AOT-biomaps 2.9.318__py3-none-any.whl → 2.9.323__py3-none-any.whl

AOT_biomaps/AOT_Acoustic/AcousticTools.py

@@ -157,8 +157,6 @@ def calculate_envelope_squared(field):
         print(f"Erreur dans calculate_envelope_squared: {e}")
         raise
 
-
-
 def getPattern(pathFile):
     """
     Get the pattern from a file path.

AOT_biomaps/AOT_Experiment/ExperimentTools.py

@@ -0,0 +1,60 @@
+import numpy as np
+
+def calc_mat_os(xm, fx, dx, bool_active_list, signal_type):
+    num_els = len(xm)
+    
+    # Cas limite : Fréquence nulle (Décimation 0)
+    if fx == 0:
+        if signal_type == 'cos':
+            # cos(0) = 1 -> Tout est actif
+            mask = np.ones(num_els, dtype=bool)
+        else:
+            # sin(0) = 0 -> Tout est inactif
+            mask = np.zeros(num_els, dtype=bool)
+    else:
+        # Calcul normal pour fx > 0
+        half_period_elements = round(1 / (2 * fx * dx))
+        
+        # Sécurité : si fx est tellement grand que half_period < 1
+        half_period_elements = max(1, half_period_elements)
+        
+        indices = np.arange(num_els)
+        if signal_type == 'cos':
+            mask = ((indices // half_period_elements) % 2 == 0)
+        else:
+            # Déphasage de 90° pour le sinus : on décale d'une demi-demi-période
+            shift = half_period_elements // 2
+            mask = (((indices + shift) // half_period_elements) % 2 == 0)
+            
+    return np.tile(mask[:, np.newaxis], (1, bool_active_list.shape[1]))
+
+def convert_to_hex_list(matrix):
+    """
+    Convertit une matrice binaire en liste de strings hexa (paquets de 4 bits).
+    Chaque colonne devient une chaîne de caractères.
+    """
+    n_els, n_scans = matrix.shape
+    
+    # 1. Padding pour s'assurer que n_els est multiple de 4
+    remainder = n_els % 4
+    if remainder != 0:
+        padding = np.zeros((4 - remainder, n_scans))
+        matrix = np.vstack([matrix, padding])
+    
+    # 2. Reshape pour isoler des blocs de 4 bits (nibbles)
+    # Shape résultante : (Nombre de blocs, 4 bits, Nombre de scans)
+    blocks = matrix.reshape(-1, 4, n_scans)
+    
+    # 3. Calcul de la valeur décimale de chaque bloc (0 à 15)
+    # On considère le premier élément comme le bit de poids faible (LSB)
+    weights = np.array([1, 2, 4, 8]).reshape(1, 4, 1)
+    dec_values = np.sum(blocks * weights, axis=1).astype(int)
+    
+    # 4. Conversion en caractères Hexadécimaux
+    # On définit la table de conversion pour la rapidité
+    hex_table = np.array(list("0123456789abcdef"))
+    hex_matrix = hex_table[dec_values]
+    
+    # 5. Assemblage des chaînes (de l'élément N vers 0 pour l'ordre Shift Register standard)
+    return ["".join(hex_matrix[::-1, col]) for col in range(n_scans)]
+

AOT_biomaps/AOT_Experiment/Tomography.py

@@ -2,6 +2,7 @@ from ._mainExperiment import Experiment
 from AOT_biomaps.AOT_Acoustic.AcousticEnums import WaveType
 from AOT_biomaps.AOT_Acoustic.StructuredWave import StructuredWave
 from AOT_biomaps.Config import config
+from AOT_biomaps.AOT_Experiment.ExperimentTools import calc_mat_os, convert_to_hex_list
 import os
 import psutil
 import numpy as np
@@ -273,7 +274,7 @@ class Tomography(Experiment):
                     line = f"({coords}, {angles})\n"
                     file.write(line)
 
-    def generateActiveList(self, N):
+    def generateActiveList(self, N = None, decimations = None, angles = None):
         """
         Génère une liste de patterns d'activation équilibrés et réguliers.
         Args:
@@ -281,11 +282,16 @@ class Tomography(Experiment):
         Returns:
             list: Liste de strings au format "hex_angle".
         """
-        if N < 1:
-            raise ValueError("N must be a positive integer.")
-        self.patterns = self._generate_patterns(N)
+        if decimations is not None and angles is not None:
+            self._genereate_patterns_from_decimations(decimations, angles)
+        elif N is not None and N > 1:
+            self.patterns = self._generate_patterns(N)
+        else:
+            raise ValueError("Either N (>=2) or both decimations and angles must be provided for pattern generation.")
         if not self._check_patterns(self.patterns):
             raise ValueError("Generated patterns failed validation.")
+        
+    
 
     def selectAngles(self, angles):
 
@@ -337,7 +343,76 @@ class Tomography(Experiment):
             self.AOsignal_withoutTumor = self.AOsignal_withoutTumor[:, indices]
         self.AcousticFields = newAcousticFields
 
-    def _generate_patterns(self, N):
+    def _genereate_patterns_from_decimations(self, decimations, angles):
+        if isinstance(decimations, list): decimations = np.array(decimations)
+        if isinstance(angles, list): angles = np.array(angles)
+
+        angles = np.sort(angles)
+        decimations = np.sort(decimations)
+
+        num_elements = self.params.acoustic['num_elements']
+        dx_mm = self.params.general['dx'] * 1e3
+
+        # --- Calcul du nombre de Scans ---
+        if 0 in decimations:
+            Nscans = 4 * angles.shape[0] * (decimations.shape[0] - 1) + angles.shape[0]
+            offSet = angles.shape[0]
+        else:
+            Nscans = 4 * angles.shape[0] * decimations.shape[0]
+            offSet = 0
+
+        ActiveLIST = np.ones((num_elements, Nscans))
+        Xm = np.arange(1, num_elements + 1) * dx_mm
+        dFx = 1 / (num_elements * dx_mm)
+
+        # On traite séparément les décimations non nulles pour la boucle
+        active_decimations = decimations[decimations != 0]
+
+        for i_dec in range(len(active_decimations)):
+            idx_base = (np.arange(len(angles))) + (i_dec * 4 * len(angles)) + offSet
+            
+            Icos   = idx_base
+            Incos  = idx_base + len(angles)
+            Isin   = idx_base + 2 * len(angles)
+            Insin  = idx_base + 3 * len(angles)
+
+            fx = dFx * active_decimations[i_dec]
+
+            # Remplissage des 4 phases
+            valid_icos = Icos[Icos < Nscans]
+            if valid_icos.size > 0:
+                ActiveLIST[:, valid_icos] = calc_mat_os(Xm, fx, dx_mm, ActiveLIST[:, valid_icos], 'cos')
+                if (Incos < Nscans).any():
+                    ActiveLIST[:, Incos[Incos < Nscans]] = 1 - ActiveLIST[:, valid_icos]
+
+            valid_isin = Isin[Isin < Nscans]
+            if valid_isin.size > 0:
+                ActiveLIST[:, valid_isin] = calc_mat_os(Xm, fx, dx_mm, ActiveLIST[:, valid_isin], 'sin')
+                if (Insin < Nscans).any():
+                    ActiveLIST[:, Insin[Insin < Nscans]] = 1 - ActiveLIST[:, valid_isin]
+
+        # --- Conversion au format attendu ---
+        # 1. On convertit toute la matrice en liste de strings Hexa
+        hexa_list = convert_to_hex_list(ActiveLIST)
+
+        # 2. Fonction interne de formatage d'angle (pour coller à votre ancien code)
+        def format_angle(a):
+            return f"{'1' if a < 0 else '0'}{abs(a):02d}"
+
+        # 3. Construction de la liste de dictionnaires
+        patterns = []
+        for i in range(Nscans):
+            # On retrouve l'angle correspondant à l'index i
+            # La logique est cyclique sur la taille de 'angles'
+            angle_val = angles[i % len(angles)]
+            
+            hex_pattern = hexa_list[i]
+            pair = f"{hex_pattern}_{format_angle(angle_val)}"
+            patterns.append({"fileName": pair})
+
+        return patterns
+    
+    def _generate_patterns(self, N,angles = None):
         def format_angle(a):
             return f"{'1' if a < 0 else '0'}{abs(a):02d}"
 
@@ -348,7 +423,13 @@ class Tomography(Experiment):
             return hex_string
 
         num_elements = self.params.acoustic['num_elements']
-        angle_choices = list(range(-20, 21))
+        if angles is None:
+            angle_choices = list(range(-20, 21))
+        else:
+            # convert np.array to list if necessary
+            if isinstance(angles, np.ndarray):
+                angles = angles.tolist()
+            angle_choices = angles
 
         # 1. Trouver TOUS les diviseurs PAIRS de num_elements (y compris num_elements)
         divs = [d for d in range(2, num_elements + 1) if num_elements % d == 0 and d % 2 == 0]
@@ -451,7 +532,7 @@ class Tomography(Experiment):
             divergence_deg (float): Angle d'ouverture du masque pour suivre l'élargissement du faisceau.
                                     0.0 = Droit, 0.5 = Légère ouverture (conseillé).
         """
-        print(f"Application de l'apodisation (Alpha={alpha}, Div={divergence_deg}°) sur {len(self.AcousticFields)} champs...")
+        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']
 
@@ -512,7 +593,7 @@ class Tomography(Experiment):
             # 8. Mise à jour de l'objet
             self.AcousticFields[i].field = field_apodized
 
-        print("Apodisation terminée.")
+        print("Apodisation done.")
 
     # PRIVATE METHODS
     def _generateAcousticFields_STRUCT_CPU(self, fieldDataPath=None, show_log=False, nameBlock=None):

AOT_biomaps/AOT_Recon/ReconTools.py

@@ -221,7 +221,6 @@ def calculate_memory_requirement(SMatrix, y):
     # --- 3. Final Result ---
     return total_bytes / (1024 ** 3)
 
-
 def check_gpu_memory(device_index, required_memory, show_logs=True):
     """Check if enough memory is available on the specified GPU."""
     free_memory, _ = torch.cuda.mem_get_info(f"cuda:{device_index}")
@@ -252,7 +251,6 @@ def _backward_projection(SMatrix, e_p, c_p):
                     total += SMatrix[_t, _z, _x, _n] * e_p[_t, _n]
             c_p[_z, _x] = total
 
-
 def _build_adjacency_sparse(Z, X, device, corner=(0.5 - np.sqrt(2) / 4) / np.sqrt(2), face=0.5 - np.sqrt(2) / 4,dtype=torch.float32):
     rows, cols, weights = [], [], []
     for z in range(Z):
@@ -273,7 +271,6 @@ def _build_adjacency_sparse(Z, X, device, corner=(0.5 - np.sqrt(2) / 4) / np.sqr
     index, values = coalesce(index, values, m=Z*X, n=Z*X)
     return index, values
 
-
 def power_method(P, PT, data, Z, X, n_it=10):
     x = torch.randn(Z * X, device=data.device)
     x = x / torch.norm(x)

AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.318'
+__version__ = '2.9.323'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -176,6 +176,11 @@ def initialize(process=None):
 
 
 
+
+
+
+
+
 
 
 

{aot_biomaps-2.9.318.dist-info → aot_biomaps-2.9.323.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.318
+Version: 2.9.323
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.318.dist-info → aot_biomaps-2.9.323.dist-info}/RECORD

@@ -1,16 +1,17 @@
 AOT_biomaps/Config.py,sha256=ghEOP1n8aO1pR-su13wMeAZAxZRfry5hH67NbtZ8SqI,3614
 AOT_biomaps/Settings.py,sha256=v8fPhnvvcfBJP29m1RLOTEr3jndGLGwbUiORXmsj2Bo,2853
-AOT_biomaps/__init__.py,sha256=JzWlV3kQ0eqvYRCkDaPawjpBhG0lagMhcLDnBLaY5Fs,4298
+AOT_biomaps/__init__.py,sha256=CzNrJamLw5SZZ9fGeXRnGrBUqSj90vh2wZx1792YWto,4308
 AOT_biomaps/AOT_Acoustic/AcousticEnums.py,sha256=s5kXa6jKzbS4btwbubrVcynLOr0yg5tth5vL_FGfbMk,1802
-AOT_biomaps/AOT_Acoustic/AcousticTools.py,sha256=al7xXKMY5e-qQQ7nrQVPVAmqYiB320OluNlY6ti8iKc,7539
+AOT_biomaps/AOT_Acoustic/AcousticTools.py,sha256=h2sCtGVcDtyLtEF1q7sLZmuWivWmesVGUBPnW-ndQqc,7535
 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/ExperimentTools.py,sha256=BkHSX_foyyj5UrHZWQH5F9DGeV8o2fkp3euEbcvE4vA,2399
 AOT_biomaps/AOT_Experiment/Focus.py,sha256=B2nBawmv-NG2AWJx9zgQ8GlN6aFB9FwTSqX-M-phKXg,3193
-AOT_biomaps/AOT_Experiment/Tomography.py,sha256=JO-yLOSnCd8Da2HC9uJ1uI0GD-_Ca1PX9URzAk_EAiQ,31149
+AOT_biomaps/AOT_Experiment/Tomography.py,sha256=-7HfRDPchTRwxm0SObU_pGN3FH4HN6b1WJvLuacGzFU,34672
 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
@@ -25,7 +26,7 @@ AOT_biomaps/AOT_Recon/BayesianRecon.py,sha256=RnnPa-tTcvirwiNPnCRZnSM4NWeEEltYET
 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/ReconTools.py,sha256=py1zKVEa0j7EfmcNZS2lpVQwzlkY6rRWsDQ8izWlme4,19872
 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
@@ -41,7 +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-2.9.318.dist-info/METADATA,sha256=ynPqtHAnkFQBks7GrB91EadzCQxdCC7PFc0kHG3H-Zo,700
-aot_biomaps-2.9.318.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aot_biomaps-2.9.318.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
-aot_biomaps-2.9.318.dist-info/RECORD,,
+aot_biomaps-2.9.323.dist-info/METADATA,sha256=9n72wEg-tUeIC9EWY6rFRJCpFwBOnly-3IQZSVdvLts,700
+aot_biomaps-2.9.323.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.323.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.323.dist-info/RECORD,,