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Forward simulation of the helix is black #84

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gschlafly opened this issue Jan 11, 2024 · 1 comment
Open

Forward simulation of the helix is black #84

gschlafly opened this issue Jan 11, 2024 · 1 comment
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@gschlafly
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def simulate_helix_images():
    optical_info = setup_optical_parameters(
        "config_settings/optical_config_helix.json")
    optical_system = {'optical_info': optical_info}  
    simulator = ForwardModel(optical_system, backend=BACKEND)
    # Volume creation
    helix_path = "objects/Helix/Helix1.h5"
    volume_GT = BirefringentVolume.init_from_file(
        helix_path, BackEnds.PYTORCH, optical_info)
    visualize_volume(volume_GT, optical_info)
    simulator.forward_model(volume_GT)
    simulator.view_images()

image

image

{
    "volume_shape"      : [3, 7, 7],
    "axial_voxel_size_um"     : 1.0,
    "cube_voxels"       : true,
    "pixels_per_ml"     : 17,
    "n_micro_lenses"    : 1,
    "n_voxels_per_ml"   : 1,
    "M_obj"             : 60,
    "na_obj"            : 1.2,
    "n_medium"          : 1.52,
    "wavelength"        : 0.550,
    "camera_pix_pitch"  : 6.5,
}
@gschlafly gschlafly added the invalid This doesn't seem right label Jan 11, 2024
@gschlafly gschlafly self-assigned this Jan 11, 2024
@gschlafly
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gschlafly commented Jan 11, 2024

With a 3x3 MLA and 5x5 MLA, the images are no longer black. However, notably the center lenslet is not black, confirming that the 1x1 MLA should not be black.
image
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