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

Fixed detector positioning in msot acuity echo #149

Merged
merged 2 commits into from
Jun 14, 2022
Merged

Fixed detector positioning in msot acuity echo #149

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0286fe9
Fixed detector positioning in msot acuity echo
kdreher Jun 9, 2022
1e46e54
Fixed x-position shift of illumination in update_settings_for_use_of_…
kdreher Jun 14, 2022
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
6 changes: 2 additions & 4 deletions simpa/core/device_digital_twins/pa_devices/ithera_msot_acuity.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,7 @@ def __init__(self, device_position_mm: np.ndarray = None,
self.probe_height_mm = 43.2
self.focus_in_field_of_view_mm = 8
self.detection_geometry_position_vector = np.add(self.device_position_mm,
np.array([0, 0,
self.probe_height_mm +
self.focus_in_field_of_view_mm]))
np.array([0, 0, self.focus_in_field_of_view_mm]))

if field_of_view_extent_mm is None:
self.field_of_view_extent_mm = np.asarray([-(2 * np.sin(0.34 / 40 * 128) * 40) / 2,
Expand Down Expand Up @@ -190,7 +188,7 @@ def update_settings_for_use_of_model_based_volume_creator(self, global_settings)
self.set_detection_geometry(detection_geometry)
for illumination_geom in self.illumination_geometries:
illumination_geom.device_position_mm = np.add(illumination_geom.device_position_mm,
np.array([0, 0, probe_size_mm]))
np.array([width_shift_for_structures_mm, 0, probe_size_mm]))
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I do not understand where this is coming from exactly.. Is it for "sliding" a probe along the x-axis to potentially simulate multiple areas of the same tissue model?

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

No this comes from the check if the volume is not wide enough. Then the volume is enlarged on both sides and the structures are shifted accordingly so that they are still in the middle of the volume. Then, the device position also needs to be shifted by the same width. The device itself and the detection geometry were already shifted by that width but not the illumination


background_settings = Settings({
Tags.MOLECULE_COMPOSITION: TISSUE_LIBRARY.heavy_water(),
Expand Down