Skip to content

Using custom dataset labels don't show up #1586

@CharlieFengCN

Description

@CharlieFengCN

Hi I'm using Unetr to run another public binary classification dataset - ATLAS R2.0 I made sure my json file is fine but why aren't my labels showing up when I do the data visualization This is my process for data extraction and image

`train_transforms = Compose(
[
LoadImaged(keys=["image", "label"]),
EnsureChannelFirstd(keys=["image", "label"]),
Orientationd(keys=["image", "label"], axcodes="RAS"),
ScaleIntensityRanged(
keys=["image"],
a_min=-50,
a_max=100,
b_min=0.0,
b_max=1.0,
clip=True,
),
# Spacingd(keys=["image", "label"], pixdim=(2.0, 2.0, 0.1), mode=("bilinear", "nearest")),
# CropForegroundd(keys=["image", "label"], source_key="image"),
# CenterSpatialCropd(keys=['image', 'label'], roi_size=(512,512,12)),
# Resize(spatial_size=(400, 400, 12)),
ResizeWithPadOrCropd(keys=["image", "label"], spatial_size=(197,233,189)),
RandCropByPosNegLabeld(
keys=["image", "label"],
label_key="label",
spatial_size=(96, 96, 96),
pos=1,
neg=1,
num_samples=8,
image_key="image",
image_threshold=0,
),
# RandAffined(
# keys=["image", "label"],
# mode=("bilinear", "nearest"),
# prob=1.0,
# spatial_size=(512, 512, 16),
# translate_range=(40, 40, 2),
# rotate_range=(np.pi / 36, np.pi / 36, np.pi / 4),
# scale_range=(0.15, 0.15, 0.15),
# padding_mode="border",
# ),
# RandGaussianNoised(keys=["image"], prob=0.10, std=0.1),
RandFlipd(
keys=["image", "label"],
spatial_axis=[0],
prob=0.10,
),
RandFlipd(
keys=["image", "label"],
spatial_axis=[1],
prob=0.10,
),
RandFlipd(
keys=["image", "label"],
spatial_axis=[2],
prob=0.10,
),
RandRotate90d(
keys=["image", "label"],
prob=0.10,
max_k=3,
),
RandShiftIntensityd(
keys=["image"],
offsets=0.10,
prob=0.50,
),
# CenterSpatialCropd(keys=['image', 'label'], roi_size=(352,352,16))
]
)
val_transforms = Compose(
[
LoadImaged(keys=["image", "label"]),
EnsureChannelFirstd(keys=["image", "label"]),
Orientationd(keys=["image", "label"], axcodes="RAS"),
# Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 0.1), mode=("bilinear", "nearest")),
ScaleIntensityRanged(
keys=["image"],
a_min=-50,
a_max=100,
b_min=0.0,
b_max=1.0,
clip=True,
),
# CropForegroundd(keys=["image", "label"], source_key="image"),
# Resize(spatial_size=(400, 400, 12)),
ResizeWithPadOrCropd(keys=["image", "label"], spatial_size=(197,233,189)),

    # Rotate90d(keys=["image", "label"], k=1),
    # CenterSpatialCropd(keys=['image', 'label'], roi_size=(352,352,16)),
    # Flipd(keys=["image", "label"], spatial_axis=[0]),
]

) data_dir = r"/home/FCN/code/data"
split_json = "/dataset.json"

datasets = data_dir + split_json
datalist = load_decathlon_datalist(datasets, True, "training")
val_files = load_decathlon_datalist(datasets, True, "validation")
train_ds = CacheDataset(
data=datalist,
transform=train_transforms,
cache_num=24,
cache_rate=1.0,
num_workers=8,
)
device_ids = [i for i in range(torch.cuda.device_count())]
train_loader = DataLoader(train_ds, batch_size=1, shuffle=True, num_workers=0, pin_memory=True)
val_ds = CacheDataset(data=val_files, transform=val_transforms, cache_num=6, cache_rate=1.0, num_workers=4)
val_loader = DataLoader(val_ds, batch_size=1, shuffle=False, num_workers=0, pin_memory=True)

print(len(train_loader))
print(len(val_loader))`

`check_ds = Dataset(data=val_files, transform=val_transforms)
check_loader = DataLoader(check_ds, batch_size=1)
check_data = first(check_loader)
image, label = (check_data["image"][0][0], check_data["label"][0][0])
print(f"image shape: {image.shape}, label shape: {label.shape}")

plot the slice [:, :, 80]

plt.figure("check", (12, 6))
plt.subplot(1, 2, 1)
plt.title("image")
plt.imshow(image[:, :, 80], cmap="gray")
plt.subplot(1, 2, 2)
plt.title("label")
plt.imshow(label[:, :,80])
plt.show()`

image

image

Please tell me what's wrong . Thanks very much

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions