careamics 0.1.0rc6__py3-none-any.whl → 0.1.0rc7__py3-none-any.whl

careamics/models/lvae/likelihoods.py

@@ -0,0 +1,312 @@
+"""
+Script containing modules for definining different likelihood functions (as nn.Module).
+"""
+
+import math
+from typing import Dict, Literal, Tuple, Union
+
+import numpy as np
+import torch
+from torch import nn
+
+
+class LikelihoodModule(nn.Module):
+    """
+    The base class for all likelihood modules.
+    It defines the fundamental structure and methods for specialized likelihood models.
+    """
+
+    def distr_params(self, x):
+        return None
+
+    def set_params_to_same_device_as(self, correct_device_tensor):
+        pass
+
+    @staticmethod
+    def logvar(params):
+        return None
+
+    @staticmethod
+    def mean(params):
+        return None
+
+    @staticmethod
+    def mode(params):
+        return None
+
+    @staticmethod
+    def sample(params):
+        return None
+
+    def log_likelihood(self, x, params):
+        return None
+
+    def forward(
+        self, input_: torch.Tensor, x: torch.Tensor
+    ) -> Tuple[torch.Tensor, Dict[str, torch.Tensor]]:
+
+        distr_params = self.distr_params(input_)
+        mean = self.mean(distr_params)
+        mode = self.mode(distr_params)
+        sample = self.sample(distr_params)
+        logvar = self.logvar(distr_params)
+
+        if x is None:
+            ll = None
+        else:
+            ll = self.log_likelihood(x, distr_params)
+
+        dct = {
+            "mean": mean,
+            "mode": mode,
+            "sample": sample,
+            "params": distr_params,
+            "logvar": logvar,
+        }
+
+        return ll, dct
+
+
+class GaussianLikelihood(LikelihoodModule):
+    r"""
+    A specialize `LikelihoodModule` for Gaussian likelihood.
+
+    Specifically, in the LVAE model, the likelihood is defined as:
+        p(x|z_1) = N(x|\mu_{p,1}, \sigma_{p,1}^2)
+    """
+
+    def __init__(
+        self,
+        ch_in: int,
+        color_channels: int,
+        predict_logvar: Literal[None, "pixelwise", "global", "channelwise"] = None,
+        logvar_lowerbound: float = None,
+        conv2d_bias: bool = True,
+    ):
+        """
+        Constructor.
+
+        Parameters
+        ----------
+        predict_logvar: Literal[None, 'global', 'pixelwise', 'channelwise'], optional
+            If not `None`, it expresses how to compute the log-variance.
+            Namely:
+            - if `pixelwise`, log-variance is computed for each pixel.
+            - if `global`, log-variance is computed as the mean of all pixel-wise entries.
+            - if `channelwise`, log-variance is computed as the average over the channels.
+            Default is `None`.
+        logvar_lowerbound: float, optional
+            The lowerbound value for log-variance. Default is `None`.
+        conv2d_bias: bool, optional
+            Whether to use bias term in convolutions. Default is `True`.
+        """
+        super().__init__()
+
+        # If True, then we also predict pixelwise logvar.
+        self.predict_logvar = predict_logvar
+        self.logvar_lowerbound = logvar_lowerbound
+        self.conv2d_bias = conv2d_bias
+        assert self.predict_logvar in [None, "global", "pixelwise", "channelwise"]
+
+        # logvar_ch_needed = self.predict_logvar is not None
+        # self.parameter_net = nn.Conv2d(ch_in,
+        #                                color_channels * (1 + logvar_ch_needed),
+        #                                kernel_size=3,
+        #                                padding=1,
+        #                                bias=self.conv2d_bias)
+        self.parameter_net = nn.Identity()
+
+        print(
+            f"[{self.__class__.__name__}] PredLVar:{self.predict_logvar} LowBLVar:{self.logvar_lowerbound}"
+        )
+
+    def get_mean_lv(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
+        """
+        Given the output of the top-down pass, compute the mean and log-variance of the
+        Gaussian distribution defining the likelihood.
+
+        Parameters
+        ----------
+        x: torch.Tensor
+            The input tensor to the likelihood module, i.e., the output of the top-down pass.
+        """
+        # Feed the output of the top-down pass to a parameter network
+        # This network can be either a Conv2d or Identity module
+        x = self.parameter_net(x)
+
+        if self.predict_logvar is not None:
+            # Get pixel-wise mean and logvar
+            mean, lv = x.chunk(2, dim=1)
+
+            # Optionally, compute the global or channel-wise logvar
+            if self.predict_logvar in ["channelwise", "global"]:
+                if self.predict_logvar == "channelwise":
+                    # logvar should be of the following shape (batch, num_channels, ). Other dims would be singletons.
+                    N = np.prod(lv.shape[:2])
+                    new_shape = (*mean.shape[:2], *([1] * len(mean.shape[2:])))
+                elif self.predict_logvar == "global":
+                    # logvar should be of the following shape (batch, ). Other dims would be singletons.
+                    N = lv.shape[0]
+                    new_shape = (*mean.shape[:1], *([1] * len(mean.shape[1:])))
+                else:
+                    raise ValueError(
+                        f"Invalid value for self.predict_logvar:{self.predict_logvar}"
+                    )
+
+                lv = torch.mean(lv.reshape(N, -1), dim=1)
+                lv = lv.reshape(new_shape)
+
+            # Optionally, clip log-var to a lower bound
+            if self.logvar_lowerbound is not None:
+                lv = torch.clip(lv, min=self.logvar_lowerbound)
+        else:
+            mean = x
+            lv = None
+        return mean, lv
+
+    def distr_params(self, x: torch.Tensor) -> Dict[str, torch.Tensor]:
+        """
+        Get parameters (mean, log-var) of the Gaussian distribution defined by the likelihood.
+
+        Parameters
+        ----------
+        x: torch.Tensor
+            The input tensor to the likelihood module, i.e., the output of the top-down pass.
+        """
+        mean, lv = self.get_mean_lv(x)
+        params = {
+            "mean": mean,
+            "logvar": lv,
+        }
+        return params
+
+    @staticmethod
+    def mean(params):
+        return params["mean"]
+
+    @staticmethod
+    def mode(params):
+        return params["mean"]
+
+    @staticmethod
+    def sample(params):
+        # p = Normal(params['mean'], (params['logvar'] / 2).exp())
+        # return p.rsample()
+        return params["mean"]
+
+    @staticmethod
+    def logvar(params):
+        return params["logvar"]
+
+    def log_likelihood(self, x, params):
+        if self.predict_logvar is not None:
+            logprob = log_normal(x, params["mean"], params["logvar"])
+        else:
+            logprob = -0.5 * (params["mean"] - x) ** 2
+        return logprob
+
+
+def log_normal(
+    x: torch.Tensor, mean: torch.Tensor, logvar: torch.Tensor
+) -> torch.Tensor:
+    """
+    Compute the log-probability at `x` of a Gaussian distribution
+    with parameters `(mean, exp(logvar))`.
+
+    NOTE: In the case of LVAE, the log-likeihood formula becomes:
+        \\mathbb{E}_{z_1\\sim{q_\\phi}}[\\log{p_\theta(x|z_1)}]=-\frac{1}{2}(\\mathbb{E}_{z_1\\sim{q_\\phi}}[\\log{2\\pi\\sigma_{p,0}^2(z_1)}] +\\mathbb{E}_{z_1\\sim{q_\\phi}}[\frac{(x-\\mu_{p,0}(z_1))^2}{\\sigma_{p,0}^2(z_1)}])
+
+    Parameters
+    ----------
+    x: torch.Tensor
+        The ground-truth tensor. Shape is (batch, channels, dim1, dim2).
+    mean: torch.Tensor
+        The inferred mean of distribution. Shape is (batch, channels, dim1, dim2).
+    logvar: torch.Tensor
+        The inferred log-variance of distribution. Shape has to be either scalar or broadcastable.
+    """
+    var = torch.exp(logvar)
+    log_prob = -0.5 * (
+        ((x - mean) ** 2) / var + logvar + torch.tensor(2 * math.pi).log()
+    )
+    return log_prob
+
+
+class NoiseModelLikelihood(LikelihoodModule):
+
+    def __init__(
+        self,
+        ch_in: int,
+        color_channels: int,
+        data_mean: Union[Dict[str, torch.Tensor], torch.Tensor],
+        data_std: Union[Dict[str, torch.Tensor], torch.Tensor],
+        noiseModel: nn.Module,
+    ):
+        super().__init__()
+        self.parameter_net = (
+            nn.Identity()
+        )  # nn.Conv2d(ch_in, color_channels, kernel_size=3, padding=1)
+        self.data_mean = data_mean
+        self.data_std = data_std
+        self.noiseModel = noiseModel
+
+    def set_params_to_same_device_as(self, correct_device_tensor):
+        if isinstance(self.data_mean, torch.Tensor):
+            if self.data_mean.device != correct_device_tensor.device:
+                self.data_mean = self.data_mean.to(correct_device_tensor.device)
+                self.data_std = self.data_std.to(correct_device_tensor.device)
+        elif isinstance(self.data_mean, dict):
+            for key in self.data_mean.keys():
+                self.data_mean[key] = self.data_mean[key].to(
+                    correct_device_tensor.device
+                )
+                self.data_std[key] = self.data_std[key].to(correct_device_tensor.device)
+
+    def get_mean_lv(self, x):
+        return self.parameter_net(x), None
+
+    def distr_params(self, x):
+        mean, lv = self.get_mean_lv(x)
+        # mean, lv = x.chunk(2, dim=1)
+
+        params = {
+            "mean": mean,
+            "logvar": lv,
+        }
+        return params
+
+    @staticmethod
+    def mean(params):
+        return params["mean"]
+
+    @staticmethod
+    def mode(params):
+        return params["mean"]
+
+    @staticmethod
+    def sample(params):
+        # p = Normal(params['mean'], (params['logvar'] / 2).exp())
+        # return p.rsample()
+        return params["mean"]
+
+    def log_likelihood(self, x: torch.Tensor, params: Dict[str, torch.Tensor]):
+        """
+        Compute the log-likelihood given the parameters `params` obtained from the reconstruction tensor and the target tensor `x`.
+        """
+        predicted_s_denormalized = (
+            params["mean"] * self.data_std["target"] + self.data_mean["target"]
+        )
+        x_denormalized = x * self.data_std["target"] + self.data_mean["target"]
+        # predicted_s_cloned = predicted_s_denormalized
+        # predicted_s_reduced = predicted_s_cloned.permute(1, 0, 2, 3)
+
+        # x_cloned = x_denormalized
+        # x_cloned = x_cloned.permute(1, 0, 2, 3)
+        # x_reduced = x_cloned[0, ...]
+        # import pdb;pdb.set_trace()
+        likelihoods = self.noiseModel.likelihood(
+            x_denormalized, predicted_s_denormalized
+        )
+        # likelihoods = self.noiseModel.likelihood(x, params['mean'])
+        logprob = torch.log(likelihoods)
+        return logprob