Skip to content

update instance segmentation visualisation #57

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

Open
Marei33 wants to merge 8 commits into
base: dev
Choose a base branch
from
Open

update instance segmentation visualisation #57

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
a630e6c
delete conda env from rules and default configfile from the workflows
Marei33 Jun 24, 2026
2ec6291
change instance segmentation visualization
Marei33 Jun 11, 2026
a21d1fb
exclude landmark plot in this branch for better understanding
Marei33 Jun 25, 2026
f7f6f79
save fixed_prealigned as pdf
Marei33 Jun 26, 2026
62dcee4
make plot format optional: png, pdf or None (set via individual save_…
Marei33 Jun 26, 2026
aa5e3e4
move matching plots to plots subfolder
Marei33 Jun 29, 2026
3b3f929
Set test config maxiter to 100 and update matchmaker_vis.svg
Marei33 Jun 29, 2026
09435a8
update matchmaker visualisation with elastic registration example
Marei33 Jun 30, 2026
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 examples/register_config_test_elastic.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@ coherent_point_drift:

ILP:
min_neighbours: 10
max_dist: 30
max_dist: 15

mobie_export: False
mobie_export: True
semantic_seg: True
mobie_dataset_name: "platy1_muscles_stardist"
59 changes: 45 additions & 14 deletions matchmaker/cpd_nonrigid_registration.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,33 +11,67 @@
get_attrs
)


from matchmaker.utils import overlay_pcds, visualize_displacement_field, extract_centroids, run_cpd, create_pcd



def cpd_from_images(fixed_img, fixed_resolution, moving_img, moving_resolution, output_dir, w, beta, lmd, maxiter):
fixed_labels, fixed_center_coords = extract_centroids(fixed_img, fixed_resolution)
moving_labels, moving_center_coord = extract_centroids(moving_img, moving_resolution)

fixed_pcd = create_pcd(fixed_center_coords, fixed_labels)
moving_pcd = create_pcd(moving_center_coord, moving_labels)

overlay_pcds(fixed_pcd, moving_pcd, projection="xz", save_path = output_dir / "pcds_before_registration_xz.png")
overlay_pcds(fixed_pcd, moving_pcd, projection="yz", save_path = output_dir / "pcds_before_registration_yz.png")
overlay_pcds(fixed_pcd, moving_pcd, projection="xy", save_path = output_dir / "pcds_before_registration_xy.png")
overlay_pcds(fixed_pcd, moving_pcd, projection="xz", save_path=output_dir / "plots/pcds_before_registration_xz.png")
overlay_pcds(fixed_pcd, moving_pcd, projection="yz", save_path=output_dir / "plots/pcds_before_registration_yz.png")
overlay_pcds(fixed_pcd, moving_pcd, projection="xy", save_path=output_dir / "plots/pcds_before_registration_xy.png")

logging.info(f"Point cloud registration with parameters w={w}, beta={beta}, lmd={lmd}, maxiter={maxiter}")

registered_pcd = run_cpd(fixed_pcd, moving_pcd, w, beta, lmd, maxiter)

overlay_pcds(fixed_pcd, registered_pcd, projection="xz", save_path = output_dir / "pcds_after_registration_xz.png")
overlay_pcds(fixed_pcd, registered_pcd, projection="yz", save_path = output_dir / "pcds_after_registration_yz.png")
overlay_pcds(fixed_pcd, registered_pcd, projection="xy", save_path = output_dir / "pcds_after_registration_xy.png")
overlay_pcds(
fixed_pcd,
registered_pcd,
projection="xz",
save_path=output_dir / "plots/pcds_after_registration_xz.png",
)
overlay_pcds(
fixed_pcd,
registered_pcd,
projection="yz",
save_path=output_dir / "plots/pcds_after_registration_yz.png",
)
overlay_pcds(
fixed_pcd,
registered_pcd,
projection="xy",
save_path=output_dir / "plots/pcds_after_registration_xy.png",
)

visualize_displacement_field(moving_pcd, registered_pcd, projection="xz", save_path = output_dir / "displacement_field_xz.png")
visualize_displacement_field(moving_pcd, registered_pcd, projection="yz", save_path = output_dir / "displacement_field_yz.png")
visualize_displacement_field(moving_pcd, registered_pcd, projection="xy", save_path = output_dir / "displacement_field_xy.png")
visualize_displacement_field(
moving_pcd,
registered_pcd,
projection="xz",
save_path=output_dir / "plots/displacement_field_xz.png",
)
visualize_displacement_field(
moving_pcd,
registered_pcd,
projection="xz",
save_path=output_dir / "plots/displacement_field_xz.pdf",
)
visualize_displacement_field(
moving_pcd,
registered_pcd,
projection="yz",
save_path=output_dir / "plots/displacement_field_yz.png",
)
visualize_displacement_field(
moving_pcd,
registered_pcd,
projection="xy",
save_path=output_dir / "plots/displacement_field_xy.png",
)

o3d.t.io.write_point_cloud(str(output_dir / "fixed_pcd.pcd"), fixed_pcd, write_ascii=True)
o3d.t.io.write_point_cloud(str(output_dir / "moving_pcd.pcd"), moving_pcd, write_ascii=True)
Expand Down Expand Up @@ -90,8 +124,5 @@ def main(fixed_path, fixed_key, moving_path, moving_key, output_dir, w, beta, lm
)





if __name__ == "__main__":
main()
16 changes: 6 additions & 10 deletions matchmaker/match_pointclouds.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,6 @@
from matchmaker.utils import sparse_ilp_matching, write_index_pairs, plot_matching_qc




def match_points(fixed_pcd, registered_pcd, output_dir, max_dist, min_neighbours):

logging.info(f"Number of points in fixed pcd: {len(fixed_pcd.point.positions)}")
Expand Down Expand Up @@ -44,16 +42,14 @@ def match_points(fixed_pcd, registered_pcd, output_dir, max_dist, min_neighbours
]

if swap_order:
plot_matching_qc(pos_2, pos_1, output_dir / "point_matching_xz.png", pairs=matched_idx_pairs, projection="xz")
plot_matching_qc(pos_2, pos_1, output_dir / "point_matching_yz.png", pairs=matched_idx_pairs, projection="yz")
plot_matching_qc(pos_2, pos_1, output_dir / "point_matching_xy.png", pairs=matched_idx_pairs, projection="xy")
plot_matching_qc(pos_2, pos_1, output_dir / "plots/point_matching_xz.png", pairs=matched_idx_pairs, projection="xz")
plot_matching_qc(pos_2, pos_1, output_dir / "plots/point_matching_yz.png", pairs=matched_idx_pairs, projection="yz")
plot_matching_qc(pos_2, pos_1, output_dir / "plots/point_matching_xy.png", pairs=matched_idx_pairs, projection="xy")

else:
plot_matching_qc(pos_1, pos_2, output_dir / "point_matching_xz.png", pairs=matched_idx_pairs, projection="xz")
plot_matching_qc(pos_1, pos_2, output_dir / "point_matching_yz.png", pairs=matched_idx_pairs, projection="yz")
plot_matching_qc(pos_1, pos_2, output_dir / "point_matching_xy.png", pairs=matched_idx_pairs, projection="xy")


plot_matching_qc(pos_1, pos_2, output_dir / "plots/point_matching_xz.png", pairs=matched_idx_pairs, projection="xz")
plot_matching_qc(pos_1, pos_2, output_dir / "plots/point_matching_yz.png", pairs=matched_idx_pairs, projection="yz")
plot_matching_qc(pos_1, pos_2, output_dir / "plots/point_matching_xy.png", pairs=matched_idx_pairs, projection="xy")

return matched_idx_pairs, matched_label_pairs

Expand Down
Loading