AOT-biomaps 2.9.373__py3-none-any.whl → 2.9.374__py3-none-any.whl

AOT_biomaps/AOT_Acoustic/_mainAcoustic.py

@@ -106,7 +106,7 @@ class AcousticField(ABC):
                 'Nx': int(np.round((params.general['Xrange'][1] - params.general['Xrange'][0])/params.general['dx'])),
                 'Ny': int(np.round((params.general['Yrange'][1] - params.general['Yrange'][0])/params.general['dy']))  if params.general['Yrange'] is not None else 1,
                 'Nz': int(np.round((params.general['Zrange'][1] - params.general['Zrange'][0])/params.general['dz'])),
-                'Nt': params.general['Nt'] if 'Nt' in params.general else None,
+                'Nt': (params.general['Nt'])*int(float(params.acoustic['f_AQ']))/int(float(params.acoustic['f_saving'])) if 'Nt' in params.general else None,
                 'probeWidth': params.acoustic['num_elements'] * params.acoustic['element_width'],
                 'IsAbsorbingMedium': params.acoustic['isAbsorbingMedium'],
             }
@@ -511,34 +511,45 @@ class AcousticField(ABC):
         try:
             # --- 1. Grid setup ---
             dx = self.params['dx']
+            air_margin = 20 
             if dx >= self.params['element_width']:
                 dx = self.params['element_width'] / 2
                 if self.params['width_phantom'] is not None:
-                    Nx = int(np.round((self.params['width_phantom'])/dx))
+                    pva_nx = int(np.round((self.params['width_phantom'])/dx))
+                    Nx = pva_nx + 2 * air_margin
                 else:
                     Nx = int(round((self.params['Xrange'][1] - self.params['Xrange'][0]) / dx))
                 if self.params['height_phantom'] is not None:
-                    Nz = int(np.round((self.params['height_phantom'])/dx))
+                    Nz = int(np.round((self.params['height_phantom'])/dx))  
                 else:
                     Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / dx))
             else:
                 if self.params['width_phantom'] is not None:
-                    Nx = int(np.round((self.params['width_phantom'])/self.params['dx']))
+                    pva_nx  = int(np.round((self.params['width_phantom'])/self.params['dx']))
+                    Nx = pva_nx + 2 * air_margin
                 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']))
                 else:
                     Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / self.params['dz']))
-
+           
             # --- 2. Time and space factors ---
-            self.factorT = int(np.ceil(self.params['f_AQ'] / self.params['f_saving']))
-            self.factorX = int(np.ceil(Nx / self.params['Nx']))
-            self.factorZ = int(np.ceil(Nz / self.params['Nz']))
+            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']))
 
             # --- 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)
+
 
             source = kSource()
             source.p_mask = np.zeros((Nx, Nz))
@@ -548,18 +559,16 @@ class AcousticField(ABC):
             sensor.mask = np.ones((Nx, Nz))
 
             # --- 5. PML setup ---
-            total_size_z = next_power_of_2(Nz)
-            pml_z_size = (total_size_z - Nz) // 2
-            pml_z_size = max(pml_z_size, 50)    # Ensure a minimum PML size of 50 grid points to avoid parasitic reflections
+            pml_size = 50 
 
-            # --- 6. Simulation options ---
+            # --- 7. Simulation options ---
             simulation_options = SimulationOptions(
-                pml_inside=False,
-                pml_size=[0, pml_z_size],
-                use_sg=False,
-                save_to_disk=True,
-                input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
-                output_filename=os.path.join(gettempdir(), "KwaveOUT.h5")
+            pml_inside=False, # PML ajoutée autour de la grille Air+PVA
+            pml_size=[pml_size, 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")
             )
 
             execution_options = SimulationExecutionOptions(
@@ -569,12 +578,12 @@ class AcousticField(ABC):
             )
 
             # --- 7. Call specialized function to set up source.p_mask and source.p ---
-            self._SetUpSource(source, Nx, dx, self.factorT)
+            self._SetUpSource(source, Nx, dx, factorT)
 
             # --- 8. Run simulation ---
             sensor_data = kspaceFirstOrder2D(
                 kgrid=kgrid,
-                medium=self.medium,
+                medium=medium,
                 source=source,
                 sensor=sensor,
                 simulation_options=simulation_options,
@@ -583,7 +592,11 @@ class AcousticField(ABC):
 
             # --- 9. Post-process results ---
             data = sensor_data['p'].reshape(kgrid.Nt, Nz, Nx)
-            return data
+
+            if factorT != 1 or factorX != 1 or factorZ != 1:
+                return reshape_field(data, [factorT, factorX, factorZ])
+            else:
+                return data
             
         except Exception as e:
             print(f"Error generating 2D acoustic field: {e}")

AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.373'
+__version__ = '2.9.374'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -235,5 +235,6 @@ def initialize(process=None):
 
 
 
+
 
 

{aot_biomaps-2.9.373.dist-info → aot_biomaps-2.9.374.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.373
+Version: 2.9.374
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.373.dist-info → aot_biomaps-2.9.374.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=fgpEUPXUQbaCtMxY_uHJtjrQTvQBwltYoAQtHk1zCuM,4408
+AOT_biomaps/__init__.py,sha256=eegeRt9p4KDthViG3c8Q2wMit5HW0lYzfCC2O36Rm2w,4410
 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
@@ -8,7 +8,7 @@ AOT_biomaps/AOT_Acoustic/IrregularWave.py,sha256=yZhtxkR6zlciRcEpdTR0BAhvgQl40XH
 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/__init__.py,sha256=t9M2rRqa_L9pk7W2FeELTkHEMuP4DBr4gBRldMqsQbg,491
-AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=M0CKApSCuKiCupj9pf9uOEhuuzJVNSlLvhgTpBQN5Q8,46128
+AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=5QKOZBpeuNCFCzQHYF0kwtUZxaBjAIWc7BQf0vgVAh8,46710
 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-2.9.373.dist-info/METADATA,sha256=pJCjnmUoIHGqV_s_popa7BNlrTn4LPP3h7mxRqlUiTQ,700
-aot_biomaps-2.9.373.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aot_biomaps-2.9.373.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
-aot_biomaps-2.9.373.dist-info/RECORD,,
+aot_biomaps-2.9.374.dist-info/METADATA,sha256=UbVZd3QiaNI5Hod1HgbgEoA-L4uBi7-Jh4NhQa4-HJs,700
+aot_biomaps-2.9.374.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.374.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.374.dist-info/RECORD,,