From a5a293534f4f316cd9fddb4d3764857b01e354b9 Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Thu, 17 Oct 2024 15:34:35 +0200
Subject: [PATCH] add timstof preset

---
 .../config_presets/dev_presets_timstof.yml    | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 src/depiction_targeted_preproc/app/config_presets/dev_presets_timstof.yml

diff --git a/src/depiction_targeted_preproc/app/config_presets/dev_presets_timstof.yml b/src/depiction_targeted_preproc/app/config_presets/dev_presets_timstof.yml
new file mode 100644
index 0000000..0b2dae5
--- /dev/null
+++ b/src/depiction_targeted_preproc/app/config_presets/dev_presets_timstof.yml
@@ -0,0 +1,30 @@
+# No baseline correction
+baseline_correction: null
+# No peak picking
+pick_peaks: null
+# No peak filtering (we only filter for calibration below)
+filter_peaks: null
+# The calibration settings:
+# - less max distance (6x less)
+# - percentile based filtering for distance smoothing
+# - filter a low number of peaks for each filtering
+calibration:
+  method:
+    calibration_method: RegressShift
+    max_distance: 500
+    max_distance_unit: ppm
+    reg_model_type: linear_siegelslopes
+    reg_model_unit: mz
+    spatial_smoothing:
+      type: PercentileFilter
+      kernel_size: 5
+      percentile: 0.25
+      kernel_shape: square
+    min_points: 3
+    peak_filtering:
+      filters:
+        # TODO try something snr based next as this would be easier to interpretate
+        - method: FilterNHighestIntensityPartitioned
+          max_count: 300
+          n_partitions: 10
+  n_jobs: 10