Resolve merge conflict: accepted and merged changes from both branches

README.md

@@ -46,16 +46,19 @@ import spyrit
 ```
 
 ## Examples
-Simple reconstruction examples can be found in [spyrit/test/tuto_core_2d.py](https://github.com/openspyrit/spyrit/blob/master/spyrit/test/tuto_core_2d.py).
+Simple reconstruction examples can be found in [tutorial](https://github.com/openspyrit/spyrit/blob/master/spyrit/tutorial). 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/openspyrit/spyrit/blob/master/spyrit/tutorial/tuto_core_2d_short.ipynb)
+
 
 # API Documentation
 https://spyrit.readthedocs.io/
 
 # Contributors (alphabetical order)
+* Juan Abascal - [Website](https://juanabascal78.wixsite.com/juan-abascal-webpage)
 * Thomas Baudier
 * Sebastien Crombez
 * Nicolas Ducros - [Website](https://www.creatis.insa-lyon.fr/~ducros/WebPage/index.html)
-* Antonio Tomas Lorente Mur - [Website](https://www.creatis.insa-lyon.fr/~lorente/)
+* Antonio Tomas Lorente Mur - [Website]( https://sites.google.com/view/antonio-lorente-mur/)
 * Fadoua Taia-Alaoui
 
 # How to cite?

spyrit/core/prep.py

@@ -302,8 +302,8 @@ def sigma(self, x: torch.tensor) -> torch.tensor:
             :attr:`x`: batch of images in the Hadamard domain
             
         Shape:
-            - Input: :math:`(B,2*M)` where :math:`B` is the batch dimension
-            - Output: :math:`(B, M)`
+            - Input: :math:`(*,2*M)` :math:`*` indicates one or more dimensions
+            - Output: :math:`(*, M)`
             
         Example:
             >>> x = torch.rand([10,2*400], dtype=torch.float)
@@ -312,7 +312,7 @@ def sigma(self, x: torch.tensor) -> torch.tensor:
             torch.Size([10, 400])
             
         """
-        x = x[:,self.even_index] + x[:,self.odd_index]
+        x = x[...,self.even_index] + x[...,self.odd_index]
         x = 4*x/(self.alpha**2) # Cov is in [-1,1] so *4
         return x
 

spyrit/core/recon.py

@@ -744,109 +744,146 @@ def reconstruct_expe(self, x):
 
         return x
 
-class PositiveParameters(nn.Module):
-    def __init__(self, size, val_min=1e-6):
-        super(PositiveParameters, self).__init__()
-        self.val_min = torch.tensor(val_min)
-        self.params = nn.Parameter(torch.abs(val_min*torch.ones(size,1)), requires_grad=True)
+#%%===========================================================================================
+class DCDRUNet(DCNet):
+# ===========================================================================================
+    r""" Denoised completion reconstruction network based on DRUNet wich concatenates a 
+        noise level map to the input
+    
+    .. math:
         
-    def forward(self):
-        return torch.abs(self.params)
-
-class PositiveMonoIncreaseParameters(PositiveParameters):
-    def __init__(self, size, val_min=0.000001):
-        super().__init__(size, val_min)
     
-    def forward(self):
-        # cumsum in opposite order
-        return super().forward().cumsum(dim=0).flip(dims=[0])
+    Args:
+        :attr:`noise`: Acquisition operator (see :class:`~spyrit.core.noise`) 
+        
+        :attr:`prep`: Preprocessing operator (see :class:`~spyrit.core.prep`)
+        
+        :attr:`sigma`: UPDATE!! Tikhonov reconstruction operator of type 
+        :class:`~spyrit.core.recon.TikhonovMeasurementPriorDiag()`
+        
+        :attr:`denoi` (optional): Image denoising operator 
+        (see :class:`~spyrit.core.nnet`). 
+        Default :class:`~spyrit.core.nnet.Identity`
+
+        :attr:`noise_level` (optional): Noise level in the range [0, 255], default is noise_level=5
 
-# class PositiveMonoDecreaseParameters(nn.Module):
-#     def __init__(self, size, val_min=1e-6):
-#         super(PositiveMonoDecreaseParameters, self).__init__()
-#         self.val_min = torch.tensor(val_min)
-#         self.params = nn.Parameter(torch.abs(val_min*torch.ones(size,1)), requires_grad=True)
-#         self.device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
+    
+    Input / Output:
+        :attr:`input`: Ground-truth images with concatenated noise level map with 
+         shape :math:`(B,C+1,H,W)` 
+        
+        :attr:`output`: Reconstructed images with shape :math:`(B,C,H,W)`
+    
+    Attributes:
+        :attr:`Acq`: Acquisition operator initialized as :attr:`noise`
         
-#     def forward(self):
-#         for i in range(1, len(self.params)):
-#             self.params[i].data = torch.clamp(self.params[i].data, min=self.val_min.to(self.device), max=self.params[i-1].data)
-#         return torch.abs(self.params)
+        :attr:`PreP`: Preprocessing operator initialized as :attr:`prep`
+        
+        :attr:`DC_Layer`: Data consistency layer initialized as :attr:`tikho`
+        
+        :attr:`Denoi`: Image (DRUNet architecture type) denoising operator 
+        initialized as :attr:`denoi`
 
+    
+    Example:
+        >>> B, C, H, M = 10, 1, 64, 64**2
+        >>> Ord = np.ones((H,H))
+        >>> meas = HadamSplit(M, H, Ord)
+        >>> noise = NoNoise(meas)
+        >>> prep = SplitPoisson(1.0, M, H*H)
+        >>> sigma = np.random.random([H**2, H**2])
+        >>> n_channels = 1                   # 1 for grayscale image    
+        >>> model_drunet_path = './spyrit/drunet/model_zoo/drunet_gray.pth'
+        >>> denoi_drunet = drunet(in_nc=n_channels+1, out_nc=n_channels, nc=[64, 128, 256, 512], nb=4, act_mode='R',                     
+            downsample_mode="strideconv", upsample_mode="convtranspose") 
+        >>> recnet = DCDRUNet(noise,prep,sigma,denoi_drunet)
+        >>> z = recnet(x)
+        >>> print(z.shape)
+        torch.Size([10, 1, 64, 64])
+    """
 
-class UPGD(PinvNet):
     def __init__(self, 
                  noise, 
                  prep, 
-                 denoi=nn.Identity(),
-                 num_iter = 6, 
-                 lamb = 1e-5, 
-                 lamb_min = 1e-6, 
-                 split=False):
-        super(UPGD, self).__init__(noise, prep, denoi)
-        self.num_iter = num_iter
-        self.lamb = lamb
-        self.lamb_min = lamb_min
-        # Set a trainable tensor for the regularization parameter with dimension num_iter
-        # and constrained to be positive with clamp(min=0.0, max=None)        
-        self.lambs = PositiveMonoIncreaseParameters(num_iter, lamb_min) # shape lambs = [num_iter,1]
-        #self.noise = noise
-        self.split = split
-
+                 sigma, 
+                 denoi=nn.Identity(), 
+                 noise_level=5):
+        super().__init__(noise, prep, sigma, denoi)
+        self.register_buffer('noise_level', torch.FloatTensor([noise_level/255.]))
+
     def reconstruct(self, x):
         r""" Reconstruction step of a reconstruction network
-        
-        Same as :meth:`reconstruct` reconstruct except that:
-            
-            1. The regularization parameter is trainable
             
         Args:
             :attr:`x`: raw measurement vectors
         
         Shape:
-            :attr:`x`: :math:`(BC,2M)`
+            :attr:`x`: raw measurement vectors with shape :math:`(BC,2M)`
             
-            :attr:`output`: :math:`(BC,1,H,W)`
+            :attr:`output`: reconstructed images with shape :math:`(BC,1,H,W)`
+        
+        Example:
+            >>> B, C, H, M = 10, 1, 64, 64**2
+            >>> Ord = np.ones((H,H))
+            >>> meas = HadamSplit(M, H, Ord)
+            >>> noise = NoNoise(meas)
+            >>> prep = SplitPoisson(1.0, M, H*H)
+            >>> sigma = np.random.random([H**2, H**2])
+            >>> n_channels = 1                   # 1 for grayscale image    
+            >>> model_drunet_path = './spyrit/drunet/model_zoo/drunet_gray.pth'
+            >>> denoi_drunet = drunet(in_nc=n_channels+1, out_nc=n_channels, nc=[64, 128, 256, 512], nb=4, act_mode='R',                     
+                downsample_mode="strideconv", upsample_mode="convtranspose") 
+            >>> recnet = DCDRUNet(noise,prep,sigma,denoi_drunet)
+            >>> x = torch.rand((B*C,2*M), dtype=torch.float)
+            >>> z = recnet.reconstruct(x)
+            >>> print(z.shape)
+            torch.Size([10, 1, 64, 64])
         """
-
-        # Measurement operator
-        #if self.split:
-        #    meas = super().Acq.meas_op     
-        #else:
-            #meas = self.Acq.meas_op        
-        meas = self.acqu.meas_op
-
         # x of shape [b*c, 2M]
-        bc, _ = x.shape    
-
-        # First estimate: Pseudo inverse
-        # Preprocessing in the measurement domain
-        x = self.prep(x) # [5, 1024]
-
-        # Save measurements
-        m = x.clone() # [5, 1024]
-
+
+        bc, _ = x.shape
+
+        # Preprocessing
+        var_noi = self.prep.sigma(x)
+        x = self.prep(x) # shape x = [b*c, M]
+
         # measurements to image domain processing
-        x = self.pinv(x, self.acqu.meas_op)  # [5, 4096]         # shape x = [b*c,N]
-        #x = x.view(bc,1,self.acqu.meas_op.h, self.acqu.meas_op.w)   # shape x = [b*c,1,h,w]
-
-        # Unroll network
-        # Ensure step size is positive and monotonically decreasing and larger than self.lamb!
-        lambs = self.lambs()
-        for n in range(self.num_iter):
-            # Projection onto the measurement space
-            proj = self.acqu.meas_op.forward_H(x) # [5, 1024]
-
-            # Residual
-            res = proj - m # [5, 1024]
+        x_0 = torch.zeros((bc, self.Acq.meas_op.N), device=x.device)
+        x = self.tikho(x, x_0, var_noi, self.Acq.meas_op)
+        x = x.view(bc,1,self.Acq.meas_op.h, self.Acq.meas_op.w)   # shape x = [b*c,1,h,w]
+
+        # Image domain denoising
+        x = self.concat_noise_map(x)
+        x = self.denoi(x)             
+
+        return x        
 
-            # Gradient step
-            x = x + lambs[n]*self.acqu.meas_op.H_adjoint(res) # [5, 4096]
+    def concat_noise_map(self, x):
+        r""" Concatenation of noise level map to reconstructed images
+            
+        Args:
+            :attr:`x`: reconstructed images from the reconstruction layer
+        
+        Shape:
+            :attr:`x`: reconstructed images with shape :math:`(BC,1,H,W)`
+            
+            :attr:`output`: reconstructed images with concatenated noise level map with shape :math:`(BC,2,H,W)`
+        """
 
-            # Denoising step
-            x = x.view(bc,1,self.acqu.meas_op.h, self.acqu.meas_op.w) # [5, 1, 64, 64]
-            x = self.denoi(x)
-            x = x.view(bc, self.acqu.meas_op.N) # [5, 4096]
-        return x            
-
+        b, c, h, w = x.shape
+        x = 0.5*(x + 1)
+        x = torch.cat((x, self.noise_level.expand(b, 1, h, w)), dim=1)
+        return x 
 
+    def set_noise_level(self, noise_level):
+        r""" Reset noise level value
+            
+        Args:
+            :attr:`noise_level`: noise level value in the range [0, 255] 
+        
+        Shape:
+            :attr:`noise_level`: float value noise level :math:`(1)`
+            
+            :attr:`output`: noise level tensor with shape :math:`(1)`
+        """
+        self.noise_level = torch.FloatTensor([noise_level/255.])