fmt and fix ex energy parsing

Author: beykyle

src/exfor_tools/distribution.py

@@ -552,18 +552,10 @@ def to_json(self, citation: str = "") -> str:
         return json.dumps(data, indent=4)
 
     @classmethod
-    def from_json(cls, json_data: list):
-        """
-        Constructs a list of AngularDistribution objects from JSON data.
-        Parameters:
-        json_data: list
-            A list of dictionaries containing the JSON data.
-        Returns:
-            list:
-            A list of AngularDistribution objects.
-        """
+    def from_json(cls, json_file):
+        data = json.load(json_file)
         measurements = []
-        for measurement in json_data:
+        for measurement in data:
             subentry = measurement["EXFORAccessionNumber"]
             quantity = data_types_json.get(measurement["type"], "unknown")
             x_units = measurement["data"]["angle-units"]

src/exfor_tools/exfor_entry.py

@@ -3,23 +3,23 @@
 """
 
 import numpy as np
-
-from x4i3.exfor_reactions import X4Reaction
 from x4i3.exfor_column_parsing import (
     errorSuffix,
     resolutionFWSuffix,
     resolutionHWSuffix,
 )
-from .db import __EXFOR_DB__
+from x4i3.exfor_reactions import X4Reaction
 
-from .parsing import quantity_matches, quantity_symbols
-from .distribution import AngularDistribution
 from . import reaction as rxn
+from .db import __EXFOR_DB__
+from .distribution import AngularDistribution
+from .parsing import quantity_matches, quantity_symbols
 
 
 def attempt_parse_subentry(MeasurementClass, *args, **kwargs):
     failed_parses = {}
     measurements = []
+    measurements = MeasurementClass.parse_subentry(*args, **kwargs)
     try:
         measurements = MeasurementClass.parse_subentry(*args, **kwargs)
     except Exception as e:
@@ -92,7 +92,6 @@ def extract_err_analysis(common_subent):
 
 
 class ExforEntry:
-
     def __init__(
         self,
         entry: str,
@@ -173,7 +172,6 @@ def __init__(
         self.failed_parses = {}
 
         for key, data_set in entry_datasets.items():
-
             if not isinstance(data_set.reaction[0], X4Reaction):
                 # TODO handle ReactionCombinations
                 continue
@@ -189,7 +187,6 @@ def __init__(
                 and filter_subentries(data_set, **filter_kwargs)
                 and rxn.is_match(self.reaction, data_set, self.vocal)
             ):
-
                 measurements, failed_parses = attempt_parse_subentry(
                     MeasurementClass,
                     key[1],

src/exfor_tools/parsing.py

@@ -1,10 +1,10 @@
 from functools import reduce
 
 import numpy as np
-
 from x4i3.exfor_column_parsing import (
     X4ColumnParser,
     X4IndependentColumnPair,
+    X4MissingErrorColumnPair,
     angDistUnits,
     angleParserList,
     baseDataKeys,
@@ -19,10 +19,8 @@
     resolutionFWSuffix,
     resolutionHWSuffix,
     variableSuffix,
-    X4MissingErrorColumnPair,
 )
 
-
 # these are the supported quantities at the moment
 quantity_matches = {
     "dXS/dA": [["DA"], ["PAR", "DA"]],
@@ -113,7 +111,6 @@ def parse_differential_data(
     # parse errors
     xs_err = []
     for label in data_error_columns:
-
         # parse error column
         err_parser = X4ColumnParser(
             match_labels=reduce(
@@ -162,10 +159,12 @@ def parse_ex_energy(data_set):
     if missing_Ex:
         return Ex, Ex, None
 
-    if Ex[0][-3:] == "-CM":
-        raise NotImplementedError("Incident energy in CM frame!")
-
     Ex_err = reduce(condenseColumn, [c.getError(data_set) for c in energyExParserList])
+    missing_Ex_err = np.all([a is None for a in Ex_err[2:]])
+    if missing_Ex_err:
+        Ex_err = np.zeros_like(Ex)
+        return Ex, Ex_err, Ex_units
+
     if Ex_err[1] != Ex_units:
         raise ValueError(
             f"Inconsistent units for Ex and Ex error: {Ex_units} and {Ex_err[1]}"