AOT-biomaps 2.9.217__tar.gz → 2.9.219__tar.gz

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/AOT_biomaps/AOT_Experiment/_mainExperiment.py

@@ -301,11 +301,6 @@ class Experiment(ABC):
             n_acquisitions_per_event = int([line.split(":")[1].strip() for line in cdh_content if "Number of acquisitions per event" in line][0])
             num_elements = int([line.split(":")[1].strip() for line in cdh_content if "Number of US transducers" in line][0])
 
-            print(f"Nombre de scans : {n_scans}")
-            print(f"Nombre d'acquisitions par événement : {n_acquisitions_per_event}")
-            print(f"Nombre d'éléments US : {num_elements}")
-
-
             # Initialisation des structures
             AO_signal = np.zeros((n_acquisitions_per_event, n_scans), dtype=np.float32)
             active_lists = []

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/RelativeDifferences.py

@@ -9,26 +9,24 @@ def _Omega_RELATIVE_DIFFERENCE_CPU(theta_flat, index, values, gamma):
     theta_k = theta_flat[k_idx]
     diff = theta_k - theta_j
     abs_diff = np.abs(diff)
-
     denom = theta_k + theta_j + gamma * abs_diff + 1e-8
     num = diff ** 2
-
+    psi_pair = num / denom
+    psi_pair = values * psi_pair
     # First derivative ∂U/∂θ_j
     dpsi = (2 * diff * denom - num * (1 + gamma * np.sign(diff))) / (denom ** 2)
     grad_pair = values * (-dpsi)  # Note the negative sign: U contains ψ(θ_k, θ_j), seeking ∂/∂θ_j
-
     # Second derivative ∂²U/∂θ_j² (numerically stable, approximate treatment)
     d2psi = (2 * denom ** 2 - 4 * diff * denom * (1 + gamma * np.sign(diff))
                 + 2 * num * (1 + gamma * np.sign(diff)) ** 2) / (denom ** 3 + 1e-8)
     hess_pair = values * d2psi
-
     grad_U = np.zeros_like(theta_flat)
     hess_U = np.zeros_like(theta_flat)
-
     np.add.at(grad_U, j_idx, grad_pair)
     np.add.at(hess_U, j_idx, hess_pair)
-
-    return grad_U, hess_U
+    # Compute U_value
+    U_value = 0.5 * np.sum(psi_pair)
+    return grad_U, hess_U, U_value
 
 def _Omega_RELATIVE_DIFFERENCE_GPU(theta_flat, index, values, device, gamma):
     j_idx, k_idx = index
@@ -38,26 +36,24 @@ def _Omega_RELATIVE_DIFFERENCE_GPU(theta_flat, index, values, device, gamma):
     abs_diff = torch.abs(diff)
     denom = theta_k + theta_j + gamma * abs_diff + 1e-8
     num = diff ** 2
-
+    psi_pair = num / denom
+    psi_pair = values * psi_pair
     # Compute gradient contributions
     dpsi = (2 * diff * denom - num * (1 + gamma * torch.sign(diff))) / (denom ** 2)
     grad_pair = values * (-dpsi)
-
     # Compute Hessian contributions
     d2psi = (2 * denom ** 2 - 4 * diff * denom * (1 + gamma * torch.sign(diff))
              + 2 * num * (1 + gamma * torch.sign(diff)) ** 2) / (denom ** 3 + 1e-8)
     hess_pair = values * d2psi
-
     # Initialize gradient and Hessian on the correct device
     grad_U = torch.zeros_like(theta_flat, device=device)
     hess_U = torch.zeros_like(theta_flat, device=device)
-
     # Accumulate gradient contributions
     grad_U.index_add_(0, j_idx, grad_pair)
     grad_U.index_add_(0, k_idx, -grad_pair)
-
     # Accumulate Hessian contributions
     hess_U.index_add_(0, j_idx, hess_pair)
     hess_U.index_add_(0, k_idx, hess_pair)
-
-    return grad_U, hess_U
+    # Compute U_value
+    U_value = 0.5 * psi_pair.sum()
+    return grad_U, hess_U, U_value

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/AOT_biomaps/AOT_Recon/AlgebraicRecon.py

@@ -700,29 +700,46 @@ class AlgebraicRecon(Recon):
         if withTumor:
             if self.experiment.AOsignal_withTumor is None:
                 raise ValueError("AO signal with tumor is not available. Please generate AO signal with tumor the experiment first in the experiment object.")
-            else:
-                y = self.experiment.AOsignal_withTumor
         else:
             if self.experiment.AOsignal_withoutTumor is None:
                 raise ValueError("AO signal without tumor is not available. Please generate AO signal without tumor the experiment first in the experiment object.")
-            else:
-                y = self.experiment.AOsignal_withoutTumor
 
         if self.optimizer.value == OptimizerType.MLEM.value:
-            self.reconPhantom, self.indices = MLEM(SMatrix=self.SMatrix, 
-                                                    y=y,
-                                                    numIterations=self.numIterations,
-                                                    isSavingEachIteration=self.isSavingEachIteration,
-                                                    withTumor=withTumor,
-                                                    use_multi_gpu= self.isMultiGPU,
-                                                    use_numba= self.isMultiCPU,
-                                                    max_saves=self.maxSaves
-                                                    )
+            if withTumor:
+                self.reconPhantom, self.indices = MLEM(SMatrix=self.SMatrix, 
+                                                        y=self.experiment.AOsignal_withTumor,
+                                                        numIterations=self.numIterations,
+                                                        isSavingEachIteration=self.isSavingEachIteration,
+                                                        withTumor=withTumor,
+                                                        use_multi_gpu= self.isMultiGPU,
+                                                        use_numba= self.isMultiCPU,
+                                                        max_saves=self.maxSaves
+                                                        )
+            else:
+                self.reconLaser, self.indices = MLEM(SMatrix=self.SMatrix, 
+                                                        y=self.experiment.AOsignal_withoutTumor,
+                                                        numIterations=self.numIterations,
+                                                        isSavingEachIteration=self.isSavingEachIteration,
+                                                        withTumor=withTumor,
+                                                        use_multi_gpu= self.isMultiGPU,
+                                                        use_numba= self.isMultiCPU,
+                                                        max_saves=self.maxSaves
+                                                        )
         elif self.optimizer.value == OptimizerType.LS.value:
             if self.alpha is None:
                 raise ValueError("Alpha (regularization parameter) must be set for LS reconstruction.")
-            self.reconPhantom, self.indices = LS(SMatrix=self.SMatrix,
-                                                y=y, 
+            if withTumor:
+                self.reconPhantom, self.indices = LS(SMatrix=self.SMatrix,
+                                                y=self.experiment.AOsignal_withTumor, 
+                                                numIterations=self.numIterations, 
+                                                isSavingEachIteration=self.isSavingEachIteration, 
+                                                withTumor=withTumor,
+                                                alpha=self.alpha,
+                                                max_saves=self.maxSaves,
+                                                )
+            else:
+                self.reconLaser, self.indices = LS(SMatrix=self.SMatrix,
+                                                y=self.experiment.AOsignal_withoutTumor, 
                                                 numIterations=self.numIterations, 
                                                 isSavingEachIteration=self.isSavingEachIteration, 
                                                 withTumor=withTumor,

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/AOT_biomaps/AOT_Recon/PrimalDualRecon.py

@@ -148,12 +148,6 @@ class PrimalDualRecon(AlgebraicRecon):
 
 
     def _convexReconPython(self, withTumor):
-        if withTumor:
-            y=self.experiment.AOsignal_withTumor
-
-        else:
-            y=self.experiment.AOsignal_withoutTumor
-
         if self.optimizer == OptimizerType.CP_TV:
             if withTumor:
                 self.reconPhantom, self.indices = CP_TV(

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/AOT_biomaps/__init__.py

@@ -82,7 +82,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.217'
+__version__ = '2.9.219'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -251,6 +251,8 @@ def initialize(process=None):
 
 
 
+
+
 
 
 

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/AOT_biomaps.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.217
+Version: 2.9.219
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.217
+Version: 2.9.219
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.217 → aot_biomaps-2.9.219}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AOT_biomaps',
-    version='2.9.217',
+    version='2.9.219',
     packages=find_packages(),
     include_package_data=True,
     install_requires=[
@@ -226,6 +226,8 @@ setup(
 
 
 
+
+