correctly implementation

fgcz · Jun 6, 2024 · 54f89e7 · 54f89e7
1 parent 8725b0b
commit 54f89e7
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/src/depiction/spectrum/peak_picking/ms_peak_picker_wrapper.py b/src/depiction/spectrum/peak_picking/ms_peak_picker_wrapper.py
@@ -5,12 +5,8 @@
 from dataclasses import dataclass
 from typing import TYPE_CHECKING
 
-import loguru
 import ms_peak_picker
 import numpy as np
-import scipy
-
-from depiction.spectrum.peak_picking.basic_peak_picker import BasicPeakPicker
 
 if TYPE_CHECKING:
     from numpy.typing import NDArray
@@ -31,7 +27,7 @@ def pick_peaks(self, mz_arr: NDArray[float], int_arr: NDArray[float]) -> tuple[N
         peak_mz = np.array([peak.mz for peak in peak_list])
         peak_int = np.array([peak.intensity for peak in peak_list])
 
-        if self.peak_filtering is not None:
+        if self.peak_filtering is not None and len(peak_mz) > 0:
             peak_mz, peak_int = self.peak_filtering.filter_peaks(
                 spectrum_mz_arr=mz_arr,
                 spectrum_int_arr=int_arr,

diff --git a/src/depiction_targeted_preproc/workflow/proc/pick_peaks.py b/src/depiction_targeted_preproc/workflow/proc/pick_peaks.py
@@ -22,8 +22,8 @@ def proc_pick_peaks(
 ) -> None:
     config = PipelineParameters.parse_yaml(config_path)
 
-    # TODO configurable
-    peak_filtering = FilterNHighestIntensityPartitioned(max_count=200, n_partitions=8),
+    # TODO configurable filtering
+    peak_filtering = FilterNHighestIntensityPartitioned(max_count=200, n_partitions=8)
     parallel_config = ParallelConfig(n_jobs=config.n_jobs, task_size=None)
 
     match config.peak_picker: