compensation matrix reformatting

ark/mibi/rosetta_utils.py

@@ -1,4 +1,5 @@
 import os
+import json
 
 import numpy as np
 import pandas as pd
@@ -11,6 +12,31 @@
 from ark.utils.misc_utils import verify_same_elements
 
 
+def transform_compensation_json(json_path, comp_mat_path):
+    """Converts the JSON file from ionpath into a compensation matrix
+
+    Args:
+        json_path: path to json file
+        comp_mat_path: path to comp matrix
+
+    returns:
+        pd.DataTable: matrix with sources channels as rows and target channels as columns"""
+
+    with open(json_path) as f:
+        data = json.load(f)['Data']
+
+    comp_mat = pd.read_csv(comp_mat_path, index_col=0)
+
+    for i in range(len(data)):
+        current_data = data[i]
+        source = current_data['DonorMass']
+        target = current_data['RecipientMass']
+        val = current_data['Percent'] / 100
+        comp_mat.loc[source, str(target)] = val
+
+    comp_mat.to_csv(comp_mat_path)
+
+
 def compensate_matrix_simple(raw_inputs, comp_coeffs):
     """Perform compensation on the raw data using the supplied compensation values