AOT-biomaps 2.9.215__tar.gz → 2.9.291__tar.gz

{aot_biomaps-2.9.215 → aot_biomaps-2.9.291}/AOT_biomaps/AOT_Experiment/Tomography.py

@@ -7,6 +7,8 @@ import psutil
 import numpy as np
 import matplotlib.pyplot as plt
 from tqdm import trange
+import h5py
+from scipy.io import loadmat
 
 class Tomography(Experiment):
     def __init__(self, **kwargs):
@@ -433,3 +435,71 @@ class Tomography(Experiment):
             listAcousticFields.append(AcousticField)
             progress_bar.set_postfix_str("")
         return listAcousticFields
+
+    def load_experimentalAO(self, pathAO, withTumor = True, h5name='AOsignal'):
+        """
+        Load experimental AO signals from specified file paths.
+        Args:
+            path_withTumor: Path to the AO signal with tumor.
+            path_withoutTumor: Path to the AO signal without tumor.
+        """
+        if not os.path.exists(pathAO):
+            raise FileNotFoundError(f"File {pathAO} not found.")
+
+        if pathAO.endswith('.npy'):
+            ao_signal = np.load(pathAO)
+        elif pathAO.endswith('.h5'):
+            with h5py.File(pathAO, 'r') as f:
+                if h5name not in f:
+                    raise KeyError(f"Dataset '{h5name}' not found in the HDF5 file.")
+                ao_signal = f[h5name][:]
+        elif pathAO.endswith('.mat'):
+            mat_data = loadmat(pathAO)
+            if h5name not in mat_data:
+                raise KeyError(f"Dataset '{h5name}' not found in the .mat file.")
+            ao_signal = mat_data[h5name]
+        elif pathAO.endswith('.hdr'):
+            ao_signal = self._loadAOSignal(pathAO)
+        else:
+            raise ValueError("Unsupported file format. Supported formats are: .npy, .h5, .mat, .hdr")
+        
+        if withTumor:
+            self.AOsignal_withTumor = ao_signal
+        else:
+            self.AOsignal_withoutTumor = ao_signal
+
+    def check_experimentalAO(self, activeListPath, withTumor=True):
+        """
+        Check if the experimental AO signals are correctly initialized.
+        """
+        if withTumor:
+            if self.AOsignal_withTumor is None:
+                raise ValueError("Experimental AOsignal with tumor is not initialized. Please load the experimental AO signal with tumor first.")
+        else:
+            if self.AOsignal_withoutTumor is None:
+                raise ValueError("Experimental AOsignal without tumor is not initialized. Please load the experimental AO signal without tumor first.")
+        if self.AcousticFields is not None:
+            # get min time shape between all AO signals
+            print()
+            
+            if self.AcousticFields[0].field.shape[0] > self.AOsignal_withTumor.shape[0]:
+                self.cutAcousticFields(max_t=self.AOsignal_withTumor.shape[0]/float(self.params.acoustic['f_saving']))
+            else:
+                for i in range(len(self.AcousticFields)):
+                    min_time_shape = min(self.AcousticFields[i].field.shape[0])
+                if withTumor:
+                    self.AOsignal_withTumor = self.AOsignal_withTumor[:min_time_shape, :]
+                else:
+                    self.AOsignal_withoutTumor = self.AOsignal_withoutTumor[:min_time_shape, :]
+
+            for field in self.AcousticFields:                        
+                if activeListPath is not None:
+                    with open(activeListPath, 'r') as file:
+                        lines = file.readlines()
+                        expected_name = lines[self.AcousticFields.index(field)].strip()
+                        nameField = field.getName_field()
+                        if nameField.startswith("field_"):
+                            nameField = nameField[len("field_"):]
+                        if nameField != expected_name:
+                            raise ValueError(f"Field name {nameField} does not match the expected name {expected_name} from the active list.")
+        print("Experimental AO signals are correctly initialized.")

{aot_biomaps-2.9.215 → aot_biomaps-2.9.291}/AOT_biomaps/AOT_Experiment/_mainExperiment.py

@@ -77,7 +77,6 @@ class Experiment(ABC):
                 raise ValueError(f"Field {field.getName_field()} has an invalid shape: {field.field.shape}. Expected shape to be at least ({max_sample},).")
             self.AcousticFields[i].field = field.field[min_sample:max_sample, :, :]
 
-
     def addNoise(self, noiseType='gaussian', noiseLvl=0.1, withTumor=True):
         """
         Ajoute du bruit (gaussien ou poisson) au signal AO sélectionné.
@@ -293,32 +292,46 @@ class Experiment(ABC):
         if AOsignalPath.endswith(".cdh"):
             with open(AOsignalPath, "r") as file:
                 cdh_content = file.readlines()
+            
+            cdf_path = AOsignalPath.replace(".cdh", ".cdf")
 
-            # Extraction des paramètres
-            n_events = int([line.split(":")[1].strip() for line in cdh_content if "Number of events" in line][0])
-            n_acquisitions = int([line.split(":")[1].strip() for line in cdh_content if "Number of acquisitions per event" in line][0])
+            # Extraire les paramètres depuis le fichier .cdh
+            n_scans = int([line.split(":")[1].strip() for line in cdh_content if "Number of events" in line][0])
+            n_acquisitions_per_event = int([line.split(":")[1].strip() for line in cdh_content if "Number of acquisitions per event" in line][0])
             num_elements = int([line.split(":")[1].strip() for line in cdh_content if "Number of US transducers" in line][0])
 
-            # Initialisation avec la bonne forme : (n_acquisitions, n_events)
-            AOsignal_matrix = np.zeros((n_acquisitions, n_events), dtype=np.float32)
+            # Initialisation des structures
+            AO_signal = np.zeros((n_acquisitions_per_event, n_scans), dtype=np.float32)
+            active_lists = []
+            angles = []
+
+            # Lecture du fichier binaire
+            with open(cdf_path, "rb") as file:
+                for j in trange(n_scans, desc="Lecture des événements"):
+                    # Lire l'activeList : 48 caractères hex = 24 bytes
+                    active_list_bytes = file.read(24)
+                    active_list_hex = active_list_bytes.hex()
+                    active_lists.append(active_list_hex)
 
-            with open(AOsignalPath.replace(".cdh", ".cdf"), "rb") as file:
-                hex_length = (num_elements + 3) // 4
-                for event in range(n_events):
-                    file.read(hex_length // 2)  # Sauter l'en-tête de l'événement
-                    signal = np.frombuffer(file.read(n_acquisitions * 4), dtype=np.float32)
-                    AOsignal_matrix[:, event] = signal  # Remplir par colonne
-                    
-            AOsignal_matrix = AOsignal_matrix
+                    # Lire l'angle (1 byte signé)
+                    angle_byte = file.read(1)
+                    angle = np.frombuffer(angle_byte, dtype=np.int8)[0]
+                    angles.append(angle)
+
+                    # Lire le signal AO (float32)
+                    data = np.frombuffer(file.read(n_acquisitions_per_event * 4), dtype=np.float32)
+                    if len(data) != n_acquisitions_per_event:
+                        raise ValueError(f"Erreur à l'événement {j} : attendu {n_acquisitions_per_event}, obtenu {len(data)}")
+                    AO_signal[:, j] = data
+
+            return AO_signal
 
-            return AOsignal_matrix
 
         elif AOsignalPath.endswith(".npy"):
             return np.load(AOsignalPath)  # Supposé déjà au bon format
         else:
             raise ValueError("Format de fichier non supporté. Utilisez .cdh/.cdf ou .npy.")
 
-
     def saveAOsignals_Castor(self, save_directory, withTumor=True):
         if withTumor:
             AO_signal = self.AOsignal_withTumor
@@ -345,10 +358,10 @@ class Experiment(ABC):
         header_content = (
             f"Data filename: {'AOSignals_withTumor.cdf' if withTumor else 'AOSignals_withoutTumor.cdf'}\n"
             f"Number of events: {nScan}\n"
-            f"Number of acquisitions per event: {AO_signal.shape[1]}\n"
+            f"Number of acquisitions per event: {AO_signal.shape[0]}\n"
             f"Start time (s): 0\n"
             f"Duration (s): 1\n"
-            f"Acquisition frequency (Hz): {1/self.AcousticFields[0].kgrid.dt}\n"
+            f"Acquisition frequency (Hz): {self.params.acoustic['f_saving']}\n"
             f"Data mode: histogram\n"
             f"Data type: AOT\n"
             f"Number of US transducers: {self.params.acoustic['num_elements']}"

{aot_biomaps-2.9.215 → aot_biomaps-2.9.291}/AOT_biomaps/AOT_Recon/AOT_Optimizers/DEPIERRO.py

@@ -1,6 +1,8 @@
 from AOT_biomaps.AOT_Recon.ReconEnums import PotentialType
-from AOT_biomaps.AOT_Recon.ReconTools import _build_adjacency_sparse
+from AOT_biomaps.AOT_Recon.ReconTools import _build_adjacency_sparse, calculate_memory_requirement, check_gpu_memory
 from AOT_biomaps.Config import config
+
+import warnings
 import numpy as np
 import torch
 from tqdm import trange
@@ -11,9 +13,42 @@ if config.get_process() == 'gpu':
     except ImportError:
         raise ImportError("torch_scatter and torch_sparse are required for GPU processing. Please install them using 'pip install torch-scatter torch-sparse' with correct link (follow instructions https://github.com/LucasDuclos/AcoustoOpticTomography/edit/main/README.md).")
 
-def _DEPIERRO_GPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration, withTumor, max_saves=5000):
-    # Initialisation du device
-    device = torch.device(f"cuda:{config.select_best_gpu()}")
+def DEPIERRO(
+        SMatrix,
+        y, 
+        numIterations,
+        beta,
+        sigma,
+        isSavingEachIteration,
+        withTumor, 
+        max_saves, 
+        show_logs):
+        """
+        This method implements the DEPIERRO algorithm using either CPU or single-GPU PyTorch acceleration.
+        Multi-GPU and Multi-CPU modes are not implemented for this algorithm.
+        """
+        try:
+            tumor_str = "WITH" if withTumor else "WITHOUT"
+            # Auto-select device and method
+            if device is None:
+                if torch.cuda.is_available() and check_gpu_memory(config.select_best_gpu(), calculate_memory_requirement(SMatrix, y), show_logs=show_logs):
+                    device = torch.device(f"cuda:{config.select_best_gpu()}")
+                    use_gpu = True
+                else:
+                    device = torch.device("cpu")
+                    use_gpu = False
+            else:
+                use_gpu = device.type == "cuda"
+            # Dispatch to the appropriate implementation
+            if use_gpu:
+                return _DEPIERRO_GPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration, tumor_str, device, max_saves, show_logs)
+            else:
+                return _DEPIERRO_CPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration, tumor_str, device, max_saves, show_logs)
+        except Exception as e:
+            print(f"Error in MLEM: {type(e).__name__}: {e}")
+            return None, None
+
+def _DEPIERRO_GPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration, tumor_str, device, max_saves, show_logs=True):
     # Conversion des données en tenseurs PyTorch (float64)
     A_matrix_torch = torch.tensor(SMatrix, dtype=torch.float64, device=device)
     y_torch = torch.tensor(y, dtype=torch.float64, device=device)
@@ -33,7 +68,7 @@ def _DEPIERRO_GPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration,
     # Construction de la matrice d'adjacence
     adj_index, adj_values = _build_adjacency_sparse(Z, X, device=device, dtype=torch.float64)
     # Description pour la barre de progression
-    description = f"AOT-BioMaps -- Bayesian Reconstruction Tomography: DE PIERRO (Sparse QUADRATIC β:{beta:.4f}, σ:{sigma:.4f}) ---- {'WITH' if withTumor else 'WITHOUT'} TUMOR ---- processing on single GPU no.{torch.cuda.current_device()}"
+    description = f"AOT-BioMaps -- Bayesian Reconstruction Tomography: DE PIERRO (Sparse QUADRATIC β:{beta:.4f}, σ:{sigma:.4f}) ---- {tumor_str} TUMOR ---- processing on single GPU no.{torch.cuda.current_device()}"
     # Configuration pour la sauvegarde des itérations
     saved_indices = [0]
 
@@ -47,7 +82,8 @@ def _DEPIERRO_GPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration,
             save_indices.append(numIterations - 1)
 
     # Boucle principale MAP-EM
-    for it in trange(numIterations, desc=description):
+    iterator = trange(numIterations, desc=description) if show_logs else range(numIterations)
+    for it in iterator:
         theta_p = matrix_theta_torch[-1]
         theta_p_flat = theta_p.reshape(-1)
         # Étape 1 : Projection avant
@@ -92,7 +128,7 @@ def _DEPIERRO_GPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration,
     else:
         return matrix_theta_torch[-1].cpu().numpy(), None
 
-def _DEPIERRO_CPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration, withTumor, max_saves=5000):
+def _DEPIERRO_CPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration, tumor_str, device, max_saves, show_logs=True):
     try:
         if beta is None or sigma is None:
             raise ValueError("Depierro95 optimizer requires beta and sigma parameters.")
@@ -120,9 +156,10 @@ def _DEPIERRO_CPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration,
             if save_indices[-1] != numIterations - 1:
                 save_indices.append(numIterations - 1)
 
-        description = f"AOT-BioMaps -- Bayesian Reconstruction Tomography: DE PIERRO (Sparse QUADRATIC β:{beta:.4f}, σ:{sigma:.4f}) ---- {'WITH' if withTumor else 'WITHOUT'} TUMOR ---- processing on single CPU ----"
+        description = f"AOT-BioMaps -- Bayesian Reconstruction Tomography: DE PIERRO (Sparse QUADRATIC β:{beta:.4f}, σ:{sigma:.4f}) ---- {tumor_str} TUMOR ---- processing on single CPU ----"
 
-        for p in trange(numIterations, desc=description):
+        iterator = trange(numIterations, desc=description) if show_logs else range(numIterations)
+        for it in iterator:
             theta_p = matrix_theta[-1]
             theta_p_flat = theta_p.reshape(-1)
             q_flat = np.dot(A_flat, theta_p_flat)
@@ -141,9 +178,9 @@ def _DEPIERRO_CPU(SMatrix, y, numIterations, beta, sigma, isSavingEachIteration,
             theta_p_plus_1_flat = np.clip(theta_p_plus_1_flat, a_min=0, a_max=None)
             theta_next = theta_p_plus_1_flat.reshape(Z, X)
             matrix_theta[-1] = theta_next
-            if isSavingEachIteration and p in save_indices:
+            if isSavingEachIteration and it in save_indices:
                 I_reconMatrix.append(theta_next.copy())
-                saved_indices.append(p)
+                saved_indices.append(it)
 
         if isSavingEachIteration:
             return I_reconMatrix, saved_indices