AOT-biomaps 2.9.138__py3-none-any.whl → 2.9.279__py3-none-any.whl

AOT_biomaps/AOT_Recon/_mainRecon.py

@@ -10,7 +10,7 @@ from abc import ABC, abstractmethod
 
 
 class Recon(ABC):
-    def __init__(self, experiment, saveDir = None, isGPU = config.get_process() == 'gpu',  isMultiGPU =  True if config.numGPUs > 1 else False, isMultiCPU = True):
+    def __init__(self, experiment, saveDir = None, isGPU = config.get_process() == 'gpu', isMultiCPU = True):
         self.reconPhantom = None
         self.reconLaser = None
         self.experiment = experiment
@@ -18,9 +18,9 @@ class Recon(ABC):
         self.saveDir = saveDir
         self.MSE = None
         self.SSIM = None
+        self.CRC = None
 
         self.isGPU = isGPU
-        self.isMultiGPU = isMultiGPU
         self.isMultiCPU = isMultiCPU
 
         if str(type(self.experiment)) != str(Tomography):
@@ -30,38 +30,101 @@ class Recon(ABC):
     def run(self,withTumor = True):
         pass
 
-    def calculateCRC(self,iteration,ROI_mask = None):
+    def save(self, withTumor=True, overwrite=False, date=None, show_logs=True):
         """
-        Computes the Contrast Recovery Coefficient (CRC) for a given ROI.
+        Save the reconstruction results (reconPhantom is with tumor, reconLaser is without tumor) and indices of the saved recon results, in numpy format.
+
+        Args:
+            withTumor (bool): If True, saves reconPhantom. If False, saves reconLaser. Default is True.
+            overwrite (bool): If False, does not save if the file already exists. Default is False.
+
+        Warnings:
+            reconPhantom and reconLaser are lists of 2D numpy arrays, each array corresponding to one iteration.
         """
-        if self.reconType is ReconType.Analytic:
-            raise TypeError(f"Impossible to calculate CRC with analytical reconstruction")
-        elif self.reconType is None:
-            raise ValueError("Run reconstruction first")
+        isExisting, filepath = self.checkExistingFile(date=date)
+        if isExisting and not overwrite:
+            return
         
+        filename = 'reconPhantom.npy' if withTumor else 'reconLaser.npy'
+        filepathRecon = os.path.join(filepath, filename)
+
+        if withTumor:
+            if not self.reconPhantom or len(self.reconPhantom) == 0:
+                raise ValueError("Reconstructed phantom is empty. Run reconstruction first.")
+            np.save(filepathRecon, np.array(self.reconPhantom))
+        else:
+            if not self.reconLaser or len(self.reconLaser) == 0:
+                raise ValueError("Reconstructed laser is empty. Run reconstruction first.")
+            np.save(filepathRecon, np.array(self.reconLaser))
+
+        if self.indices is not None and len(self.indices) > 0:
+            filepathIndices = os.path.join(filepath, "indices.npy")
+            np.save(filepathIndices, np.array(self.indices))
+
+        if show_logs:
+            print(f"Reconstruction results saved to {os.path.dirname(filepath)}")
+
+    @abstractmethod
+    def checkExistingFile(self, date = None):
+        pass
+
+    def calculateCRC(self, use_ROI=True):
+        """
+        Computes the Contrast Recovery Coefficient (CRC) for all ROIs combined or globally.
+        For analytic reconstruction: returns a single CRC value.
+        For iterative reconstruction: returns a list of CRC values (one per iteration).
+        If iteration is specified, returns CRC for that specific iteration only.
+
+        :param iteration: Specific iteration index (optional). If None, computes for all iterations.
+        :param use_ROI: If True, computes CRC for all ROIs combined. If False, computes global CRC.
+        :return: CRC value or list of CRC values.
+        """
+        if self.reconType is None:
+            raise ValueError("Run reconstruction first")
+
         if self.reconLaser is None or self.reconLaser == []:
             raise ValueError("Reconstructed laser is empty. Run reconstruction first.")
-        if isinstance(self.Laser,list) and len(self.Laser) == 1:
-            raise ValueError("Reconstructed Image without tumor is a single frame. Run reconstruction with isSavingEachIteration=True to get a sequence of frames.")
         if self.reconPhantom is None or self.reconPhantom == []:
             raise ValueError("Reconstructed phantom is empty. Run reconstruction first.")
-        if isinstance(self.reconPhantom, list) and len(self.reconPhantom) == 1:
-            raise ValueError("Reconstructed Image with tumor is a single frame. Run reconstruction with isSavingEachIteration=True to get a sequence of frames.")
-        
+
+        # Handle empty reconstructions
         if self.reconLaser is None or self.reconLaser == []:
             print("Reconstructed laser is empty. Running reconstruction without tumor...")
-            self.run(withTumor = False, isSavingEachIteration=True)
-        if ROI_mask is not None:
-            recon_ratio = np.mean(self.reconPhantom[iteration][ROI_mask]) / np.mean(self.reconLaser[iteration][ROI_mask])
-            lambda_ratio = np.mean(self.experiment.OpticImage.phantom[ROI_mask]) / np.mean(self.experiment.OpticImage.laser[ROI_mask]) 
+            self.run(withTumor=False, isSavingEachIteration=True)
+
+        # Get the ROI mask(s) from the phantom if needed
+        if use_ROI:
+            self.experiment.OpticImage.find_ROI()
+            global_mask = np.logical_or.reduce(self.experiment.OpticImage.maskList)
+
+        # Analytic reconstruction case
+        if self.reconType is ReconType.Analytic:
+            if use_ROI:
+                recon_ratio = np.mean(self.reconPhantom[global_mask]) / np.mean(self.reconLaser[global_mask])
+                lambda_ratio = np.mean(self.experiment.OpticImage.phantom[global_mask]) / np.mean(self.experiment.OpticImage.laser.intensity[global_mask])
+            else:
+                recon_ratio = np.mean(self.reconPhantom) / np.mean(self.reconLaser)
+                lambda_ratio = np.mean(self.experiment.OpticImage.phantom) / np.mean(self.experiment.OpticImage.laser.intensity)
+
+            self.CRC =(recon_ratio - 1) / (lambda_ratio - 1)
+
+        # Iterative reconstruction case
         else:
-            recon_ratio = np.mean(self.reconPhantom[iteration]) / np.mean(self.reconLaser[iteration])
-            lambda_ratio = np.mean(self.experiment.OpticImage.phantom) / np.mean(self.experiment.OpticImage.laser)
-        
-        # Compute CRC
-        CRC = (recon_ratio - 1) / (lambda_ratio - 1)
-        return CRC
-    
+            iterations = range(len(self.reconPhantom))
+
+            crc_list = []
+            for it in iterations:
+                if use_ROI:
+                    recon_ratio = np.mean(self.reconPhantom[it][global_mask]) / np.mean(self.reconLaser[it][global_mask])
+                    lambda_ratio = np.mean(self.experiment.OpticImage.phantom[global_mask]) / np.mean(self.experiment.OpticImage.laser.intensity[global_mask])
+                else:
+                    recon_ratio = np.mean(self.reconPhantom[it]) / np.mean(self.reconLaser[it])
+                    lambda_ratio = np.mean(self.experiment.OpticImage.phantom) / np.mean(self.experiment.OpticImage.laser.intensity)
+
+                crc_list.append((recon_ratio - 1) / (lambda_ratio - 1))
+
+            self.CRC = crc_list
+
     def calculateMSE(self):
         """
         Calculate the Mean Squared Error (MSE) of the reconstruction.
@@ -76,7 +139,7 @@ class Recon(ABC):
         if self.reconType in (ReconType.Analytic, ReconType.DeepLearning):
             self.MSE = mse(self.experiment.OpticImage.phantom, self.reconPhantom)
 
-        elif self.reconType in (ReconType.Algebraic, ReconType.Bayesian):
+        elif self.reconType in (ReconType.Algebraic, ReconType.Bayesian, ReconType.Convex):
             self.MSE = []
             for theta in self.reconPhantom:
                 self.MSE.append(mse(self.experiment.OpticImage.phantom, theta))
@@ -102,10 +165,9 @@ class Recon(ABC):
                 data_range = theta.max() - theta.min()
                 ssim_value = ssim(self.experiment.OpticImage.phantom, theta, data_range=data_range)
                 self.SSIM.append(ssim_value)
- 
-    def show(self, withTumor=True, savePath=None):
-        fig, axs = plt.subplots(1, 2, figsize=(20, 10))
+    
 
+    def show(self, withTumor=True, savePath=None):
         if withTumor:
             if self.reconPhantom is None or self.reconPhantom == []:
                 raise ValueError("Reconstructed phantom with tumor is empty. Run reconstruction first.")
@@ -113,9 +175,31 @@ class Recon(ABC):
                 image = self.reconPhantom[-1]
             else:
                 image = self.reconPhantom
-            # Phantom original
+            if self.experiment.OpticImage is None:
+                fig, axs = plt.subplots(1, 1, figsize=(10, 10))
+            else:
+                fig, axs = plt.subplots(1, 2, figsize=(20, 10))
+                # Phantom original
+                im1 = axs[1].imshow(
+                    self.experiment.OpticImage.phantom,
+                    cmap='hot',
+                    vmin=0,
+                    vmax=1,
+                    extent=(
+                        self.experiment.params.general['Xrange'][0],
+                        self.experiment.params.general['Xrange'][1],
+                        self.experiment.params.general['Zrange'][1],
+                        self.experiment.params.general['Zrange'][0]
+                    ),
+                    aspect='equal'  
+                )
+                axs[1].set_title("Phantom with tumor")
+                axs[1].set_xlabel("x (mm)", fontsize=12)
+                axs[1].set_ylabel("z (mm)", fontsize=12)
+                axs[1].tick_params(axis='both', which='major', labelsize=8)
+            # Phantom reconstruit
             im0 = axs[0].imshow(
-                self.experiment.OpticImage.phantom,
+                image,
                 cmap='hot',
                 vmin=0,
                 vmax=1,
@@ -127,29 +211,11 @@ class Recon(ABC):
                 ),
                 aspect='equal'  
             )
-            axs[0].set_title("Phantom with tumor")
+            axs[0].set_title("Reconstructed phantom with tumor")
             axs[0].set_xlabel("x (mm)", fontsize=12)
             axs[0].set_ylabel("z (mm)", fontsize=12)
             axs[0].tick_params(axis='both', which='major', labelsize=8)
-            # Phantom reconstruit
-            im1 = axs[1].imshow(
-                image,
-                cmap='hot',
-                vmin=0,
-                vmax=1,
-                extent=(
-                    self.experiment.params.general['Xrange'][0],
-                    self.experiment.params.general['Xrange'][1],
-                    self.experiment.params.general['Zrange'][1],
-                    self.experiment.params.general['Zrange'][0]
-                ),
-                aspect='equal'  
-            )
-            axs[1].set_title("Reconstructed phantom with tumor")
-            axs[1].set_xlabel("x (mm)", fontsize=12)
-            axs[1].set_ylabel("z (mm)", fontsize=12)
-            axs[1].tick_params(axis='both', which='major', labelsize=8)
-            axs[1].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
+            axs[0].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
         else:
             if self.reconLaser is None or self.reconLaser == []:
                 raise ValueError("Reconstructed laser without tumor is empty. Run reconstruction first.")
@@ -157,9 +223,31 @@ class Recon(ABC):
                 image = self.reconLaser[-1]
             else:
                 image = self.reconLaser
-            # Laser original
+            if self.experiment.OpticImage is None:
+                fig, axs = plt.subplots(1, 1, figsize=(10, 10))
+            else:
+                fig, axs = plt.subplots(1, 2, figsize=(20, 10))
+                # Laser original
+                im1 = axs[1].imshow(
+                    self.experiment.OpticImage.laser.intensity,
+                    cmap='hot',
+                    vmin=0,
+                    vmax=np.max(self.experiment.OpticImage.laser.intensity),
+                    extent=(
+                        self.experiment.params.general['Xrange'][0],
+                        self.experiment.params.general['Xrange'][1],
+                        self.experiment.params.general['Zrange'][1],
+                        self.experiment.params.general['Zrange'][0]
+                    ),
+                    aspect='equal'  
+                )
+                axs[1].set_title("Laser without tumor")
+                axs[1].set_xlabel("x (mm)", fontsize=12)
+                axs[1].set_ylabel("z (mm)", fontsize=12)
+                axs[1].tick_params(axis='both', which='major', labelsize=8)
+            # Laser reconstruit
             im0 = axs[0].imshow(
-                self.experiment.OpticImage.laser.intensity,
+                image,
                 cmap='hot',
                 vmin=0,
                 vmax=np.max(self.experiment.OpticImage.laser.intensity),
@@ -169,36 +257,18 @@ class Recon(ABC):
                     self.experiment.params.general['Zrange'][1],
                     self.experiment.params.general['Zrange'][0]
                 ),
-                aspect='equal'  
+                aspect='equal'
             )
-            axs[0].set_title("Laser without tumor")
+            axs[0].set_title("Reconstructed laser without tumor")
             axs[0].set_xlabel("x (mm)", fontsize=12)
             axs[0].set_ylabel("z (mm)", fontsize=12)
             axs[0].tick_params(axis='both', which='major', labelsize=8)
-            # Laser reconstruit
-            im1 = axs[1].imshow(
-                image,
-                cmap='hot',
-                vmin=0,
-                vmax=np.max(self.experiment.OpticImage.laser.intensity),
-                extent=(
-                    self.experiment.params.general['Xrange'][0],
-                    self.experiment.params.general['Xrange'][1],
-                    self.experiment.params.general['Zrange'][1],
-                    self.experiment.params.general['Zrange'][0]
-                ),
-                aspect='equal'
-            )
-            axs[1].set_title("Reconstructed laser without tumor")
-            axs[1].set_xlabel("x (mm)", fontsize=12)
-            axs[1].set_ylabel("z (mm)", fontsize=12)
-            axs[1].tick_params(axis='both', which='major', labelsize=8)
-            axs[1].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
+            axs[0].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
 
         # Colorbar commune
         fig.subplots_adjust(bottom=0.2)
         cbar_ax = fig.add_axes([0.25, 0.08, 0.5, 0.03])
-        cbar = fig.colorbar(im1, cax=cbar_ax, orientation='horizontal')
+        cbar = fig.colorbar(im0, cax=cbar_ax, orientation='horizontal')
         cbar.set_label('Normalized Intensity', fontsize=12)
         cbar.ax.tick_params(labelsize=8)
 

AOT_biomaps/__init__.py

@@ -74,6 +74,9 @@ from .AOT_Recon.AOT_Optimizers.DEPIERRO import *
 from .AOT_Recon.AOT_Optimizers.MAPEM import *
 from .AOT_Recon.AOT_Optimizers.MLEM import *
 from .AOT_Recon.AOT_Optimizers.PDHG import *
+# SPARSE S-MATRIX
+from .AOT_Recon.AOT_SparseSMatrix.SparseSMatrix_CSR import *
+from .AOT_Recon.AOT_SparseSMatrix.SparseSMatrix_SELL import *
 # POTENTIAL FUNCTIONS
 from .AOT_Recon.AOT_PotentialFunctions.Huber import *
 from .AOT_Recon.AOT_PotentialFunctions.Quadratic import *
@@ -82,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.138'
+__version__ = '2.9.279'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -132,41 +135,6 @@ def initialize(process=None):
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
 
 
 

{aot_biomaps-2.9.138.dist-info → aot_biomaps-2.9.279.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.138
+Version: 2.9.279
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos
@@ -15,6 +15,7 @@ Requires-Dist: nvidia-ml-py3==7.352.0
 Requires-Dist: numpy==1.26.4
 Requires-Dist: torch==2.7.0
 Requires-Dist: scipy==1.13.1
+Requires-Dist: cupy-cuda12x==13.6.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: home-page

aot_biomaps-2.9.279.dist-info/RECORD

@@ -0,0 +1,47 @@
+AOT_biomaps/Config.py,sha256=ghEOP1n8aO1pR-su13wMeAZAxZRfry5hH67NbtZ8SqI,3614
+AOT_biomaps/Settings.py,sha256=v8fPhnvvcfBJP29m1RLOTEr3jndGLGwbUiORXmsj2Bo,2853
+AOT_biomaps/__init__.py,sha256=RfEi98jeLI6dtUnjRISgt1myI41kJwTXMkpSpf2VkH4,4220
+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
+AOT_biomaps/AOT_Acoustic/IrregularWave.py,sha256=yZhtxkR6zlciRcEpdTR0BAhvgQl40XHKFaF8f4VXarE,3035
+AOT_biomaps/AOT_Acoustic/PlaneWave.py,sha256=xza-rj5AUWDecLkGDxRcULrwZVWeBvGnEP2d51TyR04,1447
+AOT_biomaps/AOT_Acoustic/StructuredWave.py,sha256=jTLVlOhYLWJb5MxZPxhq3OFVlz2McoyMPBmfLvnekDU,18209
+AOT_biomaps/AOT_Acoustic/__init__.py,sha256=t9M2rRqa_L9pk7W2FeELTkHEMuP4DBr4gBRldMqsQbg,491
+AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=RdmhRF1i0KAlpsP7_wnZ7F4J27br3eUc4XR91Qq7C64,44158
+AOT_biomaps/AOT_Experiment/Focus.py,sha256=B2nBawmv-NG2AWJx9zgQ8GlN6aFB9FwTSqX-M-phKXg,3193
+AOT_biomaps/AOT_Experiment/Tomography.py,sha256=Ri83b4GMrxJO60qWsK9JInS9a7HU2Q8uqpjD3Xkl9OY,24488
+AOT_biomaps/AOT_Experiment/__init__.py,sha256=H9zMLeBLA6uhbaHohAa-2u5mDDxqJi8oE5c6tShdQp8,308
+AOT_biomaps/AOT_Experiment/_mainExperiment.py,sha256=zSfuNrsz7nhiKrGIdK6CAXjlI2T6qYC5-JXHFgPNzhc,24674
+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/AOT_biomaps_kernels.cubin,sha256=iIp_WxETL4_BCJ0zErD4xm_Kpeey3ymjafdg9kmLd-s,82528
+AOT_biomaps/AOT_Recon/AlgebraicRecon.py,sha256=ZroHGhk6Yod4_6yNSlcB5Ew5XLAGO8Bc0dW_xCVJaig,47184
+AOT_biomaps/AOT_Recon/AnalyticRecon.py,sha256=RaQ5AJ1HUmSct0BgjZ0GWSJg7SALCn3Q0laqj1yyhAE,7123
+AOT_biomaps/AOT_Recon/BayesianRecon.py,sha256=RnnPa-tTcvirwiNPnCRZnSM4NWeEEltYET-piBbp34g,12671
+AOT_biomaps/AOT_Recon/DeepLearningRecon.py,sha256=RfVcEsi4GeGqJn0_SPxwQPQx6IQjin79WKh2UarMRLI,1383
+AOT_biomaps/AOT_Recon/PrimalDualRecon.py,sha256=-7dqUxKXbHt7yR1I1kGcu1TOXn05ik6QoDDsuM0QvNU,10310
+AOT_biomaps/AOT_Recon/ReconEnums.py,sha256=KAf55RqHAr2ilt6pxFrUBGQOn-7HA8NP6TyL-1FNiXo,19714
+AOT_biomaps/AOT_Recon/ReconTools.py,sha256=RQbtK6aR0fIfIQ4wSRPIro8LEvjFG4uVCYwYSepxp44,16302
+AOT_biomaps/AOT_Recon/__init__.py,sha256=xs_argJqXKFl76xP7-jiUc1ynOEEtY7XZ0gDxD5uVZc,246
+AOT_biomaps/AOT_Recon/_mainRecon.py,sha256=exoa2UBMfMHjemxAU9dW0mhEfsP6Oe1qjSfrTrgbIcY,13125
+AOT_biomaps/AOT_Recon/AOT_Optimizers/DEPIERRO.py,sha256=qA1n722GLQJH3V8HcLr5q_GxEwBS_NRlIT3E6JZk-Ag,9479
+AOT_biomaps/AOT_Recon/AOT_Optimizers/LS.py,sha256=SvUXNnavusUFuJSPZ-Au4BQZaV2z_aRyx6w5-TpRJ9E,22719
+AOT_biomaps/AOT_Recon/AOT_Optimizers/MAPEM.py,sha256=vQLCB0L4FSXJKn2_6kdIdWrI6WZ82KuqUh7CSqBGVuo,25766
+AOT_biomaps/AOT_Recon/AOT_Optimizers/MLEM.py,sha256=n_YYZ8NbubpTe5dn_6UjCBsW6Koa0OkF5VdKzseWQeU,21279
+AOT_biomaps/AOT_Recon/AOT_Optimizers/PDHG.py,sha256=5w4klYKAct9_gnlyocIiJfDrQUdz_VhXQVSpfjrjvNU,7927
+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=ZlWaKsNPCMfy4fWxYFT2pSoKMbysQkJH4N1WbbWncq4,2493
+AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/__init__.py,sha256=RwrJdLOFbAFBFnRxo5xdlOyeZgtQRDaRWDN9-uCGUiY,84
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