Description
In the model-based volume creation, I added vessels with significant deformations (Tags.STRUCTURE_CURVATURE_FACTOR high, Tags.STRUCTURE_RADIUS_VARIATION_FACTOR high relatively to the vessel size, Tags.STRUCTURE_BIFURCATION_LENGTH_MM set within the lengths of most of the vessels). However, I simulated with different wavelengths and the deformations were different as a function of the wavelength used.
Priority
High : the results for unmixing or comparison between wavelengths may therefore be flawed
Current Behavior
When running model-based volume creation with more than one wavelength on the same structure, the variation of radius and direction of vessels seems to be changing depending on the wavelength. As I understood it, although the settings are constant, ModelBasedAdapter is run multiple times and therefore the vessel structure is added the same number of times, but the script simpa/core/utils/libraries/structure_library/VesselStructure.py defines random parameters in a stochastic way:
l.105 : radius_array.append(np.random.uniform(-1, 1) * radius_variation + radius)
l.107 : step_vector = torch.rand(3).to(self.torch_device) * 2 - 1
Screenshots
$\mu_{a}$ map at the first slice of the volume at each wavelength (800, 850, 900 nm) :
$\mu_{a}$ map at the middle slice of the volume at each wavelength (800, 850, 900 nm) :
Expected behavior
The values for $\mu_{a}$ inside each vessel should vary due to the spectral variation for each chromophores, but the map should look exactly the same.
The expected behavious is that we ensure having a consistent mask, or a consistent choice of the variation parameters along each vessel between successive scans in the scope of a unique simulation to account for the same structure.
Environment (please complete the following information):
- OS: Windows 11
- SIMPA version: 1.0.1.dev7+ga2f9a589.d20250205
- IDE: VSCode
Additional context
I don't have sufficient knowledge of the package to do a PR right now, because the problem seems a bit complicated to me, but let's discuss it if needed.
The function calculate_vessel_samples computes a position_array and a radius_array for each vessel: setting these two parameters as wavelength independant properties of vessels in the setting dictionary could be one of the ways to explore... ?
Description
In the model-based volume creation, I added vessels with significant deformations (
Tags.STRUCTURE_CURVATURE_FACTORhigh,Tags.STRUCTURE_RADIUS_VARIATION_FACTORhigh relatively to the vessel size,Tags.STRUCTURE_BIFURCATION_LENGTH_MMset within the lengths of most of the vessels). However, I simulated with different wavelengths and the deformations were different as a function of the wavelength used.Priority
High : the results for unmixing or comparison between wavelengths may therefore be flawed
Current Behavior
When running model-based volume creation with more than one wavelength on the same structure, the variation of radius and direction of vessels seems to be changing depending on the wavelength. As I understood it, although the settings are constant, ModelBasedAdapter is run multiple times and therefore the vessel structure is added the same number of times, but the script
simpa/core/utils/libraries/structure_library/VesselStructure.pydefines random parameters in a stochastic way:l.105 :
radius_array.append(np.random.uniform(-1, 1) * radius_variation + radius)l.107 :
step_vector = torch.rand(3).to(self.torch_device) * 2 - 1Screenshots
$\mu_{a}$ map at the first slice of the volume at each wavelength (800, 850, 900 nm) :
Expected behavior$\mu_{a}$ inside each vessel should vary due to the spectral variation for each chromophores, but the map should look exactly the same.
The values for
The expected behavious is that we ensure having a consistent mask, or a consistent choice of the variation parameters along each vessel between successive scans in the scope of a unique simulation to account for the same structure.
Environment (please complete the following information):
Additional context
I don't have sufficient knowledge of the package to do a PR right now, because the problem seems a bit complicated to me, but let's discuss it if needed.
The function
calculate_vessel_samplescomputes aposition_arrayand aradius_arrayfor each vessel: setting these two parameters as wavelength independant properties of vessels in the setting dictionary could be one of the ways to explore... ?