AOT-biomaps 2.9.167__py3-none-any.whl → 2.9.270__py3-none-any.whl

AOT_biomaps/AOT_Recon/ReconEnums.py

@@ -354,8 +354,33 @@ class NoiseType(Enum):
     - None: No noise is applied.
     """
     POISSON = 'poisson'
-    """Poisson noise, typically used for emission data."""
+    """Poisson noise."""
     GAUSSIAN = 'gaussian'
-    """Gaussian noise, typically used for transmission data."""
+    """Gaussian noise."""
     None_ = 'none'
     """No noise is applied."""
+
+class SMatrixType(Enum):
+    """
+    Enum for different sparsing methods used in reconstructions.
+    
+    Selection of sparsing methods:
+    - Thresholding: Sparsing based on a threshold value.
+    - TopK: Sparsing by retaining the top K values.
+    - None: No sparsing is applied.
+    """
+    DENSE = 'DENSE'
+    """No sparsing is applied."""
+    CSR = 'CSR'
+    """Sparsing based on a threshold value."""
+    COO = 'COO'
+    """Sparsing by retaining the top K values."""
+    SELL = 'SELL'
+    """Sparsing using sell C sigma method.
+    Optimized variant of ELLPACK, dividing the matrix into fixed-size "chunks" of `C` rows.
+    Non-zero elements are sorted by column within each chunk to improve memory coalescing on GPUs.
+    Rows are padded with zeros to align their length to the longest row in the chunk.
+    ** Ref : Kreutzer, M., Hager, G., Wellein, G., Fehske, H., & Bishop, A. R. (2014).
+          "A Unified Sparse Matrix Data Format for Efficient General Sparse Matrix-Vector Multiply on Modern Processors".
+          ACM Transactions on Mathematical Software, 41(2), 1–24. DOI: 10.1145/2592376.
+    """

AOT_biomaps/AOT_Recon/ReconTools.py

@@ -1,9 +1,10 @@
 import os
+from AOT_biomaps.AOT_Recon.AOT_SparseSMatrix import SparseSMatrix_CSR, SparseSMatrix_SELL
 import torch
 import numpy as np
 from numba import njit, prange
 from torch_sparse import coalesce
-import torch.nn.functional as F
+import cupyx.scipy.sparse as cpsparse
 
 def load_recon(hdr_path):
     """
@@ -78,7 +79,7 @@ def load_recon(hdr_path):
     rescale_offset = float(header.get('data rescale offset', 0))
     image = image * rescale_slope + rescale_offset
     
-    return image.T
+    return image
 
 def mse(y_true, y_pred):
     """
@@ -150,20 +151,82 @@ def ssim(img1, img2, win_size=7, k1=0.01, k2=0.03, L=1.0):
     return np.mean(ssim_map)
 
 def calculate_memory_requirement(SMatrix, y):
-    """Calculate the memory requirement for the given matrices in GB."""
-    num_elements_SMatrix = SMatrix.size
-    num_elements_y = y.size
-    num_elements_theta = SMatrix.shape[1] * SMatrix.shape[2]  # Assuming theta has shape (Z, X)
+    """
+    Calcule la mémoire requise (en Go) pour :
+    - SMatrix : Matrice (np.ndarray, CuPy CSR, SparseSMatrix_CSR ou SparseSMatrix_SELL)
+    - y : vecteur (NumPy ou CuPy, float32)
+
+    Args:
+        SMatrix: Matrix object (np.ndarray, cpsparse.csr_matrix, SparseSMatrix_CSR, or SparseSMatrix_SELL)
+        y: Vector (float32)
+    """
+    total_bytes = 0
+
+    # --- 1. Memory for SMatrix ---
+    
+    # 1.1. Custom Sparse Matrix (SELL/CSR)
+    if isinstance(SMatrix, (SparseSMatrix_SELL, SparseSMatrix_CSR)):
+        # We rely on the getMatrixSize method, which we fixed to track all host/GPU bytes.
+        # This is the most reliable way to estimate memory for custom GPU-backed structures.
+        try:
+            matrix_size_gb = SMatrix.getMatrixSize()
+            if isinstance(matrix_size_gb, dict) and 'error' in matrix_size_gb:
+                raise ValueError(f"SMatrix allocation error: {matrix_size_gb['error']}")
+            
+            # Convert GB back to bytes (1 GB = 1024^3 bytes)
+            size_SMatrix = matrix_size_gb * (1024 ** 3)
+            total_bytes += size_SMatrix
+            print(f"SMatrix (Custom Sparse) size: {matrix_size_gb:.3f} GB")
+
+        except AttributeError:
+            raise AttributeError("Custom Sparse Matrix must implement the getMatrixSize() method.")
+    
+    # 1.2. NumPy Dense Array (Standard)
+    elif isinstance(SMatrix, np.ndarray):
+        # Dense NumPy array (float32)
+        size_SMatrix = SMatrix.nbytes
+        total_bytes += size_SMatrix
+        print(f"SMatrix (NumPy Dense) size: {size_SMatrix / (1024 ** 3):.3f} GB")
+
+    # 1.3. CuPy CSR Matrix (Standard Sparse CuPy)
+    # Note: Requires CuPy to be imported, which is usually done outside this function.
+    # Assuming 'cpsparse.csr_matrix' is available in the environment if this path is taken.
+    elif 'cupy.sparse' in str(type(SMatrix)): # Using string check for type safety outside CuPy context
+        # CuPy CSR matrix structure: data (float32), indices (int32), indptr (int32)
+        nnz = SMatrix.nnz
+        num_rows = SMatrix.shape[0]
+        size_data = nnz * 4        # float32 = 4 bytes
+        size_indices = nnz * 4     # int32 = 4 bytes
+        size_indptr = (num_rows + 1) * 4 # int32 = 4 bytes
+        size_SMatrix = size_data + size_indices + size_indptr
+        total_bytes += size_SMatrix
+        print(f"SMatrix (CuPy CSR) size: {size_SMatrix / (1024 ** 3):.3f} GB")
+
+    else:
+        raise ValueError("SMatrix must be a np.ndarray, cpsparse.csr_matrix, or a custom SparseSMatrix object (CSR/SELL).")
+
+    # --- 2. Memory for Vector y ---
+    
+    # Check if y is a CuPy array or NumPy array (assuming float32 based on docstring)
+    if hasattr(y, 'nbytes'):
+        size_y = y.nbytes
+        total_bytes += size_y
+        print(f"Vector y size: {size_y / (1024 ** 3):.3f} GB")
+    else:
+        # Fallback if object doesn't expose nbytes (e.g., custom buffer), but usually array objects do.
+        raise ValueError("Vector y must be an array type exposing the .nbytes attribute.")
 
-    # Calculate total memory requirement in GB
-    total_memory = (num_elements_SMatrix + num_elements_y + num_elements_theta) * 32 / 8 / 1024**3
-    return total_memory
 
-def check_gpu_memory(device_index, required_memory):
+    # --- 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, total_memory = torch.cuda.mem_get_info(f"cuda:{device_index}")
+    free_memory, _ = torch.cuda.mem_get_info(f"cuda:{device_index}")
     free_memory_gb = free_memory / 1024**3
-    print(f"Free memory on GPU {device_index}: {free_memory_gb:.2f} GB, Required memory: {required_memory:.2f} GB")
+    if show_logs:
+        print(f"Free memory on GPU {device_index}: {free_memory_gb:.2f} GB, Required memory: {required_memory:.2f} GB")
     return free_memory_gb >= required_memory
 
 @njit(parallel=True)
@@ -270,3 +333,48 @@ def prox_F_star(y, sigma, a):
 def prox_G(x, tau, K):
     return torch.clamp(x - tau * K, min=0)
 
+def filter_radon(f, N, filter_type, Fc):
+    """
+    Implémente les filtres pour la rétroprojection filtrée (iRadon).
+    Inspirée de la fonction MATLAB FilterRadon de Mamouna Bocoum.
+
+    Paramètres :
+    ------------
+    f : np.ndarray
+        Vecteur des fréquences (ex: f_t ou f_z).
+    N : int
+        Taille du filtre (longueur de f).
+    filter_type : str
+        Type de filtre : 'ram-lak', 'shepp-logan', 'cosine', 'hamming', 'hann'.
+    Fc : float
+        Fréquence de coupure.
+
+    Retourne :
+    -----------
+    FILTER : np.ndarray
+        Filtre appliqué aux fréquences.
+    """
+    FILTER = np.abs(f)
+
+    if filter_type == 'ram-lak':
+        pass  # FILTER = |f| (déjà calculé)
+    elif filter_type == 'shepp-logan':
+        # Évite la division par zéro
+        with np.errstate(divide='ignore', invalid='ignore'):
+            FILTER = FILTER * (np.sinc(2 * f / (2 * Fc)))  # sin(2πf/(2Fc))/(2πf/(4Fc)) = sinc(2f/(2Fc))
+        FILTER[np.isnan(FILTER)] = 1.0  # Pour f=0
+    elif filter_type == 'cosine':
+        FILTER = FILTER * np.cos(2 * np.pi * f / (4 * Fc))
+    elif filter_type == 'hamming':
+        FILTER = FILTER * (0.54 + 0.46 * np.cos(2 * np.pi * f / Fc))
+    elif filter_type == 'hann':
+        FILTER = FILTER * (1 + np.cos(2 * np.pi * f / (4 * Fc))) / 2
+    else:
+        raise ValueError(f"Type de filtre inconnu : {filter_type}")
+
+    # Coupure des fréquences au-delà de Fc
+    FILTER[np.abs(f) > Fc] = 0
+    # Atténuation exponentielle (optionnelle, comme dans le code MATLAB)
+    FILTER = FILTER * np.exp(-2 * (np.abs(f) / Fc)**10)
+
+    return FILTER

AOT_biomaps/AOT_Recon/__init__.py

@@ -9,3 +9,4 @@ from .ReconTools import *
 
 
 
+

AOT_biomaps/AOT_Recon/_mainRecon.py

@@ -10,7 +10,7 @@ from abc import ABC, abstractmethod
 
 
 class Recon(ABC):
-    def __init__(self, experiment, saveDir = None, isGPU = config.get_process() == 'gpu',  isMultiGPU =  True if config.numGPUs > 1 else False, isMultiCPU = True):
+    def __init__(self, experiment, saveDir = None, isGPU = config.get_process() == 'gpu', isMultiCPU = True):
         self.reconPhantom = None
         self.reconLaser = None
         self.experiment = experiment
@@ -21,7 +21,6 @@ class Recon(ABC):
         self.CRC = None
 
         self.isGPU = isGPU
-        self.isMultiGPU = isMultiGPU
         self.isMultiCPU = isMultiCPU
 
         if str(type(self.experiment)) != str(Tomography):
@@ -31,7 +30,7 @@ class Recon(ABC):
     def run(self,withTumor = True):
         pass
 
-    def save(self, withTumor=True, overwrite=False):
+    def save(self, withTumor=True, overwrite=False, date=None, show_logs=True):
         """
         Save the reconstruction results (reconPhantom is with tumor, reconLaser is without tumor) and indices of the saved recon results, in numpy format.
 
@@ -42,23 +41,31 @@ class Recon(ABC):
         Warnings:
             reconPhantom and reconLaser are lists of 2D numpy arrays, each array corresponding to one iteration.
         """
-        should_save, filepath = self.checkExistingFile(withTumor, overwrite)
-        if not should_save:
+        isExisting, filepath = self.checkExistingFile(date=date)
+        if isExisting and not overwrite:
             return
+        
+        filename = 'reconPhantom.npy' if withTumor else 'reconLaser.npy'
+        filepathRecon = os.path.join(filepath, filename)
 
         if withTumor:
             if not self.reconPhantom or len(self.reconPhantom) == 0:
                 raise ValueError("Reconstructed phantom is empty. Run reconstruction first.")
-            np.save(filepath, np.array(self.reconPhantom))
+            np.save(filepathRecon, np.array(self.reconPhantom))
         else:
             if not self.reconLaser or len(self.reconLaser) == 0:
                 raise ValueError("Reconstructed laser is empty. Run reconstruction first.")
-            np.save(filepath, np.array(self.reconLaser))
+            np.save(filepathRecon, np.array(self.reconLaser))
 
-        print(f"Reconstruction results saved to {os.path.dirname(filepath)}")
+        if self.indices is not None and len(self.indices) > 0:
+            filepathIndices = os.path.join(filepath, "indices.npy")
+            np.save(filepathIndices, np.array(self.indices))
+
+        if show_logs:
+            print(f"Reconstruction results saved to {os.path.dirname(filepath)}")
 
     @abstractmethod
-    def checkExistingFile(self, withTumor=True, overwrite=False):
+    def checkExistingFile(self, date = None):
         pass
 
     def calculateCRC(self, use_ROI=True):
@@ -132,7 +139,7 @@ class Recon(ABC):
         if self.reconType in (ReconType.Analytic, ReconType.DeepLearning):
             self.MSE = mse(self.experiment.OpticImage.phantom, self.reconPhantom)
 
-        elif self.reconType in (ReconType.Algebraic, ReconType.Bayesian):
+        elif self.reconType in (ReconType.Algebraic, ReconType.Bayesian, ReconType.Convex):
             self.MSE = []
             for theta in self.reconPhantom:
                 self.MSE.append(mse(self.experiment.OpticImage.phantom, theta))
@@ -158,10 +165,9 @@ class Recon(ABC):
                 data_range = theta.max() - theta.min()
                 ssim_value = ssim(self.experiment.OpticImage.phantom, theta, data_range=data_range)
                 self.SSIM.append(ssim_value)
- 
-    def show(self, withTumor=True, savePath=None):
-        fig, axs = plt.subplots(1, 2, figsize=(20, 10))
+    
 
+    def show(self, withTumor=True, savePath=None):
         if withTumor:
             if self.reconPhantom is None or self.reconPhantom == []:
                 raise ValueError("Reconstructed phantom with tumor is empty. Run reconstruction first.")
@@ -169,9 +175,31 @@ class Recon(ABC):
                 image = self.reconPhantom[-1]
             else:
                 image = self.reconPhantom
-            # Phantom original
+            if self.experiment.OpticImage is None:
+                fig, axs = plt.subplots(1, 1, figsize=(10, 10))
+            else:
+                fig, axs = plt.subplots(1, 2, figsize=(20, 10))
+                # Phantom original
+                im1 = axs[1].imshow(
+                    self.experiment.OpticImage.phantom,
+                    cmap='hot',
+                    vmin=0,
+                    vmax=1,
+                    extent=(
+                        self.experiment.params.general['Xrange'][0],
+                        self.experiment.params.general['Xrange'][1],
+                        self.experiment.params.general['Zrange'][1],
+                        self.experiment.params.general['Zrange'][0]
+                    ),
+                    aspect='equal'  
+                )
+                axs[1].set_title("Phantom with tumor")
+                axs[1].set_xlabel("x (mm)", fontsize=12)
+                axs[1].set_ylabel("z (mm)", fontsize=12)
+                axs[1].tick_params(axis='both', which='major', labelsize=8)
+            # Phantom reconstruit
             im0 = axs[0].imshow(
-                self.experiment.OpticImage.phantom,
+                image,
                 cmap='hot',
                 vmin=0,
                 vmax=1,
@@ -183,29 +211,11 @@ class Recon(ABC):
                 ),
                 aspect='equal'  
             )
-            axs[0].set_title("Phantom with tumor")
+            axs[0].set_title("Reconstructed phantom with tumor")
             axs[0].set_xlabel("x (mm)", fontsize=12)
             axs[0].set_ylabel("z (mm)", fontsize=12)
             axs[0].tick_params(axis='both', which='major', labelsize=8)
-            # Phantom reconstruit
-            im1 = axs[1].imshow(
-                image,
-                cmap='hot',
-                vmin=0,
-                vmax=1,
-                extent=(
-                    self.experiment.params.general['Xrange'][0],
-                    self.experiment.params.general['Xrange'][1],
-                    self.experiment.params.general['Zrange'][1],
-                    self.experiment.params.general['Zrange'][0]
-                ),
-                aspect='equal'  
-            )
-            axs[1].set_title("Reconstructed phantom with tumor")
-            axs[1].set_xlabel("x (mm)", fontsize=12)
-            axs[1].set_ylabel("z (mm)", fontsize=12)
-            axs[1].tick_params(axis='both', which='major', labelsize=8)
-            axs[1].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
+            axs[0].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
         else:
             if self.reconLaser is None or self.reconLaser == []:
                 raise ValueError("Reconstructed laser without tumor is empty. Run reconstruction first.")
@@ -213,9 +223,31 @@ class Recon(ABC):
                 image = self.reconLaser[-1]
             else:
                 image = self.reconLaser
-            # Laser original
+            if self.experiment.OpticImage is None:
+                fig, axs = plt.subplots(1, 1, figsize=(10, 10))
+            else:
+                fig, axs = plt.subplots(1, 2, figsize=(20, 10))
+                # Laser original
+                im1 = axs[1].imshow(
+                    self.experiment.OpticImage.laser.intensity,
+                    cmap='hot',
+                    vmin=0,
+                    vmax=np.max(self.experiment.OpticImage.laser.intensity),
+                    extent=(
+                        self.experiment.params.general['Xrange'][0],
+                        self.experiment.params.general['Xrange'][1],
+                        self.experiment.params.general['Zrange'][1],
+                        self.experiment.params.general['Zrange'][0]
+                    ),
+                    aspect='equal'  
+                )
+                axs[1].set_title("Laser without tumor")
+                axs[1].set_xlabel("x (mm)", fontsize=12)
+                axs[1].set_ylabel("z (mm)", fontsize=12)
+                axs[1].tick_params(axis='both', which='major', labelsize=8)
+            # Laser reconstruit
             im0 = axs[0].imshow(
-                self.experiment.OpticImage.laser.intensity,
+                image,
                 cmap='hot',
                 vmin=0,
                 vmax=np.max(self.experiment.OpticImage.laser.intensity),
@@ -225,36 +257,18 @@ class Recon(ABC):
                     self.experiment.params.general['Zrange'][1],
                     self.experiment.params.general['Zrange'][0]
                 ),
-                aspect='equal'  
+                aspect='equal'
             )
-            axs[0].set_title("Laser without tumor")
+            axs[0].set_title("Reconstructed laser without tumor")
             axs[0].set_xlabel("x (mm)", fontsize=12)
             axs[0].set_ylabel("z (mm)", fontsize=12)
             axs[0].tick_params(axis='both', which='major', labelsize=8)
-            # Laser reconstruit
-            im1 = axs[1].imshow(
-                image,
-                cmap='hot',
-                vmin=0,
-                vmax=np.max(self.experiment.OpticImage.laser.intensity),
-                extent=(
-                    self.experiment.params.general['Xrange'][0],
-                    self.experiment.params.general['Xrange'][1],
-                    self.experiment.params.general['Zrange'][1],
-                    self.experiment.params.general['Zrange'][0]
-                ),
-                aspect='equal'
-            )
-            axs[1].set_title("Reconstructed laser without tumor")
-            axs[1].set_xlabel("x (mm)", fontsize=12)
-            axs[1].set_ylabel("z (mm)", fontsize=12)
-            axs[1].tick_params(axis='both', which='major', labelsize=8)
-            axs[1].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
+            axs[0].tick_params(axis='y', which='both', left=False, right=False, labelleft=False)
 
         # Colorbar commune
         fig.subplots_adjust(bottom=0.2)
         cbar_ax = fig.add_axes([0.25, 0.08, 0.5, 0.03])
-        cbar = fig.colorbar(im1, cax=cbar_ax, orientation='horizontal')
+        cbar = fig.colorbar(im0, cax=cbar_ax, orientation='horizontal')
         cbar.set_label('Normalized Intensity', fontsize=12)
         cbar.ax.tick_params(labelsize=8)
 

AOT_biomaps/__init__.py

@@ -74,6 +74,9 @@ from .AOT_Recon.AOT_Optimizers.DEPIERRO import *
 from .AOT_Recon.AOT_Optimizers.MAPEM import *
 from .AOT_Recon.AOT_Optimizers.MLEM import *
 from .AOT_Recon.AOT_Optimizers.PDHG import *
+# SPARSE S-MATRIX
+from .AOT_Recon.AOT_SparseSMatrix.SparseSMatrix_CSR import *
+from .AOT_Recon.AOT_SparseSMatrix.SparseSMatrix_SELL import *
 # POTENTIAL FUNCTIONS
 from .AOT_Recon.AOT_PotentialFunctions.Huber import *
 from .AOT_Recon.AOT_PotentialFunctions.Quadratic import *
@@ -82,7 +85,7 @@ from .AOT_Recon.AOT_PotentialFunctions.RelativeDifferences import *
 from .Config import config
 from .Settings import *
 
-__version__ = '2.9.167'
+__version__ = '2.9.270'
 __process__ = config.get_process()
 
 def initialize(process=None):
@@ -131,76 +134,3 @@ def initialize(process=None):
 
 
 
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{aot_biomaps-2.9.167.dist-info → aot_biomaps-2.9.270.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AOT_biomaps
-Version: 2.9.167
+Version: 2.9.270
 Summary: Acousto-Optic Tomography
 Home-page: https://github.com/LucasDuclos/AcoustoOpticTomography
 Author: Lucas Duclos
@@ -15,6 +15,7 @@ Requires-Dist: nvidia-ml-py3==7.352.0
 Requires-Dist: numpy==1.26.4
 Requires-Dist: torch==2.7.0
 Requires-Dist: scipy==1.13.1
+Requires-Dist: cupy-cuda12x==13.6.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: home-page

aot_biomaps-2.9.270.dist-info/RECORD

@@ -0,0 +1,47 @@
+AOT_biomaps/Config.py,sha256=ghEOP1n8aO1pR-su13wMeAZAxZRfry5hH67NbtZ8SqI,3614
+AOT_biomaps/Settings.py,sha256=v8fPhnvvcfBJP29m1RLOTEr3jndGLGwbUiORXmsj2Bo,2853
+AOT_biomaps/__init__.py,sha256=iEepgwL2rWJA8lbRj13CVqHYGC2VHsTf6zp7mQFm480,4202
+AOT_biomaps/AOT_Acoustic/AcousticEnums.py,sha256=s5kXa6jKzbS4btwbubrVcynLOr0yg5tth5vL_FGfbMk,1802
+AOT_biomaps/AOT_Acoustic/AcousticTools.py,sha256=al7xXKMY5e-qQQ7nrQVPVAmqYiB320OluNlY6ti8iKc,7539
+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
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+AOT_biomaps/AOT_Experiment/Tomography.py,sha256=Ri83b4GMrxJO60qWsK9JInS9a7HU2Q8uqpjD3Xkl9OY,24488
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