don't fail on "empty" spectra

fgcz · Jun 18, 2024 · f2ce95c · f2ce95c
1 parent 6d47748
commit f2ce95c
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/src/depiction/tools/pick_peaks.py b/src/depiction/tools/pick_peaks.py
@@ -1,5 +1,7 @@
 import argparse
 
+from loguru import logger
+
 from depiction.parallel_ops import ParallelConfig, WriteSpectraParallel
 from depiction.spectrum.peak_filtering import FilterByIntensity
 from depiction.spectrum.peak_picking import BasicInterpolatedPeakPicker
@@ -31,7 +33,10 @@ def _operation(
         for spectrum_index in spectra_ids:
             mz_arr, int_arr, coords = reader.get_spectrum_with_coords(spectrum_index)
             peak_mz, peak_int = peak_picker.pick_peaks(mz_arr, int_arr)
-            writer.add_spectrum(peak_mz, peak_int, coords)
+            if len(peak_mz) > 0:
+                writer.add_spectrum(peak_mz, peak_int, coords)
+            else:
+                logger.warning(f"Dropped spectrum {spectrum_index} as no peaks were found")
 
 
 def debug_diagnose_threshold_correspondence(