(PR #29) Refactor/modify results parsers

- Moved parsers out to utility file. These will be used in the new monitors.
- Replaced cycle number entry in parsed data with length of discharge capacities (cycle number key not guaranteed in results)

aiida_aurora/utils/cycling_analysis.py

@@ -1,99 +1,17 @@
 import itertools
 import json
 
-import numpy as np
-
 from aiida.common.exceptions import AiidaException
-from aiida.orm import ArrayData, CalcJobNode, QueryBuilder, RemoteData
-
-
-def get_data_from_raw(jsdata):
-    "Extract raw data from json file."
-    if not isinstance(jsdata, dict):
-        raise TypeError('jsdata should be a dictionary')
-    if len(jsdata["steps"]) > 1:
-        raise NotImplementedError('Analysis of multiple steps is not implemented.')
-
-    raw_data = jsdata["steps"][0]["data"]
-
-    # extract raw data
-    t = np.array([ts["uts"] for ts in raw_data]) - raw_data[0]["uts"]
-    Ewe = np.array([ts["raw"]["Ewe"]["n"] for ts in raw_data])
-    I = np.array([ts["raw"]["I"]["n"] for ts in raw_data])
-    cn = np.array([ts["raw"]["cycle number"] for ts in raw_data])
-
-    # find indices of sign changes in I
-    idx = np.where(np.diff(np.sign(I)) != 0)[0]
-
-    # integrate and store charge and discharge currents
-    Qc, Qd = [], []
-    for ii in range(len(idx) - 1):
-        i0, ie = idx[ii], idx[ii + 1]
-        q = np.trapz(I[i0:ie], t[i0:ie])
-        if q > 0:
-            Qc.append(q)
-        else:
-            Qd.append(abs(q))
-    data = {
-        'time': t,
-        'Ewe': Ewe,
-        'I': I,
-        'cn': cn,
-        'time-cycles': t[idx[2::2]],
-        'Qd': np.array(Qd),
-        'Qc': np.array(Qc)
-    }
-    return data
+from aiida.orm import CalcJobNode, QueryBuilder, RemoteData
 
-
-def get_data_from_results(array_node):
-    "Extract data from parsed ArrayData node."
-    if not isinstance(array_node, ArrayData):
-        raise TypeError('array_node should be an ArrayData')
-
-    # collect data
-    t = array_node.get_array('step0_uts')
-    t -= t[0]
-    Ewe = array_node.get_array('step0_Ewe_n')
-    I = array_node.get_array('step0_I_n')
-    cn = array_node.get_array('step0_cycle_number')
-
-    # find indices of sign changes in I
-    idx = np.where(np.diff(np.sign(I)) != 0)[0]
-
-    # integrate and store charge and discharge currents
-    Qc, Qd = [], []
-    for ii in range(len(idx) - 1):
-        i0, ie = idx[ii], idx[ii + 1]
-        q = np.trapz(I[i0:ie], t[i0:ie])
-        if q > 0:
-            Qc.append(q)
-        else:
-            Qd.append(abs(q))
-    data = {
-        'time': t,
-        'Ewe': Ewe,
-        'I': I,
-        'cn': cn,
-        'time-cycles': t[idx[2::2]],
-        'Qd': np.array(Qd),
-        'Qc': np.array(Qc)
-    }
-    return data
-
-
-def get_capacities(data_dic, discharge=True):
-    if discharge:
-        return data_dic['Qd']
-    else:
-        return data_dic['Qc']
+from .parsers import get_data_from_raw, get_data_from_results
 
 
 def analyze_cycling_results(data, consecutive_cycles, threshold, discharge):
     """Analyse cycling results.
     `data` should be a dictionary generated by `get_data_from_*`.
     """
-    Qs = get_capacities(data, discharge=discharge)
+    Qs = data['Qd'] if discharge else data['Qc']
     print(f"  capacities:          {Qs}")
     print(f"  relative capacities: {Qs / Qs[0]}")
 

aiida_aurora/utils/parsers.py

@@ -0,0 +1,76 @@
+import numpy as np
+
+from aiida.orm import ArrayData
+
+
+def get_data_from_raw(jsdata):
+    "Extract raw data from json file."
+    if not isinstance(jsdata, dict):
+        raise TypeError('jsdata should be a dictionary')
+    if len(jsdata["steps"]) > 1:
+        raise NotImplementedError('Analysis of multiple steps is not implemented.')
+
+    raw_data = jsdata["steps"][0]["data"]
+
+    # extract raw data
+    t = np.array([ts["uts"] for ts in raw_data]) - raw_data[0]["uts"]
+    Ewe = np.array([ts["raw"]["Ewe"]["n"] for ts in raw_data])
+    I = np.array([ts["raw"]["I"]["n"] for ts in raw_data])
+
+    # find indices of sign changes in I
+    idx = np.where(np.diff(np.sign(I)) != 0)[0]
+
+    # integrate and store charge and discharge currents
+    Qc, Qd = [], []
+    for ii in range(len(idx) - 1):
+        i0, ie = idx[ii], idx[ii + 1]
+        q = np.trapz(I[i0:ie], t[i0:ie])
+        if q > 0:
+            Qc.append(q)
+        else:
+            Qd.append(abs(q))
+
+    return {
+        'time': t,
+        'Ewe': Ewe,
+        'I': I,
+        'cn': len(Qd),
+        'time-cycles': t[idx[2::2]],
+        'Qd': np.array(Qd),
+        'Qc': np.array(Qc),
+    }
+
+
+def get_data_from_results(array_node):
+    "Extract data from parsed ArrayData node."
+    if not isinstance(array_node, ArrayData):
+        raise TypeError('array_node should be an ArrayData')
+
+    # collect data
+    t = array_node.get_array('step0_uts')
+    t -= t[0]
+    Ewe = array_node.get_array('step0_Ewe_n')
+    I = array_node.get_array('step0_I_n')
+
+    # find indices of sign changes in I
+    idx = np.where(np.diff(np.sign(I)) != 0)[0]
+
+    # integrate and store charge and discharge currents
+    Qc, Qd = [], []
+    for ii in range(len(idx) - 1):
+        i0, ie = idx[ii], idx[ii + 1]
+        q = np.trapz(I[i0:ie], t[i0:ie])
+        if q > 0:
+            Qc.append(q)
+        else:
+            Qd.append(abs(q))
+
+    return {
+        'time': t,
+        'Ewe': Ewe,
+        'I': I,
+        'cn': len(Qd),
+        'time-cycles': t[idx[2::2]],
+        'Qd': np.array(Qd),
+        'Qc': np.array(Qc),
+    }