From ae5b717a1991ba0f9f5cff8f25590341edd41d31 Mon Sep 17 00:00:00 2001
From: Sean Colby <seanmcolby@gmail.com>
Date: Tue, 11 Jun 2024 15:09:36 -0700
Subject: [PATCH] Handle nans for missing calibrant ions

---
 deimos/calibration.py | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/deimos/calibration.py b/deimos/calibration.py
index ce54a6c..80ff771 100644
--- a/deimos/calibration.py
+++ b/deimos/calibration.py
@@ -17,13 +17,24 @@
             1221.990636,
             1521.971475,
         ],
-        "ccs": [121.3, 153.7, 203, 243.6, 282.2, 317],
+        "ccs": [121.30, 153.73, 202.96, 243.64, 282.20, 316.96],
         "q": [1, 1, 1, 1, 1, 1],
     },
     "neg": {
-        "mz": [301.998139, 601.978977, 1033.988109, 1333.968947, 1633.949786],
-        "ccs": [140, 180.8, 255.3, 284.8, 319],
-        "q": [1, 1, 1, 1, 1, 1],
+        "mz": [
+            # 112.985587,
+            301.998139,
+            601.978977,
+            1033.988109,
+            1333.968947,
+            1633.949786,
+        ],
+        "ccs": [
+            # 108.23,
+            140.04, 180.77, 255.34, 284.76, 319.03],
+        "q": [
+            # 1, 
+            1, 1, 1, 1, 1],
     },
 }
 
@@ -301,7 +312,7 @@ def calibrate_ccs(
 def tunemix(
     features,
     mz=[112.985587, 301.998139, 601.978977, 1033.988109, 1333.968947, 1633.949786],
-    ccs=[108.4, 139.8, 179.9, 254.2, 283.6, 317.7],
+    ccs=[108.23, 140.04, 180.77, 255.34, 284.76, 319.03],
     q=[1, 1, 1, 1, 1, 1],
     buffer_mass=28.013,
     mz_tol=200e-6,
@@ -487,6 +498,10 @@ def map_mz_to_ccs(mz, mode="pos", tol=15e-3):
         map_mz_to_ccs(x, mode=mode, tol=tol) for x in im_cal["theoretical"].values
     ]
 
+    # Drop missing
+    tof_cal = tof_cal.dropna(axis=0).reset_index(drop=True)
+    im_cal = im_cal.dropna(axis=0).reset_index(drop=True)
+
     return tof_cal, im_cal