Merge pull request #112 from PolarizedLightFieldMicroscopy/mbl_2024

MBL September 2024

.vscode/settings.json

@@ -5,4 +5,11 @@
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
     "python.testing.autoTestDiscoverOnSaveEnabled": true,
-}
+    "files.exclude": {
+        "**/__pycache__/": true,
+        "**/*.pyc": true,
+        "**/*.pyo": true,
+        ".pytest_cache/": true
+    },
+    "editor.wordWrap": "on",  // Wrap long lines
+}

README.md

@@ -1,6 +1,6 @@
 ![python versions](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)
 [![Run Pytest](https://github.com/PolarizedLightFieldMicroscopy/forward-model/actions/workflows/pytest-action.yml/badge.svg)](https://github.com/PolarizedLightFieldMicroscopy/forward-model/actions/workflows/pytest-action.yml)
-# GeoBirT
+# BirTomo: Birefringence Tomography
 Polarized light field microscopy forward model and inverse model using geometrical optics and Jones Calculus.
 
 ## Installation

config/iter_config.json

@@ -1,5 +1,5 @@
 {
-    "n_epochs": 100,
+    "num_iterations": 100,
     "regularization_weight": 0.1,
     "lr": 1e-3,
     "lr_birefringence": 1e-3,

config/iter_config_sphere.json

@@ -1,5 +1,5 @@
 {
-    "n_epochs": 200,
+    "num_iterations": 200,
     "regularization_weight": 0.5,
     "lr": 1e-3,
     "lr_birefringence": 1e-3,
@@ -13,11 +13,12 @@
         ["birefringence active negative penalty", 1000],
         ["birefringence mask", 0]
     ],
+    "nerf_mode": false,
     "from_simulation": true,
     "vox_indices_by_mla_idx_path": "",
     "mla_rays_at_once": true,
     "two_optic_axis_components": true,
-    "free_memory_by_del_large_arrays": true,
+    "free_memory_by_del_large_arrays": false,
     "save_rays": false,
     "save_freq": 20,
     "output_posfix": "",

examples/reconstruction_basic.py

@@ -0,0 +1,94 @@
+# %% Importing necessary libraries
+import os
+import numpy as np
+import torch
+from VolumeRaytraceLFM.abstract_classes import BackEnds
+from VolumeRaytraceLFM.simulations import ForwardModel
+from VolumeRaytraceLFM.birefringence_implementations import BirefringentVolume
+from VolumeRaytraceLFM.volumes import volume_args
+from VolumeRaytraceLFM.setup_parameters import (
+    setup_optical_parameters,
+    setup_iteration_parameters,
+)
+from VolumeRaytraceLFM.reconstructions import ReconstructionConfig, Reconstructor
+from VolumeRaytraceLFM.utils.file_utils import (
+    create_unique_directory,
+)
+
+# %% Configuration paramters to be changed
+simulate = True
+
+# Volume creation arguments, see src/VolumeRaytraceLFM/volumes/volume_args.py for more options
+volume_gt_creation_args = volume_args.voxel_args
+volume_initial_creation_args = volume_args.random_pos_args
+
+# Paths to the optical and iteration configuration files
+optical_config_file = os.path.join("..", "config", "optical_config_voxel.json")
+iter_config_file = os.path.join("..", "config", "iter_config_reg.json")
+
+# Path to the directory where the reconstruction will be saved
+recon_output_dir = os.path.join("..", "reconstructions", "voxel")
+recon_output_dir_postfix = "postfix"
+recon_directory = create_unique_directory(recon_output_dir, postfix=recon_output_dir_postfix)
+
+# Whether to continue a previous reconstruction
+continue_recon = False
+recon_file_path = r"to be alterned.h5"
+
+# For loading forward images that were saved in a previous reconstruction folder
+measurement_dir = os.path.join(recon_output_dir, "to be altered")
+
+BACKEND = BackEnds.PYTORCH
+DEVICE = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+
+print(f"Using device: {DEVICE}")
+
+# %% Simulate or load forward images
+optical_info = setup_optical_parameters(optical_config_file)
+
+if simulate:
+    optical_system = {"optical_info": optical_info}
+    simulator = ForwardModel(optical_system, backend=BACKEND)
+    volume_GT = BirefringentVolume(
+        backend=BACKEND,
+        optical_info=optical_info,
+        volume_creation_args=volume_gt_creation_args,
+    )
+    simulator.forward_model(volume_GT)
+    simulator.view_images()
+    ret_image_meas = simulator.ret_img.detach().numpy()
+    azim_image_meas = simulator.azim_img.detach().numpy()
+else:
+    ret_image_meas = np.load(os.path.join(measurement_dir, "ret_image.npy"))
+    azim_image_meas = np.load(os.path.join(measurement_dir, "azim_image.npy"))
+    volume_GT = None
+
+# %% Run reconstruction
+recon_optical_info = optical_info.copy()
+iteration_params = setup_iteration_parameters(iter_config_file)
+if continue_recon:
+    initial_volume = BirefringentVolume.init_from_file(recon_file_path, BACKEND, recon_optical_info)
+else:
+    initial_volume = BirefringentVolume(
+        backend=BACKEND,
+        optical_info=recon_optical_info,
+        volume_creation_args=volume_initial_creation_args,
+    )
+recon_config = ReconstructionConfig(
+    recon_optical_info,
+    ret_image_meas,
+    azim_image_meas,
+    initial_volume,
+    iteration_params,
+    gt_vol=volume_GT
+)
+recon_config.save(recon_directory)
+reconstructor = Reconstructor(
+    recon_config,
+    output_dir=recon_directory,
+    device=DEVICE
+)
+reconstructor.reconstruct(plot_live=True)
+print("Reconstruction complete")
+
+# %%

examples/simulation_basic.py

@@ -5,21 +5,25 @@
 from VolumeRaytraceLFM.birefringence_implementations import BirefringentVolume
 from VolumeRaytraceLFM.volumes import volume_args
 from VolumeRaytraceLFM.setup_parameters import setup_optical_parameters
+from VolumeRaytraceLFM.visualization.plotting_volume import visualize_volume
 
 # %% Setting up the optical system
 BACKEND = BackEnds.PYTORCH
-optical_info = setup_optical_parameters("../config/optical_config_sphere.json")
+optical_info = setup_optical_parameters("config/optical_config_sphere.json")
 optical_system = {"optical_info": optical_info}
 print(optical_info)
 
 # %% Create the simulator and volume
-simulator = ForwardModel(optical_system, backend=BACKEND)
 volume = BirefringentVolume(
     backend=BACKEND,
     optical_info=optical_info,
-    volume_creation_args=volume_args.sphere_args2,
+    volume_creation_args=volume_args.shell_small_args,
 )
+plotly_figure = volume.plot_lines_plotly(draw_spheres=True)
+plotly_figure.show()
+
 # %% Image the volume
+simulator = ForwardModel(optical_system, backend=BACKEND)
 simulator.rays.prepare_for_all_rays_at_once()
 start_time = time.perf_counter()
 simulator.rays.reset_timing_info()

src/VolumeRaytraceLFM/abstract_classes.py

@@ -477,8 +477,8 @@ def rays_through_vol(pixels_per_ml, naObj, nMedium, volume_ctr_um):
                                     pixel behind each lenslet
             naObj (float): numerical aperture of the objective lens
             nMedium (float): refractive index of the volume
-            volume_ctr_um (np.array): 3D vector containing the coordinates of the center of the
-                                volume in volume space units (um)
+            volume_ctr_um (np.array): 3D vector containing the coordinates of the center
+                                        of the volume in volume space units (um)
         Returns:
             ray_enter (np.array): (3, X, X) array where (3, i, j) gives the coordinates
                                     within the volume ray entrance plane for which the
@@ -909,8 +909,7 @@ def _filter_invalid_rays(
                 )
 
     def compute_ray_collisions(self, ray_enter, ray_exit, voxel_size_um, vol_shape):
-        """
-        Computes parameters for collisions of rays with voxels.
+        """Computes parameters for collisions of rays with voxels.
         For each ray defined by start (ray_enter) and end (ray_exit) points,
         calculates the intersected voxels and lengths of intersections within
         a volume of given shape (vol_shape) and voxel size (voxel_size_um).