AOT-biomaps 2.9.370__py3-none-any.whl → 2.9.372__py3-none-any.whl

AOT_biomaps/AOT_Acoustic/_mainAcoustic.py

@@ -93,6 +93,8 @@ class AcousticField(ABC):
                 'num_elements': params.acoustic['num_elements'],
                 'element_width': params.acoustic['element_width'],
                 'element_height': params.acoustic['element_height'],
+                'height_phantom': params.acoustic['phantom']['height'] if 'phantom' in params.acoustic and 'height' in params.acoustic['phantom'] else None,
+                'width_phantom': params.acoustic['phantom']['width'] if 'phantom' in params.acoustic and 'width' in params.acoustic['phantom'] else None,
                 'Xrange': params.general['Xrange'],
                 'Yrange': params.general['Yrange'],
                 'Zrange': params.general['Zrange'],
@@ -104,6 +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,
                 'probeWidth': params.acoustic['num_elements'] * params.acoustic['element_width'],
                 'IsAbsorbingMedium': params.acoustic['isAbsorbingMedium'],
             }
@@ -114,8 +117,11 @@ class AcousticField(ABC):
 
                 self.params['f_AQ'] = int(1/self.kgrid.dt)
             else:
-                Nt = ceil((self.params['Zrange'][1] - self.params['Zrange'][0])*float(params.acoustic['f_AQ']) / self.params['c0'])
-
+                if self.params['Nt'] is None:
+                    Nt = ceil((self.params['Zrange'][1] - self.params['Zrange'][0])*float(params.acoustic['f_AQ']) / self.params['c0'])
+                    self.params['Nt'] = Nt
+                else:
+                    Nt = self.params['Nt']
                 self.kgrid.setTime(Nt,1/float(params.acoustic['f_AQ']))
                 self.params['f_AQ'] = int(float(params.acoustic['f_AQ']))
 
@@ -505,13 +511,25 @@ class AcousticField(ABC):
         try:
             # --- 1. Grid setup ---
             dx = self.params['dx']
-            if dx >= self.params['element_width']*2:
+            if dx >= self.params['element_width']:
                 dx = self.params['element_width'] / 2
-                Nx = int(round((self.params['Xrange'][1] - self.params['Xrange'][0]) / dx))
-                Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / dx))
+                if self.params['width_phantom'] is not None:
+                    Nx = int(np.round((self.params['width_phantom'])/dx))
+                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))
+                else:
+                    Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / dx))
             else:
-                Nx = self.params['Nx']
-                Nz = self.params['Nz']
+                if self.params['width_phantom'] is not None:
+                    Nx = int(np.round((self.params['width_phantom'])/self.params['dx']))
+                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']))
@@ -530,17 +548,15 @@ class AcousticField(ABC):
             sensor.mask = np.ones((Nx, Nz))
 
             # --- 5. PML setup ---
-            total_size_x = next_power_of_2(Nx)
             total_size_z = next_power_of_2(Nz)
-            pml_x_size = (total_size_x - Nx) // 2
             pml_z_size = (total_size_z - Nz) // 2
-            pml_x_size = max(pml_x_size, 50)    # Ensure a minimum PML size of 50 grid points to avoid parasitic reflections
             pml_z_size = max(pml_z_size, 50)    # Ensure a minimum PML size of 50 grid points to avoid parasitic reflections
 
             # --- 6. Simulation options ---
             simulation_options = SimulationOptions(
                 pml_inside=False,
-                pml_size=[pml_x_size, pml_z_size],
+                pml_size=[0, pml_z_size],
+                pml_header=True,
                 use_sg=False,
                 save_to_disk=True,
                 input_filename=os.path.join(gettempdir(), "KwaveIN.h5"),
@@ -583,11 +599,23 @@ class AcousticField(ABC):
             dx = self.params['dx']
             if dx >= self.params['element_width']:
                 dx = self.params['element_width'] / 2
-                Nx = int(round((self.params['Xrange'][1] - self.params['Xrange'][0]) / dx))
-                Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / dx))
+                if self.params['width_phantom'] is not None:
+                    Nx = int(np.round((self.params['width_phantom'])/dx))
+                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))
+                else:
+                    Nz = int(round((self.params['Zrange'][1] - self.params['Zrange'][0]) / dx))
             else:
-                Nx = self.params['Nx']
-                Nz = self.params['Nz']
+                if self.params['width_phantom'] is not None:
+                    Nx = int(np.round((self.params['width_phantom'])/self.params['dx']))
+                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 (common) ---
             factorT = int(np.ceil(self.params['f_AQ'] / self.params['f_saving']))

AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.370'
+__version__ = '2.9.372'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -231,6 +231,8 @@ def initialize(process=None):
 
 
 
+
+
 
 
 

{aot_biomaps-2.9.370.dist-info → aot_biomaps-2.9.372.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.370
+Version: 2.9.372
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.370.dist-info → aot_biomaps-2.9.372.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=Zm2g5BaW_0Ai5njolsGHMC-7d92ILbQbYSINrhPC-yM,4402
+AOT_biomaps/__init__.py,sha256=kQwtDEc16hDG55-_3fja8dSj4Rht8ze0DBNbXxO9lXs,4406
 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=RdmhRF1i0KAlpsP7_wnZ7F4J27br3eUc4XR91Qq7C64,44158
+AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=z_fnwPXixDt-fO-TR-AXXrjGhgxJhjC8l9YkBWX3aME,46162
 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-2.9.370.dist-info/METADATA,sha256=rLuQ3BEnaedh8dUlK226kHbiG_y0GEHl3IEamse4Q3M,700
-aot_biomaps-2.9.370.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aot_biomaps-2.9.370.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
-aot_biomaps-2.9.370.dist-info/RECORD,,
+aot_biomaps-2.9.372.dist-info/METADATA,sha256=LCSOt-pw_o2CG-ehSjE0G70PZHMCzs8eBIh1sVT5sNY,700
+aot_biomaps-2.9.372.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.372.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.372.dist-info/RECORD,,