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Merge pull request #523 from yfukai/geff_update
Adding data conversion function for GEFF format
2 parents 03a8684 + 2f266a1 commit 76e6ad1

6 files changed

Lines changed: 689 additions & 9 deletions

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‎docs/examples/file_export.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 8,
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"id": "b12fc821",
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"metadata": {},
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"outputs": [],
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"source": [
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"from laptrack import LapTrack\n",
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"from laptrack import data_conversion\n",
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"from laptrack import datasets\n",
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"import geff"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "5fec4807",
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"metadata": {},
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"outputs": [],
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"source": [
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"lt = LapTrack(\n",
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" metric=\"sqeuclidean\",\n",
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" cutoff=15**2,\n",
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" splitting_metric=\"sqeuclidean\",\n",
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" merging_metric=\"sqeuclidean\",\n",
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" splitting_cutoff=15**2,\n",
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" merging_cutoff=15**2,\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "49ae32cc",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/fukai/projects/laptrack/src/laptrack/_tracking.py:808: FutureWarning: The parameter only_coordinate_cols will be False by default in the major release.\n",
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" warnings.warn(\n"
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]
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}
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],
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"source": [
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"spots_df = datasets.simple_tracks()\n",
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"track_df, split_df, merge_df = lt.predict_dataframe(\n",
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" spots_df, coordinate_cols=[\"position_x\", \"position_y\"], frame_col=\"frame\"\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "8fe2bf20",
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"metadata": {},
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"outputs": [],
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"source": [
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"tree_geff = data_conversion.convert_dataframes_to_geff_networkx(\n",
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" track_df,\n",
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" split_df,\n",
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" merge_df,\n",
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" coordinate_cols=[\"position_x\", \"position_y\"],\n",
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" frame_col=\"frame\",\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"id": "56da38ad",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"{'frame': 0,\n",
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" 'position_x': np.float64(178.4125746427294),\n",
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" 'position_y': np.float64(185.18866073671265)}"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"tree_geff.nodes[0]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"id": "3329e792",
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"metadata": {},
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"outputs": [],
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"source": [
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"geff.write_nx(tree_geff, \"/tmp/tree.geff\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9274242d",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "laptrack-py3.13",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎noxfile.py‎

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@@ -80,7 +80,7 @@ def safety(session: Session) -> None:
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def mypy(session: Session) -> None:
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"""Type-check using mypy."""
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args = session.posargs or ["src", "tests", "docs/conf.py"]
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session.install(".")
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session.install(".[all]")
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session.install("mypy", "pytest")
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session.run("mypy", *args)
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if not session.posargs:
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@session(python=python_versions)
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def tests(session: Session) -> None:
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"""Run the test suite."""
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session.install(".")
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session.install(".[all]")
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session.install("coverage[toml]", "pytest", "pytest-datadir", "pygments")
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try:
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session.install("ray")
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@session(python=python_versions)
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def typeguard(session: Session) -> None:
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"""Runtime type checking using Typeguard."""
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session.install(".")
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session.install(".[all]")
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session.install("pytest", "pytest-datadir", "typeguard", "pygments", "ray")
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session.run("pytest", f"--typeguard-packages={package}", *session.posargs)
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def docs_build(session: Session) -> None:
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"""Build the documentation."""
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args = session.posargs or ["docs", "docs/_build"]
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session.install(".", *doc_build_packages)
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session.install(".[all]", *doc_build_packages)
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build_dir = Path("docs", "_build")
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if build_dir.exists():
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def docs(session: Session) -> None:
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"""Build and serve the documentation with live reloading on file changes."""
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args = session.posargs or ["--open-browser", "docs", "docs/_build"]
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session.install(".", *doc_build_packages)
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session.install(".[all]", *doc_build_packages)
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build_dir = Path("docs", "_build")
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if build_dir.exists():

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