0.1)
statistics = Statistics(epochs)
for epoch in range(epochs):
scheduler.step()
train_loss, train_acc = train(net, optimizer, trainloader, criterion,
epoch)
test_loss, test_acc = test(net, valloader, criterion, epoch)
# Reporting
print(
'[{:d}] main/loss: {:.3f} main/acc: {:.3f}, main/validation/loss: {:.3f}, main/validation/acc: {:.3f}'
.format(epoch + 1, train_loss, train_acc, test_loss, test_acc))
statistics(epoch + 1, train_loss, train_acc, test_loss, test_acc)
writer.add_scalar('main/loss', train_loss, epoch + 1)
writer.add_scalar('main/acc', train_acc, epoch + 1)
writer.add_scalar('main/validation/loss', test_loss, epoch + 1)
writer.add_scalar('main/validation/acc', test_acc, epoch + 1)
torch.save(net.state_dict(),
os.path.join(ABEJA_TRAINING_RESULT_DIR, 'model.pth'))
def train(train_run = (True,True), restore = False, epoch = 0):
disc_train_run,segm_train_run = train_run
train_run = disc_train_run or segm_train_run
if not train_run:
FLAGS.batch_size = 1
FLAGS.num_epochs = 1
train_run = disc_train_run or segm_train_run
timestr = time.strftime("TRAIN/%d_%b_%Y_%H_%M",time.localtime()) if train_run else time.strftime("TEST/%d_%b_%Y_%H_%M",time.localtime())
timestr = timestr + "_EPOCH_%d"%epoch
# Location to log to.
split = 'TRAIN' if train_run else 'TEST'
# We just run from the saved model directory for demoing.
FLAGS.run_dir = FLAGS.mod_dir
filestr = FLAGS.run_dir + "tensorlogs/" + timestr + '/'
ft.directoryFixer(filestr + 'patches/')
print("Running from: " + filestr)
tf.reset_default_graph()
discriminator = DiscNet(disc_train_run,restore,timestr,split)
tf.reset_default_graph()
segmenter = SegNet(segm_train_run,restore,timestr)
# Starts the input generator
print("\rSTARTING INPUT GENERATION THREADS...")
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess = discriminator.sess, coord = coord)
print("STARTING TRAINING...")
step = 0
full_pats = 0
epoch = 0
disc_losses = []
segm_losses = []
try:
while not coord.should_stop():
# Run the network and write summaries
try:
orig_img,orig_lab,img_pat,lab_pat,disc_log,count,disc_loss = discriminator.run()
disc_losses.append(disc_loss)
except IndexError:
break
# Epoch done.
img_pat = np.reshape(img_pat,(-1,FLAGS.patch_size,FLAGS.patch_size,3))
lab_pat = np.reshape(lab_pat,(-1,FLAGS.patch_size,FLAGS.patch_size,1))
disc_log = np.squeeze(disc_log)
# Do some processing, create new array with only patches we need.
new_imgs = []
new_labs = []
for x in range(len(disc_log)):
if(disc_log[x] == 1):
new_imgs.append(img_pat[x])
new_labs.append(lab_pat[x])
new_imgs = np.array(new_imgs)
new_labs = np.array(new_labs)
imgs_labs_losses = []
if(np.sum(disc_log) > 0):
seg_log,seg_loss,per_pat_loss = segmenter.run(new_imgs,new_labs,count)
segm_losses.append(seg_loss)
# Train on the worst 1/2 images twice.
if train_run:
im_loss = zip(new_imgs,new_labs,per_pat_loss)
[imgs_labs_losses.append(im_lab_loss) for im_lab_loss in im_loss]
# Do some more processing, weave the resultant patches into an array
# of the resultant logit map
y = 0
if not train_run:
full_pats = np.zeros(shape = lab_pat.shape)
for x in range(len(disc_log)):
if(disc_log[x] == 1):
full_pats[x] = seg_log[y]
y+=1
orig_img = np.squeeze(orig_img).astype('uint8')
orig_lab = util.cpu_colorize(np.squeeze(orig_lab))
# Go from patches to full image logit map.
result = patches_to_image(full_pats)
img = Image.fromarray(util.cpu_colorize(result))
img.save(filestr + '%d_log.png'%step)
img = Image.fromarray(orig_img)
img.save(filestr + '%d_img.png'%step)
img = Image.fromarray(orig_lab)
img.save(filestr + '%d_lab.png'%step)
for x in range(new_imgs.shape[0]):
img = Image.fromarray(np.squeeze(new_imgs[x]).astype(np.uint8))
img.save(filestr + 'patches/' + '%d_%d_img_pat.png'%(step,x))
img = Image.fromarray(np.squeeze(util.cpu_colorize(new_labs[x])))
img.save(filestr + 'patches/' + '%d_%d_lab_pat.png'%(step,x))
img = Image.fromarray(np.squeeze(util.cpu_colorize(seg_log[x])))
img.save(filestr + 'patches/' + '%d_%d_lab_pat.png'%(step,x))
step +=1
# Train on bad patches over again.
if segm_train_run:
imgs_labs_losses.sort(key = lambda tup: tup[2])
iterval = 0
while len(imgs_labs_losses) > 1:
iterval += 1
imgs_labs_losses = imgs_labs_losses[len(imgs_labs_losses)//2:]
generator.perturb(imgs_labs_losses)
new_imgs = []
new_labs = []
[(new_imgs.append(new_img),new_labs.append(new_lab)) for new_img,new_lab,_ in imgs_labs_losses]
# Run through 10 patches at a time as a batch.
for x in range(len(new_imgs)//10 + 1):
print('\rTRAINING ON HARD EXAMPLES %d/%d ITER %d'%(x,len(new_imgs)//10+1,iterval),end='')
_ = segmenter.run(new_imgs[x*10:(x+1)*10],new_labs[x*10:(x+1)*10],0,False)
print('\rDONE TRAINING HARD EXAMPLES')
except KeyboardInterrupt:
pass
finally:
if train_run:
discriminator.save()
segmenter.save()
coord.request_stop()
coord.join(threads)
discriminator.close()
segmenter.close()
return np.mean(disc_losses),np.mean(segm_losses)
def main(_run, _config, world_size, rank, init_method, datadir, batch_size,
num_workers, outdir_suffix, outdir, lr, wd, warmup, num_epochs,
nsamples):
cudnn.benchmark = True
device = torch.device('cuda:0') # device is set by CUDA_VISIBLE_DEVICES
torch.cuda.set_device(device)
# rank 0 creates experiment observer
is_master = rank == 0
# rank joins process group
print('rank', rank, 'init_method', init_method)
dist.init_process_group('nccl',
rank=rank,
world_size=world_size,
init_method=init_method)
# actual training stuff
train = make_loader(
pt.join(datadir, '') if datadir else None,
batch_size,
device,
world_size,
rank,
num_workers,
# this the parameter based on which augmentation is applied to the data
gpu_augmentation=False,
image_rng=None,
nsamples=nsamples)
# lr is scaled linearly to original batch size of 256
# world_batch_size = world_size * batch_size
# k = world_batch_size / 256
# lr = k * lr
# outdir stuff
if outdir is None:
outdir = pt.join(ROOT, '../exp/', outdir_suffix)
model = Net(num_classes=500, batch_size=batch_size)
print('\n network parameters ', len(list(model.parameters())))
model = model.to(device)
model = nn.parallel.DistributedDataParallel(model, device_ids=[device])
#model = Unpacker(model)
optimizer, policy = make_policy(num_epochs, model, lr, 0.9, wd)
# loss for autoencoder
loss = L1Loss(output_key='output', target_key='target_image').to(device)
# this loss is for classifier
classifier_loss = CrossEntropyLoss(output_key='probs',
target_key='label').to(device)
trainer = Trainer(model,
optimizer,
loss,
classifier_loss,
rank,
AccuracyMetric(output_key='softmax_output',
target_key='label'),
policy,
None,
train,
None,
outdir,
snapshot_interval=4 if is_master else None,
quiet=True if not is_master else False)
print('\n Number of epochs are: ', num_epochs)
start = datetime.now()
with train:
trainer.train(num_epochs, start_epoch=0)
print("Training complete in: " + str(datetime.now() - start))
def main(_run, _config, world_size, rank, init_method, datadir, batch_size,
val_batch_size, num_workers, outdir, outdir_prefix, lr, wd,
bn_momentum, bn_correct, warmup, num_epochs, resume, finetune, size,
nsamples):
cudnn.benchmark = True
device = torch.device('cuda:0') # device is set by CUDA_VISIBLE_DEVICES
torch.cuda.set_device(device)
# rank 0 creates experiment observer
is_master = rank == 0
# rank joins process group
print('rank', rank, 'init_method', init_method)
dist.init_process_group('nccl',
rank=rank,
world_size=world_size,
init_method=init_method)
# actual training stuff
train = make_loader(
pt.join(datadir, '') if datadir else None,
batch_size,
device,
world_size,
rank,
num_workers,
size,
# this the parameter based on which augmentation is applied to the data
gpu_augmentation=False,
image_rng=None,
nsamples=nsamples)
# lr is scaled linearly to original batch size of 256
world_batch_size = world_size * batch_size
k = world_batch_size / 256
lr = k * lr
# outdir stuff
if outdir is None:
outdir = pt.join(outdir_prefix, '%dgpu' % (world_size, ))
model = Net(num_classes=1000, batch_size=batch_size)
model = model.to(device)
model = nn.parallel.DistributedDataParallel(model, device_ids=[device])
#model = Unpacker(model)
optimizer, policy = make_policy(num_epochs, model, lr, 0.9)
print('\n policy defined')
# loss for autoencoder
loss = L1Loss(output_key='output', target_key='target_image').to(device)
# this loss is for classifier
classifier_loss = CrossEntropyLoss(output_key='probs',
target_key='label').to(device)
trainer = Trainer(model,
optimizer,
loss,
None,
policy,
None,
train,
None,
outdir,
snapshot_interval=5 if is_master else None,
quiet=rank != 0)
print('\n trainer has been initialized')
start = datetime.now()
with train:
trainer.train(num_epochs, start_epoch=0)
print("Training complete in: " + str(datetime.now() - start))
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--cuda', default=False, action="store_true")
parser.add_argument('--force', default=False, action="store_true")
parser.add_argument('--threads', default=os.cpu_count(), type=int)
args = parser.parse_args()
logger.debug(args)
num_classes = 3
logger.info(f"... setting up models ...")
create_folder("results/benchmark")
model_dict = {
"model_segnet_1":
SegNet(num_classes=num_classes, n_init_features=1),
"model_segnet_2":
SegNet(num_classes=num_classes, n_init_features=2),
"model_segnet_3":
SegNet(num_classes=num_classes, n_init_features=3),
# "mid_ssma_2": FusionNet(fusion="ssma", bottleneck=16, fusion_activ="sigmoid", num_classes=num_classes, decoders="single", branches=2),
"mid_custom_2":
FusionNet(fusion="custom",
bottleneck=16,
fusion_activ="softmax",
num_classes=num_classes,
decoders="single",
branches=2),
# "dual_ssma_2": FusionNet(fusion="ssma", bottleneck=16, fusion_activ="sigmoid", num_classes=num_classes, decoders="multi", branches=2),