konfai 1.1.3__py3-none-any.whl → 1.1.4__py3-none-any.whl

konfai/data/augmentation.py

@@ -134,7 +134,6 @@ class EulerTransform(DataAugmentation):
                                                                                    
 class Translate(EulerTransform):
     
-    @config("Translate")
     def __init__(self, t_min: float = -10, t_max = 10, is_int: bool = False):
         super().__init__()
         self.t_min = t_min
@@ -152,7 +151,6 @@ class Translate(EulerTransform):
 
 class Rotate(EulerTransform):
 
-    @config("Rotate")
     def __init__(self, a_min: float = 0, a_max: float = 360, is_quarter: bool = False):
         super().__init__()
         self.a_min = a_min
@@ -174,7 +172,6 @@ class Rotate(EulerTransform):
 
 class Scale(EulerTransform):
 
-    @config("Scale")
     def __init__(self, s_std: float = 0.2):
         super().__init__()
         self.s_std = s_std
@@ -187,7 +184,6 @@ class Scale(EulerTransform):
 
 class Flip(DataAugmentation):
 
-    @config("Flip")
     def __init__(self, f_prob: Union[list[float], None] = [0.33, 0.33 ,0.33]) -> None:
         super().__init__()
         self.f_prob = f_prob
@@ -211,7 +207,6 @@ class Flip(DataAugmentation):
 
 class ColorTransform(DataAugmentation):
 
-    @config("ColorTransform")
     def __init__(self, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.matrix: dict[int, list[torch.Tensor]] = {}
@@ -236,7 +231,6 @@ class ColorTransform(DataAugmentation):
 
 class Brightness(ColorTransform):
 
-    @config("Brightness")
     def __init__(self, b_std: float, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.b_std = b_std
@@ -248,7 +242,6 @@ class Brightness(ColorTransform):
 
 class Contrast(ColorTransform):
 
-    @config("Contrast")
     def __init__(self, c_std: float, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.c_std = c_std
@@ -260,7 +253,6 @@ class Contrast(ColorTransform):
 
 class LumaFlip(ColorTransform):
 
-    @config("LumaFlip")
     def __init__(self, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.v = torch.tensor([1, 1, 1, 0])/torch.sqrt(torch.tensor(3)) 
@@ -285,7 +277,6 @@ class HUE(ColorTransform):
     
 class Saturation(ColorTransform):
 
-    @config("Saturation")
     def __init__(self, s_std: float, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.s_std = s_std
@@ -372,7 +363,6 @@ class Saturation(ColorTransform):
 
 class Noise(DataAugmentation):
 
-    @config("Noise")
     def __init__(self, n_std: float, noise_step: int=1000, beta_start: float = 1e-4, beta_end: float = 0.02, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.n_std = n_std
@@ -427,7 +417,6 @@ class Noise(DataAugmentation):
 
 class CutOUT(DataAugmentation):
 
-    @config("CutOUT")
     def __init__(self, c_prob: float, cutout_size: int, value: float, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         self.c_prob = c_prob
@@ -458,7 +447,6 @@ class CutOUT(DataAugmentation):
 
 class Elastix(DataAugmentation):
 
-    @config("Elastix")
     def __init__(self, grid_spacing: int = 16, max_displacement: int = 16) -> None:
         super().__init__()
         self.grid_spacing = grid_spacing
@@ -529,7 +517,6 @@ class Elastix(DataAugmentation):
 
 class Permute(DataAugmentation):
 
-    @config("Permute")
     def __init__(self, prob_permute: Union[list[float], None] = [0.5 ,0.5]) -> None:
         super().__init__()
         self._permute_dims = torch.tensor([[0, 2, 1, 3], [0, 3, 1, 2]])
@@ -567,7 +554,6 @@ class Permute(DataAugmentation):
 
 class Mask(DataAugmentation):
 
-    @config("Mask")
     def __init__(self, mask: str, value: float, groups: Union[list[str], None] = None) -> None:
         super().__init__(groups)
         if mask is not None:

konfai/data/data_manager.py

@@ -217,7 +217,6 @@ class Subset():
         else:
             names_filtred = names
         size = len(names_filtred)
-        
         index = []
         if self.subset is None:
             index = list(range(0, size))
@@ -226,15 +225,24 @@ class Subset():
                 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):
-                validation_names = []
+                train_names = []
                 with open(self.subset, "r") as f:
                     for name in f:
-                        validation_names.append(name.strip())
+                        train_names.append(name.strip())
                 index = []
                 for i, name in enumerate(names_filtred):
-                    if name in validation_names:
+                    if name in train_names:
                         index.append(i)
-            
+            elif self.subset.startswith("~") and os.path.exists(self.subset[1:]):
+                exclude_names = []
+                with open(self.subset[1:], "r") as f:
+                    for name in f:
+                        exclude_names.append(name.strip())
+                index = []
+                for i, name in enumerate(names_filtred):
+                    if name not in exclude_names:
+                        index.append(i)
+
         elif isinstance(self.subset, list):
             if len(self.subset) > 0:
                 if isinstance(self.subset[0], int):

konfai/evaluator.py

@@ -102,7 +102,7 @@ class Evaluator(DistributedObject):
         result = {}
         for output_group in self.metrics:
             for target_group in self.metrics[output_group]:
-                targets = [data_dict[group][0].to(0) if torch.cuda.is_available() else data_dict[group][0] for group in target_group.split("/") if group in data_dict]
+                targets = [data_dict[group][0].to(0) if torch.cuda.is_available() else data_dict[group][0] for group in target_group.split(";") if group in data_dict]
                 name = data_dict[output_group][1][0]
                 for metric in self.metrics[output_group][target_group]:
                     result["{}:{}:{}".format(output_group, target_group, metric.__class__.__name__)] = metric(data_dict[output_group][0].to(0) if torch.cuda.is_available() else data_dict[output_group][0], *targets).item()
@@ -135,8 +135,11 @@ class Evaluator(DistributedObject):
                 f"Available groups: {sorted(groupsDest)}"
             )
 
-        target_groups = {target for targets in self.metrics.values() for target in targets}
-        missing_targets = target_groups - set(groupsDest)
+        target_groups = []
+        for i in {target for targets in self.metrics.values() for target in targets}:
+            for u in i.split(";"):
+                target_groups.append(u)
+        missing_targets = set(target_groups) - set(groupsDest)
         if missing_targets:
             raise EvaluatorError(
                 f"The following metric target groups are missing from 'groupsDest': {sorted(missing_targets)}. ",

konfai/models/segmentation/NestedUNet.py

@@ -31,7 +31,6 @@ class NestedUNet(network.Network):
             self.add_module("Softmax", torch.nn.Softmax(dim=1))
             self.add_module("Argmax", blocks.ArgMax(dim=1))
 
-    @config("NestedUNet")
     def __init__(   self,
                     optimizer : network.OptimizerLoader = network.OptimizerLoader(),
                     schedulers : network.LRSchedulersLoader = network.LRSchedulersLoader(),

konfai/models/segmentation/UNet.py

@@ -38,7 +38,6 @@ class UNetBlock(network.ModuleArgsDict):
 
 class UNet(network.Network):
 
-    @config("UNet")
     def __init__(   self,
                     optimizer : network.OptimizerLoader = network.OptimizerLoader(),
                     schedulers : network.LRSchedulersLoader = network.LRSchedulersLoader(),

konfai/network/network.py

@@ -157,7 +157,7 @@ class Measure():
         outputs_group_rename = {}
         
         modules = []
-        for i,_ in model.named_modules():
+        for i,_,_ in model.named_ModuleArgsDict():
             modules.append(i)
 
         for output_group in self.outputsCriterions.keys():
@@ -167,11 +167,12 @@ class Measure():
                     "Please check that the name matches exactly a submodule or output of your model architecture."
                 )
             for target_group in self.outputsCriterions[output_group]:
-                if target_group not in group_dest:
-                    raise MeasureError(
-                        f"The target_group '{target_group}' defined in 'outputsCriterions.{output_group}.targetsCriterions' was not found in the available destination groups.",
-                        "This target_group is expected for loss or metric computation, but was not loaded in 'group_dest'.",
-                        f"Please make sure that the group '{target_group}' is defined in 'Dataset:groups_src:...:groups_dest:'{target_group}'' and correctly loaded from the dataset.")
+                for target_group_tmp in target_group.split(";"): 
+                    if target_group_tmp not in group_dest:
+                        raise MeasureError(
+                            f"The target_group '{target_group_tmp}' defined in 'outputsCriterions.{output_group}.targetsCriterions' was not found in the available destination groups.",
+                            "This target_group is expected for loss or metric computation, but was not loaded in 'group_dest'.",
+                            f"Please make sure that the group '{target_group_tmp}' is defined in 'Dataset:groups_src:...:groups_dest:'{target_group_tmp}'' and correctly loaded from the dataset.")
                 for criterion in self.outputsCriterions[output_group][target_group]:
                     if not self.outputsCriterions[output_group][target_group][criterion].isTorchCriterion:
                         outputs_group_rename[output_group] = criterion.init(model, output_group, target_group)
@@ -189,7 +190,7 @@ class Measure():
 
     def update(self, output_group: str, output : torch.Tensor, data_dict: dict[str, torch.Tensor], it: int, nb_patch: int, training: bool) -> None:
         for target_group in self.outputsCriterions[output_group]:
-            target = [data_dict[group].to(output[0].device).detach() for group in target_group.split("/") if group in data_dict]
+            target = [data_dict[group].to(output[0].device).detach() for group in target_group.split(";") if group in data_dict]
 
             for criterion, criterionsAttr in self.outputsCriterions[output_group][target_group].items():
                 if it >= criterionsAttr.stepStart and (criterionsAttr.stepStop is None or it <= criterionsAttr.stepStop):
@@ -928,6 +929,16 @@ class Network(ModuleArgsDict, ABC):
             if isinstance(module, ModuleArgsDict):
                 module._training = state
 
+class MinimalModel(Network):
+    
+    def __init__(self, model: Network, optimizer : OptimizerLoader = OptimizerLoader(),
+                    schedulers : LRSchedulersLoader = LRSchedulersLoader(),
+                    outputsCriterions: dict[str, TargetCriterionsLoader] = {"default" : TargetCriterionsLoader()},
+                    patch : Union[ModelPatch, None] = None,
+                    dim : int = 3, nb_batch_per_step = 1, init_type = "normal", init_gain = 0.02):
+        super().__init__(1, optimizer, schedulers, outputsCriterions, patch, nb_batch_per_step, init_type, init_gain, dim)
+        self.add_module("Model", model)
+
 class ModelLoader():
 
     @config("Model")
@@ -937,11 +948,13 @@ class ModelLoader():
     def getModel(self, train : bool = True, DL_args: Union[str, None] = None, DL_without=["optimizer", "schedulers", "nb_batch_per_step", "init_type", "init_gain"]) -> Network:
         if not DL_args:
             DL_args="{}.Model".format(KONFAI_ROOT())
-        model = partial(getattr(importlib.import_module(self.module), self.name), config = None, DL_args=DL_args)
-        if not train: 
-            model = partial(model, DL_without = DL_without)
-        return model()
-
+        DL_args += "."+self.name
+        model = config(DL_args)(getattr(importlib.import_module(self.module), self.name))(config = None,  DL_without = DL_without if not train else [])
+        if not isinstance(model, Network):
+            model = config(DL_args)(partial(MinimalModel, model))(config = None,  DL_without = DL_without+["model"] if not train else [])
+            model.setName(self.name)
+        return model
+    
 class CPU_Model():
 
     def __init__(self, model: Network) -> None:

konfai/predictor.py

@@ -258,7 +258,6 @@ class _Predictor():
         desc = lambda : "Prediction : {}".format(description(self.modelComposite))
         self.dataloader_prediction.dataset.load("Prediction")
         with tqdm.tqdm(iterable = enumerate(self.dataloader_prediction), leave=True, desc = desc(), total=len(self.dataloader_prediction), ncols=0) as batch_iter:
-            dist.barrier()
             for it, data_dict in batch_iter:
                 with torch.amp.autocast('cuda', enabled=self.autocast):
                     input = self.getInput(data_dict)
@@ -272,7 +271,7 @@ class _Predictor():
 
                     batch_iter.set_description(desc())
                     self.it += 1
-
+        
     def _predict_log(self, data_dict : dict[str, tuple[torch.Tensor, int, int, int]]):
         measures = DistributedObject.getMeasure(self.world_size, self.global_rank, self.local_rank, {"" : self.modelComposite.module}, 1)
         

konfai/trainer.py

@@ -34,7 +34,7 @@ class EarlyStoppingBase:
 class EarlyStopping(EarlyStoppingBase):
 
     @config("EarlyStopping")
-    def __init__(self, monitor: Union[list[str], None] = [], patience=10, min_delta=0.0, mode="min"):
+    def __init__(self, monitor: Union[list[str], None] = [], patience: int=10, min_delta: float=0.0, mode: str="min"):
         super().__init__()
         self.monitor = [] if monitor is None else monitor
         self.patience = patience

konfai/utils/config.py

@@ -3,7 +3,7 @@ import ruamel.yaml
 import inspect 
 import collections
 from copy import deepcopy
-from typing import Union, Literal, get_origin, get_args
+from typing import Union, Literal, get_origin, get_args, Any
 import torch
 from konfai import CONFIG_FILE
 from konfai.utils.utils import ConfigError
@@ -175,8 +175,11 @@ def config(key : Union[str, None] = None):
                     os.environ['KONFAI_CONFIG_VARIABLE'] = "False"
                     kwargs = {} 
                     for param in list(inspect.signature(function).parameters.values())[len(args):]:
-
+                        if param.name in without:
+                            continue
+                        
                         annotation = param.annotation
+
                         # --- support Literal ---
                         if get_origin(annotation) is Literal:
                             allowed_values = get_args(annotation)
@@ -192,11 +195,10 @@ def config(key : Union[str, None] = None):
                             for i in annotation.__args__:
                                 annotation = i
                                 break
-                        if param.name in without:
-                            continue
+                        
                         if not annotation == inspect._empty:
                             if annotation not in [int, str, bool, float, torch.Tensor]:
-                                if str(annotation).startswith("list") or str(annotation).startswith("tuple") or str(annotation).startswith("typing.Tuple") or str(annotation).startswith("typing.List"):
+                                if str(annotation).startswith("list") or str(annotation).startswith("tuple") or str(annotation).startswith("typing.Tuple") or str(annotation).startswith("typing.List") or str(annotation).startswith("typing.Sequence"):
                                     elem_type = annotation.__args__[0]
                                     values = config.getValue(param.name, param.default)
                                     if getattr(elem_type, '__origin__', None) is Union:
@@ -221,7 +223,7 @@ def config(key : Union[str, None] = None):
                                 elif str(annotation).startswith("dict"):
                                     if annotation.__args__[0] == str:
                                         values = config.getValue(param.name, param.default)
-                                        if values is not None and annotation.__args__[1] not in [int, str, bool, float]:
+                                        if values is not None and annotation.__args__[1] not in [int, str, bool, float, Any]:
                                             try:
                                                 kwargs[param.name] = {value : annotation.__args__[1](config = filename, DL_args = key_tmp+"."+param.name+"."+value) for value in values}
                                             except ValueError as e:
@@ -229,6 +231,7 @@ def config(key : Union[str, None] = None):
                                             except Exception as e:
                                                 raise ConfigError("{} {}".format(values, e))
                                         else:
+
                                             kwargs[param.name] = values
                                     else: 
                                         raise ConfigError("Config: The config only supports types : config(Object), int, str, bool, float, list[int], list[str], list[bool], list[float], dict[str, Object]")
@@ -236,7 +239,7 @@ def config(key : Union[str, None] = None):
                                     try:
                                         kwargs[param.name] = annotation(config = filename, DL_args = key_tmp)
                                     except Exception as e:
-                                        raise ConfigError("Failed to instantiate {} with type {}, error {} ".format(param.name, annotation.__name__, e))
+                                        raise ConfigError("Failed to instantiate {} with type {}, error {} ".format(param.name, annotation, e))
                                     
                                     if os.environ['KONFAI_CONFIG_VARIABLE'] == "True":
                                         os.environ['KONFAI_CONFIG_VARIABLE'] = "False"

konfai/utils/utils.py

@@ -21,7 +21,7 @@ import sys
 import re
 
 
-def description(model, modelEMA = None, showMemory: bool = True) -> str:
+def description(model, modelEMA = None, showMemory: bool = True, train: bool = True) -> str:
     values_desc = lambda weights, values: " ".join(["{}({:.2f}) : {:.6f}".format(name.split(":")[-1], weight, value) for (name, value), weight in zip(values.items(), weights.values())])
     model_desc = lambda model : "("+" ".join(["{}({:.6f}) : {}".format(name, network.optimizer.param_groups[0]['lr'] if network.optimizer is not None else 0, values_desc(network.measure.getLastWeights(), network.measure.getLastValues())) for name, network in model.module.getNetworks().items() if network.measure is not None])+")"
     result = "Loss {}".format(model_desc(model))
@@ -33,9 +33,9 @@ def description(model, modelEMA = None, showMemory: bool = True) -> str:
     return result
 
 def _getModule(classpath : str, type : str) -> tuple[str, str]:
-    if len(classpath.split("_")) > 1:
-        module = ".".join(classpath.split("_")[:-1])
-        name = classpath.split("_")[-1] 
+    if len(classpath.split(":")) > 1:
+        module = ".".join(classpath.split(":")[:-1])
+        name = classpath.split(":")[-1] 
     else:
         module = "konfai."+type+("." if len(classpath.split(".")) > 2 else "")+".".join(classpath.split(".")[:-1])
         name = classpath.split(".")[-1]

{konfai-1.1.3.dist-info → konfai-1.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: konfai
-Version: 1.1.3
+Version: 1.1.4
 Summary: Modular and configurable Deep Learning framework with YAML and PyTorch
 Author-email: Valentin Boussot <boussot.v@gmail.com>
 License-Expression: Apache-2.0

{konfai-1.1.3.dist-info → konfai-1.1.4.dist-info}/RECORD

@@ -1,11 +1,11 @@
 konfai/__init__.py,sha256=YXG-wpSEXWs6Jt3BDI77V4r89gEUNX-6lxW9btj5VYI,851
-konfai/evaluator.py,sha256=rAhfdRemMjzC3VoaqyQKJR0SBekuLDiLT1nhblH8RQk,8293
+konfai/evaluator.py,sha256=G8tXI-g8yTxBZXmESpRW7B5UEI4SMXq47fsGksU0G0M,8394
 konfai/main.py,sha256=xhCIs3VKXxNCgyyN616K-VANEFCsZZRR-l8LIMHlmPw,2597
-konfai/predictor.py,sha256=SgHs_gylsyVtQ41DBRBRmcpHIMg2ghLbxELbQBxjjFY,22747
-konfai/trainer.py,sha256=GCi8oRgTlbZxwKfmJlS2S4VU1yj1pCl6QeAWNwdSFPs,20223
+konfai/predictor.py,sha256=R9ohOqEcSoq6Wu9Yv3pkerVfm6qSotd4aICe7ctOsU0,22728
+konfai/trainer.py,sha256=gJ7qmU302M3Mevq3l1aIdPpey5C3prtibD69LyxbnAg,20240
 konfai/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-konfai/data/augmentation.py,sha256=kp4HyMSGflbuHbOsNiXBxszLFSuOZ4zRRQT0cHNIVUI,32620
-konfai/data/data_manager.py,sha256=oG73iHT5qV52UTWQPC3MKjsjaQHJUOAPF1WA-XeTmUE,29700
+konfai/data/augmentation.py,sha256=ruvS7ykFveOZBe2Mv_TOU5a8AzUgH7gfTipwqYgRM7k,32293
+konfai/data/data_manager.py,sha256=TCQFZ_zpRHYIomPOotG8U_I0DfpjhSaajb7ypd6fyRU,30103
 konfai/data/patching.py,sha256=oq43r3JlS9hw-pnzpjT3epvXJxEKqiQEtFVZPjY9Jic,15749
 konfai/data/transform.py,sha256=ZZoxft0V8t-DaKjF3OsIFezz41B8_xwPqBvYCYwF0dk,26471
 konfai/metric/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -20,20 +20,20 @@ konfai/models/generation/gan.py,sha256=-GoKxHm3W9NdD4U77UcJrG5TfOZ3NWFUZG663kt2X
 konfai/models/generation/vae.py,sha256=_3JYVT2ojZ0P98tYcD2ny7a-gWVUmnByLDhY7i-n_4g,4719
 konfai/models/registration/registration.py,sha256=18EiWt4RJIXLyFtqU-kHjV1sMnQRm9mxAA6_-2B1YqI,6313
 konfai/models/representation/representation.py,sha256=RwQYoxtdph440-t_ZLelykl0hkUAD1zdspQaLkgxb-0,2677
-konfai/models/segmentation/NestedUNet.py,sha256=6XGizAIc4bDL8vx4AHW8BBFjUvovRYcjdMBHsN4ViNo,4301
-konfai/models/segmentation/UNet.py,sha256=JhKyGuaFXY7thJcbQ2mWGuIBtNdUhh5FoacpWDZ0N1k,4065
+konfai/models/segmentation/NestedUNet.py,sha256=wutcHYpZkOm8FqPPt5zifD6dGSDlhB9zIBlibzVyAYY,4275
+konfai/models/segmentation/UNet.py,sha256=Uei51-_0Le24ZJs9tbuL6hQn66kigkfbaLSMlH38els,4045
 konfai/network/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 konfai/network/blocks.py,sha256=RaTI0Lrvq1V-GIFei-WTUB6wlg4LydZksAyJ8DMk40M,13502
-konfai/network/network.py,sha256=SnwQUKFTZZU8zuix5sm0vW8s0G3h6Fa8pHoIcwC984Q,46512
+konfai/network/network.py,sha256=YCPfgQ7EuRiTgAlMlQTx5ospluO4aiqSbsdU4GdLiMA,47467
 konfai/utils/ITK.py,sha256=OxTieDNNYHGkn7zxJsAG-6ecRG1VYMvn1dlBbBe1DOs,13955
 konfai/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-konfai/utils/config.py,sha256=OsCUqgNaPX56nD_MpJ2WRpiQ7xxqHonfPYaS9VGtsl8,12413
+konfai/utils/config.py,sha256=f7o83ix5_oNbr2pki-Czqr-yHi-8n92ZL64nlo0XGwA,12514
 konfai/utils/dataset.py,sha256=6ZzevdhJ7e5zlXATAVwSh9O6acKXM7gYNxkMAa5DrmM,36351
 konfai/utils/registration.py,sha256=v1srEBOcgDnHrx0YtsK6bcj0yCMH7wNeaQ3wC7gEvOw,8898
-konfai/utils/utils.py,sha256=Laq8bGc5mGKFZlJIkHxa-BrC9uR2F7MTRuL4YFAIxQY,23439
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