fix: data normalization and improve handling of runs in JcampMSConver…

…ter (#220)

* Fix data normalization and improve handling of runs in JcampMSConverter

* Add unit test for JCAMP single point handling in the last line

* Update requirements.txt to use specific branch of nmrglue

* Change nmrglue version for unit test in CI

chem_spectra/lib/converter/jcamp/ms.py

@@ -1,5 +1,6 @@
 from chem_spectra.lib.converter.jcamp.data_parse import make_ms_data_xsys
 from chem_spectra.lib.converter.share import reduce_pts
+import numpy as np
 
 MARGIN = 1
 THRESHOLD_MS = 0.05
@@ -78,12 +79,19 @@ def __get_ratio(self, spc):
 
         return ratio, noise_ratio
 
+    # Guarantees that the data passed to `reduce_pts` and subsequent operations
+    # conforms to the expected structure.
+    def __normalize_data(self, data):
+        if isinstance(data, np.ndarray) and data.ndim == 3 and data.shape[0] == 1:
+            return data[0]
+        return data
+
     def __decode(self, runs):
         spectra = []
         best_ratio, best_idx, backup_ratio, backup_idx = 0, 0, 0, 0
         for idx, data in enumerate(runs):
+            data = self.__normalize_data(data)
             spectra.append(reduce_pts(data))
-
             ratio, noise_ratio = self.__get_ratio(data)
             if (best_ratio < ratio) and (noise_ratio <= 50.0):
                 best_idx = idx
@@ -117,4 +125,4 @@ def __set_datatables(self):
                     )
                 )
             dts.append({'dt': dt, 'pts': pts})
-        return dts
+        return dts

environment.yml

@@ -88,5 +88,5 @@ dependencies:
       - werkzeug==3.0.3
       - wrapt==1.16.0
       - zipp==3.19.2
-      - -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
+      - -e git+https://github.com/ComPlat/nmrglue.git@Refactor-parse_xy_xy-standardize-output-3D-arrays#egg=nmrglue
 prefix: /home/eln/anaconda3/envs/python-v38

requirements.txt

@@ -19,7 +19,7 @@ matplotlib==3.7.3
 mccabe==0.6.1
 more-itertools==7.2.0
 # -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
--e git+https://github.com/ComPlat/nmrglue.git@stable_version#egg=nmrglue
+-e git+https://github.com/ComPlat/nmrglue.git@Refactor-parse_xy_xy-standardize-output-3D-arrays#egg=nmrglue
 netCDF4==1.5.3
 numpy==1.22.4
 olefile==0.46