repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
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ML-Doctor | ML-Doctor-main/demoloader/DCGAN.py | import torch.nn as nn
class Generator(nn.Module):
def __init__(self, ngpu=1, nc=3, nz=100, ngf=64):
super(Generator, self).__init__()
self.ngpu = ngpu
self.main = nn.Sequential(
# input is Z, going into a convolution
nn.ConvTranspose2d(nz, ngf * 8, 4, 1, 0, bias=Fals... | 4,237 | 29.934307 | 82 | py |
ML-Doctor | ML-Doctor-main/utils/define_models.py | import torch
import torch.nn as nn
import torch.nn.functional as F
class attrinf_attack_model(nn.Module):
def __init__(self, inputs, outputs):
super(attrinf_attack_model, self).__init__()
self.classifier = nn.Linear(inputs, outputs)
def forward(self, x):
x = torch.flatten(x, 1)
... | 4,227 | 24.017751 | 130 | py |
ML-Doctor | ML-Doctor-main/doctor/modsteal.py | import torch
import torch.nn.functional as F
from math import *
from tqdm import tqdm
class train_steal_model():
def __init__(self, train_loader, test_loader, target_model, attack_model, TARGET_PATH, ATTACK_PATH, device, batch_size, loss, optimizer):
self.device = device
self.batch_size = batch_si... | 4,341 | 33.188976 | 141 | py |
ML-Doctor | ML-Doctor-main/doctor/attrinf.py | import torch
import pickle
import torch.nn as nn
import torch.optim as optim
from utils.define_models import *
from sklearn.metrics import f1_score
class attack_training():
def __init__(self, device, attack_trainloader, attack_testloader, target_model, TARGET_PATH, ATTACK_PATH):
self.device = device
... | 6,547 | 34.978022 | 120 | py |
ML-Doctor | ML-Doctor-main/doctor/modinv.py | import time
import torch
import random
import numpy as np
import torch.nn as nn
import torch.utils.data
from torch.autograd import Variable
class ccs_inversion(object):
'''
Model inversion is a kind of data reconstruct attack.
This class we implement the attack on neural network,
the attack goal is t... | 8,409 | 36.713004 | 148 | py |
ML-Doctor | ML-Doctor-main/doctor/meminf.py | import os
import glob
import torch
import pickle
import numpy as np
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import torch.backends.cudnn as cudnn
np.set_printoptions(threshold=np.inf)
from opacus import PrivacyEngine
from torch.optim import lr_scheduler
from sklearn.metrics imp... | 31,612 | 37.042118 | 183 | py |
IVOS-ATNet | IVOS-ATNet-master/config.py | import os
class Config(object):
def __init__(self):
################################ C ##################################
# DAVIS path
self.davis_dataset_dir = '/home/yuk/data_ssd/datasets/DAVIS'
self.test_gpu_id = 2
self.test_metric_list = ['J', 'J_AND_F']
#######... | 1,329 | 40.5625 | 95 | py |
IVOS-ATNet | IVOS-ATNet-master/eval_real-world.py | from davisinteractive.session import DavisInteractiveSession
from davisinteractive import utils as interactive_utils
from davisinteractive.dataset import Davis
from davisinteractive.metrics import batched_jaccard
from libs import custom_transforms as tr, davis2017_torchdataset
import os
import numpy as np
from PIL im... | 17,873 | 50.2149 | 147 | py |
IVOS-ATNet | IVOS-ATNet-master/eval_davis-framework.py | from davisinteractive.session import DavisInteractiveSession
from davisinteractive import utils as interactive_utils
from davisinteractive.dataset import Davis
from davisinteractive.metrics import batched_jaccard
from libs import custom_transforms as tr, davis2017_torchdataset
import os
import numpy as np
from PIL im... | 17,800 | 50.005731 | 147 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/ltm_transfer.py |
import torch
import torch.nn as nn
import torch.nn.functional as F
class LTM_transfer(nn.Module):
def __init__(self,md=4, stride=1):
super(LTM_transfer, self).__init__()
self.md = md #displacement (default = 4pixels)
self.range = (md*2 + 1) ** 2 #(default = (4x2+1)**2 = 81)
self.... | 3,767 | 38.25 | 153 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/atnet.py | import torch
import torch.nn as nn
import torch.nn.functional as F
from networks.deeplab.aspp import ASPP
from networks.deeplab.backbone.resnet import SEResNet50
from networks.correlation_package.correlation import Correlation
from networks.ltm_transfer import LTM_transfer
class ATnet(nn.Module):
def __init__(se... | 16,091 | 38.153285 | 144 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/__init__.py | # | 1 | 1 | 1 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/aspp.py | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
class _ASPPModule(nn.Module):
def __init__(self, inplanes, planes, kernel_size, padding, dilation, BatchNorm, pretrained):
super(_ASPPModule, self).__... | 4,257 | 38.425926 | 139 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/decoder.py | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
class Decoder(nn.Module):
def __init__(self, num_classes, backbone, BatchNorm):
super(Decoder, self).__init__()
if backbone == 'resnet' or bac... | 2,280 | 39.017544 | 107 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/deeplab.py | import torch
import torch.nn as nn
import torch.nn.functional as F
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
from networks.deeplab.aspp import build_aspp
from networks.deeplab.decoder import build_decoder
from networks.deeplab.backbone import build_backbone
class DeepLab(nn.Module):... | 2,493 | 33.638889 | 93 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/__init__.py | # | 1 | 1 | 1 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/backbone/resnet.py | import math
import torch.nn as nn
import torch.utils.model_zoo as model_zoo
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
class Bottleneck(nn.Module):
expansion = 4
def __init__(self, inplanes, planes, stride=1, dilation=1, downsample=None, BatchNorm=None):
super(Bottle... | 9,076 | 36.979079 | 130 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/backbone/drn.py | import torch.nn as nn
import math
import torch.utils.model_zoo as model_zoo
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
webroot = 'https://tigress-web.princeton.edu/~fy/drn/models/'
model_urls = {
'resnet50': 'https://download.pytorch.org/models/resnet50-19c8e357.pth',
'drn-c... | 14,657 | 35.372208 | 100 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/backbone/__init__.py | from networks.deeplab.backbone import resnet, xception, drn, mobilenet
def build_backbone(backbone, output_stride, BatchNorm):
if backbone == 'resnet':
return resnet.ResNet101(output_stride, BatchNorm)
elif backbone == 'xception':
return xception.AlignedXception(output_stride, BatchNorm)
el... | 522 | 36.357143 | 70 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/backbone/xception.py | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.model_zoo as model_zoo
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
def fixed_padding(inputs, kernel_size, dilation):
kernel_size_effective = kernel_size + (kernel_size - 1) * (dilatio... | 11,561 | 39.145833 | 116 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/backbone/mobilenet.py | import torch
import torch.nn.functional as F
import torch.nn as nn
import math
from networks.deeplab.sync_batchnorm.batchnorm import SynchronizedBatchNorm2d
import torch.utils.model_zoo as model_zoo
def conv_bn(inp, oup, stride, BatchNorm):
return nn.Sequential(
nn.Conv2d(inp, oup, 3, stride, 1, bias=False... | 5,398 | 34.519737 | 110 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/sync_batchnorm/replicate.py | # -*- coding: utf-8 -*-
# File : replicate.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import functools
from torch.nn.parallel.dat... | 3,218 | 35.579545 | 115 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/sync_batchnorm/unittest.py | # -*- coding: utf-8 -*-
# File : unittest.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import unittest
import numpy as np
from torc... | 834 | 26.833333 | 157 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/sync_batchnorm/batchnorm.py | # -*- coding: utf-8 -*-
# File : batchnorm.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import collections
import torch
import torc... | 12,932 | 44.861702 | 116 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/sync_batchnorm/comm.py | # -*- coding: utf-8 -*-
# File : comm.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import queue
import collections
import threading
... | 4,440 | 33.161538 | 117 | py |
IVOS-ATNet | IVOS-ATNet-master/networks/deeplab/sync_batchnorm/__init__.py | # -*- coding: utf-8 -*-
# File : __init__.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
from .batchnorm import SynchronizedBatchNorm1... | 447 | 36.333333 | 96 | py |
IVOS-ATNet | IVOS-ATNet-master/libs/custom_transforms.py | import numpy as np
import torch
class Normalize_ApplymeanvarImage(object):
def __init__(self, mean, var, change_channels=False):
self.mean = mean
self.var = var
self.change_channels = change_channels
def __call__(self, sample):
for elem in sample.keys():
if 'image'... | 1,272 | 25.520833 | 132 | py |
IVOS-ATNet | IVOS-ATNet-master/libs/utils.py | import os
import numpy as np
import cv2
from davisinteractive.utils.operations import bresenham
def mkdir(paths):
if not isinstance(paths, (list, tuple)):
paths = [paths]
for path in paths:
if not os.path.isdir(path):
os.makedirs(path)
class logger:
def __init__(self, log_fil... | 5,600 | 35.37013 | 120 | py |
IVOS-ATNet | IVOS-ATNet-master/libs/__init__.py | # | 1 | 1 | 1 | py |
IVOS-ATNet | IVOS-ATNet-master/libs/utils_torch.py | import torch
def combine_masks_with_batch(masks, n_obj, th=0.5, return_as_onehot = False):
""" Combine mask for different objects.
Different methods are the following:
* `max_per_pixel`: Computes the final mask taking the pixel with the highest
probability for every object.
# ... | 1,315 | 34.567568 | 84 | py |
IVOS-ATNet | IVOS-ATNet-master/libs/analyze_report.py | """ Analyse Global Summary
"""
import os
import json
import matplotlib.pyplot as plt
def analyze_summary(fname, metric = 'J_AND_F'):
METRIC_TXT = {'J': 'J',
'F': 'F',
'J_AND_F': 'J&F',}
with open(fname, 'r') as fp:
summary = json.load(fp)
print('AUC: \t{:.3f}'.... | 1,721 | 32.115385 | 122 | py |
IVOS-ATNet | IVOS-ATNet-master/libs/davis2017_torchdataset.py | from __future__ import division
import os
import numpy as np
import cv2
from libs import utils
from torch.utils.data import Dataset
import json
from PIL import Image
class DAVIS2017(Dataset):
"""DAVIS 2017 dataset constructed using the PyTorch built-in functionalities"""
def __init__(self,
... | 13,111 | 42.417219 | 153 | py |
GraphLoG | GraphLoG-main/pretrain_graphlog.py | import argparse
from loader import MoleculeDataset
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from tqdm import tqdm
import numpy as np
import os, sys
import pdb
import copy
import random
from model import GNN, ProjectNet
from sklearn.metrics import roc_auc_score
... | 22,536 | 43.364173 | 118 | py |
GraphLoG | GraphLoG-main/batch.py | import torch
from torch_geometric.data import Data, Batch
class BatchMasking(Data):
r"""A plain old python object modeling a batch of graphs as one big
(dicconnected) graph. With :class:`torch_geometric.data.Data` being the
base class, all its methods can also be used here.
In addition, single graphs c... | 8,940 | 38.043668 | 190 | py |
GraphLoG | GraphLoG-main/dataloader.py | import torch.utils.data
from torch.utils.data.dataloader import default_collate
from batch import BatchSubstructContext, BatchMasking, BatchAE
class DataLoaderSubstructContext(torch.utils.data.DataLoader):
r"""Data loader which merges data objects from a
:class:`torch_geometric.data.dataset` to a mini-batch.
... | 2,503 | 36.939394 | 89 | py |
GraphLoG | GraphLoG-main/model.py | import torch
from torch_geometric.nn import MessagePassing
from torch_geometric.utils import add_self_loops, degree, softmax
from torch_geometric.nn import global_add_pool, global_mean_pool, global_max_pool, GlobalAttention, Set2Set
import torch.nn.functional as F
from torch_scatter import scatter_add
from torch_geomet... | 15,224 | 36.967581 | 129 | py |
GraphLoG | GraphLoG-main/finetune.py | import argparse
from loader import MoleculeDataset
from torch_geometric.data import DataLoader
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.optim.lr_scheduler import StepLR
from tqdm import tqdm
import os, sys
import numpy as np
import random
from model i... | 11,223 | 40.724907 | 129 | py |
GraphLoG | GraphLoG-main/splitters.py | import torch
import random
import numpy as np
from itertools import compress
from rdkit.Chem.Scaffolds import MurckoScaffold
from collections import defaultdict
from sklearn.model_selection import StratifiedKFold
# splitter function
def generate_scaffold(smiles, include_chirality=False):
"""
Obtain Bemis-Murc... | 14,949 | 41.351275 | 179 | py |
GraphLoG | GraphLoG-main/util.py | import torch
import copy
import random
import networkx as nx
import numpy as np
from torch_geometric.utils import convert
from loader import graph_data_obj_to_nx_simple, nx_to_graph_data_obj_simple
from rdkit import Chem
from rdkit.Chem import AllChem
from loader import mol_to_graph_data_obj_simple, \
graph_data_ob... | 11,865 | 41.378571 | 100 | py |
GraphLoG | GraphLoG-main/loader.py | import os
import torch
import pickle
import collections
import math
import pandas as pd
import numpy as np
import networkx as nx
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import AllChem
from rdkit import DataStructs
from rdkit.Chem.rdMolDescriptors import GetMorganFingerprintAsBitVect
fr... | 56,150 | 41.250564 | 165 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/setup.py | """Setup script for python packaging."""
import site
import sys
from setuptools import setup
# enable installing package for user
# https://github.com/pypa/pip/issues/7953#issuecomment-645133255
site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
setup(
name="imgx",
version="0.1.0",
description="",
auth... | 593 | 22.76 | 64 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/run_test_ensemble.py | """Script to launch ensemble on test set results."""
import argparse
import json
from collections import defaultdict
from functools import partial
from pathlib import Path
import jax
import jax.numpy as jnp
import numpy as np
import pandas as pd
import SimpleITK as sitk # noqa: N813
from absl import logging
from omeg... | 7,072 | 31.296804 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/run_test.py | """Script to launch evaluation on test sets."""
import argparse
import json
from pathlib import Path
import jax
import numpy as np
from absl import logging
from omegaconf import OmegaConf
from imgx import TEST_SPLIT
from imgx.device import broadcast_to_local_devices
from imgx.exp import Experiment
from imgx.exp.train... | 5,684 | 30.236264 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/math_util.py | """Module for math functions."""
import jax
import jax.numpy as jnp
def logits_to_mask(x: jnp.ndarray, axis: int) -> jnp.ndarray:
"""Transform logits to one hot mask.
The one will be on the class having largest logit.
Args:
x: logits.
axis: axis of num_classes.
Returns:
One... | 471 | 18.666667 | 61 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/run_valid.py | """Script to launch evaluation on validation tests."""
import argparse
from pathlib import Path
from typing import List
import jax
from absl import logging
from omegaconf import OmegaConf
from imgx import VALID_SPLIT
from imgx.device import broadcast_to_local_devices
from imgx.exp import Experiment
from imgx.exp.trai... | 3,106 | 24.891667 | 74 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/config.py | """Module for configuration related functions."""
from typing import Dict
def flatten_dict(d: Dict, parent_key: str = "", sep: str = "_") -> Dict:
"""Flat a nested dict.
Args:
d: dict to flat.
parent_key: key of the parent.
sep: separation string.
Returns:
flatten dict.
... | 603 | 23.16 | 72 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/__init__.py | """A Jax-based DL toolkit for biomedical and bioinformatics applications."""
from pathlib import Path
# machine error
EPS = 1.0e-5
NAN_MASK = "nan_mask"
# path for all non-tensorflow-dataset data sets
DIR_DATA = Path("datasets")
# splits
TRAIN_SPLIT = "train"
VALID_SPLIT = "valid"
TEST_SPLIT = "test"
# jax device
... | 657 | 21.689655 | 76 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/run_train.py | """Script to launch training."""
from pathlib import Path
import hydra
import jax
import wandb
from absl import logging
from omegaconf import DictConfig, OmegaConf
from imgx import VALID_SPLIT
from imgx.config import flatten_dict
from imgx.exp import Experiment
from imgx.exp.train_state import get_eval_params_and_sta... | 5,235 | 29.619883 | 76 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/device.py | """Module to handle multi-devices."""
from typing import Optional, Tuple, Union
import chex
import jax
import jax.numpy as jnp
def broadcast_to_local_devices(value: chex.ArrayTree) -> chex.ArrayTree:
"""Broadcasts an object to all local devices.
Args:
value: value to be broadcast.
Returns:
... | 3,095 | 25.689655 | 92 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/metric/area.py | """Metrics to measure foreground area."""
import jax.numpy as jnp
def class_proportion(mask: jnp.ndarray) -> jnp.ndarray:
"""Calculate proportion per class.
Args:
mask: shape = (batch, d1, ..., dn, num_classes).
Returns:
Proportion, shape = (batch, num_classes).
"""
reduce_axes ... | 590 | 27.142857 | 70 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/metric/distribution.py | """Metric functions for probability distributions."""
import jax.numpy as jnp
def normal_kl(
p_mean: jnp.ndarray,
p_log_variance: jnp.ndarray,
q_mean: jnp.ndarray,
q_log_variance: jnp.ndarray,
) -> jnp.ndarray:
"""Compute the KL divergence between two 1D normal distributions.
Although the inp... | 3,097 | 29.07767 | 75 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/metric/dice.py | """Metric functions for image segmentation."""
import jax.numpy as jnp
def dice_score(
mask_pred: jnp.ndarray,
mask_true: jnp.ndarray,
) -> jnp.ndarray:
"""Soft Dice score, larger is better.
Args:
mask_pred: soft mask with probabilities, (batch, ..., num_classes).
mask_true: one hot t... | 1,407 | 28.333333 | 75 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/metric/surface_distance.py | """Surface distance metric.
Functions are all numpy based, as they rely on scipy and not jittable for JAX.
References:
https://github.com/deepmind/surface-distance
https://github.com/Project-MONAI/MONAI/blob/dev/monai/metrics/surface_distance.py
"""
from functools import partial
from itertools import combinat... | 13,562 | 33.336709 | 89 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/metric/__init__.py | """Module for metrics."""
from imgx.metric.area import class_proportion
from imgx.metric.centroid import centroid_distance
from imgx.metric.dice import dice_score, iou
from imgx.metric.surface_distance import (
aggregated_surface_distance,
average_surface_distance,
hausdorff_distance,
normalized_surface... | 636 | 25.541667 | 50 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/metric/centroid.py | """Metric centroid distance."""
from typing import Optional, Tuple
import jax.numpy as jnp
def get_coordinate_grid(shape: Tuple[int, ...]) -> jnp.ndarray:
"""Generate a grid with given shape.
This function is not jittable as the output depends on the value of shapes.
Args:
shape: shape of the g... | 3,160 | 28.542056 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/augmentation.py | """Image augmentation functions."""
from functools import partial
from typing import Callable, Dict, Sequence
import jax
import numpy as np
from jax import numpy as jnp
from jax.scipy.ndimage import map_coordinates
from omegaconf import DictConfig
from imgx import IMAGE, LABEL
from imgx.datasets import FOREGROUND_RAN... | 12,812 | 26.793926 | 77 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/iterator.py | """Dataset related classes and functions."""
from functools import partial
from typing import Callable, Dict, Iterator, Optional, Tuple
import jax
import jax.numpy as jnp
import jax.scipy
import jmp
import tensorflow as tf
import tensorflow_datasets as tfds
from absl import logging
from omegaconf import DictConfig
fr... | 8,041 | 31.297189 | 91 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/util.py | """Util functions for image.
Some are adapted from
https://github.com/google-research/scenic/blob/03735eb81f64fd1241c4efdb946ea6de3d326fe1/scenic/dataset_lib/dataset_utils.py
"""
import functools
import queue
import threading
from typing import Any, Callable, Dict, Generator, Iterable, Tuple
import chex
import jax
im... | 11,835 | 32.247191 | 123 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/__init__.py | """Dataset module to build tensorflow datasets."""
from collections import namedtuple
from pathlib import Path
from imgx.datasets.amos_ct.amos_ct_dataset_builder import (
AMOS_CT_IMAGE_SHAPE,
AMOS_CT_IMAGE_SPACING,
AMOS_NUM_CLASSES,
AMOS_TFDS_FOLD,
)
from imgx.datasets.male_pelvic_mr.male_pelvic_mr_dat... | 1,471 | 22 | 73 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/preprocess.py | """Preprocess functions using sitk."""
from pathlib import Path
from typing import List, Optional, Tuple
import numpy as np
import SimpleITK as sitk # noqa: N813
from imgx.datasets.util import (
get_center_crop_shape_from_bbox,
get_center_pad_shape,
)
from imgx.metric.surface_distance import get_binary_mask_... | 9,837 | 32.80756 | 82 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/amos_ct/__init__.py | """AMOS dataset.
https://arxiv.org/abs/2206.08023
https://zenodo.org/record/7155725#.Y4ndMuzP2rN
"""
| 103 | 13.857143 | 46 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/amos_ct/amos_ct_dataset_builder.py | """AMOS CT image dataset."""
import json
from pathlib import Path
from typing import Dict, Generator, List, Tuple
import numpy as np
import tensorflow_datasets as tfds
from imgx import IMAGE, LABEL, TEST_SPLIT, TRAIN_SPLIT, UID, VALID_SPLIT
from imgx.datasets.preprocess import load_and_preprocess_image_and_label
_D... | 7,208 | 33.004717 | 177 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/male_pelvic_mr/male_pelvic_mr_dataset_builder.py | """male_pelvic_mr dataset."""
from pathlib import Path
from typing import Dict, Generator, List, Tuple
import numpy as np
import pandas as pd
import tensorflow_datasets as tfds
from imgx import IMAGE, LABEL, TEST_SPLIT, TRAIN_SPLIT, UID, VALID_SPLIT
from imgx.datasets.preprocess import load_and_preprocess_image_and_... | 6,514 | 31.738693 | 180 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/datasets/male_pelvic_mr/__init__.py | """Male pelvic MR dataset.
https://arxiv.org/abs/2209.05160
"""
| 65 | 12.2 | 32 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/diffusion/variance_schedule.py | """Variance schedule for diffusion models."""
from __future__ import annotations
import enum
import numpy as np
from jax import numpy as jnp
class DiffusionBetaSchedule(enum.Enum):
"""Class to define beta schedule."""
LINEAR = enum.auto()
QUADRADIC = enum.auto()
COSINE = enum.auto()
WARMUP10 = ... | 4,844 | 29.093168 | 77 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/diffusion/gaussian_diffusion.py | """Gaussian diffusion related functions.
https://github.com/WuJunde/MedSegDiff/blob/master/guided_diffusion/gaussian_diffusion.py
https://github.com/hojonathanho/diffusion/blob/master/diffusion_tf/diffusion_utils_2.py
"""
import dataclasses
import enum
from typing import Callable, Iterator, Sequence, Tuple, Union
imp... | 27,736 | 33.413151 | 92 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/diffusion/__init__.py | """Diffusion related functions."""
| 35 | 17 | 34 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/conf/__init__.py | """Package for config files."""
| 32 | 15.5 | 31 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/loss/cross_entropy.py | """Loss functions for classification."""
import jax
import jax.numpy as jnp
import optax
def mean_cross_entropy(
logits: jnp.ndarray,
mask_true: jnp.ndarray,
) -> jnp.ndarray:
"""Cross entropy.
Args:
logits: unscaled prediction, (batch, ..., num_classes).
mask_true: one hot targets, (... | 1,352 | 26.06 | 72 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/loss/dice.py | """Loss functions for image segmentation."""
import jax
import jax.numpy as jnp
def mean_with_background(batch_cls_loss: jnp.ndarray) -> jnp.ndarray:
"""Return average with background class.
Args:
batch_cls_loss: shape (batch, num_classes).
Returns:
Mean loss of shape (1,).
"""
r... | 2,386 | 27.082353 | 75 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/loss/__init__.py | """Package for loss functions."""
from imgx.loss.cross_entropy import mean_cross_entropy, mean_focal_loss
from imgx.loss.dice import mean_dice_loss
__all__ = [
"mean_cross_entropy",
"mean_focal_loss",
"mean_dice_loss",
]
| 234 | 22.5 | 71 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/model/unet_3d_slice_time.py | """UNet for segmentation."""
import dataclasses
from typing import Callable, List, Tuple
import haiku as hk
import jax
from jax import numpy as jnp
from imgx.model.basic import instance_norm, sinusoidal_positional_embedding
from imgx.model.unet_3d_slice import Conv2dNormAct, Conv2dPool
@dataclasses.dataclass
class ... | 7,105 | 31.153846 | 95 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/model/unet_3d_time.py | """UNet for segmentation."""
import dataclasses
from typing import Callable, List, Tuple
import haiku as hk
import jax
from jax import numpy as jnp
from imgx.model.basic import instance_norm, sinusoidal_positional_embedding
from imgx.model.unet_3d import Conv3dNormAct, Conv3dPool
@dataclasses.dataclass
class TimeCo... | 6,438 | 30.10628 | 95 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/model/unet_3d_slice.py | """UNet for segmentation."""
import dataclasses
from typing import Callable, List, Tuple
import haiku as hk
import jax
from jax import numpy as jnp
from imgx.model.basic import instance_norm
@dataclasses.dataclass
class Conv2dNormAct(hk.Module):
"""Block with conv2d-norm-act."""
out_channels: int
kerne... | 7,387 | 27.635659 | 85 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/model/__init__.py | """Package for models."""
from imgx.model.unet_3d import Unet3d # noqa: F401
from imgx.model.unet_3d_slice import Unet3dSlice # noqa: F401
from imgx.model.unet_3d_slice_time import Unet3dSliceTime # noqa: F401
from imgx.model.unet_3d_time import Unet3dTime # noqa: F401
SUPPORTED_VISION_MODELS = [
"Unet3d",
... | 701 | 27.08 | 71 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/model/unet_3d.py | """UNet for segmentation."""
import dataclasses
from typing import Callable, List, Tuple
import haiku as hk
import jax
from jax import numpy as jnp
from imgx.model.basic import instance_norm
@dataclasses.dataclass
class Conv3dNormAct(hk.Module):
"""Block with conv3d-norm-act."""
out_channels: int
kerne... | 6,811 | 26.691057 | 85 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/model/basic.py | """Basic functions and modules."""
import haiku as hk
from jax import numpy as jnp
def layer_norm(x: jnp.ndarray) -> jnp.ndarray:
"""Applies a unique LayerNorm at the last axis.
Args:
x: input
Returns:
Normalised input.
"""
return hk.LayerNorm(axis=-1, create_scale=True, create_o... | 2,088 | 26.486842 | 74 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/train_state.py | """Training state and checkpoints."""
import pickle
from pathlib import Path
from typing import Optional, Tuple
import chex
import haiku as hk
import jax
import jax.numpy as jnp
import jmp
import numpy as np
import optax
from imgx.device import broadcast_to_local_devices, get_first_replica_values
CHECKPOINT_ATTRS = ... | 6,560 | 30.695652 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/optim.py | """Module for optimization."""
import logging
from typing import Tuple
import jax
import jax.numpy as jnp
import optax
from omegaconf import DictConfig
def ema_update(
ema_value: jnp.ndarray,
current_value: jnp.ndarray,
decay: float,
step: jnp.ndarray,
) -> jnp.ndarray:
"""Implements exponential ... | 3,308 | 30.216981 | 79 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/experiment.py | """Module for launching experiments."""
import logging
from functools import partial
from pathlib import Path
from typing import Callable, Dict, Mapping, Optional, Tuple, Union
import chex
import haiku as hk
import jax
import jax.numpy as jnp
import jmp
import optax
import tensorflow as tf
from omegaconf import DictCo... | 13,642 | 30.801865 | 79 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/loss.py | """Module for building models and losses."""
from typing import Callable, Dict, Tuple
import haiku as hk
import jax
import jax.numpy as jnp
from omegaconf import DictConfig
from imgx import IMAGE, LABEL
from imgx.datasets import NUM_CLASSES_MAP
from imgx.diffusion.gaussian_diffusion import (
DiffusionModelOutputT... | 11,245 | 30.858357 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/model.py | """Module for building models."""
import haiku as hk
from omegaconf import DictConfig
from imgx.datasets import IMAGE_SHAPE_MAP, NUM_CLASSES_MAP
from imgx.diffusion.gaussian_diffusion import (
DiffusionBetaSchedule,
DiffusionModelOutputType,
DiffusionModelVarianceType,
DiffusionSpace,
GaussianDiffu... | 3,969 | 32.644068 | 75 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/mixed_precision.py | """Mixed precision related functions."""
from functools import partial
import chex
import haiku as hk
import jax
import jax.numpy as jnp
import jmp
from imgx import model
from imgx.model import CONFIG_NAME_TO_MODEL_CLS_NAME
def get_mixed_precision_policy(use_mp: bool) -> jmp.Policy:
"""Return general mixed prec... | 2,956 | 29.173469 | 78 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/eval.py | """Module for building evaluation functions."""
import json
from functools import partial
from pathlib import Path
from typing import Callable, Dict, Iterable, Optional, Tuple
import chex
import haiku as hk
import jax
import numpy as np
import pandas as pd
from jax import numpy as jnp
from omegaconf import DictConfig
... | 16,503 | 31.746032 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/imgx/exp/__init__.py | """Module to manage experiments."""
from imgx.exp.experiment import Experiment
__all__ = ["Experiment"]
| 105 | 20.2 | 42 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_dataset_util.py | """Tests for image utils of datasets."""
from typing import Tuple
import chex
import numpy as np
import pytest
from chex._src import fake
from imgx.datasets.util import (
get_center_crop_shape,
get_center_crop_shape_from_bbox,
get_center_pad_shape,
get_foreground_range,
try_to_get_center_crop_shap... | 9,387 | 23.968085 | 77 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_metric_centroid_distance.py | """Test centroid distance functions."""
from typing import Optional, Tuple
import chex
import numpy as np
from absl.testing import parameterized
from chex._src import fake
from imgx.metric import centroid_distance
from imgx.metric.centroid import get_centroid, get_coordinate_grid
# Set `FLAGS.chex_n_cpu_devices` C... | 10,714 | 28.68144 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_metric_area.py | """Test area functions."""
import chex
import numpy as np
from absl.testing import parameterized
from chex._src import fake
from imgx.metric.area import class_proportion
# Set `FLAGS.chex_n_cpu_devices` CPU devices for all tests.
def setUpModule() -> None: # pylint: disable=invalid-name
"""Fake multi-devices."... | 1,794 | 27.492063 | 76 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_model_basic.py | """Test basic functions for model."""
import chex
import jax
from absl.testing import parameterized
from chex._src import fake
from imgx.model.basic import sinusoidal_positional_embedding
# Set `FLAGS.chex_n_cpu_devices` CPU devices for all tests.
def setUpModule() -> None: # pylint: disable=invalid-name
"""Fak... | 1,478 | 27.442308 | 78 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_diffusion_gaussian.py | """Test Gaussian diffusion related classes and functions."""
from typing import Tuple
import chex
import haiku as hk
import jax
import jax.numpy as jnp
from absl.testing import parameterized
from chex._src import fake
from imgx.diffusion.gaussian_diffusion import (
DiffusionBetaSchedule,
DiffusionModelOutputT... | 19,693 | 33.250435 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_loss_cross_entropy.py | """Test dice loss functions."""
import chex
import jax
import numpy as np
from absl.testing import parameterized
from chex._src import fake
from imgx.loss import mean_cross_entropy, mean_focal_loss
# Set `FLAGS.chex_n_cpu_devices` CPU devices for all tests.
def setUpModule() -> None: # pylint: disable=invalid-name... | 5,017 | 27.511364 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_train_state.py | """Test TrainState and related functions."""
from pathlib import Path
from typing import Dict
import chex
import jax.numpy as jnp
import jax.random
import jmp
import pytest
from chex._src import fake
from imgx.device import broadcast_to_local_devices
from imgx.exp import train_state
def setUpModule() -> None: # p... | 3,895 | 30.934426 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_exp_model.py | """Test mixed precision related functions in factory."""
import haiku as hk
import pytest
from omegaconf import DictConfig
from imgx.exp.model import build_vision_model
from imgx.model import MODEL_CLS_NAME_TO_CONFIG_NAME, SUPPORTED_VISION_MODELS
DUMMY_TASK_CONFIG = {
"name": "segmentation",
"diffusion": {
... | 1,733 | 24.5 | 77 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_dataset_augmentation.py | """Test function for data augmentation."""
from typing import Tuple
import chex
import jax
import jax.numpy as jnp
import numpy as np
from absl.testing import parameterized
from chex._src import fake
from imgx import IMAGE, LABEL
from imgx.datasets import FOREGROUND_RANGE
from imgx.datasets.augmentation import (
... | 23,132 | 29.081925 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_loss_dice.py | """Test dice loss functions."""
import chex
import jax
import numpy as np
from absl.testing import parameterized
from chex._src import fake
from imgx.loss import mean_dice_loss
# Set `FLAGS.chex_n_cpu_devices` CPU devices for all tests.
def setUpModule() -> None: # pylint: disable=invalid-name
"""Fake multi-de... | 5,992 | 29.42132 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_diffusion_variance_schedule.py | """Test Gaussian diffusion related classes and functions."""
import chex
import jax.numpy as jnp
from absl.testing import parameterized
from chex._src import fake
from imgx.diffusion.variance_schedule import (
DiffusionBetaSchedule,
downsample_beta_schedule,
get_beta_schedule,
)
# Set `FLAGS.chex_n_cpu... | 2,208 | 27.320513 | 60 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_exp_mixed_precision.py | """Test mixed precision related functions in factory."""
import haiku as hk
import pytest
from imgx import model
from imgx.exp.mixed_precision import set_mixed_precision_policy
from imgx.model import MODEL_CLS_NAME_TO_CONFIG_NAME
from imgx.model import __all__ as all_model_classes
@pytest.mark.parametrize(
"mode... | 938 | 31.37931 | 80 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_metric_surface_distance.py | """Test loss functions."""
from functools import partial
from typing import Callable, List, Tuple, Union
import chex
import jax
import numpy as np
from absl.testing import parameterized
from imgx.metric.surface_distance import (
aggregated_surface_distance,
average_surface_distance,
get_binary_mask_bound... | 31,405 | 31.444215 | 88 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_metric_dice.py | """Test dice score metric related functions."""
import chex
import jax
import numpy as np
from absl.testing import parameterized
from chex._src import fake
from imgx.metric import dice_score, iou
# Set `FLAGS.chex_n_cpu_devices` CPU devices for all tests.
def setUpModule() -> None: # pylint: disable=invalid-name
... | 4,360 | 25.430303 | 77 | py |
ImgX-DiffSeg | ImgX-DiffSeg-main/tests/unit/test_model_unet_3d_time.py | """Test Unet related classes and functions."""
from typing import Tuple
import chex
import haiku as hk
import jax
import jax.numpy as jnp
from absl.testing import parameterized
from chex._src import fake
from imgx.model import Unet3dSliceTime, Unet3dTime
# Set `FLAGS.chex_n_cpu_devices` CPU devices for all tests.
d... | 6,305 | 27.278027 | 80 | py |
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