AOT-biomaps 2.9.376__py3-none-any.whl → 2.9.378__py3-none-any.whl

AOT_biomaps/AOT_Acoustic/StructuredWave.py

@@ -109,7 +109,8 @@ class StructuredWave(AcousticField):
         try:
             super().__init__(**kwargs)
             self.waveType = WaveType.StructuredWave
-            self.kgrid.setTime(int(self.kgrid.Nt*1.5),self.kgrid.dt) # Extend the time grid to allow for delays
+            if  self.params['Nt'] is None:
+                self.kgrid.setTime(int(self.kgrid.Nt*1.5),self.kgrid.dt) # Extend the time grid to allow for delays
             if space_0 is not None and space_1 is not None and move_head_0_2tail is not None and move_tail_1_2head is not None and angle_deg is not None:
                 self.pattern = self.PatternParams(space_0, space_1, move_head_0_2tail, move_tail_1_2head, self.params['num_elements'] // 4)
                 self.angle = angle_deg

AOT_biomaps/AOT_Acoustic/_mainAcoustic.py

@@ -123,7 +123,6 @@ class AcousticField(ABC):
                 else:
                     Nt = self.params['Nt']
                 self.kgrid.setTime(Nt,1/float(params.acoustic['f_AQ']))
-                print(f" NT kgrid : {self.kgrid.Nt} ")
                 self.params['f_AQ'] = int(float(params.acoustic['f_AQ']))
 
             self._generate_burst_signal()
@@ -146,7 +145,7 @@ class AcousticField(ABC):
             self.medium = None
 
         self.waveType = None
-        self.field = None   
+        self.field = None  
 
     def __str__(self):
         """
@@ -514,7 +513,7 @@ class AcousticField(ABC):
             dx = self.params['dx']
             air_margin = 20 
             if dx >= self.params['element_width']:
-                dx = self.params['element_width'] / 2
+                dx = self.params['element_width']/2
                 if self.params['width_phantom'] is not None:
                     pva_nx = int(np.round((self.params['width_phantom'])/dx))
                     Nx = pva_nx + 2 * air_margin
@@ -531,29 +530,46 @@ class AcousticField(ABC):
                 else:
                     Nx = int(round((self.params['Xrange'][1] - self.params['Xrange'][0]) / self.params['dx']))
                 if self.params['height_phantom'] is not None:
-                    Nz = int(np.round((self.params['height_phantom'])/self.params['dz']))
+                    Nz = int(np.round((self.params['height_phantom'])/self.params['dx']))
                 else:
-                    Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / self.params['dz']))
-           
+                    Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / self.params['dx']))
+            
+            Nx_final = int(round((self.params['Xrange'][1] - self.params['Xrange'][0]) / self.params['dx']))
+            Nz_final = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / self.params['dx']))
             # --- 2. Time and space factors ---
             factorT = int(np.ceil(self.params['f_AQ'] / self.params['f_saving']))
-            factorX = int(np.ceil(Nx / self.params['Nx']))
-            factorZ = int(np.ceil(Nz / self.params['Nz']))
+            factorX = int(np.ceil(self.params['dx'] / dx))
+            factorZ = factorX
 
             # --- 3. Grid and source initialization ---
             kgrid = kWaveGrid([Nx, Nz], [dx, dx])
-            kgrid.setTime(self.kgrid.Nt, 1 / self.params['f_AQ'])
-            
-            medium = kWaveMedium()
-            medium.sound_speed = np.full((Nx, Nz), 343.0)
-            medium.density = np.full((Nx, Nz), 1.2)
-            x_start, x_end = air_margin, air_margin + pva_nx
-            medium.sound_speed[x_start:x_end, :] = self.params['c0'] # 1540 m/s
-            medium.density[x_start:x_end, :] = self.params.get('density', 1000.0)
+
+            # --- CORRECTIF : Définition du Medium avec hétérogénéité ---
+            # Initialisation en float32 (essentiel pour GPU)
+            c_map = np.full((Nx, Nz), 343.0, dtype=np.float32)  # Air par défaut
+            rho_map = np.full((Nx, Nz), 1.2, dtype=np.float32)
+
+            # Insertion du bloc de PVA
+            x_start = air_margin
+            x_end = air_margin + pva_nx
+            c_map[x_start:x_end, :] = self.params['c0']
+            rho_map[x_start:x_end, :] = self.params.get('density', 1000.0)
+
+            medium = kWaveMedium(sound_speed=c_map, density=rho_map)
+
+            # --- CORRECTIF : Recalcul du pas de temps (CFL) ---
+            # k-Wave a besoin d'un dt basé sur la vitesse MAXIMALE (1540 m/s)
+            c_mean = np.mean(c_map[:, 0]) # mean speed at z=0
+            c_max = np.max(c_map)
+            cfl = 0.3 # Valeur de sécurité
+            dt = cfl * dx / c_max
+            kgrid.setTime(self.kgrid.Nt, dt)
 
 
             source = kSource()
             source.p_mask = np.zeros((Nx, Nz))
+            # Appel à la méthode spécialisée
+            self._SetUpSource(self,source, Nx, dt, dx, c_mean,factorT)  # factorT=1 pour simplifier
 
             # --- 4. Sensor setup ---
             sensor = kSensor()
@@ -565,11 +581,14 @@ class AcousticField(ABC):
             # --- 7. Simulation options ---
             simulation_options = SimulationOptions(
             pml_inside=False, # PML ajoutée autour de la grille Air+PVA
-            pml_size=[pml_size, pml_size],
+            pml_size=[1, pml_size],
             use_sg=False,
             save_to_disk=True,
             input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
-            output_filename=os.path.join(gettempdir(), "KwaveOUT.h5")
+            output_filename=os.path.join(gettempdir(), "KwaveOUT.h5"),
+            smooth_c0 = True,
+            smooth_rho0 = True,
+            smooth_p0 = True
             )
 
             execution_options = SimulationExecutionOptions(
@@ -578,9 +597,6 @@ class AcousticField(ABC):
                 show_sim_log=show_log
             )
 
-            # --- 7. Call specialized function to set up source.p_mask and source.p ---
-            self._SetUpSource(source, Nx, dx, factorT)
-
             # --- 8. Run simulation ---
             sensor_data = kspaceFirstOrder2D(
                 kgrid=kgrid,
@@ -593,16 +609,18 @@ class AcousticField(ABC):
 
             # --- 9. Post-process results ---
             data = sensor_data['p'].reshape(kgrid.Nt, Nz, Nx)
-
             if factorT != 1 or factorX != 1 or factorZ != 1:
-                return reshape_field(data, [factorT, factorX, factorZ])
+                data = reshape_field(data, [factorT, factorX, factorZ])
+                xStart = (Nx//2)//factorX - (Nx_final//2)
+                return data[:, :Nz_final, xStart:xStart+Nx_final]
             else:
-                return data
+                return data[:, :Nz_final, xStart:xStart+Nx_final]
             
         except Exception as e:
             print(f"Error generating 2D acoustic field: {e}")
             return None
     
+    
     def _generate_acoustic_field_KWAVE_3D(self, isGPU=True, show_log=True):
         """
         Generate a 3D acoustic field using k-Wave.

AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.376'
+__version__ = '2.9.378'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -237,6 +237,8 @@ def initialize(process=None):
 
 
 
+
+
 
 
 

{aot_biomaps-2.9.376.dist-info → aot_biomaps-2.9.378.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.376
+Version: 2.9.378
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.376.dist-info → aot_biomaps-2.9.378.dist-info}/RECORD

@@ -1,14 +1,14 @@
 AOT_biomaps/Config.py,sha256=ghEOP1n8aO1pR-su13wMeAZAxZRfry5hH67NbtZ8SqI,3614
 AOT_biomaps/Settings.py,sha256=v8fPhnvvcfBJP29m1RLOTEr3jndGLGwbUiORXmsj2Bo,2853
-AOT_biomaps/__init__.py,sha256=_ENzaj3wC6AiL-lT89XklXCQJiP6Lar7-ZLadcQW6_E,4414
+AOT_biomaps/__init__.py,sha256=S_KfEFZ_eCoqy0gfMeQgnrb9rnTBdwdU8Q_avyhpNLI,4418
 AOT_biomaps/AOT_Acoustic/AcousticEnums.py,sha256=s5kXa6jKzbS4btwbubrVcynLOr0yg5tth5vL_FGfbMk,1802
 AOT_biomaps/AOT_Acoustic/AcousticTools.py,sha256=7kuWIIGyzZPQrzRI0zVvdwNUp7qKUE67yCYOMzSb0Ug,8283
 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=DRTjD-zrmX12FHrvwOeEo-Rk1fHYm9gfCcebz4WhtXc,18930
+AOT_biomaps/AOT_Acoustic/StructuredWave.py,sha256=CpmvyHmwVvYuGhC1bL6VDQERC70gDQNgIdKNZI22Zpw,18978
 AOT_biomaps/AOT_Acoustic/__init__.py,sha256=t9M2rRqa_L9pk7W2FeELTkHEMuP4DBr4gBRldMqsQbg,491
-AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=TKaMqVcpa4pUvcxbQstgKVoWqrXUCaWQDY576PjxvoA,46771
+AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=tGsCSJXrGs25M0IWf6qRKniQ1KAgU3fAHi-n48prDFw,47696
 AOT_biomaps/AOT_Experiment/ExperimentTools.py,sha256=aFvJw6J_jfFVTDFnG7J3a61SHEgORdZKZS0UI82VMaY,2637
 AOT_biomaps/AOT_Experiment/Focus.py,sha256=B2nBawmv-NG2AWJx9zgQ8GlN6aFB9FwTSqX-M-phKXg,3193
 AOT_biomaps/AOT_Experiment/Tomography.py,sha256=9mJDwV9WVphoX8drL7MgN3WhS6fjYwS6HWQD3x1CrVs,37625
@@ -42,7 +42,7 @@ AOT_biomaps/AOT_Recon/AOT_PotentialFunctions/__init__.py,sha256=RwrJdLOFbAFBFnRx
 AOT_biomaps/AOT_Recon/AOT_SparseSMatrix/SparseSMatrix_CSR.py,sha256=RACc2P5oxmp0uPLAGnNj9mEtAxa_OlepNgCawKij3jI,12062
 AOT_biomaps/AOT_Recon/AOT_SparseSMatrix/SparseSMatrix_SELL.py,sha256=ti3dZQsb_Uu62C7Bn65Z-yf-R5NKCFsmnBT5GlLd_HY,15138
 AOT_biomaps/AOT_Recon/AOT_SparseSMatrix/__init__.py,sha256=8nou-hqjQjuCTLhoL5qv4EM_lMPFviAZAZKSPhi84jE,67
-aot_biomaps-2.9.376.dist-info/METADATA,sha256=OE--N73pyqCMv7YjXsBORjCnJStdj7VDcc_Jso2kQvA,700
-aot_biomaps-2.9.376.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aot_biomaps-2.9.376.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
-aot_biomaps-2.9.376.dist-info/RECORD,,
+aot_biomaps-2.9.378.dist-info/METADATA,sha256=y50KhGuRlcPegJxI1-vSusy6byZECPWGUDpsACtCNDI,700
+aot_biomaps-2.9.378.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.378.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.378.dist-info/RECORD,,