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Multi-surfaces-based flattening #13

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784eda8
refactor: multi-surfaces support
huangziwei Mar 3, 2026
e5d6be4
refactor: backward compatibility and variable name clarity
huangziwei Mar 3, 2026
f4af776
refactor: auto select two nearest surfaces for flattening
huangziwei Mar 3, 2026
b4746a7
refactor: more backward compatiblity fix; update: all notebooks with …
huangziwei Mar 3, 2026
6c2f525
fix: unwarpers also use the new surface selector
huangziwei Mar 3, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -29,5 +29,6 @@ venv/
*.swo

dev/
ref/

*copy*
48 changes: 28 additions & 20 deletions notebooks/example.api.high.ipynb
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44 changes: 31 additions & 13 deletions notebooks/example.api.low.ipynb
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Expand Up @@ -13,11 +13,10 @@
"import matplotlib.pyplot as plt\n",
"from matplotlib.colors import Normalize\n",
"\n",
"from pywarper.surface import fit_sac_surface, build_mapping\n",
"from pywarper.surface import fit_surface, build_mapping # fit_sac_surface is also available as a legacy alias\n",
"from pywarper.warpers import warp_nodes, normalize_nodes, warp_skeleton\n",
"from pywarper.stats import get_convex_hull, get_hull_centroid, get_xy_center_of_mass\n",
"from pywarper.utils import read_sumbul_et_al_chat_bands\n",
"\n"
"from pywarper.utils import read_sumbul_et_al_chat_bands\n"
]
},
{
Expand Down Expand Up @@ -54,8 +53,11 @@
"outputs": [],
"source": [
"# Fit surfaces with pygridfit under the hood\n",
"off_sac_surface, xgridmax, ygridmax = fit_sac_surface(x=off_sac['x'], y=off_sac['y'], z=off_sac['z'], smoothness=15)\n",
"on_sac_surface, xgridmin, ygridmin = fit_sac_surface(x=on_sac['x'], y=on_sac['y'], z=on_sac['z'], smoothness=15)"
"off_sac_surface, xgridmax, ygridmax = fit_surface(x=off_sac['x'], y=off_sac['y'], z=off_sac['z'], smoothness=15)\n",
"on_sac_surface, xgridmin, ygridmin = fit_surface(x=on_sac['x'], y=on_sac['y'], z=on_sac['z'], smoothness=15)\n",
"# legacy API\n",
"# off_sac_surface, xgridmax, ygridmax = fit_sac_surface(x=off_sac['x'], y=off_sac['y'], z=off_sac['z'], smoothness=15)\n",
"# on_sac_surface, xgridmin, ygridmin = fit_sac_surface(x=on_sac['x'], y=on_sac['y'], z=on_sac['z'], smoothness=15)"
]
},
{
Expand All @@ -68,17 +70,32 @@
"name": "stdout",
"output_type": "stream",
"text": [
"↳ mapping ON (min) surface …\n",
" done in 0.01 seconds.\n",
"↳ mapping OFF (max) surface …\n",
" done in 0.01 seconds.\n"
"↳ mapping 'on_sac' surface …\n",
" done in 0.02 seconds.\n",
"↳ mapping 'off_sac' surface …\n",
" done in 0.02 seconds.\n"
]
}
],
"source": [
"# fit quasi-conformally mapping\n",
"arbor_boundaries = np.array([skel.nodes[:, 0].min(), skel.nodes[:, 0].max(), skel.nodes[:, 1].min(), skel.nodes[:, 1].max()])\n",
"surface_mapping = build_mapping(on_sac_surface, off_sac_surface, arbor_boundaries, conformal_jump=2, n_anchors=16, verbose=True)"
"surface_mapping = build_mapping( \n",
" {\"on_sac\": on_sac_surface, \"off_sac\": off_sac_surface}, \n",
" bounds=arbor_boundaries, \n",
" conformal_jump=2, \n",
" n_anchors=16, \n",
" verbose=True,\n",
")\n",
"# legacy API\n",
"# surface_mapping = build_mapping(\n",
"# on_sac_surface=on_sac_surface,\n",
"# off_sac_surface=off_sac_surface,\n",
"# bounds=arbor_boundaries,\n",
"# conformal_jump=2,\n",
"# n_anchors=16,\n",
"# verbose=True,\n",
"# )"
]
},
{
Expand All @@ -92,7 +109,8 @@
"output_type": "stream",
"text": [
"[pywarper] Warping skeleton...\n",
" done in 0.36 seconds.\n",
"[pywarper] Flattening with surfaces: \"on_sac\" (z=41.31) and \"off_sac\" (z=56.00)\n",
" done in 0.29 seconds.\n",
"[skeliner] Warning: 58 nodes have zero radius; they were ignored when picking the estimator.\n"
]
}
Expand Down Expand Up @@ -268,7 +286,7 @@
{
"data": {
"text/plain": [
"<matplotlib.legend.Legend at 0x117041310>"
"<matplotlib.legend.Legend at 0x119bb5310>"
]
},
"execution_count": 8,
Expand Down Expand Up @@ -338,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Last updated: 2026-02-16 16:06:33 CET\n",
"Last updated: 2026-03-03 15:40:46 CET\n",
"\n",
"Python implementation: CPython\n",
"Python version : 3.13.11\n",
Expand Down
62 changes: 46 additions & 16 deletions notebooks/example.unwarp.ipynb
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Expand Up @@ -10,10 +10,10 @@
"import skeliner as sk\n",
"import matplotlib.pyplot as plt\n",
"\n",
"from pywarper.surface import fit_sac_surface, build_mapping\n",
"from pywarper.surface import fit_surface, build_mapping # fit_sac_surface is also available as a legacy alias\n",
"from pywarper.warpers import warp_nodes, normalize_nodes, warp_skeleton\n",
"from pywarper.utils import read_sumbul_et_al_chat_bands\n",
"from pywarper.unwarper import unwarp_nodes, unwarp_skeleton\n"
"from pywarper.unwarper import unwarp_nodes, unwarp_skeleton"
]
},
{
Expand Down Expand Up @@ -48,8 +48,11 @@
"outputs": [],
"source": [
"# Fit surfaces with pygridfit under the hood\n",
"off_sac_surface, xgridmax, ygridmax = fit_sac_surface(x=off_sac['x'], y=off_sac['y'], z=off_sac['z'], smoothness=15)\n",
"on_sac_surface, xgridmin, ygridmin = fit_sac_surface(x=on_sac['x'], y=on_sac['y'], z=on_sac['z'], smoothness=15)\n"
"off_sac_surface, xgridmax, ygridmax = fit_surface(x=off_sac['x'], y=off_sac['y'], z=off_sac['z'], smoothness=15)\n",
"on_sac_surface, xgridmin, ygridmin = fit_surface(x=on_sac['x'], y=on_sac['y'], z=on_sac['z'], smoothness=15)\n",
"# legacy API\n",
"# off_sac_surface, xgridmax, ygridmax = fit_sac_surface(x=off_sac['x'], y=off_sac['y'], z=off_sac['z'], smoothness=15)\n",
"# on_sac_surface, xgridmin, ygridmin = fit_sac_surface(x=on_sac['x'], y=on_sac['y'], z=on_sac['z'], smoothness=15)"
]
},
{
Expand All @@ -61,17 +64,32 @@
"name": "stdout",
"output_type": "stream",
"text": [
"↳ mapping ON (min) surface …\n",
" done in 0.02 seconds.\n",
"↳ mapping OFF (max) surface …\n",
" done in 0.02 seconds.\n"
"↳ mapping 'on_sac' surface …\n",
" done in 0.01 seconds.\n",
"↳ mapping 'off_sac' surface …\n",
" done in 0.01 seconds.\n"
]
}
],
"source": [
"# fit quasi-conformally mapping\n",
"arbor_boundaries = np.array([skel.nodes[:, 0].min(), skel.nodes[:, 0].max(), skel.nodes[:, 1].min(), skel.nodes[:, 1].max()])\n",
"surface_mapping = build_mapping(on_sac_surface, off_sac_surface, arbor_boundaries, conformal_jump=2, n_anchors=16, verbose=True)\n"
"surface_mapping = build_mapping(\n",
" {\"on_sac\": on_sac_surface, \"off_sac\": off_sac_surface},\n",
" bounds=arbor_boundaries,\n",
" conformal_jump=2,\n",
" n_anchors=16,\n",
" verbose=True,\n",
")\n",
"# legacy API\n",
"# surface_mapping = build_mapping(\n",
"# on_sac_surface=on_sac_surface,\n",
"# off_sac_surface=off_sac_surface,\n",
"# bounds=arbor_boundaries,\n",
"# conformal_jump=2,\n",
"# n_anchors=16,\n",
"# verbose=True,\n",
"# )"
]
},
{
Expand All @@ -84,7 +102,8 @@
"output_type": "stream",
"text": [
"[pywarper] Warping skeleton...\n",
" done in 0.40 seconds.\n",
"[pywarper] Flattening with surfaces: \"on_sac\" (z=41.31) and \"off_sac\" (z=56.00)\n",
" done in 0.28 seconds.\n",
"[skeliner] Warning: 58 nodes have zero radius; they were ignored when picking the estimator.\n"
]
}
Expand Down Expand Up @@ -113,6 +132,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"[pywarper] Unwarping with surfaces: \"on_sac\" (z=41.31) and \"off_sac\" (z=56.00)\n",
"[pywarper] Unwarping with surfaces: \"on_sac\" (z=41.31) and \"off_sac\" (z=56.00)\n",
"Skeleton local_ls error (mean / p95 / max): 0.0060 / 0.0257 / 0.0664\n",
"Skeleton optimize error on subset (mean / p95 / max): 5.2062e-04 / 1.9949e-03 / 2.6957e-02\n"
]
Expand Down Expand Up @@ -145,6 +166,7 @@
" on_sac_pos=0,\n",
" off_sac_pos=12,\n",
" conformal_jump=2,\n",
" verbose=True,\n",
")\n",
"\n",
"# option 2: inverse-by-optimization (iterative; use subset for notebook speed)\n",
Expand All @@ -159,6 +181,7 @@
" max_evals_per_point=100,\n",
" convergence_tol=1e-9,\n",
" bound_xy_to_map=True,\n",
" verbose=True,\n",
")\n",
"\n",
"err_skel_local = np.linalg.norm(unwarped_skel_local - skel.nodes, axis=1)\n",
Expand Down Expand Up @@ -203,7 +226,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -248,17 +271,23 @@
"])\n",
"\n",
"# these are the coordinates that would be annotated in warped space\n",
"annot_prenorm, _, _ = warp_nodes(annot_orig, surface_mapping, conformal_jump=2)\n",
"annot_prenorm, median_depths = warp_nodes(annot_orig, surface_mapping, conformal_jump=2)\n",
"annot_warped = normalize_nodes(\n",
" annot_prenorm,\n",
" med_z_on=med_z_on,\n",
" med_z_off=med_z_off,\n",
" median_depths=median_depths,\n",
")\n",
"# legacy API\n",
"# annot_warped = normalize_nodes(\n",
"# annot_prenorm,\n",
"# med_z_on=med_z_on,\n",
"# med_z_off=med_z_off,\n",
"# )\n",
"\n",
"annot_unwarped_local = unwarp_nodes(\n",
" annot_warped,\n",
" surface_mapping,\n",
" conformal_jump=2,\n",
" verbose=True,\n",
")\n",
"annot_unwarped_opt = unwarp_nodes(\n",
" annot_warped,\n",
Expand All @@ -268,6 +297,7 @@
" max_evals_per_point=100,\n",
" convergence_tol=1e-9,\n",
" bound_xy_to_map=True,\n",
" verbose=True,\n",
")\n",
"\n",
"err_ann_local = np.linalg.norm(annot_unwarped_local - annot_orig, axis=1)\n",
Expand Down Expand Up @@ -301,7 +331,7 @@
"ax.set_xlabel('X (μm)')\n",
"ax.set_ylabel('Z (μm)')\n",
"ax.legend(frameon=False, loc='best')\n",
"fig.tight_layout()\n"
"fig.tight_layout()"
]
},
{
Expand Down Expand Up @@ -371,7 +401,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Last updated: 2026-02-16 16:06:53 CET\n",
"Last updated: 2026-03-03 15:57:32 CET\n",
"\n",
"Python implementation: CPython\n",
"Python version : 3.13.11\n",
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "hatchling.build"

[project]
name = "pywarper"
version = "0.2.5"
version = "0.3.0"
description = "Conformal mapping-based warping of retinal morphologies."
authors = []
requires-python = ">=3.10.0"
Expand Down
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