Wildcard import (#1411)

add `__all__` and `remove import *`. Update CONTRIBUTING.md

CONTRIBUTING.md

@@ -73,6 +73,13 @@ License information: all source code files should start with this paragraph:
 
 ```
 
+##### Exporting modules
+
+If you intend for any variables/functions/classes to be available outside of the file with the edited functionality, then:
+
+- Create or append to the `__all__` variable (in the file in which functionality has been added), and
+- Add to the `__init__.py` file.
+
 #### Unit testing
 MONAI tests are located under `tests/`.
 

monai/apps/__init__.py

@@ -9,5 +9,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .datasets import *
-from .utils import *
+from .datasets import CrossValidation, DecathlonDataset, MedNISTDataset
+from .utils import check_hash, download_and_extract, download_url, extractall

monai/config/__init__.py

@@ -9,5 +9,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .deviceconfig import *
-from .type_definitions import *
+from .deviceconfig import (
+    USE_COMPILED,
+    get_gpu_info,
+    get_system_info,
+    print_config,
+    print_debug_info,
+    print_gpu_info,
+    print_system_info,
+)
+from .type_definitions import IndexSelection, KeysCollection

monai/config/deviceconfig.py

@@ -38,6 +38,16 @@
 psutil, has_psutil = optional_import("psutil")
 psutil_version = psutil.__version__ if has_psutil else "NOT INSTALLED or UNKNOWN VERSION."
 
+__all__ = [
+    "print_config",
+    "get_system_info",
+    "print_system_info",
+    "get_gpu_info",
+    "print_gpu_info",
+    "print_debug_info",
+    "USE_COMPILED",
+]
+
 
 def get_config_values():
     """

monai/config/type_definitions.py

@@ -11,6 +11,8 @@
 
 from typing import Collection, Hashable, Iterable, Union
 
+__all__ = ["KeysCollection", "IndexSelection"]
+
 """Commonly used concepts
 This module provides naming and type specifications for commonly used concepts
 within the MONAI package. The intent is to explicitly identify information

monai/data/__init__.py

@@ -22,14 +22,38 @@
     ZipDataset,
 )
 from .decathlon_datalist import load_decathlon_datalist, load_decathlon_properties
-from .grid_dataset import *
-from .image_reader import *
+from .grid_dataset import GridPatchDataset, PatchDataset
+from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader
 from .iterable_dataset import IterableDataset
 from .nifti_reader import NiftiDataset
 from .nifti_saver import NiftiSaver
 from .nifti_writer import write_nifti
 from .png_saver import PNGSaver
 from .png_writer import write_png
-from .synthetic import *
+from .synthetic import create_test_image_2d, create_test_image_3d
 from .thread_buffer import ThreadBuffer
-from .utils import *
+from .utils import (
+    DistributedSampler,
+    compute_importance_map,
+    compute_shape_offset,
+    correct_nifti_header_if_necessary,
+    create_file_basename,
+    dense_patch_slices,
+    get_random_patch,
+    get_valid_patch_size,
+    is_supported_format,
+    iter_patch,
+    iter_patch_slices,
+    json_hashing,
+    list_data_collate,
+    partition_dataset,
+    partition_dataset_classes,
+    pickle_hashing,
+    rectify_header_sform_qform,
+    select_cross_validation_folds,
+    set_rnd,
+    sorted_dict,
+    to_affine_nd,
+    worker_init_fn,
+    zoom_affine,
+)

monai/data/utils.py

@@ -39,6 +39,32 @@
 
 nib, _ = optional_import("nibabel")
 
+__all__ = [
+    "get_random_patch",
+    "iter_patch_slices",
+    "dense_patch_slices",
+    "iter_patch",
+    "get_valid_patch_size",
+    "list_data_collate",
+    "worker_init_fn",
+    "set_rnd",
+    "correct_nifti_header_if_necessary",
+    "rectify_header_sform_qform",
+    "zoom_affine",
+    "compute_shape_offset",
+    "to_affine_nd",
+    "create_file_basename",
+    "compute_importance_map",
+    "is_supported_format",
+    "partition_dataset",
+    "partition_dataset_classes",
+    "select_cross_validation_folds",
+    "DistributedSampler",
+    "json_hashing",
+    "pickle_hashing",
+    "sorted_dict",
+]
+
 
 def get_random_patch(
     dims: Sequence[int], patch_size: Sequence[int], rand_state: Optional[np.random.RandomState] = None

monai/engines/__init__.py

@@ -9,7 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .evaluator import *
-from .multi_gpu_supervised_trainer import *
-from .trainer import *
-from .utils import *
+from .evaluator import EnsembleEvaluator, Evaluator, SupervisedEvaluator
+from .multi_gpu_supervised_trainer import create_multigpu_supervised_evaluator, create_multigpu_supervised_trainer
+from .trainer import GanTrainer, SupervisedTrainer, Trainer
+from .utils import CommonKeys, GanKeys, default_make_latent, default_prepare_batch, get_devices_spec

monai/engines/utils.py

@@ -13,6 +13,8 @@
 
 import torch
 
+__all__ = ["CommonKeys", "GanKeys", "get_devices_spec", "default_prepare_batch", "default_make_latent"]
+
 
 class CommonKeys:
     """

monai/handlers/__init__.py

@@ -23,5 +23,5 @@
 from .stats_handler import StatsHandler
 from .surface_distance import SurfaceDistance
 from .tensorboard_handlers import TensorBoardImageHandler, TensorBoardStatsHandler
-from .utils import *
+from .utils import all_gather, stopping_fn_from_loss, stopping_fn_from_metric
 from .validation_handler import ValidationHandler

monai/inferers/__init__.py

@@ -9,5 +9,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .inferer import *
+from .inferer import Inferer, SimpleInferer, SlidingWindowInferer
 from .utils import sliding_window_inference

monai/metrics/__init__.py

@@ -10,8 +10,8 @@
 # limitations under the License.
 
 from .confusion_matrix import ConfusionMatrixMetric, compute_confusion_matrix_metric, get_confusion_matrix
-from .hausdorff_distance import *
+from .hausdorff_distance import HausdorffDistanceMetric, compute_hausdorff_distance, compute_percent_hausdorff_distance
 from .meandice import DiceMetric, compute_meandice
 from .rocauc import compute_roc_auc
 from .surface_distance import SurfaceDistanceMetric, compute_average_surface_distance
-from .utils import *
+from .utils import do_metric_reduction, get_mask_edges, get_surface_distance, ignore_background

monai/metrics/confusion_matrix.py

@@ -14,7 +14,7 @@
 
 import torch
 
-from monai.metrics.utils import *
+from monai.metrics.utils import do_metric_reduction, ignore_background
 from monai.utils import MetricReduction
 
 

monai/metrics/hausdorff_distance.py

@@ -15,7 +15,7 @@
 import numpy as np
 import torch
 
-from monai.metrics.utils import *
+from monai.metrics.utils import do_metric_reduction, get_mask_edges, get_surface_distance, ignore_background
 from monai.utils import MetricReduction
 
 __all__ = ["HausdorffDistanceMetric", "compute_hausdorff_distance", "compute_percent_hausdorff_distance"]

monai/metrics/meandice.py

@@ -14,7 +14,7 @@
 
 import torch
 
-from monai.metrics.utils import *
+from monai.metrics.utils import do_metric_reduction, ignore_background
 from monai.utils import MetricReduction
 
 

monai/metrics/surface_distance.py

@@ -15,7 +15,7 @@
 import numpy as np
 import torch
 
-from monai.metrics.utils import *
+from monai.metrics.utils import do_metric_reduction, get_mask_edges, get_surface_distance, ignore_background
 from monai.utils import MetricReduction
 
 

monai/networks/__init__.py

@@ -9,4 +9,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .utils import *
+from .utils import (
+    eval_mode,
+    icnr_init,
+    normal_init,
+    normalize_transform,
+    one_hot,
+    pixelshuffle,
+    predict_segmentation,
+    slice_channels,
+    to_norm_affine,
+    train_mode,
+)

monai/networks/blocks/__init__.py

@@ -25,4 +25,4 @@
     SEResNetBottleneck,
     SEResNeXtBottleneck,
 )
-from .upsample import *
+from .upsample import SubpixelUpsample, Subpixelupsample, SubpixelUpSample, Upsample, UpSample

monai/networks/layers/__init__.py

@@ -9,8 +9,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .convutils import *
-from .factories import *
-from .filtering import *
-from .simplelayers import *
-from .spatial_transforms import *
+from .convutils import calculate_out_shape, gaussian_1d, polyval, same_padding, stride_minus_kernel_padding
+from .factories import Act, Conv, Dropout, LayerFactory, Norm, Pad, Pool, split_args
+from .filtering import BilateralFilter
+from .simplelayers import (
+    LLTM,
+    ChannelPad,
+    Flatten,
+    GaussianFilter,
+    HilbertTransform,
+    Reshape,
+    SkipConnection,
+    separable_filtering,
+)
+from .spatial_transforms import AffineTransform, grid_count, grid_grad, grid_pull, grid_push

monai/networks/nets/__init__.py

@@ -11,16 +11,16 @@
 
 from .ahnet import AHNet
 from .autoencoder import AutoEncoder
-from .basic_unet import *
-from .classifier import *
+from .basic_unet import BasicUNet, BasicUnet, Basicunet
+from .classifier import Classifier, Critic, Discriminator
 from .densenet import DenseNet, densenet121, densenet169, densenet201, densenet264
-from .dynunet import *
-from .fullyconnectednet import *
+from .dynunet import DynUNet, DynUnet, Dynunet
+from .fullyconnectednet import FullyConnectedNet, VarFullyConnectedNet
 from .generator import Generator
 from .highresnet import HighResBlock, HighResNet
 from .regressor import Regressor
 from .segresnet import SegResNet, SegResNetVAE
 from .senet import SENet, se_resnet50, se_resnet101, se_resnet152, se_resnext50_32x4d, se_resnext101_32x4d, senet154
-from .unet import *
+from .unet import UNet, Unet, unet
 from .varautoencoder import VarAutoEncoder
 from .vnet import VNet

monai/networks/nets/classifier.py

@@ -17,6 +17,8 @@
 from monai.networks.layers.factories import Act, Norm, split_args
 from monai.networks.nets.regressor import Regressor
 
+__all__ = ["Classifier", "Discriminator", "Critic"]
+
 
 class Classifier(Regressor):
     """

monai/networks/nets/dynunet.py

@@ -12,9 +12,10 @@
 
 from typing import List, Optional, Sequence, Union
 
+import torch
 import torch.nn as nn
 
-from monai.networks.blocks.dynunet_block import *
+from monai.networks.blocks.dynunet_block import UnetBasicBlock, UnetOutBlock, UnetResBlock, UnetUpBlock
 
 __all__ = ["DynUNet", "DynUnet", "Dynunet"]
 

monai/networks/nets/fullyconnectednet.py

@@ -17,6 +17,8 @@
 from monai.networks.blocks import ADN
 from monai.networks.layers.factories import Act
 
+__all__ = ["FullyConnectedNet", "VarFullyConnectedNet"]
+
 
 def _get_adn_layer(
     act: Optional[Union[Tuple, str]], dropout: Optional[Union[Tuple, str, float]], ordering: Optional[str]

monai/networks/nets/segresnet.py

@@ -13,9 +13,10 @@
 
 import numpy as np
 import torch
+import torch.nn as nn
 import torch.nn.functional as F
 
-from monai.networks.blocks.segresnet_block import *
+from monai.networks.blocks.segresnet_block import ResBlock, get_conv_layer, get_norm_layer, get_upsample_layer
 from monai.networks.layers.factories import Act, Dropout
 from monai.utils import UpsampleMode
 

monai/networks/nets/unet.py

@@ -19,6 +19,8 @@
 from monai.networks.layers.simplelayers import SkipConnection
 from monai.utils import alias, export
 
+__all__ = ["UNet", "Unet", "unet"]
+
 
 @export("monai.networks.nets")
 @alias("Unet")

monai/optimizers/__init__.py

@@ -10,4 +10,4 @@
 # limitations under the License.
 
 from .novograd import Novograd
-from .utils import *
+from .utils import generate_param_groups