AOT-biomaps 2.9.369__tar.gz → 2.9.371__tar.gz

{aot_biomaps-2.9.369 → aot_biomaps-2.9.371}/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-2.9.369 → aot_biomaps-2.9.371}/AOT_biomaps/AOT_Recon/AnalyticRecon.py

@@ -18,91 +18,6 @@ class AnalyticRecon(Recon):
         self.Lc = Lc # in meters
         self.AOsignal_demoldulated = None
 
-    def parse_and_demodulate(self, withTumor=True):
-
-        if withTumor:
-            AOsignal = self.experiment.AOsignal_withTumor
-        else:
-            AOsignal = self.experiment.AOsignal_withoutTumor
-        delta_x = self.experiment.params.general['dx']  # en m 
-        n_piezos = self.experiment.params.acoustic['num_elements']
-        demodulated_data = {}
-        structured_buffer = {} 
-
-        for i in trange(len(self.experiment.AcousticFields), desc="Demodulating AO signals"):   
-            label = self.experiment.AcousticFields[i].getName_field()
-            
-            parts = label.split("_")
-            hex_pattern = parts[0]
-            angle_code = parts[-1]
-            
-            # Angle
-            if angle_code.startswith("1"):
-                angle_deg = -int(angle_code[1:])
-            else:
-                angle_deg = int(angle_code)
-            angle_rad = np.deg2rad(angle_deg)
-            
-            # Onde Plane (f_s = 0)
-            if set(hex_pattern.lower().replace(" ", "")) == {'f'}:
-                fs_key = 0.0 # fs_key est en mm^-1 (0.0 mm^-1)
-                demodulated_data[(fs_key, angle_rad)] = np.array(AOsignal[:,i])
-                continue
-                
-            # Onde Structurée
-            profile = hex_to_binary_profile(hex_pattern, n_piezos)
-            
-            # Calcul FS (Fréquence de Structuration)
-            ft_prof = np.fft.fft(profile)
-            # On regarde uniquement la partie positive non DC
-            idx_max = np.argmax(np.abs(ft_prof[1:len(profile)//2])) + 1
-            freqs = np.fft.fftfreq(len(profile), d=delta_x)
-            
-            # freqs est en m^-1 car delta_x est en mètres.
-            fs_m_inv = abs(freqs[idx_max]) 
-            
-            # *** CORRECTION 1: Conversion de f_s en mm^-1 (mm^-1 est utilisé dans iRadon) ***
-            fs_key = fs_m_inv / 1000.0 # Fréquence spatiale en mm^-1
-
-            
-            if fs_key == 0: continue
-
-            # Calcul de la Phase (Shift)
-            phase = get_phase_deterministic(profile)
-            
-            # Stockage par (fs, theta) et phase
-            key = (fs_key, angle_rad)
-            if key not in structured_buffer:
-                structured_buffer[key] = {}
-            
-            # La moyenne est nécessaire si plusieurs acquisitions ont la même phase (pour le SNR) 
-            if phase in structured_buffer[key]:
-                structured_buffer[key][phase] = (structured_buffer[key][phase] + np.array(AOsignal[:,i])) / 2
-            else:
-                structured_buffer[key][phase] = np.array(AOsignal[:,i])
-
-
-        
-        for (fs, theta), phases in structured_buffer.items():
-            s0 = phases.get(0.0, 0)
-            s_pi_2 = phases.get(np.pi/2, 0)
-            s_pi = phases.get(np.pi, 0)
-            s_3pi_2 = phases.get(3*np.pi/2, 0)
-
-            # Assurer que les zéros sont des vecteurs de la bonne taille
-            example = next(val for val in phases.values() if not isinstance(val, int))
-            if isinstance(s0, int): s0 = np.zeros_like(example)
-            if isinstance(s_pi, int): s_pi = np.zeros_like(example)
-            if isinstance(s_pi_2, int): s_pi_2 = np.zeros_like(example)
-            if isinstance(s_3pi_2, int): s_3pi_2 = np.zeros_like(example)
-
-            real = s0 - s_pi
-            imag = s_pi_2 - s_3pi_2 
-              
-            demodulated_data[(fs, theta)] = (real - 1j * imag) / (2/np.pi)
-            
-        return demodulated_data
-
     def run(self, processType = ProcessType.PYTHON, withTumor= True):
         """
         This method is a placeholder for the analytic reconstruction process.

{aot_biomaps-2.9.369 → aot_biomaps-2.9.371}/AOT_biomaps/AOT_Recon/_mainRecon.py

@@ -1,12 +1,13 @@
 from AOT_biomaps.Config import config
-from AOT_biomaps.AOT_Experiment.Tomography import Tomography
+from AOT_biomaps.AOT_Experiment.Tomography import Tomography, hex_to_binary_profile
 from .ReconEnums import ReconType
-from .ReconTools import mse, ssim
+from .ReconTools import mse, ssim, get_phase_deterministic
 
 import os
 import numpy as np
 import matplotlib.pyplot as plt
 from abc import ABC, abstractmethod
+from tqdm import trange
 
 
 class Recon(ABC):
@@ -166,7 +167,6 @@ class Recon(ABC):
                 ssim_value = ssim(self.experiment.OpticImage.phantom, theta, data_range=data_range)
                 self.SSIM.append(ssim_value)
     
-
     def show(self, withTumor=True, savePath=None, scale='same'):
         """
         Display the reconstructed images.
@@ -308,4 +308,87 @@ class Recon(ABC):
 
         plt.show()
 
+    def parse_and_demodulate(self, withTumor=True):
 
+        if withTumor:
+            AOsignal = self.experiment.AOsignal_withTumor
+        else:
+            AOsignal = self.experiment.AOsignal_withoutTumor
+        delta_x = self.experiment.params.general['dx']  # en m 
+        n_piezos = self.experiment.params.acoustic['num_elements']
+        demodulated_data = {}
+        structured_buffer = {} 
+
+        for i in trange(len(self.experiment.AcousticFields), desc="Demodulating AO signals"):   
+            label = self.experiment.AcousticFields[i].getName_field()
+            
+            parts = label.split("_")
+            hex_pattern = parts[0]
+            angle_code = parts[-1]
+            
+            # Angle
+            if angle_code.startswith("1"):
+                angle_deg = -int(angle_code[1:])
+            else:
+                angle_deg = int(angle_code)
+            angle_rad = np.deg2rad(angle_deg)
+            
+            # Onde Plane (f_s = 0)
+            if set(hex_pattern.lower().replace(" ", "")) == {'f'}:
+                fs_key = 0.0 # fs_key est en mm^-1 (0.0 mm^-1)
+                demodulated_data[(fs_key, angle_rad)] = np.array(AOsignal[:,i])
+                continue
+                
+            # Onde Structurée
+            profile = hex_to_binary_profile(hex_pattern, n_piezos)
+            
+            # Calcul FS (Fréquence de Structuration)
+            ft_prof = np.fft.fft(profile)
+            # On regarde uniquement la partie positive non DC
+            idx_max = np.argmax(np.abs(ft_prof[1:len(profile)//2])) + 1
+            freqs = np.fft.fftfreq(len(profile), d=delta_x)
+            
+            # freqs est en m^-1 car delta_x est en mètres.
+            fs_m_inv = abs(freqs[idx_max]) 
+            
+            # *** CORRECTION 1: Conversion de f_s en mm^-1 (mm^-1 est utilisé dans iRadon) ***
+            fs_key = fs_m_inv / 1000.0 # Fréquence spatiale en mm^-1
+
+            
+            if fs_key == 0: continue
+
+            # Calcul de la Phase (Shift)
+            phase = get_phase_deterministic(profile)
+            
+            # Stockage par (fs, theta) et phase
+            key = (fs_key, angle_rad)
+            if key not in structured_buffer:
+                structured_buffer[key] = {}
+            
+            # La moyenne est nécessaire si plusieurs acquisitions ont la même phase (pour le SNR) 
+            if phase in structured_buffer[key]:
+                structured_buffer[key][phase] = (structured_buffer[key][phase] + np.array(AOsignal[:,i])) / 2
+            else:
+                structured_buffer[key][phase] = np.array(AOsignal[:,i])
+
+
+        
+        for (fs, theta), phases in structured_buffer.items():
+            s0 = phases.get(0.0, 0)
+            s_pi_2 = phases.get(np.pi/2, 0)
+            s_pi = phases.get(np.pi, 0)
+            s_3pi_2 = phases.get(3*np.pi/2, 0)
+
+            # Assurer que les zéros sont des vecteurs de la bonne taille
+            example = next(val for val in phases.values() if not isinstance(val, int))
+            if isinstance(s0, int): s0 = np.zeros_like(example)
+            if isinstance(s_pi, int): s_pi = np.zeros_like(example)
+            if isinstance(s_pi_2, int): s_pi_2 = np.zeros_like(example)
+            if isinstance(s_3pi_2, int): s_3pi_2 = np.zeros_like(example)
+
+            real = s0 - s_pi
+            imag = s_pi_2 - s_3pi_2 
+              
+            demodulated_data[(fs, theta)] = (real - 1j * imag) / (2/np.pi)
+            
+        return demodulated_data

{aot_biomaps-2.9.369 → aot_biomaps-2.9.371}/AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.369'
+__version__ = '2.9.371'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -230,6 +230,8 @@ def initialize(process=None):
 
 
 
+
+
 
 
 

{aot_biomaps-2.9.369 → aot_biomaps-2.9.371}/AOT_biomaps.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.369
+Version: 2.9.371
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.369 → aot_biomaps-2.9.371}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.369
+Version: 2.9.371
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.369 → aot_biomaps-2.9.371}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AOT_biomaps',
-    version='2.9.369',
+    version='2.9.371',
     packages=find_packages(),
     include_package_data=True,
     
@@ -388,6 +388,8 @@ setup(
 
 
 
+
+