TSV to Parquet & rename _correlations Fix #247, #91

src/rbc/bids/metrics.py

@@ -89,13 +89,13 @@ def export_metrics(
             outputs.timeseries[atl],
             suffix="timeseries",
             desc="mean",
-            extension=".tsv",
+            extension=".parquet",
             atlas=bids_safe_label(atl),
         )
         mex.save(
-            outputs.correlation_matrix[atl],
-            suffix="correlations",
+            outputs.connectome[atl],
+            suffix="connectome",
             desc="pearson",
-            extension=".tsv",
+            extension=".parquet",
             atlas=bids_safe_label(atl),
         )

src/rbc/core/metrics/timeseries.py

@@ -11,6 +11,7 @@
 from typing import NamedTuple
 
 import numpy as np
+import polars as pl
 
 from rbc.core.niwrap import generate_exec_folder
 
@@ -113,7 +114,7 @@ class TimeseriesOutputs(NamedTuple):
     """Outputs from :func:`compute_timeseries`."""
 
     timeseries: Path
-    correlation_matrix: Path
+    connectome: Path
     labels: np.ndarray
 
 
@@ -134,7 +135,7 @@ def compute_timeseries(
             *in_file*.
 
     Returns:
-        :class:`TimeseriesOutputs` containing paths to the TSV files and
+        :class:`TimeseriesOutputs` containing paths to the Parquet files and
         the ROI labels array.
     """
     import nibabel as nib
@@ -163,14 +164,19 @@ def compute_timeseries(
     out_dir.mkdir(parents=True, exist_ok=True)
 
     stem = in_file.name.split(".nii")[0]
-    ts_path = out_dir / f"{stem}_timeseries.tsv"
-    corr_path = out_dir / f"{stem}_correlation_matrix.tsv"
+    ts_path = out_dir / f"{stem}_timeseries.parquet"
+    corr_path = out_dir / f"{stem}_connectome.parquet"
 
-    np.savetxt(ts_path, ts, delimiter="\t")
-    np.savetxt(corr_path, corr, delimiter="\t")
+    # ROIs
+    roi_names = [str(label) for label in labels]
+    # Timepoints
+    tp_names = [str(i) for i in range(ts.shape[1])]
+
+    pl.DataFrame(ts, schema=tp_names).write_parquet(ts_path)
+    pl.DataFrame(corr, schema=roi_names).write_parquet(corr_path)
 
     return TimeseriesOutputs(
         timeseries=ts_path,
-        correlation_matrix=corr_path,
+        connectome=corr_path,
         labels=labels,
     )

src/rbc/workflows/metrics.py

@@ -39,8 +39,8 @@ class MetricsOutputs(NamedTuple):
         reho: Raw ReHo map.
         reho_smooth: Smoothed ReHo map.
         reho_zscored: Z-scored (smoothed) ReHo map.
-        timeseries: Atlas-based mean timeseries TSV.
-        correlation_matrix: Pairwise correlation matrix TSV.
+        timeseries: Atlas-based mean timeseries file.
+        connectome: Pairwise connectome file.
     """
 
     alff: Path
@@ -53,7 +53,7 @@ class MetricsOutputs(NamedTuple):
     reho_smooth: Path
     reho_zscored: Path
     timeseries: dict[str, Path]
-    correlation_matrix: dict[str, Path]
+    connectome: dict[str, Path]
 
 
 def single_session_metrics(
@@ -127,7 +127,5 @@ def single_session_metrics(
         reho_smooth=reho_smooth_path,
         reho_zscored=reho_zscored_path,
         timeseries={label: ts.timeseries for label, ts in ts_outputs.items()},
-        correlation_matrix={
-            label: ts.correlation_matrix for label, ts in ts_outputs.items()
-        },
+        connectome={label: ts.connectome for label, ts in ts_outputs.items()},
     )

tests/full_pipeline/longitudinal/test_all.py

@@ -62,7 +62,7 @@ def test_longitudinal_all_produces_derivatives(
     assert list(func.glob(f"{_STEM}_space-longitudinal_*_alff.nii.gz")), (
         f"Missing ALFF\n--- file tree ---\n{tree}"
     )
-    assert list(func.glob(f"{_STEM}_space-longitudinal_*_timeseries.tsv")), (
+    assert list(func.glob(f"{_STEM}_space-longitudinal_*_timeseries.parquet")), (
         f"Missing timeseries\n--- file tree ---\n{tree}"
     )
 

tests/full_pipeline/longitudinal/test_metrics.py

@@ -58,8 +58,8 @@ def test_longitudinal_metrics_timeseries_exist(
     func = longitudinal_pipeline_data / f"sub-{_SUB}" / f"ses-{_SES}" / "func"
     tree = _file_tree(longitudinal_pipeline_data)
 
-    timeseries = list(func.glob(f"{_STEM}_space-longitudinal_*_timeseries.tsv"))
-    assert timeseries, f"No timeseries TSV found\n--- file tree ---\n{tree}"
+    timeseries = list(func.glob(f"{_STEM}_space-longitudinal_*_timeseries.parquet"))
+    assert timeseries, f"No timeseries Parquet found\n--- file tree ---\n{tree}"
 
-    correlations = list(func.glob(f"{_STEM}_space-longitudinal_*_correlations.tsv"))
-    assert correlations, f"No correlation TSV found\n--- file tree ---\n{tree}"
+    correlations = list(func.glob(f"{_STEM}_space-longitudinal_*_connectome.parquet"))
+    assert correlations, f"No connectome Parquet found\n--- file tree ---\n{tree}"

tests/integration/test_all.py

@@ -189,10 +189,10 @@ def _assert_derivatives_exist(output_dir: Path) -> None:
     assert qc_files, f"No QC quality TSV files found\n--- file tree ---\n{tree}"
 
     # -- Metrics --
-    assert list(func.glob(f"{bold_stem}_space-*_*_timeseries.tsv")), (
+    assert list(func.glob(f"{bold_stem}_space-*_*_timeseries.parquet")), (
         f"No timeseries TSV files found\n--- file tree ---\n{tree}"
     )
-    assert list(func.glob(f"{bold_stem}_space-*_*_correlations.tsv")), (
+    assert list(func.glob(f"{bold_stem}_space-*_*_connectome.parquet")), (
         f"No correlation matrix TSV files found\n--- file tree ---\n{tree}"
     )
 

tests/unit/bids/test_exports.py

@@ -90,8 +90,8 @@ def _make_metrics_outputs(w: Path, atlases: list[str]) -> MetricsOutputs:
         reho=_dummy(w, "reho.nii.gz"),
         reho_smooth=_dummy(w, "reho_smooth.nii.gz"),
         reho_zscored=_dummy(w, "reho_z.nii.gz"),
-        timeseries={a: _dummy(w, f"ts_{a}.tsv") for a in atlases},
-        correlation_matrix={a: _dummy(w, f"corr_{a}.tsv") for a in atlases},
+        timeseries={a: _dummy(w, f"ts_{a}.parquet") for a in atlases},
+        connectome={a: _dummy(w, f"connectome_{a}.parquet") for a in atlases},
     )
 
 

tests/unit/core/test_timeseries.py

@@ -5,6 +5,7 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
+import polars as pl
 import pytest
 
 from rbc.core.metrics.timeseries import (
@@ -247,7 +248,7 @@ def _make_nifti(self, data: np.ndarray, path: Path) -> None:
         img.to_filename(str(path))
 
     def test_round_trip(self, tmp_path: Path) -> None:
-        """Should produce TSV files that can be loaded back."""
+        """Should produce Parquet files that can be loaded back."""
         rng = np.random.default_rng(20)
         data = rng.standard_normal((4, 4, 4, 10))
         atlas = np.zeros((4, 4, 4), dtype=np.int16)
@@ -262,13 +263,13 @@ def test_round_trip(self, tmp_path: Path) -> None:
         result = compute_timeseries(in_file, atlas_file)
 
         assert result.timeseries.exists()
-        assert result.correlation_matrix.exists()
+        assert result.connectome.exists()
         assert len(result.labels) == 2
 
-        ts_loaded = np.loadtxt(result.timeseries, delimiter="\t")
+        ts_loaded = pl.read_parquet(result.timeseries)
         assert ts_loaded.shape == (2, 10)
 
-        corr_loaded = np.loadtxt(result.correlation_matrix, delimiter="\t")
+        corr_loaded = pl.read_parquet(result.connectome)
         assert corr_loaded.shape == (2, 2)
 
     def test_output_naming(self, tmp_path: Path) -> None:
@@ -285,8 +286,8 @@ def test_output_naming(self, tmp_path: Path) -> None:
 
         result = compute_timeseries(in_file, atlas_file)
 
-        assert result.timeseries.name == "sub-01_bold_timeseries.tsv"
-        assert result.correlation_matrix.name == "sub-01_bold_correlation_matrix.tsv"
+        assert result.timeseries.name == "sub-01_bold_timeseries.parquet"
+        assert result.connectome.name == "sub-01_bold_connectome.parquet"
 
     def test_custom_out_dir(self, tmp_path: Path) -> None:
         """Should write to a custom output directory."""
@@ -304,7 +305,7 @@ def test_custom_out_dir(self, tmp_path: Path) -> None:
         result = compute_timeseries(in_file, atlas_file, out_dir=out_dir)
 
         assert result.timeseries.parent == out_dir
-        assert result.correlation_matrix.parent == out_dir
+        assert result.connectome.parent == out_dir
 
     def test_labels_in_output(self, tmp_path: Path) -> None:
         """Output labels should match the atlas ROI labels."""