AOT-biomaps 2.9.217__py3-none-any.whl → 2.9.219__py3-none-any.whl

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/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/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/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/__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.dist-info → aot_biomaps-2.9.219.dist-info}/METADATA

@@ -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.dist-info → aot_biomaps-2.9.219.dist-info}/RECORD

@@ -1,6 +1,6 @@
 AOT_biomaps/Config.py,sha256=ghEOP1n8aO1pR-su13wMeAZAxZRfry5hH67NbtZ8SqI,3614
 AOT_biomaps/Settings.py,sha256=v8fPhnvvcfBJP29m1RLOTEr3jndGLGwbUiORXmsj2Bo,2853
-AOT_biomaps/__init__.py,sha256=a5-mladvHgmA_M1WKbypLCFGpl5fYpD17MwJ4SLWkv4,4304
+AOT_biomaps/__init__.py,sha256=38jdZ4Xsj9DQtz91An6hfnZq6apgWu5JkmlaeQ4el30,4308
 AOT_biomaps/AOT_Acoustic/AcousticEnums.py,sha256=s5kXa6jKzbS4btwbubrVcynLOr0yg5tth5vL_FGfbMk,1802
 AOT_biomaps/AOT_Acoustic/AcousticTools.py,sha256=al7xXKMY5e-qQQ7nrQVPVAmqYiB320OluNlY6ti8iKc,7539
 AOT_biomaps/AOT_Acoustic/FocusedWave.py,sha256=3kGKKDx_3Msy5COYqIwzROPORGWvNjw8UsDanBfkMXE,11037
@@ -12,17 +12,17 @@ AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=RdmhRF1i0KAlpsP7_wnZ7F4J27br3eU
 AOT_biomaps/AOT_Experiment/Focus.py,sha256=B2nBawmv-NG2AWJx9zgQ8GlN6aFB9FwTSqX-M-phKXg,3193
 AOT_biomaps/AOT_Experiment/Tomography.py,sha256=LoQ304X9pUwpGn_BqNx1JijRFBFtI5Vz2R7bFIKyYKM,20954
 AOT_biomaps/AOT_Experiment/__init__.py,sha256=H9zMLeBLA6uhbaHohAa-2u5mDDxqJi8oE5c6tShdQp8,308
-AOT_biomaps/AOT_Experiment/_mainExperiment.py,sha256=Jv25qvTyh4FU1POC1PIyodvLCi-wfRCeiLoR3RfpklI,24886
+AOT_biomaps/AOT_Experiment/_mainExperiment.py,sha256=1iB1gqWuPFE_jPUPQI9bb380qPmMP1FLE3SSLMlB5xw,24678
 AOT_biomaps/AOT_Optic/Absorber.py,sha256=jEodzRy7gkEH-wbazVasRQiri0dU16BfapmR-qnTSvM,867
 AOT_biomaps/AOT_Optic/Laser.py,sha256=uzQwxswjU0kZWix3CmZLoWmhsBa3VhN27STprNv-xB8,2986
 AOT_biomaps/AOT_Optic/OpticEnums.py,sha256=b349_JyjHqQohmjK4Wke-A_HLGaqb3_BKbyUqFC4jxY,499
 AOT_biomaps/AOT_Optic/__init__.py,sha256=HSUVhfz0NzwHHZZ9KP9Xyfu33IgP_rYJX86J-gEROlo,321
 AOT_biomaps/AOT_Optic/_mainOptic.py,sha256=Wk63CcgWbU-ygMfjNK80islaUbGGJpTXgZY3_C2KQNY,8179
-AOT_biomaps/AOT_Recon/AlgebraicRecon.py,sha256=kebjUSqbyMGIZ-X57GV3zgkUunh2r41RxIbHaKY71w8,41412
+AOT_biomaps/AOT_Recon/AlgebraicRecon.py,sha256=g1JEwsi2BFljptPNzNhe0qKiua2DVYNYVUb6zMPrsWU,42833
 AOT_biomaps/AOT_Recon/AnalyticRecon.py,sha256=vjeTUnaZrtnLHnx6goseeJsd165KbSugQYwUXJFXapU,7596
 AOT_biomaps/AOT_Recon/BayesianRecon.py,sha256=WeE_512cBVOB__72132Ifvgb0E40gkjmQTXnwY_cZtk,16357
 AOT_biomaps/AOT_Recon/DeepLearningRecon.py,sha256=RfVcEsi4GeGqJn0_SPxwQPQx6IQjin79WKh2UarMRLI,1383
-AOT_biomaps/AOT_Recon/PrimalDualRecon.py,sha256=RM7yssmQkrNggU_RHZmgXp36ecu0nbLCTSh_G24ii8E,10090
+AOT_biomaps/AOT_Recon/PrimalDualRecon.py,sha256=RiQBHZrZ3CICb4GxwBJVIdNrKfkZz7o9RJLNYnl-XlA,9945
 AOT_biomaps/AOT_Recon/ReconEnums.py,sha256=oyT9qIfEpE_ChPQihM8-6b0UOtNmuE4weUpO8lJCB38,18641
 AOT_biomaps/AOT_Recon/ReconTools.py,sha256=zPGwoDHX5H7v78onHAlFwZ8OdjZVsX6PAJFrTiikqEc,10608
 AOT_biomaps/AOT_Recon/__init__.py,sha256=LDbNpsjS8_TJrXMKzkpzSAj5trVuCW57AWQaJBrzd0I,244
@@ -35,9 +35,9 @@ AOT_biomaps/AOT_Recon/AOT_Optimizers/PDHG.py,sha256=5w4klYKAct9_gnlyocIiJfDrQUdz
 AOT_biomaps/AOT_Recon/AOT_Optimizers/__init__.py,sha256=tNGVulINaqQZzcs5cvCMAT5ypGdoFWRnxtl9y7ePECk,106
 AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/Huber.py,sha256=dRd1t5OBag_gVmfji3L0QrA1GJ_702LcCkLH32Bot0M,3285
 AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/Quadratic.py,sha256=wTbzcXxMdEl9ReEXrL43DOJQecokBwJYU_s2kQUASZY,2545
-AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/RelativeDifferences.py,sha256=dgB3Vt40S5D1VerHr-h-YnzB5xNCt6amE19-C0zyIpU,2253
+AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/RelativeDifferences.py,sha256=ZlWaKsNPCMfy4fWxYFT2pSoKMbysQkJH4N1WbbWncq4,2493
 AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/__init__.py,sha256=RwrJdLOFbAFBFnRxo5xdlOyeZgtQRDaRWDN9-uCGUiY,84
-aot_biomaps-2.9.217.dist-info/METADATA,sha256=brSxYFUSU9Q3wZC2LleSVDbMvvYk5pjzdAdZQMptPzE,663
-aot_biomaps-2.9.217.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aot_biomaps-2.9.217.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
-aot_biomaps-2.9.217.dist-info/RECORD,,
+aot_biomaps-2.9.219.dist-info/METADATA,sha256=l0YeqS4U6dqjUzoYiOWl0r-gjEed92_LwnWGDajLEtA,663
+aot_biomaps-2.9.219.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.219.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.219.dist-info/RECORD,,