Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Axial dimension of voxels can be larger #109

Merged
merged 2 commits into from
Sep 23, 2024
Merged

Axial dimension of voxels can be larger #109

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
15b0506
Plot scaled MIP with axial voxel size differs
gschlafly Sep 23, 2024
69d4889
Test axial voxels on spicule
gschlafly Sep 23, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions config/spicule/iter_config.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"n_epochs": 10,
"n_epochs": 100,
"regularization_weight": 0.5,
"lr": 1e-3,
"lr_birefringence": 1e-3,
Expand All @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions config/spicule/optical_config.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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,
Expand Down
2 changes: 1 addition & 1 deletion recon_scripts/spicule.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,6 @@ def recon_spicule(
init_vol_path = None
recon_spicule(
init_vol_path,
"debug",
"axial_voxels",
load_rays=True
)
7 changes: 3 additions & 4 deletions src/VolumeRaytraceLFM/abstract_classes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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).
Expand Down
8 changes: 6 additions & 2 deletions src/VolumeRaytraceLFM/reconstructions.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down