AOT-biomaps 2.9.186__py3-none-any.whl → 2.9.294__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
@@ -21,7 +21,6 @@ class Recon(ABC):
         self.CRC = None
 
         self.isGPU = isGPU
-        self.isMultiGPU = isMultiGPU
         self.isMultiCPU = isMultiCPU
 
         if str(type(self.experiment)) != str(Tomography):
@@ -31,7 +30,7 @@ class Recon(ABC):
     def run(self,withTumor = True):
         pass
 
-    def save(self, withTumor=True, overwrite=False, date=None):
+    def save(self, withTumor=True, overwrite=False, date=None, show_logs=True):
         """
         Save the reconstruction results (reconPhantom is with tumor, reconLaser is without tumor) and indices of the saved recon results, in numpy format.
 
@@ -62,7 +61,8 @@ class Recon(ABC):
             filepathIndices = os.path.join(filepath, "indices.npy")
             np.save(filepathIndices, np.array(self.indices))
 
-        print(f"Reconstruction results saved to {os.path.dirname(filepath)}")
+        if show_logs:
+            print(f"Reconstruction results saved to {os.path.dirname(filepath)}")
 
     @abstractmethod
     def checkExistingFile(self, date = None):
@@ -165,10 +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.")
@@ -176,9 +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,
@@ -190,29 +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.")
@@ -220,9 +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),
@@ -232,36 +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__ = '2.9.186'
+__version__ = '2.9.294'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -135,74 +138,6 @@ def initialize(process=None):
 
 
 
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{aot_biomaps-2.9.186.dist-info → aot_biomaps-2.9.294.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.186
+Version: 2.9.294
 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-2.9.294.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=86X2xRJNI72niePVEmyZMqO0Y4vQeag7ZSHPM3kc4Pk,4250
+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=Li4HdWpr65ONf82FqFAjZ8w3ob9UuJucDWGAAvBF77Q,83680
+AOT_biomaps/AOT_Recon/AlgebraicRecon.py,sha256=CGBXZyYEZ3TOTFOKSt-h7NGuFbuI9PNr3YTWTbSLxDo,46832
+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=JbFhxiyUoSTnlJgHbOWIfUUwhwfZoi39RJMnfkagegY,16504
+AOT_biomaps/AOT_Recon/ReconEnums.py,sha256=KAf55RqHAr2ilt6pxFrUBGQOn-7HA8NP6TyL-1FNiXo,19714
+AOT_biomaps/AOT_Recon/ReconTools.py,sha256=A4IQV7IETu9MgYr7hjLNPTImzjf8CEU4cZ2e0EgJNWA,19878
+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=bCu1rKzFXPbYQ7jV3L3E_jVQpb6LIEC5MIlN1-mCNdY,22814
+AOT_biomaps/AOT_Recon/AOT_Optimizers/MAPEM.py,sha256=vQLCB0L4FSXJKn2_6kdIdWrI6WZ82KuqUh7CSqBGVuo,25766
+AOT_biomaps/AOT_Recon/AOT_Optimizers/MLEM.py,sha256=v5wITKacemu_hY391-cZDSpw4R95XqyLGivQWa-gOOc,21254
+AOT_biomaps/AOT_Recon/AOT_Optimizers/PDHG.py,sha256=oSojwug5mcZedKOWAV7YPMlCp0Qy_Aed0fjHRuyZWpo,28622
+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
+AOT_biomaps/AOT_Recon/AOT_SparseSMatrix/SparseSMatrix_CSR.py,sha256=RACc2P5oxmp0uPLAGnNj9mEtAxa_OlepNgCawKij3jI,12062
+AOT_biomaps/AOT_Recon/AOT_SparseSMatrix/SparseSMatrix_SELL.py,sha256=WTqHBeglUxRx-jy6CcoETgqYSSHYTwi2zR5NrJcPXGU,14449
+AOT_biomaps/AOT_Recon/AOT_SparseSMatrix/__init__.py,sha256=8nou-hqjQjuCTLhoL5qv4EM_lMPFviAZAZKSPhi84jE,67
+aot_biomaps-2.9.294.dist-info/METADATA,sha256=8c8tnkhnARdI6acSPSrB1FQloxgjuoNHKslkkgIq7xM,700
+aot_biomaps-2.9.294.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.294.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.294.dist-info/RECORD,,

aot_biomaps-2.9.186.dist-info/RECORD

@@ -1,43 +0,0 @@
-AOT_biomaps/Config.py,sha256=ghEOP1n8aO1pR-su13wMeAZAxZRfry5hH67NbtZ8SqI,3614
-AOT_biomaps/Settings.py,sha256=v8fPhnvvcfBJP29m1RLOTEr3jndGLGwbUiORXmsj2Bo,2853
-AOT_biomaps/__init__.py,sha256=Do2yZDpPCTLSkc3c8N_PXUsI-93MG7hfYvmhEmutaos,4242
-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=LlHBxGYmTsM1gQVaJXlUxIOsqg6zTIPBAZK46v3UUiE,18205
-AOT_biomaps/AOT_Acoustic/__init__.py,sha256=t9M2rRqa_L9pk7W2FeELTkHEMuP4DBr4gBRldMqsQbg,491
-AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=YZK5KnG60CyHlQaxYg-J4tGVY3SzJPB4t8uvNwU1HMI,43934
-AOT_biomaps/AOT_Experiment/Focus.py,sha256=B2nBawmv-NG2AWJx9zgQ8GlN6aFB9FwTSqX-M-phKXg,3193
-AOT_biomaps/AOT_Experiment/Tomography.py,sha256=H3DZKSzoGZlV9gEpRyCgIW7KPn-qZn3V2RTmf6DUrmE,20901
-AOT_biomaps/AOT_Experiment/__init__.py,sha256=H9zMLeBLA6uhbaHohAa-2u5mDDxqJi8oE5c6tShdQp8,308
-AOT_biomaps/AOT_Experiment/_mainExperiment.py,sha256=SbDmSNQoNS5G0-QwpV94KeV6XtdN5xzfFCnQPQWrH1Y,21891
-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=sMuH3Sg5OOzcVUoOHtaeyrq3BNK5lNcuS_WkqcDppME,38696
-AOT_biomaps/AOT_Recon/AnalyticRecon.py,sha256=vjeTUnaZrtnLHnx6goseeJsd165KbSugQYwUXJFXapU,7596
-AOT_biomaps/AOT_Recon/BayesianRecon.py,sha256=iAaAn9nwkvJ3Ilip_y2ywDKShpcbWzHATznmF84mNrQ,16844
-AOT_biomaps/AOT_Recon/DeepLearningRecon.py,sha256=RfVcEsi4GeGqJn0_SPxwQPQx6IQjin79WKh2UarMRLI,1383
-AOT_biomaps/AOT_Recon/PrimalDualRecon.py,sha256=iJPXUjxvvrIJVp6bo-W87T8ZXJneRmejt-SEjKQPPC0,9451
-AOT_biomaps/AOT_Recon/ReconEnums.py,sha256=oyT9qIfEpE_ChPQihM8-6b0UOtNmuE4weUpO8lJCB38,18641
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