remove SURE

LION/losses/SURE.py

@@ -15,8 +15,11 @@ def __init__(self, noise_std: float, epsilon: Optional[float] = None) -> None:
         warnings.warn(
             "SURE expects Gaussian noise, which is not the case in noisy recosntruction of CT, so this may not work as expected"
         )
+        raise NotImplementedError(
+            "This is not working as expected, it is not implemented for CT reconstruction. See issue #144 to develop this"
+        )
 
-    def forward(self, model, noisy):
+    def forward(self, noisy, model):
 
         if model.get_input_type() != ModelInputType.IMAGE:
             raise NotImplementedError(
@@ -40,3 +43,26 @@ def forward(self, model, noisy):
     @staticmethod
     def default_epsilon(y):
         return torch.max(y) / 1000
+
+    @staticmethod
+    def cite(cite_format="MLA"):
+
+        if cite_format == "MLA":
+            print("Metzler, Christopher A., et al.")
+            print('"Unsupervised learning with Steins unbiased risk estimator."')
+            print("\x1B[3m  arXiv preprint arXiv:1805.10531 \x1B[0m")
+            print("2018")
+
+        elif cite_format == "bib":
+            string = """
+            @article{metzler2018unsupervised,
+            title={Unsupervised learning with Stein's unbiased risk estimator},
+            author={Metzler, Christopher A and Mousavi, Ali and Heckel, Reinhard and Baraniuk, Richard G},
+            journal={arXiv preprint arXiv:1805.10531},
+            year={2018}
+            }"""
+            print(string)
+        else:
+            raise AttributeError(
+                'cite_format not understood, only "MLA" and "bib" supported'
+            )

LION/optimizers/LIONsolver.py

@@ -329,7 +329,7 @@ def check_validation_ready(self, autofill=True, verbose=True):
             "validation_fn",
             expected_type=callable,
             error=False,
-            autofill=True,
+            autofill=self.validation_loader is not None,
             verbose=verbose,
             default=self.loss_fn,
         )
@@ -338,7 +338,7 @@ def check_validation_ready(self, autofill=True, verbose=True):
             "validation_freq",
             expected_type=int,
             error=False,
-            autofill=autofill,
+            autofill=self.validation_loader is not None,
             verbose=verbose,
             default=10,
         )
@@ -699,8 +699,6 @@ def epoch_step(self, epoch):
                 self.save_validation(epoch)
         elif self.verbose:
             print(f"Epoch {epoch+1} - Training loss: {self.train_loss[epoch]}")
-        elif self.validation_freq is not None and self.validation_loss is not None:
-            self.validation_loss[epoch] = self.validate()
 
     def train(self, n_epochs):
         """
@@ -719,6 +717,8 @@ def train(self, n_epochs):
 
         if self.check_validation_ready() == 0:
             self.validation_loss = np.zeros((n_epochs))
+        if self.validation_loader is None:
+            self.validation_loss = None
 
         self.model.train()
         # train loop

papers_in_LION.md

@@ -10,7 +10,9 @@ Pelt, Daniël M., and James A. Sethian. "A mixed-scale dense convolutional neura
 [https://doi.org/10.1073/pnas.1715832114](https://doi.org/10.1073/pnas.1715832114)
 
 `LION/models/CNNs/MS-D/`               Submodule with the original repo
+
 `LION/models/CNNs/MSD_pytorch.py`      the LIONmodel to load the original code
+
 `LION/models/CNNs/MSDNet.py`           Our version of the MSD_pytorch model. Uses more memory
 
 #### Learned Primal Dual (LPD)
@@ -66,6 +68,7 @@ Kiss, Maximilian B., et al. "2DeteCT-A large 2D expandable, trainable, experimen
 [https://doi.org/10.1038/s41597-023-02484-6](https://doi.org/10.1038/s41597-023-02484-6)
 
 `LION/data_loaders/2deteCT/`       Code to download and pre-process a LION version of the 2deteCT, made with the authors. 
+
 `LION/data_loaders/deteCT.py`      Pytorch DataSet
 
 #### LIDC-IDRI
@@ -74,8 +77,16 @@ Armato III, Samuel G., et al. "The lung image database consortium (LIDC) and ima
 [https://doi.org/10.1118/1.3528204](https://doi.org/10.1118/1.3528204)
 
 `LION/data_loaders/LIDC_IDRI/`     Code to pre-process a LION version of the dataset
+
 `LION/data_loaders/LIDC_IDRI.py`   Pytorch DataSet
 
 ## Loss functions
 
+#### Steins Unbased risk estimator (SURE)
+
+Metzler, Christopher A., et al. "Unsupervised learning with Stein's unbiased risk estimator." arXiv preprint arXiv:1805.10531 (2018).
+[https://doi.org/10.48550/arXiv.1805.10531](https://doi.org/10.48550/arXiv.1805.10531)
+
+`LION/losses/SURE.py`     The loss function itself. Use with `SelfSupervisedSolver`
+
 ## Misc