konfai 1.1.7__py3-none-any.whl → 1.1.9__py3-none-any.whl

konfai/data/data_manager.py

@@ -1,85 +1,114 @@
 import math
 import os
 import random
+import threading
+from abc import ABC, abstractmethod
+from collections.abc import Iterator, Mapping
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from functools import partial
+
+import numpy as np
 import torch
-from torch.utils import data
 import tqdm
-import numpy as np
-from abc import ABC
-from torch.utils.data import DataLoader, Sampler
-from typing import Union, Iterator
-from concurrent.futures import ThreadPoolExecutor, as_completed
-import threading
 from torch.cuda import device_count
-import SimpleITK as sitk
+from torch.utils import data
+from torch.utils.data import DataLoader, Sampler
 
-from konfai import KONFAI_STATE, KONFAI_ROOT
-from konfai.data.patching import DatasetPatch, DatasetManager
-from konfai.utils.config import config
-from konfai.utils.utils import memoryInfo, cpuInfo, memoryForecast, getMemory, State, SUPPORTED_EXTENSIONS, DatasetManagerError
-from konfai.utils.dataset import Dataset, Attribute
-from konfai.data.transform import TransformLoader, Transform
+from konfai import konfai_root, konfai_state
 from konfai.data.augmentation import DataAugmentationsList
+from konfai.data.patching import DatasetManager, DatasetPatch
+from konfai.data.transform import Transform, TransformLoader
+from konfai.utils.config import config
+from konfai.utils.dataset import Attribute, Dataset
+from konfai.utils.utils import (
+    SUPPORTED_EXTENSIONS,
+    DatasetManagerError,
+    State,
+    get_cpu_info,
+    get_memory,
+    get_memory_info,
+    memory_forecast,
+)
+
 
 class GroupTransform:
 
     @config()
-    def __init__(self,  transforms : Union[dict[str, TransformLoader], list[Transform]] = {"default:Normalize:Standardize:Unsqueeze:TensorCast:ResampleIsotropic:ResampleResize": TransformLoader()},
-                        patch_transforms : Union[dict[str, TransformLoader], list[Transform]] = {"default:Normalize:Standardize:Unsqueeze:TensorCast:ResampleIsotropic:ResampleResize": TransformLoader()},
-                        isInput: bool = True) -> None:
-        self._pre_transforms = transforms
-        self._post_transforms = patch_transforms
-        self.pre_transforms : list[Transform] = []
-        self.post_transforms : list[Transform] = []
-        self.isInput = isInput
-        
-    def load(self, group_src : str, group_dest : str, datasets: list[Dataset]):
-        if self._pre_transforms is not None:
-            if isinstance(self._pre_transforms, dict):
-                for classpath, transform in self._pre_transforms.items():
-                    transform = transform.getTransform(classpath, DL_args =  "{}.Dataset.groups_src.{}.groups_dest.{}.transforms".format(KONFAI_ROOT(), group_src, group_dest))
-                    transform.setDatasets(datasets)
-                    self.pre_transforms.append(transform)
-            else:
-                for transform in self._pre_transforms:
-                    transform.setDatasets(datasets)
-                    self.pre_transforms.append(transform)
-
-        if self._post_transforms is not None:
-            if isinstance(self._post_transforms, dict):
-                for classpath, transform in self._post_transforms.items():
-                    transform = transform.getTransform(classpath, DL_args = "{}.Dataset.groups_src.{}.groups_dest.{}.patch_transforms".format(KONFAI_ROOT(), group_src, group_dest))
-                    transform.setDatasets(datasets)
-                    self.post_transforms.append(transform)
-            else:
-                for transform in self._post_transforms:
-                    transform.setDatasets(datasets)
-                    self.post_transforms.append(transform)
-    
+    def __init__(
+        self,
+        transforms: dict[str, TransformLoader] = {
+            "default:Normalize:Standardize:Unsqueeze:TensorCast:ResampleIsotropic:ResampleResize": TransformLoader()
+        },
+        patch_transforms: dict[str, TransformLoader] = {
+            "default:Normalize:Standardize:Unsqueeze:TensorCast:ResampleIsotropic:ResampleResize": TransformLoader()
+        },
+        is_input: bool = True,
+    ) -> None:
+        self._transforms = transforms
+        self._patch_transforms = patch_transforms
+        self.transforms: list[Transform] = []
+        self.patch_transforms: list[Transform] = []
+        self.is_input = is_input
+
+    def load(self, group_src: str, group_dest: str, datasets: list[Dataset]):
+        if self._transforms is not None:
+            for classpath, transform_loader in self._transforms.items():
+                transform = transform_loader.get_transform(
+                    classpath,
+                    konfai_args=f"{konfai_root()}.Dataset.groups_src.{group_src}.groups_dest.{group_dest}.transforms",
+                )
+                transform.set_datasets(datasets)
+                self.transforms.append(transform)
+
+        if self._patch_transforms is not None:
+            for classpath, transform_loader in self._patch_transforms.items():
+                transform = transform_loader.get_transform(
+                    classpath,
+                    konfai_args=f"{konfai_root()}.Dataset.groups_src.{group_src}"
+                    f".groups_dest.{group_dest}.patch_transforms",
+                )
+                transform.set_datasets(datasets)
+                self.patch_transforms.append(transform)
+
     def to(self, device: int):
-        for transform in self.pre_transforms:
-            transform.setDevice(device)
-        for transform in self.post_transforms:
-            transform.setDevice(device)
+        for transform in self.transforms:
+            transform.to(device)
+        for transform in self.patch_transforms:
+            transform.to(device)
+
 
 class GroupTransformMetric(GroupTransform):
 
     @config()
-    def __init__(self, transforms : Union[dict[str, TransformLoader], list[Transform]] = {"default:Normalize:Standardize:Unsqueeze:TensorCast:ResampleIsotropic:ResampleResize": TransformLoader()}):
+    def __init__(
+        self,
+        transforms: dict[str, TransformLoader] = {
+            "default:Normalize:Standardize:Unsqueeze:TensorCast:ResampleIsotropic:ResampleResize": TransformLoader()
+        },
+    ):
         super().__init__(transforms, None)
 
+
 class Group(dict[str, GroupTransform]):
 
     @config()
-    def __init__(self, groups_dest: dict[str, GroupTransform] = {"default:group_dest": GroupTransform()}):
+    def __init__(
+        self,
+        groups_dest: dict[str, GroupTransform] = {"default:group_dest": GroupTransform()},
+    ):
         super().__init__(groups_dest)
 
+
 class GroupMetric(dict[str, GroupTransformMetric]):
 
     @config()
-    def __init__(self, groups_dest: dict[str, GroupTransformMetric] = {"default:group_dest": GroupTransformMetric()}):
+    def __init__(
+        self,
+        groups_dest: dict[str, GroupTransformMetric] = {"default:group_dest": GroupTransformMetric()},
+    ):
         super().__init__(groups_dest)
 
+
 class CustomSampler(Sampler[int]):
 
     def __init__(self, size: int, shuffle: bool = False) -> None:
@@ -87,135 +116,178 @@ class CustomSampler(Sampler[int]):
         self.shuffle = shuffle
 
     def __iter__(self) -> Iterator[int]:
-        return iter(torch.randperm(len(self)).tolist() if self.shuffle else list(range(len(self))) )
+        return iter(torch.randperm(len(self)).tolist() if self.shuffle else list(range(len(self))))
 
     def __len__(self) -> int:
         return self.size
 
+
 class DatasetIter(data.Dataset):
 
-    def __init__(self, rank: int, data : dict[str, list[DatasetManager]], map: dict[int, tuple[int, int, int]], groups_src : dict[str, Group], inlineAugmentations: bool, dataAugmentationsList : list[DataAugmentationsList], patch_size: Union[list[int], None], overlap: Union[int, None], buffer_size: int, use_cache = True) -> None:
+    def __init__(
+        self,
+        rank: int,
+        data: dict[str, list[DatasetManager]],
+        mapping: list[tuple[int, int, int]],
+        groups_src: Mapping[str, Group | GroupMetric],
+        inline_augmentations: bool,
+        data_augmentations_list: list[DataAugmentationsList],
+        patch_size: list[int] | None,
+        overlap: int | None,
+        buffer_size: int,
+        use_cache=True,
+    ) -> None:
         self.rank = rank
         self.data = data
-        self.map = map
+        self.mapping = mapping
         self.patch_size = patch_size
         self.overlap = overlap
         self.groups_src = groups_src
-        self.dataAugmentationsList = dataAugmentationsList
+        self.data_augmentations_list = data_augmentations_list
         self.use_cache = use_cache
         self.nb_dataset = len(data[list(data.keys())[0]])
         self.buffer_size = buffer_size
-        self._index_cache = list()
-        self.device = None
-        self.inlineAugmentations = inlineAugmentations
+        self._index_cache: list[int] = []
+        self.inline_augmentations = inline_augmentations
 
-    def getPatchConfig(self) -> tuple[list[int], int]:
+    def get_patch_config(self) -> tuple[list[int] | None, int | None]:
         return self.patch_size, self.overlap
-    
+
     def to(self, device: int):
         for group_src in self.groups_src:
             for group_dest in self.groups_src[group_src]:
                 self.groups_src[group_src][group_dest].to(device)
-        self.device = device
+        for data_augmentations in self.data_augmentations_list:
+            for data_augmentation in data_augmentations.data_augmentations:
+                data_augmentation.to(device)
 
-    def getDatasetFromIndex(self, group_dest: str, index: int) -> DatasetManager:
+    def get_dataset_from_index(self, group_dest: str, index: int) -> DatasetManager:
         return self.data[group_dest][index]
-    
-    def resetAugmentation(self, label):
-        if self.inlineAugmentations and len(self.dataAugmentationsList) > 0:
+
+    def reset_augmentation(self, label):
+        if self.inline_augmentations and len(self.data_augmentations_list) > 0:
             for index in range(self.nb_dataset):
                 for group_src in self.groups_src:
                     for group_dest in self.groups_src[group_src]:
-                        self.data[group_dest][index].unloadAugmentation()
-                        self.data[group_dest][index].resetAugmentation()
+                        self.data[group_dest][index].unload_augmentation()
+                        self.data[group_dest][index].reset_augmentation()
             self.load(label + " Augmentation")
 
     def load(self, label: str):
         if self.use_cache:
-            memory_init = getMemory()
+            memory_init = get_memory()
 
-            indexs = [index for index in range(self.nb_dataset)]
+            indexs = list(range(self.nb_dataset))
             if len(indexs) > 0:
                 memory_lock = threading.Lock()
-                desc = lambda : "Caching "+ label +": {} | {} | {}".format(memoryInfo(), memoryForecast(memory_init, 0, self.nb_dataset), cpuInfo())
-                pbar = tqdm.tqdm(
-                    total=len(indexs),
-                    desc=desc(),
-                    leave=False
-                )
+
+                def desc():
+                    return (
+                        f"Caching {label}: "
+                        f"{get_memory_info()} | "
+                        f"{memory_forecast(memory_init, 0, self.nb_dataset)} | "
+                        f"{get_cpu_info()}"
+                    )
+
+                pbar = tqdm.tqdm(total=len(indexs), desc=desc(), leave=False)
 
                 def process(index):
-                    self._loadData(index)
+                    self._load_data(index)
                     with memory_lock:
                         pbar.set_description(desc())
                         pbar.update(1)
-                with ThreadPoolExecutor(max_workers=os.cpu_count()//(device_count() if device_count() > 0 else 1)) as executor:
+
+                cpu_count = os.cpu_count() or 1
+                with ThreadPoolExecutor(
+                    max_workers=cpu_count // (device_count() if device_count() > 0 else 1)
+                ) as executor:
                     futures = [executor.submit(process, index) for index in indexs]
                     for _ in as_completed(futures):
                         pass
 
                 pbar.close()
-    
-    def _loadData(self, index):
+
+    def _load_data(self, index):
         if index not in self._index_cache:
             self._index_cache.append(index)
         for group_src in self.groups_src:
             for group_dest in self.groups_src[group_src]:
-                self.loadData(group_src, group_dest, index)
+                self.load_data(group_src, group_dest, index)
 
-    def loadData(self, group_src: str, group_dest : str, index : int) -> None:
-        self.data[group_dest][index].load(self.groups_src[group_src][group_dest].pre_transforms, self.dataAugmentationsList, self.device)
+    def load_data(self, group_src: str, group_dest: str, index: int) -> None:
+        self.data[group_dest][index].load(
+            self.groups_src[group_src][group_dest].transforms,
+            self.data_augmentations_list,
+        )
 
-    def _unloadData(self, index : int) -> None:
+    def _unload_data(self, index: int) -> None:
         if index in self._index_cache:
             self._index_cache.remove(index)
         for group_src in self.groups_src:
             for group_dest in self.groups_src[group_src]:
-                self.unloadData(group_dest, index)
-    
-    def unloadData(self, group_dest : str, index : int) -> None:
+                self.unload_data(group_dest, index)
+
+    def unload_data(self, group_dest: str, index: int) -> None:
         return self.data[group_dest][index].unload()
 
     def __len__(self) -> int:
-        return len(self.map)
+        return len(self.mapping)
 
-    def __getitem__(self, index : int) -> dict[str, tuple[torch.Tensor, int, int, int, str, bool]]:
+    def __getitem__(self, index: int) -> dict[str, tuple[torch.Tensor, int, int, int, str, bool]]:
         data = {}
-        x, a, p = self.map[index]
+        x, a, p = self.mapping[index]
         if x not in self._index_cache:
             if len(self._index_cache) >= self.buffer_size and not self.use_cache:
-                self._unloadData(self._index_cache[0])
-            self._loadData(x)
+                self._unload_data(self._index_cache[0])
+            self._load_data(x)
 
         for group_src in self.groups_src:
             for group_dest in self.groups_src[group_src]:
                 dataset = self.data[group_dest][x]
-                data["{}".format(group_dest)] = (dataset.getData(p, a, self.groups_src[group_src][group_dest].post_transforms, self.groups_src[group_src][group_dest].isInput), x, a, p, dataset.name, self.groups_src[group_src][group_dest].isInput)
+                data[f"{group_dest}"] = (
+                    dataset.get_data(
+                        p,
+                        a,
+                        self.groups_src[group_src][group_dest].patch_transforms,
+                        self.groups_src[group_src][group_dest].is_input,
+                    ),
+                    x,
+                    a,
+                    p,
+                    dataset.name,
+                    self.groups_src[group_src][group_dest].is_input,
+                )
         return data
 
-class Subset():
-    
-    def __init__(self, subset: Union[str, list[int], list[str], None] = None, shuffle: bool = True) -> None:
+
+class Subset:
+
+    def __init__(
+        self,
+        subset: str | list[int] | list[str] | None = None,
+        shuffle: bool = True,
+    ) -> None:
         self.subset = subset
         self.shuffle = shuffle
 
-    def __call__(self, names: list[str], infos: list[dict[str, tuple[np.ndarray, Attribute]]]) -> set[str]:
-        inter_name = set(names[0])
-        for n in names[1:]:
-            inter_name = inter_name.intersection(set(n))
-        names = sorted(list(inter_name))
-        
+    def __call__(self, names: list[str], infos: dict[str, tuple[list[int], Attribute]]) -> set[str]:
+        names = sorted(names)
+
         size = len(names)
         index = []
         if self.subset is None:
             index = list(range(0, size))
         elif isinstance(self.subset, str):
             if ":" in self.subset:
-                r = np.clip(np.asarray([int(self.subset.split(":")[0]), int(self.subset.split(":")[1])]), 0, size)
+                r = np.clip(
+                    np.asarray([int(self.subset.split(":")[0]), int(self.subset.split(":")[1])]),
+                    0,
+                    size,
+                )
                 index = list(range(r[0], r[1]))
             elif os.path.exists(self.subset):
                 train_names = []
-                with open(self.subset, "r") as f:
+                with open(self.subset) as f:
                     for name in f:
                         train_names.append(name.strip())
                 index = []
@@ -224,7 +296,7 @@ class Subset():
                         index.append(i)
             elif self.subset.startswith("~") and os.path.exists(self.subset[1:]):
                 exclude_names = []
-                with open(self.subset[1:], "r") as f:
+                with open(self.subset[1:]) as f:
                     for name in f:
                         exclude_names.append(name.strip())
                 index = []
@@ -233,200 +305,283 @@ class Subset():
                         index.append(i)
 
         elif isinstance(self.subset, list):
+            index = []
             if len(self.subset) > 0:
-                if isinstance(self.subset[0], int):
-                    if len(self.subset) == 1:
-                        index = list(range(self.subset[0], min(size, self.subset[0]+1)))
-                    else:
-                        index = self.subset
-                if isinstance(self.subset[0], str):
-                    index = []
-                    for i, name in enumerate(names):
-                        if name in self.subset:
-                            index.append(i)
+                for s in self.subset:
+                    if isinstance(s, int):
+                        index.append(s)
+                    elif isinstance(s, str):
+                        for i, name in enumerate(names):
+                            if name in self.subset:
+                                index.append(i)
         if self.shuffle:
-            index = random.sample(index, len(index))
-        return set([names[i] for i in index])
-    
+            index = random.sample(index, len(index))  # nosec B311
+        return {names[i] for i in index}
+
     def __str__(self):
-        return "Subset : " + str(self.subset) + " shuffle : "+ str(self.shuffle)
-    
+        return "Subset : " + str(self.subset) + " shuffle : " + str(self.shuffle)
+
+
 class TrainSubset(Subset):
 
     @config()
-    def __init__(self, subset: Union[str, list[int], list[str], None] = None, shuffle: bool = True) -> None:
+    def __init__(
+        self,
+        subset: str | list[int] | list[str] | None = None,
+        shuffle: bool = True,
+    ) -> None:
         super().__init__(subset, shuffle)
 
+
 class PredictionSubset(Subset):
 
     @config()
-    def __init__(self, subset: Union[str, list[int], list[str], None] = None) -> None:
+    def __init__(self, subset: str | list[int] | list[str] | None = None) -> None:
         super().__init__(subset, False)
 
+
 class Data(ABC):
-    
-    def __init__(self,  dataset_filenames : list[str], 
-                        groups_src : dict[str, Group],
-                        patch : Union[DatasetPatch, None],
-                        use_cache : bool,
-                        subset : Subset,
-                        batch_size : int,
-                        validation: Union[float, str, list[int], list[str], None] = None,
-                        inlineAugmentations: bool = False,
-                        dataAugmentationsList: dict[str, DataAugmentationsList]= {}) -> None:
+
+    @abstractmethod
+    def __init__(
+        self,
+        dataset_filenames: list[str],
+        groups_src: Mapping[str, Group | GroupMetric],
+        patch: DatasetPatch | None,
+        use_cache: bool,
+        subset: Subset,
+        batch_size: int,
+        validation: float | str | list[int] | list[str] | None,
+        inline_augmentations: bool,
+        data_augmentations_list: dict[str, DataAugmentationsList],
+    ) -> None:
         self.dataset_filenames = dataset_filenames
         self.subset = subset
         self.groups_src = groups_src
         self.patch = patch
         self.validation = validation
-        self.dataAugmentationsList = dataAugmentationsList
+        self.data_augmentations_list = data_augmentations_list
         self.batch_size = batch_size
-        self.dataSet_args = dict(groups_src=self.groups_src, inlineAugmentations=inlineAugmentations, dataAugmentationsList = list(self.dataAugmentationsList.values()), use_cache = use_cache, buffer_size=batch_size+1, patch_size=self.patch.patch_size if self.patch is not None else None, overlap=self.patch.overlap if self.patch is not None else None)
-        self.dataLoader_args = dict(num_workers=int(os.environ["KONFAI_WORKERS"]), pin_memory=True)
-        self.data : list[list[dict[str, list[DatasetManager]]], dict[str, list[DatasetManager]]] = []
-        self.map : list[list[list[tuple[int, int, int]]], list[tuple[int, int, int]]] = []
+
+        self.datasetIter = partial(
+            DatasetIter,
+            groups_src=self.groups_src,
+            inline_augmentations=inline_augmentations,
+            data_augmentations_list=list(self.data_augmentations_list.values()),
+            patch_size=self.patch.patch_size if self.patch is not None else None,
+            overlap=self.patch.overlap if self.patch is not None else None,
+            buffer_size=batch_size + 1,
+            use_cache=use_cache,
+        )
+        self.dataLoader_args = {
+            "num_workers": int(os.environ["KONFAI_WORKERS"]) if use_cache else 0,
+            "pin_memory": True,
+        }
+        self.data: list[list[dict[str, list[DatasetManager]]]] = []
+        self.mapping: list[list[list[tuple[int, int, int]]]] = []
         self.datasets: dict[str, Dataset] = {}
 
-    def _getDatasets(self, names: list[str], dataset_name: dict[str, dict[str, list[str]]]) -> tuple[dict[str, list[Dataset]], list[tuple[int, int, int]]]:
+    def _get_datasets(
+        self, names: list[str], dataset_name: dict[str, dict[str, list[str]]]
+    ) -> tuple[dict[str, list[DatasetManager]], list[tuple[int, int, int]]]:
         nb_dataset = len(names)
-        nb_patch = None
+        nb_patch: list[list[int]]
         data = {}
-        map = []
-        nb_augmentation = np.max([int(np.sum([data_augmentation.nb for data_augmentation in self.dataAugmentationsList.values()])+1), 1])
+        mapping = []
+        nb_augmentation = np.max(
+            [
+                int(np.sum([data_augmentation.nb for data_augmentation in self.data_augmentations_list.values()]) + 1),
+                1,
+            ]
+        )
         for group_src in self.groups_src:
             for group_dest in self.groups_src[group_src]:
-                data[group_dest] = [DatasetManager(i, group_src, group_dest, name, self.datasets[[filename for filename, names in dataset_name[group_src].items() if name in names][0]], patch = self.patch, pre_transforms = self.groups_src[group_src][group_dest].pre_transforms, dataAugmentationsList=list(self.dataAugmentationsList.values())) for i, name in enumerate(names)]
-                nb_patch = [[dataset.getSize(a) for a in range(nb_augmentation)] for dataset in data[group_dest]]
+                data[group_dest] = [
+                    DatasetManager(
+                        i,
+                        group_src,
+                        group_dest,
+                        name,
+                        self.datasets[
+                            [filename for filename, names in dataset_name[group_src].items() if name in names][0]
+                        ],
+                        patch=self.patch,
+                        transforms=self.groups_src[group_src][group_dest].transforms,
+                        data_augmentations_list=list(self.data_augmentations_list.values()),
+                    )
+                    for i, name in enumerate(names)
+                ]
+                nb_patch = [[dataset.get_size(a) for a in range(nb_augmentation)] for dataset in data[group_dest]]
 
         for x in range(nb_dataset):
             for y in range(nb_augmentation):
                 for z in range(nb_patch[x][y]):
-                    map.append((x, y, z))
-        return data, map
+                    mapping.append((x, y, z))
+        return data, mapping
 
-    def getGroupsDest(self):
-        groupsDest = []
+    def get_groups_dest(self):
+        groups_dest = []
         for group_src in self.groups_src:
             for group_dest in self.groups_src[group_src]:
-                groupsDest.append(group_dest)
-        return groupsDest
-    
-    def _split(map: list[tuple[int, int, int]], world_size: int) -> list[list[tuple[int, int, int]]]:
-        if len(map) == 0:
+                groups_dest.append(group_dest)
+        return groups_dest
+
+    @staticmethod
+    def _split(mapping: list[tuple[int, int, int]], world_size: int) -> list[list[tuple[int, int, int]]]:
+        if len(mapping) == 0:
             return [[] for _ in range(world_size)]
-        
-        maps = []
-        if KONFAI_STATE() == str(State.PREDICTION) or KONFAI_STATE() == str(State.EVALUATION):
-            np_map = np.asarray(map)
-            unique_index = np.unique(np_map[:, 0])
-            offset = int(np.ceil(len(unique_index)/world_size))
+
+        mappings = []
+        if konfai_state() == str(State.PREDICTION) or konfai_state() == str(State.EVALUATION):
+            np_mapping = np.asarray(mapping)
+            unique_index = np.unique(np_mapping[:, 0])
+            offset = int(np.ceil(len(unique_index) / world_size))
             if offset == 0:
                 offset = 1
             for itr in range(0, len(unique_index), offset):
-                maps.append([tuple(v) for v in np_map[np.where(np.isin(np_map[:, 0], unique_index[itr:itr+offset]))[0], :]])
+                mappings.append(
+                    [
+                        tuple(v)
+                        for v in np_mapping[
+                            np.where(np.isin(np_mapping[:, 0], unique_index[itr : itr + offset]))[0],
+                            :,
+                        ]
+                    ]
+                )
         else:
-            offset = int(np.ceil(len(map)/world_size))
+            offset = int(np.ceil(len(mapping) / world_size))
             if offset == 0:
                 offset = 1
-            for itr in range(0, len(map), offset):
-                maps.append(list(map[-offset:]) if itr+offset > len(map) else map[itr:itr+offset])
-        return maps
-    
-    def getData(self, world_size: int) -> list[list[DataLoader]]:
-        datasets: dict[str, list[(str, bool)]] = {}
+            for itr in range(0, len(mapping), offset):
+                mappings.append(list(mapping[-offset:]) if itr + offset > len(mapping) else mapping[itr : itr + offset])
+        return mappings
+
+    def get_data(self, world_size: int) -> list[list[DataLoader]]:
+        datasets: dict[str, list[tuple[str, bool]]] = {}
         if self.dataset_filenames is None or len(self.dataset_filenames) == 0:
             raise DatasetManagerError("No dataset filenames were provided")
         for dataset_filename in self.dataset_filenames:
             if dataset_filename is None:
-                raise DatasetManagerError("Invalid dataset entry: 'None' received.",
-                    "Each dataset must be a valid path string (e.g., './Dataset/', './Dataset/:mha, './Dataset/:a:mha', './Dataset/:i:mha').",
-                    "Please check your 'dataset_filenames' list for missing or null entries."
+                raise DatasetManagerError(
+                    "Invalid dataset entry: 'None' received.",
+                    "Each dataset must be a valid path string (e.g., './Dataset/', './Dataset/:mha, "
+                    "'./Dataset/:a:mha', './Dataset/:i:mha').",
+                    "Please check your 'dataset_filenames' list for missing or null entries.",
                 )
             if len(dataset_filename.split(":")) == 1:
                 filename = dataset_filename
-                format = "mha"
+                file_format = "mha"
                 append = True
             elif len(dataset_filename.split(":")) == 2:
-                filename, format = dataset_filename.split(":")
+                filename, file_format = dataset_filename.split(":")
                 append = True
             else:
-                filename, flag, format = dataset_filename.split(":")
+                filename, flag, file_format = dataset_filename.split(":")
                 append = flag == "a"
 
-            if format not in SUPPORTED_EXTENSIONS:
-                raise DatasetManagerError(f"Unsupported file format '{format}'.",
-                        f"Supported extensions are: {', '.join(SUPPORTED_EXTENSIONS)}")
-            
-            dataset = Dataset(filename, format)
+            if file_format not in SUPPORTED_EXTENSIONS:
+                raise DatasetManagerError(
+                    f"Unsupported file format '{file_format}'.",
+                    f"Supported extensions are: {', '.join(SUPPORTED_EXTENSIONS)}",
+                )
+
+            dataset = Dataset(filename, file_format)
 
             self.datasets[filename] = dataset
             for group in self.groups_src:
-                if dataset.isGroupExist(group):
+                if dataset.is_group_exist(group):
                     if group in datasets:
-                        datasets[group].append((filename, append)) 
+                        datasets[group].append((filename, append))
                     else:
                         datasets[group] = [(filename, append)]
-        modelHaveInput = False
+        model_have_input = False
         for group_src in self.groups_src:
             if group_src not in datasets:
-                
+
                 raise DatasetManagerError(
                     f"Group source '{group_src}' not found in any dataset.",
                     f"Dataset filenames provided: {self.dataset_filenames}",
-                    "Available groups across all datasets: {}".format(["{} {}".format(f, d.getGroup()) for f, d in self.datasets.items()]),
-                    f"Please check that an entry in the dataset with the name '{group_src}.{format}' exists."
+                    f"Available groups across all datasets: "
+                    "{[f'{f} {d.get_group()}' for f, d in self.datasets.items()]}"
+                    f"Please check that an entry in the dataset with the name '{group_src}.{format}' exists.",
                 )
-           
+
             for group_dest in self.groups_src[group_src]:
-                self.groups_src[group_src][group_dest].load(group_src, group_dest, [self.datasets[filename] for filename, _ in datasets[group_src]])
-                modelHaveInput |= self.groups_src[group_src][group_dest].isInput
+                self.groups_src[group_src][group_dest].load(
+                    group_src,
+                    group_dest,
+                    [self.datasets[filename] for filename, _ in datasets[group_src]],
+                )
+                model_have_input |= self.groups_src[group_src][group_dest].is_input
+        if self.patch is not None:
+            self.patch.init()
 
-        if not modelHaveInput:
+        if not model_have_input:
             raise DatasetManagerError(
-                "At least one group must be defined with 'isInput: true' to provide input to the network."
+                "At least one group must be defined with 'is_input: true' to provide input to the network."
             )
 
-        for key, dataAugmentations in self.dataAugmentationsList.items():
-            dataAugmentations.load(key, [self.datasets[filename] for filename, _ in datasets[group_src]])
+        for key, data_augmentations in self.data_augmentations_list.items():
+            data_augmentations.load(key, [self.datasets[filename] for filename, _ in datasets[group_src]])
 
-        names = set()
-        dataset_name : dict[str, dict[str, list[str]]] = {}
-        dataset_info : dict[str, dict[str, dict[str, Attribute]]] = {}
+        names: set[str] = set()
+        dataset_name: dict[str, dict[str, list[str]]] = {}
+        dataset_info: dict[str, dict[str, dict[str, tuple[list[int], Attribute]]]] = {}
         for group in self.groups_src:
-            namesByGroup = set()
+            names_by_group = set()
             if group not in dataset_name:
                 dataset_name[group] = {}
                 dataset_info[group] = {}
             for filename, _ in datasets[group]:
-                namesByGroup.update(self.datasets[filename].getNames(group))
-                dataset_name[group][filename] = self.datasets[filename].getNames(group)
-                dataset_info[group][filename] = {name: self.datasets[filename].getInfos(group, name) for name in dataset_name[group][filename]}
+                names_by_group.update(self.datasets[filename].get_names(group))
+                dataset_name[group][filename] = self.datasets[filename].get_names(group)
+                dataset_info[group][filename] = {
+                    name: self.datasets[filename].get_infos(group, name) for name in dataset_name[group][filename]
+                }
             if len(names) == 0:
-                names.update(namesByGroup)
-            else: 
-                names = names.intersection(namesByGroup)
+                names.update(names_by_group)
+            else:
+                names = names.intersection(names_by_group)
         if len(names) == 0:
-           raise DatasetManagerError(
-                f"No data was found for groups {list(self.groups_src.keys())}: although each group contains data from a dataset, there are no common dataset names shared across all groups, the intersection is empty."
-            )   
-                    
-        subset_names = set()
+            raise DatasetManagerError(
+                f"No data was found for groups {list(self.groups_src.keys())}: although each group contains data "
+                "from a dataset, there are no common dataset names shared across all groups, the intersection is empty."
+            )
+
+        subset_names: set[str] = set()
         for group in dataset_name:
-            subset_names_bygroup = set()
+            subset_names_bygroup: set[str] = set()
             for filename, append in datasets[group]:
                 if append:
-                    subset_names_bygroup.update(self.subset([dataset_name[group][filename]], [dataset_info[group][filename]]))
+                    subset_names_bygroup.update(
+                        self.subset(
+                            dataset_name[group][filename],
+                            dataset_info[group][filename],
+                        )
+                    )
                 else:
                     if len(subset_names_bygroup) == 0:
-                        subset_names_bygroup.update(self.subset([dataset_name[group][filename]], [dataset_info[group][filename]])) 
+                        subset_names_bygroup.update(
+                            self.subset(
+                                dataset_name[group][filename],
+                                dataset_info[group][filename],
+                            )
+                        )
                     else:
-                        subset_names_bygroup = subset_names_bygroup.intersection(self.subset([dataset_name[group][filename]], [dataset_info[group][filename]]))
+                        subset_names_bygroup = subset_names_bygroup.intersection(
+                            self.subset(
+                                dataset_name[group][filename],
+                                dataset_info[group][filename],
+                            )
+                        )
             if len(subset_names) == 0:
                 subset_names.update(subset_names_bygroup)
-            else: 
+            else:
                 subset_names = subset_names.intersection(subset_names_bygroup)
+
         if len(subset_names) == 0:
-            raise DatasetManagerError("All data entries were excluded by the subset filter.",
+            raise DatasetManagerError(
+                "All data entries were excluded by the subset filter.",
                 f"Dataset entries found: {', '.join(names)}",
                 f"Subset object applied: {self.subset}",
                 f"Subset requested : {', '.join(subset_names)}",
@@ -436,31 +591,38 @@ class Data(ABC):
                 "\tsubset: [0, 1]            # explicit indices",
                 "\tsubset: 0:10              # slice notation",
                 "\tsubset: ./Validation.txt  # external file",
-                "\tsubset: None              # to disable filtering"
+                "\tsubset: None              # to disable filtering",
             )
-                                        
-        data, map = self._getDatasets(list(subset_names), dataset_name)
 
-        train_map = map
-        validate_map = []
+        data, mapping = self._get_datasets(list(subset_names), dataset_name)
+
+        train_mapping = mapping
+        validate_mapping = []
         if isinstance(self.validation, float) or isinstance(self.validation, int):
             if self.validation <= 0 or self.validation >= 1:
-                raise DatasetManagerError("Validation must be a float between 0 and 1.", f"Received: {self.validation}", "Example: validation = 0.2  # for a 20% validation split")
-            
-            train_map, validate_map = map[:int(math.floor(len(map)*(1-self.validation)))], map[int(math.floor(len(map)*(1-self.validation))):]
+                raise DatasetManagerError(
+                    "Validation must be a float between 0 and 1.",
+                    f"Received: {self.validation}",
+                    "Example: validation = 0.2  # for a 20% validation split",
+                )
+
+            train_mapping, validate_mapping = (
+                mapping[: int(math.floor(len(mapping) * (1 - self.validation)))],
+                mapping[int(math.floor(len(mapping) * (1 - self.validation))) :],
+            )
         elif isinstance(self.validation, str):
             if ":" in self.validation:
-                index = list(range(int(self.subset.split(":")[0]), int(self.subset.split(":")[1])))
-                train_map = [m for m in map if m[0] not in index]
-                validate_map = [m for m in map if m[0] in index]
+                index = list(range(int(self.validation.split(":")[0]), int(self.validation.split(":")[1])))
+                train_mapping = [m for m in mapping if m[0] not in index]
+                validate_mapping = [m for m in mapping if m[0] in index]
             elif os.path.exists(self.validation):
                 validation_names = []
-                with open(self.validation, "r") as f:
+                with open(self.validation) as f:
                     for name in f:
                         validation_names.append(name.strip())
                 index = [i for i, n in enumerate(subset_names) if n in validation_names]
-                train_map = [m for m in map if m[0] not in index]
-                validate_map = [m for m in map if m[0] in index]
+                train_mapping = [m for m in mapping if m[0] not in index]
+                validate_mapping = [m for m in mapping if m[0] in index]
             else:
                 raise DatasetManagerError(
                     f"Invalid string value for 'validation': '{self.validation}'",
@@ -470,94 +632,151 @@ class Data(ABC):
                     "\t• A float between 0 and 1 (e.g., 0.2)",
                     "\t• A list of sample names or indices",
                     "The provided value is neither a valid slice nor a readable file.",
-                    "Please fix your 'validation' setting in the configuration."
-                    )
-            
+                    "Please fix your 'validation' setting in the configuration.",
+                )
+
         elif isinstance(self.validation, list):
             if len(self.validation) > 0:
                 if isinstance(self.validation[0], int):
-                    train_map = [m for m in map if m[0] not in self.validation]
-                    validate_map = [m for m in map if m[0] in self.validation]
+                    train_mapping = [m for m in mapping if m[0] not in self.validation]
+                    validate_mapping = [m for m in mapping if m[0] in self.validation]
                 elif isinstance(self.validation[0], str):
                     index = [i for i, n in enumerate(subset_names) if n in self.validation]
-                    train_map = [m for m in map if m[0] not in index]
-                    validate_map = [m for m in map if m[0] in index]
+                    train_mapping = [m for m in mapping if m[0] not in index]
+                    validate_mapping = [m for m in mapping if m[0] in index]
                 else:
-                    raise DatasetManagerError(f"Invalid list type for 'validation': elements of type '{type(self.validation[0]).__name__}' are not supported.",
-                            "Supported list element types are:",
-                            "\t• int  → list of indices (e.g., [0, 1, 2])",
-                            "\t• str  → list of sample names (e.g., ['patient01', 'patient02'])",
-                            f"Received list: {self.validation}"
-                        )
-        if len(train_map) == 0:
-            raise DatasetManagerError("No data left for training after applying the validation split.",
-                f"Dataset size: {len(map)}",
+                    raise DatasetManagerError(
+                        "Invalid list type for 'validation': elements of type "
+                        f"'{type(self.validation[0]).__name__}' are not supported.",
+                        "Supported list element types are:",
+                        "\t• int  → list of indices (e.g., [0, 1, 2])",
+                        "\t• str  → list of sample names (e.g., ['patient01', 'patient02'])",
+                        f"Received list: {self.validation}",
+                    )
+        if len(train_mapping) == 0:
+            raise DatasetManagerError(
+                "No data left for training after applying the validation split.",
+                f"Dataset size: {len(mapping)}",
                 f"Validation setting: {self.validation}",
-                "Please reduce the validation size, increase the dataset, or disable validation."
+                "Please reduce the validation size, increase the dataset, or disable validation.",
             )
 
-        if self.validation is not None and len(validate_map) == 0:
-            raise DatasetManagerError("No data left for validation after applying the validation split.",
-                f"Dataset size: {len(map)}",
+        if self.validation is not None and len(validate_mapping) == 0:
+            raise DatasetManagerError(
+                "No data left for validation after applying the validation split.",
+                f"Dataset size: {len(mapping)}",
                 f"Validation setting: {self.validation}",
-                "Please increase the validation size, increase the dataset, or disable validation."
+                "Please increase the validation size, increase the dataset, or disable validation.",
             )
-        train_maps = Data._split(train_map, world_size)
-        validate_maps = Data._split(validate_map, world_size)
-        
-        for i, (train_map, validate_map) in enumerate(zip(train_maps, validate_maps)):
-            maps = [train_map]
-            if len(validate_map):
-                maps += [validate_map]
+        train_mappings = Data._split(train_mapping, world_size)
+        validate_mappings = Data._split(validate_mapping, world_size)
+
+        for i, (train_mapping, validate_mapping) in enumerate(zip(train_mappings, validate_mappings)):
+            mappings = [train_mapping]
+            if len(validate_mapping):
+                mappings += [validate_mapping]
             self.data.append([])
-            self.map.append([])
-            for map_tmp in maps:
-                indexs = np.unique(np.asarray(map_tmp)[:, 0])
-                self.data[i].append({k:[v[it] for it in indexs] for k, v in data.items()})
-                map_tmp_array = np.asarray(map_tmp)
+            self.mapping.append([])
+            for mapping_tmp in mappings:
+                indexs = np.unique(np.asarray(mapping_tmp)[:, 0])
+                self.data[i].append({k: [v[it] for it in indexs] for k, v in data.items()})
+                mapping_tmp_array = np.asarray(mapping_tmp)
                 for a, b in enumerate(indexs):
-                    map_tmp_array[np.where(np.asarray(map_tmp_array)[:, 0] == b), 0] = a
-                self.map[i].append([(a,b,c) for a,b,c in map_tmp_array])
+                    mapping_tmp_array[np.where(np.asarray(mapping_tmp_array)[:, 0] == b), 0] = a
+                self.mapping[i].append([(a, b, c) for a, b, c in mapping_tmp_array])
+
+        data_loaders: list[list[DataLoader]] = []
+        for i, (datas, mappings) in enumerate(zip(self.data, self.mapping)):
+            data_loaders.append([])
+            for data, mapping in zip(datas, mappings):
+                data_loaders[i].append(
+                    DataLoader(
+                        dataset=self.datasetIter(
+                            rank=i,
+                            data=data,
+                            mapping=mapping,
+                        ),
+                        sampler=CustomSampler(len(mapping), self.subset.shuffle),
+                        batch_size=self.batch_size,
+                        **self.dataLoader_args,
+                    )
+                )
+        return data_loaders
 
-        dataLoaders: list[list[DataLoader]] = []
-        for i, (datas, maps) in enumerate(zip(self.data, self.map)):
-            dataLoaders.append([])
-            for data, map in zip(datas, maps):
-                dataLoaders[i].append(DataLoader(dataset=DatasetIter(rank=i, data=data, map=map, **self.dataSet_args), sampler=CustomSampler(len(map), self.subset.shuffle), batch_size=self.batch_size,**self.dataLoader_args))
-        return dataLoaders
 
 class DataTrain(Data):
 
     @config("Dataset")
-    def __init__(self,  dataset_filenames : list[str] = ["default:./Dataset"], 
-                        groups_src : dict[str, Group] = {"default:group_src" : Group()},
-                        augmentations : Union[dict[str, DataAugmentationsList], None] = {"DataAugmentation_0" : DataAugmentationsList()},
-                        inlineAugmentations: bool = False,
-                        patch : Union[DatasetPatch, None] = DatasetPatch(),
-                        use_cache : bool = True,
-                        subset : Union[TrainSubset, dict[str, TrainSubset]] = TrainSubset(),
-                        batch_size : int = 1,
-                        validation : Union[float, str, list[int], list[str]] = 0.2) -> None:
-        super().__init__(dataset_filenames, groups_src, patch, use_cache, subset, batch_size, validation, inlineAugmentations, augmentations if augmentations else {})
+    def __init__(
+        self,
+        dataset_filenames: list[str] = ["default:./Dataset"],
+        groups_src: dict[str, Group] = {"default:group_src": Group()},
+        augmentations: dict[str, DataAugmentationsList] | None = {"DataAugmentation_0": DataAugmentationsList()},
+        inline_augmentations: bool = False,
+        patch: DatasetPatch | None = DatasetPatch(),
+        use_cache: bool = True,
+        subset: TrainSubset = TrainSubset(),
+        batch_size: int = 1,
+        validation: float | str | list[int] | list[str] = 0.2,
+    ) -> None:
+        super().__init__(
+            dataset_filenames,
+            groups_src,
+            patch,
+            use_cache,
+            subset,
+            batch_size,
+            validation,
+            inline_augmentations,
+            augmentations if augmentations else {},
+        )
+
 
 class DataPrediction(Data):
 
     @config("Dataset")
-    def __init__(self,  dataset_filenames : list[str] = ["default:./Dataset"], 
-                        groups_src : dict[str, Group] = {"default" : Group()},
-                        augmentations : Union[dict[str, DataAugmentationsList], None] = {"DataAugmentation_0" : DataAugmentationsList()},
-                        patch : Union[DatasetPatch, None] = DatasetPatch(),
-                        subset : Union[PredictionSubset, dict[str, PredictionSubset]] = PredictionSubset(),
-                        batch_size : int = 1) -> None:
+    def __init__(
+        self,
+        dataset_filenames: list[str] = ["default:./Dataset"],
+        groups_src: dict[str, Group] = {"default": Group()},
+        augmentations: dict[str, DataAugmentationsList] | None = {"DataAugmentation_0": DataAugmentationsList()},
+        patch: DatasetPatch | None = DatasetPatch(),
+        subset: PredictionSubset = PredictionSubset(),
+        batch_size: int = 1,
+    ) -> None:
+
+        super().__init__(
+            dataset_filenames=dataset_filenames,
+            groups_src=groups_src,
+            patch=patch,
+            use_cache=False,
+            subset=subset,
+            batch_size=batch_size,
+            validation=None,
+            inline_augmentations=False,
+            data_augmentations_list=augmentations if augmentations else {},
+        )
 
-        super().__init__(dataset_filenames, groups_src, patch, False, subset, batch_size, dataAugmentationsList=augmentations if augmentations else {})
 
 class DataMetric(Data):
 
     @config("Dataset")
-    def __init__(self,  dataset_filenames : list[str] = ["default:./Dataset"], 
-                        groups_src : dict[str, GroupMetric] = {"default" : GroupMetric()},
-                        subset : Union[PredictionSubset, dict[str, PredictionSubset]] = PredictionSubset(),
-                        validation: Union[str, None] = None) -> None:
-
-        super().__init__(dataset_filenames=dataset_filenames, groups_src=groups_src, patch=None, use_cache=False, subset=subset, batch_size=1, validation=validation)
+    def __init__(
+        self,
+        dataset_filenames: list[str] = ["default:./Dataset"],
+        groups_src: dict[str, GroupMetric] = {"default": GroupMetric()},
+        subset: PredictionSubset = PredictionSubset(),
+        validation: str | None = None,
+    ) -> None:
+
+        super().__init__(
+            dataset_filenames=dataset_filenames,
+            groups_src=groups_src,
+            patch=None,
+            use_cache=False,
+            subset=subset,
+            batch_size=1,
+            validation=validation,
+            data_augmentations_list={},
+            inline_augmentations=False,
+        )