multimodars 0.7.2__tar.gz → 0.7.4__tar.gz

{multimodars-0.7.2 → multimodars-0.7.4}/CHANGELOG.md

@@ -3,6 +3,73 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+## [0.7.4] - 2026-10-02
+
+### Fixed
+- Alignment: the reference point is found on the full-resolution centerline and the resampling
+  is anchored on it, instead of snapping to the nearest frame-spaced sample (up to half a spacing).
+- Alignment: the reference frame, not frame 0, is placed on the reference point, matching the
+  rotation search. Frames off either end of the centerline no longer shift the rest.
+- `find_ref_frame_idx` returns the frame's position instead of its `id`.
+- Alignment: centerlines given in ascending z kept backwards tangents after being reversed, so
+  frames were rotated to face against the centerline.
+- Alignment: the resampled centerline no longer drops up to one spacing at its distal end.
+- `Centerline.resample` no longer adds a near-duplicate point before the end through float drift.
+
+### Internal
+- Alignment preprocessing uses `Centerline::resample_anchored` instead of its own copy. Shared
+  `cumulative_arc_length` / `mean_spacing` helpers replace the hand-written versions.
+
+## [0.7.3] - 2026-09-28
+Smoother anomalous ostium. The two halves of the ostial ring now meet in smooth arcs instead of
+sharp kinks, the ring's correction is faded into the aortic mesh all the way round, and the fillet
+only rounds the aorta-facing half - towards the aorta rather than back into the vessel. On
+`examples/data` the raw stitched mesh goes from 220 to 81 self-intersecting faces at the ostium
+(235 to 47 after `fix_and_remesh_stitched_mesh`). Still to do: most of the rest sit at one tip of
+the slit-like ostium, where the aortic wall touches the first millimetres of the intravascular tube.
+
+### Added
+- `stitch_ccta_to_intravascular` gained `seam_points_a` / `seam_points_b` (default 2 / 4). At both
+  seams where the ostium's aorta-facing Half A meets its coronary-facing Half B, that many Half A /
+  Half B points are replaced by a smooth arc that follows each half's own direction. Everything
+  outside those ranges stays exactly in place, so Half A's mid-section keeps its wall-thickness
+  offset from the intravascular ostium. The counts are points on the CCTA ring as cut from the
+  mesh, before it is densified; more than a half can give are reduced with a warning. Only used
+  with `prox_start_mode="highest_z"` and `proximal_is_ostium=True`.
+
+### Changed
+- `fillet_bulge` now only rounds the ostium's Half A, fading out along the seam arcs; Half B and
+  the distal seam stay direct strips (0.7.2 rounded every strut of both seams). It needs
+  `prox_start_mode="highest_z"` with `proximal_is_ostium=True`, otherwise a warning is printed and
+  the direct strip is used.
+- The two-half ostium's IV-plane clamp now runs before the seam arcs are built, so it cannot
+  flatten them back into a kink. What triggers it (ring and IV plane at least 45° apart) is
+  unchanged.
+
+### Fixed
+- The fillet's arcs bulged away from the combined centroid of both rings, which on an anomalous
+  ostium sent many of them back into the vessel (47 of 100 on `examples/data`). They now bulge
+  away from the intravascular geometry, along the ostial frame's outward normal.
+- Only Half A's displacement was faded into the surrounding aortic mesh, so the faces behind
+  Half B's moved rim folded through the intravascular tube. The whole ring's displacement is now
+  faded in.
+- A zero-length strut no longer misaligns the fillet's intermediate rings.
+- `stitch` (the one-call wrapper) failed with its default regions: it removed them with
+  `target_boundaries=1`, merging the two rims into one ring, which stitching then rejected. It now
+  keeps both rims.
+- `read_mesh` no longer falls back to face-cleanup methods that trimesh 4 removed; they could only
+  hide an error.
+
+### Internal
+- `_redistribute_ring_evenly`'s arc-length sampling moved into `_even_arclength_samples`, so
+  per-point values (the Half A weights) resample with the points.
+- `_condition_ostium_ring_two_half` and `_prepare_prox_dist_boundary_pts` also return the Half A
+  weights; `_carry_ring_weights` keeps them with their points through densification, start-point
+  rotation and winding fixes.
+- `_bulge_arc_points` is replaced by the vectorised `_fillet_arc_layers`.
+  `_taper_ring_displacement` lost `protected_pts` / `seam_damping`, which fading the whole ring
+  no longer needs.
+
 ## [0.7.2] - 2026-09-19
 More anatomical approach in creating the anomalous ostium. Takes the wall measurement to create
 and offset. This ensures that the ostium is represented like the ostium from the intravascular
@@ -162,7 +229,7 @@ kind of a dome on top of this plane.
 ### Fixed
 - `align_manual` no explicitly states `rotation_angle_deg` instead of `rotation_angle`
 
-## Changed
+### Changed
 - `align_manual`, `align_combined` and `align_three_points` all return their rotation angle now.
 
 ## [0.5.4] - 2026-08-03 Hotfix

{multimodars-0.7.2 → multimodars-0.7.4}/Cargo.lock

@@ -696,7 +696,7 @@ dependencies = [
 
 [[package]]
 name = "multimodars"
-version = "0.7.2"
+version = "0.7.4"
 dependencies = [
  "anyhow",
  "approx",

{multimodars-0.7.2 → multimodars-0.7.4}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "multimodars"
-version = "0.7.2"
+version = "0.7.4"
 edition = "2021"
 license = "MIT"
 readme = "README.md"

{multimodars-0.7.2 → multimodars-0.7.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multimodars
-Version: 0.7.2
+Version: 0.7.4
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -36,7 +36,7 @@ Project-URL: Issues, https://github.com/yungselm/multimoda-rs/issues
 > Brace for breaking changes!
 
 [![PyPI](https://img.shields.io/pypi/v/multimodars.svg)](https://pypi.org/project/multimodars)
-[![Downloads](https://static.pepy.tech/badge/multimodars)](https://pepy.tech/project/multimodars)
+<!-- [![Downloads](https://static.pepy.tech/badge/multimodars)](https://pepy.tech/project/multimodars) -->
 [![License](https://img.shields.io/pypi/l/multimodars.svg)](LICENSE)
 [![Docs](https://img.shields.io/readthedocs/multimoda-rs)](https://multimoda-rs.readthedocs.io)
 [![Tests and Build](https://github.com/yungselm/multimoda-rs/actions/workflows/CI.yml/badge.svg)](https://github.com/yungselm/multimoda-rs/actions/workflows/CI.yml)
@@ -104,7 +104,7 @@ rest, stress, dia, sys, _ = mm.from_file_full(
 # Align geometry onto a CCTA-derived centerline
 cl_raw = np.genfromtxt("examples/data/centerline_raw.csv", delimiter=",")
 centerline = mm.numpy_to_centerline(cl_raw)
-aligned_pair, cl_resampled, total_rotation_deg = mm.align_three_point(
+aligned_pair, spacing_mm, total_rotation_deg = mm.align_three_point(
     centerline, rest,
     main_ref_pt=(12.2605, -201.3643, 1751.0554),
     counterclockwise_ref_pt=(11.7567, -202.1920, 1754.7975),

{multimodars-0.7.2 → multimodars-0.7.4}/README.md

@@ -12,7 +12,7 @@
 > Brace for breaking changes!
 
 [![PyPI](https://img.shields.io/pypi/v/multimodars.svg)](https://pypi.org/project/multimodars)
-[![Downloads](https://static.pepy.tech/badge/multimodars)](https://pepy.tech/project/multimodars)
+<!-- [![Downloads](https://static.pepy.tech/badge/multimodars)](https://pepy.tech/project/multimodars) -->
 [![License](https://img.shields.io/pypi/l/multimodars.svg)](LICENSE)
 [![Docs](https://img.shields.io/readthedocs/multimoda-rs)](https://multimoda-rs.readthedocs.io)
 [![Tests and Build](https://github.com/yungselm/multimoda-rs/actions/workflows/CI.yml/badge.svg)](https://github.com/yungselm/multimoda-rs/actions/workflows/CI.yml)
@@ -80,7 +80,7 @@ rest, stress, dia, sys, _ = mm.from_file_full(
 # Align geometry onto a CCTA-derived centerline
 cl_raw = np.genfromtxt("examples/data/centerline_raw.csv", delimiter=",")
 centerline = mm.numpy_to_centerline(cl_raw)
-aligned_pair, cl_resampled, total_rotation_deg = mm.align_three_point(
+aligned_pair, spacing_mm, total_rotation_deg = mm.align_three_point(
     centerline, rest,
     main_ref_pt=(12.2605, -201.3643, 1751.0554),
     counterclockwise_ref_pt=(11.7567, -202.1920, 1754.7975),

{multimodars-0.7.2 → multimodars-0.7.4}/multimodars/_processing.py

@@ -1,31 +1,65 @@
 from __future__ import annotations
 
 from .multimodars import (
+    PyCenterline,
     PyContour,
     PyContourType,
+    PyDiscretizedVesselTree,  # noqa: F401 — re-exported for type annotations
     PyGeometry,
     PyGeometryPair,
     PyInputData,
-    PyCenterline,
-    PyDiscretizedVesselTree,  # noqa: F401 — re-exported for type annotations
-    from_file_full as _from_file_full,
-    from_file_doublepair as _from_file_doublepair,
-    from_file_singlepair as _from_file_singlepair,
-    from_file_single as _from_file_single,
-    from_array_full as _from_array_full,
-    from_array_doublepair as _from_array_doublepair,
-    from_array_singlepair as _from_array_singlepair,
-    from_array_single as _from_array_single,
-    align_three_point as _align_three_point,
-    align_manual as _align_manual,
+)
+from .multimodars import (
     align_combined as _align_combined,
-    to_obj as _to_obj,
-    read_centerline_vtp as _read_centerline_vtp,
-    find_centerline_bounded_points_simple as _find_centerline_bounded_points_simple,
-    find_proximal_distal_scaling as _find_proximal_distal_scaling,
+)
+from .multimodars import (
+    align_manual as _align_manual,
+)
+from .multimodars import (
+    align_three_point as _align_three_point,
+)
+from .multimodars import (
     build_adjacency_map as _build_adjacency_map,
+)
+from .multimodars import (
     discretize_vessel as _discretize_vessel,
 )
+from .multimodars import (
+    find_centerline_bounded_points_simple as _find_centerline_bounded_points_simple,
+)
+from .multimodars import (
+    find_proximal_distal_scaling as _find_proximal_distal_scaling,
+)
+from .multimodars import (
+    from_array_doublepair as _from_array_doublepair,
+)
+from .multimodars import (
+    from_array_full as _from_array_full,
+)
+from .multimodars import (
+    from_array_single as _from_array_single,
+)
+from .multimodars import (
+    from_array_singlepair as _from_array_singlepair,
+)
+from .multimodars import (
+    from_file_doublepair as _from_file_doublepair,
+)
+from .multimodars import (
+    from_file_full as _from_file_full,
+)
+from .multimodars import (
+    from_file_single as _from_file_single,
+)
+from .multimodars import (
+    from_file_singlepair as _from_file_singlepair,
+)
+from .multimodars import (
+    read_centerline_vtp as _read_centerline_vtp,
+)
+from .multimodars import (
+    to_obj as _to_obj,
+)
 
 _AlignLog = list[tuple[int, int, float, float, float, float, float]]
 
@@ -1035,7 +1069,10 @@ def align_three_point(
     geometry : PyGeometryPair or PyGeometry
         Single geometry or diastolic/systolic geometry pair to align.
     main_ref_pt : tuple of float
-        ``(x, y, z)`` reference point at the aortic ostium.
+        ``(x, y, z)`` reference point at the aortic ostium.  The geometry's reference
+        frame (the first frame with a reference point) is placed on the closest
+        centerline point; frames that do not fit on the centerline are left
+        unaligned and reported in a warning.
     counterclockwise_ref_pt : tuple of float
         ``(x, y, z)`` counterclockwise reference point (viewed proximal → distal).
     clockwise_ref_pt : tuple of float
@@ -1131,7 +1168,10 @@ def align_manual(
     rotation_angle_deg : float
         Rotation angle in degrees to apply.
     ref_point : tuple of float
-        ``(x, y, z)`` reference point on the centerline.
+        ``(x, y, z)`` reference point on the centerline.  The geometry's reference
+        frame (the first frame with a reference point, else frame 0) is placed on
+        the closest centerline point; frames that do not fit on the centerline are
+        left unaligned and reported in a warning.
     write : bool, optional
         Whether to write the aligned meshes to OBJ files.  Default is ``False``.
     watertight : bool, optional
@@ -1219,7 +1259,10 @@ def align_combined(
     geometry : PyGeometryPair or PyGeometry
         Single geometry or diastolic/systolic geometry pair to align.
     main_ref_pt : tuple of float
-        ``(x, y, z)`` reference point at the aortic ostium.
+        ``(x, y, z)`` reference point at the aortic ostium.  The geometry's reference
+        frame (the first frame with a reference point) is placed on the closest
+        centerline point; frames that do not fit on the centerline are left
+        unaligned and reported in a warning.
     counterclockwise_ref_pt : tuple of float
         ``(x, y, z)`` counterclockwise reference point (viewed proximal → distal).
     clockwise_ref_pt : tuple of float
@@ -1505,7 +1548,7 @@ def build_adjacency_map(
 
 
 def discretize_vessel(
-    centerline: "PyCenterline",
+    centerline: PyCenterline,
     points: list[tuple[float, float, float]],
     branch_id: int = 0,
     step_size: float = 0.5,

{multimodars-0.7.2 → multimodars-0.7.4}/multimodars/ccta/__init__.py

@@ -1,19 +1,15 @@
 from __future__ import annotations
 
-from . import stitching
-from . import scaling
-from . import labeling
-from . import centerline_prep
-from . import debug_plots as debug_plots
-from . import mesh_regions
-from . import postprocessing as _postprocessing
-
 from pathlib import Path
 from typing import TYPE_CHECKING
+
 import numpy as np
 import trimesh
 
 from ..io.write_geometries import export_section_stl as export_section_stl
+from . import centerline_prep, labeling, mesh_regions, scaling, stitching
+from . import debug_plots as debug_plots
+from . import postprocessing as _postprocessing
 
 if TYPE_CHECKING:
     from ..multimodars import PyCenterline, PyFrame, PyGeometry
@@ -264,7 +260,7 @@ def scale(
 def stitch(
     results: dict,
     geometry: PyGeometry,
-    region_remove: list[str] | str = ["anomalous_points", "proximal_points"],
+    region_remove: list[str] | str | None = None,
     prox_start_mode: str = "highest_z",
     dist_start_mode: str = "nearest_iv",
 ) -> dict:
@@ -291,12 +287,18 @@ def stitch(
     geometry : PyGeometry
         Intravascular imaging geometry whose contours define the vessel lumen
         used as the stitching target.
+    region_remove : str or list of str, optional
+        Labeled regions cut out of the CCTA mesh before stitching (default
+        ``["anomalous_points", "proximal_points"]``).
     prox_start_mode : str, optional
         How to choose index 0 of the proximal boundary ring before stitching.
-        ``"nearest_iv"`` (default) rotates to the point closest to IV point 0;
-        ``"highest_z"`` rotates to the point with the largest z-coordinate.
+        ``"highest_z"`` (default here) rotates to the point with the largest
+        z-coordinate and treats the ostium as two halves (see
+        :func:`~multimodars.ccta.stitching.stitch_ccta_to_intravascular`);
+        ``"nearest_iv"`` rotates to the point closest to IV point 0.
     dist_start_mode : str, optional
-        Same as *prox_start_mode* but for the distal boundary ring.
+        Same as *prox_start_mode* but for the distal boundary ring (default
+        ``"nearest_iv"``).
 
     Returns
     -------
@@ -304,8 +306,12 @@ def stitch(
         Stitched results dictionary with the same structure as *results*, where
         ``"mesh"`` is the stitched, hole-filled surface.
     """
+    if region_remove is None:
+        region_remove = ["anomalous_points", "proximal_points"]
+    # Cutting a segment out of the vessel opens a rim at each end, and the
+    # stitch needs both as separate rings.
     updated_results = mesh_regions.remove_labeled_points_from_mesh(
-        results, region_remove
+        results, region_remove, target_boundaries=2
     )
 
     stitched = stitching.stitch_ccta_to_intravascular(