Merge pull request #109 from PolarizedLightFieldMicroscopy/axial_voxel

Axial dimension of voxels can be larger
PolarizedLightFieldMicroscopy · Sep 23, 2024 · 2518d00 · 2518d00
2 parents 06b457f + 69d4889
commit 2518d00
Show file tree

Hide file tree

Showing 5 changed files with 14 additions and 11 deletions.
diff --git a/config/spicule/iter_config.json b/config/spicule/iter_config.json
@@ -1,5 +1,5 @@
 {
-    "n_epochs": 10,
+    "n_epochs": 100,
     "regularization_weight": 0.5,
     "lr": 1e-3,
     "lr_birefringence": 1e-3,
@@ -10,7 +10,7 @@
     "datafidelity": "euler",
     "regularization_fcns": [
         ["birefringence active L2", 10000],
-        ["birefringence active negative penalty", 1000000]
+        ["birefringence active negative penalty", 1000]
     ],
     "nerf_mode": false,
     "from_simulation": false,

diff --git a/config/spicule/optical_config.json b/config/spicule/optical_config.json
@@ -1,7 +1,7 @@
 {
     "volume_shape"      : [31, 110, 110],
-    "axial_voxel_size_um"     : 1.0,
-    "cube_voxels"       : true,
+    "axial_voxel_size_um"     : 6.75,
+    "cube_voxels"       : false,
     "pixels_per_ml"     : 16,
     "n_micro_lenses"    : 94,
     "n_voxels_per_ml"   : 1,

diff --git a/recon_scripts/spicule.py b/recon_scripts/spicule.py
@@ -131,6 +131,6 @@ def recon_spicule(
     init_vol_path = None
     recon_spicule(
         init_vol_path,
-        "debug",
+        "axial_voxels",
         load_rays=True
     )
diff --git a/src/VolumeRaytraceLFM/abstract_classes.py b/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).

diff --git a/src/VolumeRaytraceLFM/reconstructions.py b/src/VolumeRaytraceLFM/reconstructions.py
@@ -950,8 +950,12 @@ def visualize_and_save(self, ep, fig, output_dir):
                 Delta_n = volume_estimation.get_delta_n().detach().unsqueeze(0)
             else:
                 Delta_n = volume_estimation.get_delta_n().detach().unsqueeze(0)
-            mip_image = convert_volume_to_2d_mip(Delta_n)
-            mip_image_np = prepare_plot_mip(mip_image, plot=False)
+            vol_size_um = self.optical_info["voxel_size_um"]
+            rel_scaling_factor = vol_size_um[0] / vol_size_um[2]
+            mip_image = convert_volume_to_2d_mip(
+                Delta_n, scaling_factors=(1, 1, rel_scaling_factor)
+            )
+            mip_image_np = prepare_plot_mip(mip_image, plot=True)
             plot_iteration_update_gridspec(
                 self.birefringence_mip_sim,
                 self.ret_img_meas,