AOT-biomaps 2.9.312__tar.gz → 2.9.319__tar.gz

{aot_biomaps-2.9.312 → aot_biomaps-2.9.319}/AOT_biomaps/AOT_Experiment/Tomography.py

@@ -287,6 +287,56 @@ class Tomography(Experiment):
         if not self._check_patterns(self.patterns):
             raise ValueError("Generated patterns failed validation.")
 
+    def selectAngles(self, angles):
+
+        if self.AOsignal_withTumor is None and self.AOsignal_withoutTumor is None:
+            raise ValueError("AO signals are not initialized. Please load or generate the AO signals first.")
+        if self.AcousticFields is None or len(self.AcousticFields) == 0:
+            raise ValueError("AcousticFields is not initialized. Please generate the system matrix first.")
+        newAcousticFields = []
+        index = []
+        for i,field in enumerate(self.AcousticFields):
+            if field.angle in angles:
+                newAcousticFields.append(field)
+                index.append(i)
+        if self.AOsignal_withTumor is not None:
+            self.AOsignal_withTumor = self.AOsignal_withTumor[:, index]    
+        if self.AOsignal_withoutTumor is not None:
+            self.AOsignal_withoutTumor = self.AOsignal_withoutTumor[:, index]
+        self.AcousticFields = newAcousticFields
+
+    def selectPatterns(self, pattern_names):
+        if self.AOsignal_withTumor is None and self.AOsignal_withoutTumor is None:
+            raise ValueError("AO signals are not initialized. Please load or generate the AO signals first.")
+        if self.AcousticFields is None or len(self.AcousticFields) == 0:
+            raise ValueError("AcousticFields is not initialized. Please generate the system matrix first.")
+        newAcousticFields = []
+        index = []
+        for i,field in enumerate(self.AcousticFields):
+            if field.pattern.activeList in pattern_names:
+                newAcousticFields.append(field)
+                index.append(i)
+        if self.AOsignal_withTumor is not None:
+            self.AOsignal_withTumor = self.AOsignal_withTumor[:, index]    
+        if self.AOsignal_withoutTumor is not None:
+            self.AOsignal_withoutTumor = self.AOsignal_withoutTumor[:, index]
+        self.AcousticFields = newAcousticFields
+
+    def selectRandom(self,N):
+        if self.AOsignal_withTumor is None and self.AOsignal_withoutTumor is None:
+            raise ValueError("AO signals are not initialized. Please load or generate the AO signals first.")
+        if self.AcousticFields is None or len(self.AcousticFields) == 0:
+            raise ValueError("AcousticFields is not initialized. Please generate the system matrix first.")
+        if N > len(self.AcousticFields):
+            raise ValueError("N is larger than the number of available AcousticFields.")
+        indices = np.random.choice(len(self.AcousticFields), size=N, replace=False)
+        newAcousticFields = [self.AcousticFields[i] for i in indices]
+        if self.AOsignal_withTumor is not None:
+            self.AOsignal_withTumor = self.AOsignal_withTumor[:, indices]    
+        if self.AOsignal_withoutTumor is not None:
+            self.AOsignal_withoutTumor = self.AOsignal_withoutTumor[:, indices]
+        self.AcousticFields = newAcousticFields
+
     def _generate_patterns(self, N):
         def format_angle(a):
             return f"{'1' if a < 0 else '0'}{abs(a):02d}"
@@ -390,6 +440,80 @@ class Tomography(Experiment):
 
         return True
 
+    def applyApodisation(self, alpha=0.3, divergence_deg=0.5):
+        """
+        Applique une apodisation dynamique sur les champs acoustiques stockés dans l'objet.
+        L'apodisation suit l'angle d'émission et la divergence naturelle du faisceau pour
+        supprimer les lobes de diffraction (artefacts de bord) sans toucher au signal utile.
+        Args:
+            probe_width (float): Largeur physique active de la sonde (ex: 40e-3 pour 40mm).
+            alpha (float): Paramètre de Tukey (0.0=rectangle, 1.0=hann). 0.3 est un bon compromis.
+            divergence_deg (float): Angle d'ouverture du masque pour suivre l'élargissement du faisceau.
+                                    0.0 = Droit, 0.5 = Légère ouverture (conseillé).
+        """
+        print(f"Applying apodization (Alpha={alpha}, Div={divergence_deg}°) on {len(self.AcousticFields)} fields...")
+        
+        probe_width = self.params.acoustic['num_elements'] * self.params.acoustic['element_width']
+
+        for i in trange(len(self.AcousticFields), desc="Apodisation"):
+            # 1. Récupération des données et de l'angle
+            field = self.AcousticFields[i].field  # Peut être (Z, X) ou (Time, Z, X)
+            angle = self.AcousticFields[i].angle  # L'angle de l'onde plane
+
+            # 2. Récupération ou construction des axes physiques
+            nz, nx = field.shape[-2:]
+
+            if hasattr(self, 'x_axis') and self.x_axis is not None:
+                x_axis = self.x_axis
+            else:
+                # Génération par défaut centrée sur 0 (ex: -20mm à +20mm)
+                x_axis = np.linspace(-probe_width/2, probe_width/2, nx)
+
+            if hasattr(self, 'z_axis') and self.z_axis is not None:
+                z_axis = self.z_axis
+            else:
+                # Génération par défaut (ex: 0 à 40mm, basé sur un pitch standard ou arbitraire)
+                estimated_depth = 40e-3  # Valeur arbitraire si inconnue
+                z_axis = np.linspace(0, estimated_depth, nz)
+
+            # 3. Préparation des grilles pour le masque
+            Z, X = np.meshgrid(z_axis, x_axis, indexing='ij')
+
+            # 4. Calcul de la géométrie orientée (Steering)
+            angle_rad = np.deg2rad(angle)
+            X_aligned = X - Z * np.tan(angle_rad)
+
+            # 5. Calcul de la largeur dynamique du masque (Divergence)
+            div_rad = np.deg2rad(divergence_deg)
+            current_half_width = (probe_width / 2.0) + Z * np.tan(div_rad)
+
+            # 6. Normalisation et création du masque Tukey
+            X_norm = np.divide(X_aligned, current_half_width, out=np.zeros_like(X_aligned), where=current_half_width!=0)
+
+            mask = np.zeros_like(X_norm)
+            plateau_threshold = 1.0 * (1 - alpha)
+
+            # Zone centrale (plateau = 1)
+            mask[np.abs(X_norm) <= plateau_threshold] = 1.0
+
+            # Zone de transition (cosinus)
+            transition_indices = (np.abs(X_norm) > plateau_threshold) & (np.abs(X_norm) <= 1.0)
+            if np.any(transition_indices):
+                x_trans = np.abs(X_norm[transition_indices]) - plateau_threshold
+                width_trans = 1.0 * alpha
+                mask[transition_indices] = 0.5 * (1 + np.cos(np.pi * x_trans / width_trans))
+
+            # 7. Application du masque (Gestion 2D vs 3D)
+            if field.ndim == 3:
+                field_apodized = field * mask[np.newaxis, :, :]
+            else:
+                field_apodized = field * mask
+
+            # 8. Mise à jour de l'objet
+            self.AcousticFields[i].field = field_apodized
+
+        print("Apodisation done.")
+
     # PRIVATE METHODS
     def _generateAcousticFields_STRUCT_CPU(self, fieldDataPath=None, show_log=False, nameBlock=None):
         if self.patterns is None:

{aot_biomaps-2.9.312 → aot_biomaps-2.9.319}/AOT_biomaps/AOT_Recon/AOT_Optimizers/MLEM.py

@@ -547,4 +547,5 @@ def MLEM_sparseSELL_pycuda(
             try:
                 SMatrix.ctx.pop()
             except Exception:
-                pass
+                pass
+            

{aot_biomaps-2.9.312 → aot_biomaps-2.9.319}/AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.312'
+__version__ = '2.9.319'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -168,6 +168,13 @@ def initialize(process=None):
 
 
 
+
+
+
+
+
+
+
 
 
 

{aot_biomaps-2.9.312 → aot_biomaps-2.9.319}/AOT_biomaps.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.312
+Version: 2.9.319
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.312 → aot_biomaps-2.9.319}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.312
+Version: 2.9.319
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.312 → aot_biomaps-2.9.319}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AOT_biomaps',
-    version='2.9.312',
+    version='2.9.319',
     packages=find_packages(),
     include_package_data=True,
     
@@ -326,6 +326,13 @@ setup(
 
 
 
+
+
+
+
+
+
+