Aa/spectra unit

src/tools/spectra.py

@@ -23,16 +23,24 @@ class Spectra:
         ("hour", "minute"): lambda x: x * 60,
     }
 
-    def __init__(self, filepaths: list[str | Path]):
+    def __init__(
+        self,
+        filepaths: list[str | Path],
+        rtime_unit: Literal["seconds", "minute", "hour"] = "seconds",
+    ):
         """
         Initialize from a list of mzML file paths.
 
         Parameters
         ----------
         filepaths : list[str or Path]
             Paths to mzML files to parse.
+
+        rtime_unit : {'seconds', 'minute', 'hour'}
+            Target retention time unit. All parsed spectra are converted to
+            this unit. Defaults to 'seconds'.
         """
-        self.rtime_unit: str = "unknown"
+        self.rtime_unit: str = self._configure_retention_time_unit(rtime_unit)
         self.spectra = self._read_mzml_files(filepaths)
 
     def __len__(self) -> int:
@@ -69,10 +77,7 @@ def _configure_retention_time_unit(self, unit: str) -> str:
 
     def _configure_retention_time(self, rtime: float, unit: str) -> float:
         """
-        Convert a retention time value to the collection's established unit.
-
-        Sets the collection's unit from the first spectrum encountered, then converts
-        all subsequent values to match.
+        Convert a retention time value to the collection's target unit.
 
         Parameters
         ----------
@@ -84,19 +89,16 @@ def _configure_retention_time(self, rtime: float, unit: str) -> float:
         Returns
         -------
         float
-            Retention time converted to the collection's established unit.
+            Retention time converted to ``self.rtime_unit``.
         """
         unit = self._configure_retention_time_unit(unit)
 
-        # establish the target unit
-        if self.rtime_unit == "unknown":
-            self.rtime_unit = unit
-            return float(rtime)
-
         if self.rtime_unit == unit:
             return float(rtime)
 
-        return self.CONVERSIONS[(unit, self.rtime_unit)](float(rtime))
+        converted_value = self.CONVERSIONS[(unit, self.rtime_unit)](float(rtime))
+        self.rtime_unit = unit
+        return converted_value
 
     def _read_mzml_files(self, filepaths: list[str | Path]) -> "list[Spectrum]":
         """
@@ -130,7 +132,7 @@ def _read_mzml_files(self, filepaths: list[str | Path]) -> "list[Spectrum]":
                         ms_level=spec.ms_level,
                         rtime=rtime,
                         scan_index=spec.ID,
-                        file=Path(run.path_or_file),
+                        file=Path(run.path_or_file).name,
                         mz=spec.mz,
                         intensity=spec.i,
                         polarity=polarity,

tests/conftest.py

@@ -50,7 +50,8 @@ def spectra(data_dir):
             data_dir / "L01.mzML",
             data_dir / "LB01.mzML",
             data_dir / "T01A.mzML",
-        ]
+        ],
+        rtime_unit="minute",
     )
 
 

tests/test_spectra.py

@@ -39,7 +39,7 @@ def test_spectra_rtime_unit(spectra):
     assert all(sp.rtime_unit == spectra.rtime_unit for sp in spectra)
 
     s = Spectra(filepaths=[])
-    assert s.rtime_unit == "unknown"
+    assert s.rtime_unit == "seconds"
     s._configure_retention_time(1.0, "minute")
     assert s.rtime_unit == "minute"
     for unit in ("seconds", "minute", "hour"):
@@ -51,12 +51,12 @@ def test_spectra_rtime_unit(spectra):
 
 def test_spectrum_file_paths(data_dir, spectra):
     expected_files = {
-        data_dir / "Blank1A.mzML",
-        data_dir / "GAS01.mzML",
-        data_dir / "GB01.mzML",
-        data_dir / "L01.mzML",
-        data_dir / "LB01.mzML",
-        data_dir / "T01A.mzML",
+        "Blank1A.mzML",
+        "GAS01.mzML",
+        "GB01.mzML",
+        "L01.mzML",
+        "LB01.mzML",
+        "T01A.mzML",
     }
     assert {sp.file for sp in spectra} == expected_files
 
@@ -99,10 +99,12 @@ def test_match_peaks_all_matched():
 
     matches = spec._match_peaks(other, ppm_error=20)
 
-    expected = np.array([
-        [100.0, 0.5, 100.0005, 0.6],
-        [200.0, 0.8, 200.001, 0.9],
-    ])
+    expected = np.array(
+        [
+            [100.0, 0.5, 100.0005, 0.6],
+            [200.0, 0.8, 200.001, 0.9],
+        ]
+    )
     assert matches.shape == (2, 4)
     assert np.allclose(matches, expected)
 
@@ -113,12 +115,14 @@ def test_match_peaks_partial_match():
 
     matches = spec._match_peaks(other, ppm_error=10)
 
-    expected = np.array([
-        [100.0, 0.5, 100.0, 0.6],
-        [200.0, 0.8, 0.0, 0.0],
-        [300.0, 0.3, 0.0, 0.0],
-        [0.0, 0.0, 500.0, 0.7],
-    ])
+    expected = np.array(
+        [
+            [100.0, 0.5, 100.0, 0.6],
+            [200.0, 0.8, 0.0, 0.0],
+            [300.0, 0.3, 0.0, 0.0],
+            [0.0, 0.0, 500.0, 0.7],
+        ]
+    )
     assert matches.shape == (4, 4)
     assert np.allclose(matches, expected)
 
@@ -129,10 +133,12 @@ def test_match_peaks_no_match():
 
     matches = spec._match_peaks(other, ppm_error=10)
 
-    expected = np.array([
-        [100.0, 0.5, 0.0, 0.0],
-        [0.0, 0.0, 300.0, 0.8],
-    ])
+    expected = np.array(
+        [
+            [100.0, 0.5, 0.0, 0.0],
+            [0.0, 0.0, 300.0, 0.8],
+        ]
+    )
     assert matches.shape == (2, 4)
     assert np.allclose(matches, expected)
 
@@ -144,10 +150,12 @@ def test_match_peaks_closest_chosen():
     matches = spec._match_peaks(other, ppm_error=20)
 
     # 99.999 is closer to 100.0 than 100.0005
-    expected = np.array([
-        [100.0, 0.5, 100.0005, 0.6],
-        [0.0, 0.0, 99.999, 0.4],
-    ])
+    expected = np.array(
+        [
+            [100.0, 0.5, 100.0005, 0.6],
+            [0.0, 0.0, 99.999, 0.4],
+        ]
+    )
     assert matches.shape == (2, 4)
     assert np.allclose(matches, expected)
 
@@ -163,7 +171,6 @@ def test_match_peaks_abs_tol():
     assert np.allclose(with_abs_tol, [[100.0, 0.5, 100.005, 0.6]])
 
 
-
 def test_compare_spectra_empty_other():
     spec = _make_spectrum(mz=[100.0], intensity=[0.5])
     result = spec.compare_spectra(np.empty((0, 2)), ppm_error=10, function=np.dot)