AOT-biomaps 2.9.333__py3-none-any.whl → 2.9.339__py3-none-any.whl

AOT_biomaps/AOT_Experiment/Tomography.py

@@ -18,27 +18,6 @@ class Tomography(Experiment):
         self.patterns = None
         self.theta = []
         self.decimations = []
-    
-
-        for i in range(len(self.AcousticFields)):
-            profile = hex_to_binary_profile(self.AcousticFields[i].getName_field()[6:-4], self.params.acoustic['num_elements'])
-            angle = self.AcousticFields[i].angle
-            self.theta.append(angle)
-
-            if set(self.AcousticFields[i].getName_field()[6:-4].lower().replace(" ", "")) == {'f'}:
-                fs_key = 0.0 # fs_key est en mm^-1 (0.0 mm^-1)
-            else:   
-                ft_prof = np.fft.fft(profile)
-                idx_max = np.argmax(np.abs(ft_prof[1:len(profile)//2])) + 1
-                freqs = np.fft.fftfreq(len(profile), d=self.params.general['dx'])
-
-                # freqs est en m^-1 car delta_x est en mètres.
-                fs_m_inv = abs(freqs[idx_max]) 
-
-                fs_key = fs_m_inv # Fréquence spatiale en mm^-1
-
-            # fs = n * dfx  => n = fs / dfx with dfx = 1/(N*delta_x)
-            self.decimations.append(int(fs_key / (1/(len(profile)*self.params.general['dx']))))
 
     # PUBLIC METHODS
     def check(self):
@@ -85,6 +64,25 @@ class Tomography(Experiment):
         """
         if self.TypeAcoustic.value == WaveType.StructuredWave.value:
             self.AcousticFields = self._generateAcousticFields_STRUCT_CPU(fieldDataPath, show_log, nameBlock)
+            for i in range(len(self.AcousticFields)):
+                profile = hex_to_binary_profile(self.AcousticFields[i].getName_field()[6:-4], self.params.acoustic['num_elements'])
+                angle = self.AcousticFields[i].angle
+                self.theta.append(angle)
+
+                if set(self.AcousticFields[i].getName_field()[6:-4].lower().replace(" ", "")) == {'f'}:
+                    fs_key = 0.0 # fs_key est en mm^-1 (0.0 mm^-1)
+                else:   
+                    ft_prof = np.fft.fft(profile)
+                    idx_max = np.argmax(np.abs(ft_prof[1:len(profile)//2])) + 1
+                    freqs = np.fft.fftfreq(len(profile), d=self.params.general['dx'])
+
+                    # freqs est en m^-1 car delta_x est en mètres.
+                    fs_m_inv = abs(freqs[idx_max]) 
+
+                    fs_key = fs_m_inv # Fréquence spatiale en mm^-1
+
+                # fs = n * dfx  => n = fs / dfx with dfx = 1/(N*delta_x)
+                self.decimations.append(int(fs_key / (1/(len(profile)*self.params.general['dx']))))
         else:
             raise ValueError("Unsupported wave type.")
 
@@ -314,14 +312,13 @@ class Tomography(Experiment):
                 raise ValueError("Generated patterns failed validation.")
         else:
             raise ValueError("Either N (>=2) or both decimations and angles must be provided for pattern generation.")
-
-        
+      
     def saveAOsignals_matlab(self, filePath):
         ActiveList = []
         DelayLaw = []
         c = self.params.acoustic['c0']
         NbElemts = self.params.acoustic['num_elements'] 
-        pitch = self.params.acoustic['width']
+        pitch = self.params.acoustic['element_width']
 
         for i in range(len(self.AcousticFields)):
             profile = hex_to_binary_profile(self.AcousticFields[i].getName_field()[6:-4], NbElemts)
@@ -679,6 +676,7 @@ class Tomography(Experiment):
                     AcousticField.save_field(fieldDataPath)
             listAcousticFields.append(AcousticField)
             progress_bar.set_postfix_str("")
+
         return listAcousticFields
 
     def load_experimentalAO(self, pathAO, withTumor = True, h5name='AOsignal'):

AOT_biomaps/AOT_Recon/AnalyticRecon.py

@@ -24,12 +24,12 @@ class AnalyticRecon(Recon):
             AOsignal = self.experiment.AOsignal_withTumor
         else:
             AOsignal = self.experiment.AOsignal_withoutTumor
-        delta_x = self.params.acoustic['dx']  # en m 
-        n_piezos = self.params.acoustic['num_elements']
+        delta_x = self.experiment.params.general['dx']  # en m 
+        n_piezos = self.experiment.params.acoustic['num_elements']
         demodulated_data = {}
         structured_buffer = {} 
 
-        for i in tqdm(range(len(self.experiment.AcousticFields)), desc="Demodulating AO signals"):
+        for i in trange(len(self.experiment.AcousticFields), desc="Demodulating AO signals"):   
             label = self.experiment.AcousticFields[i].getName_field()
             
             parts = label.split("_")
@@ -98,11 +98,10 @@ class AnalyticRecon(Recon):
 
             real = s0 - s_pi
             imag = s_pi_2 - s_3pi_2 
-            
-            
+              
             demodulated_data[(fs, theta)] = (real - 1j * imag) / (2/np.pi)
-            self.AOsignal_demoldulated = demodulated_data
-
+            
+        return demodulated_data
 
     def run(self, processType = ProcessType.PYTHON, withTumor= True):
         """
@@ -128,6 +127,7 @@ class AnalyticRecon(Recon):
             analyticType: The type of analytic reconstruction to perform (default is iFOURIER).
         """
         if withTumor:
+            self.AOsignal_demoldulated = self.parse_and_demodulate(withTumor=True)
             if self.analyticType == AnalyticType.iFOURIER:
                 self.reconPhantom = self._iFourierRecon(self.experiment.AOsignal_withTumor)
             elif self.analyticType == AnalyticType.iRADON:
@@ -135,6 +135,7 @@ class AnalyticRecon(Recon):
             else:            
                 raise ValueError(f"Unknown analytic type: {self.analyticType}")
         else:
+            self.AOsignal_demoldulated = self.parse_and_demodulate(withTumor=False)
             if self.analyticType == AnalyticType.iFOURIER:
                 self.reconLaser = self._iFourierRecon(self.experiment.AOsignal_withoutTumor)
             elif self.analyticType == AnalyticType.iRADON:

AOT_biomaps/__init__.py

@@ -85,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.333'
+__version__ = '2.9.339'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -190,6 +190,12 @@ def initialize(process=None):
 
 
 
+
+
+
+
+
+
 
 
 

{aot_biomaps-2.9.333.dist-info → aot_biomaps-2.9.339.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.333
+Version: 2.9.339
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos

{aot_biomaps-2.9.333.dist-info → aot_biomaps-2.9.339.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=KTexXkgmJ_3hKllZPzxJIRkrNj2plmep-xD4ANfDxao,4328
+AOT_biomaps/__init__.py,sha256=r0H6FXsW0n-ethz4CgAmwp24IOM9OaxvBLKxLkZ0We0,4340
 AOT_biomaps/AOT_Acoustic/AcousticEnums.py,sha256=s5kXa6jKzbS4btwbubrVcynLOr0yg5tth5vL_FGfbMk,1802
 AOT_biomaps/AOT_Acoustic/AcousticTools.py,sha256=h2sCtGVcDtyLtEF1q7sLZmuWivWmesVGUBPnW-ndQqc,7535
 AOT_biomaps/AOT_Acoustic/FocusedWave.py,sha256=3kGKKDx_3Msy5COYqIwzROPORGWvNjw8UsDanBfkMXE,11037
@@ -11,7 +11,7 @@ AOT_biomaps/AOT_Acoustic/__init__.py,sha256=t9M2rRqa_L9pk7W2FeELTkHEMuP4DBr4gBRl
 AOT_biomaps/AOT_Acoustic/_mainAcoustic.py,sha256=RdmhRF1i0KAlpsP7_wnZ7F4J27br3eUc4XR91Qq7C64,44158
 AOT_biomaps/AOT_Experiment/ExperimentTools.py,sha256=EyTIwgxTK-FqJYlhdjgirfWCSL1kTp-IOS0tTgiAVNA,3153
 AOT_biomaps/AOT_Experiment/Focus.py,sha256=B2nBawmv-NG2AWJx9zgQ8GlN6aFB9FwTSqX-M-phKXg,3193
-AOT_biomaps/AOT_Experiment/Tomography.py,sha256=87tdUjYJbrNU2S3FT7pCsnB4jFEYZQFqD4o_FBKekkc,36689
+AOT_biomaps/AOT_Experiment/Tomography.py,sha256=3JlslI9GNZy-u0uYgf0u9qyaVAQki6cYTHhcGK33aFg,36747
 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
@@ -21,7 +21,7 @@ AOT_biomaps/AOT_Optic/__init__.py,sha256=HSUVhfz0NzwHHZZ9KP9Xyfu33IgP_rYJX86J-gE
 AOT_biomaps/AOT_Optic/_mainOptic.py,sha256=Wk63CcgWbU-ygMfjNK80islaUbGGJpTXgZY3_C2KQNY,8179
 AOT_biomaps/AOT_Recon/AOT_biomaps_kernels.cubin,sha256=JWy-bdtBTZdnNlDbJGZKwXyF-2u1wICtmlOC_YxEL6o,82528
 AOT_biomaps/AOT_Recon/AlgebraicRecon.py,sha256=CGBXZyYEZ3TOTFOKSt-h7NGuFbuI9PNr3YTWTbSLxDo,46832
-AOT_biomaps/AOT_Recon/AnalyticRecon.py,sha256=9MNztNRZuF8zM1WfJh1GaTC8b7UDb_iuh0T0LGwycUY,10905
+AOT_biomaps/AOT_Recon/AnalyticRecon.py,sha256=NKO7nE2Roq3E9HzMf_eJobm7rNQK1xzaQ0W9zXic9CY,11067
 AOT_biomaps/AOT_Recon/BayesianRecon.py,sha256=RnnPa-tTcvirwiNPnCRZnSM4NWeEEltYET-piBbp34g,12671
 AOT_biomaps/AOT_Recon/DeepLearningRecon.py,sha256=RfVcEsi4GeGqJn0_SPxwQPQx6IQjin79WKh2UarMRLI,1383
 AOT_biomaps/AOT_Recon/PrimalDualRecon.py,sha256=JbFhxiyUoSTnlJgHbOWIfUUwhwfZoi39RJMnfkagegY,16504
@@ -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-2.9.333.dist-info/METADATA,sha256=bnzNzvd1PZh5qMbP_pSbFR59oQ8YUrW4fYQmhKhY0Uo,700
-aot_biomaps-2.9.333.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-aot_biomaps-2.9.333.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
-aot_biomaps-2.9.333.dist-info/RECORD,,
+aot_biomaps-2.9.339.dist-info/METADATA,sha256=3XoTP8HukgXdJdBPQC66FjZ5q-SvOn5LhVETzFDXvfY,700
+aot_biomaps-2.9.339.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+aot_biomaps-2.9.339.dist-info/top_level.txt,sha256=6STF-lT4kaAnBHJYCripmN5mZABoHjMuY689JdiDphk,12
+aot_biomaps-2.9.339.dist-info/RECORD,,