csv file time history

CITATION.md

@@ -11,7 +11,7 @@ A BibTeX entry for LaTeX users is
 ```TeX
 @misc{PyKED,
     author = {Kyle E Niemeyer and Bryan W Weber},
-    year = 2017,
+    year = 2018,
     title = {PyKED v0.4.1},
     doi = {10.5281/zenodo.597935},
     url = {https://github.com/pr-omethe-us/PyKED},

pyked/chemked.py

@@ -2,7 +2,7 @@
 Main ChemKED module
 """
 # Standard libraries
-from os.path import exists
+from os.path import exists, isabs, dirname, join
 from collections import namedtuple
 from warnings import warn
 from copy import deepcopy
@@ -111,8 +111,10 @@ def __init__(self, yaml_file=None, dict_input=None, *, skip_validation=False):
         if yaml_file is not None:
             with open(yaml_file, 'r') as f:
                 self._properties = yaml.safe_load(f)
+            directory = dirname(yaml_file)
         elif dict_input is not None:
             self._properties = dict_input
+            directory = None
         else:
             raise NameError("ChemKED needs either a YAML filename or dictionary as input.")
 
@@ -121,7 +123,7 @@ def __init__(self, yaml_file=None, dict_input=None, *, skip_validation=False):
 
         self.datapoints = []
         for point in self._properties['datapoints']:
-            self.datapoints.append(DataPoint(point))
+            self.datapoints.append(DataPoint(point, directory))
 
         self.reference = Reference(
             volume=self._properties['reference'].get('volume'),
@@ -589,6 +591,7 @@ class DataPoint(object):
 
     Arguments:
         properties (`dict`): Dictionary adhering to the ChemKED format for ``datapoints``
+        directory (`str`, optional): Directory to look for auxiliary files
 
     Attributes:
         composition (`list`): List of dictionaries representing the species and their quantities
@@ -631,7 +634,7 @@ class DataPoint(object):
         'compression-ratio'
     ]
 
-    def __init__(self, properties):
+    def __init__(self, properties, directory=''):
         for prop in self.value_unit_props:
             if prop in properties:
                 quant = self.process_quantity(properties[prop])
@@ -685,7 +688,10 @@ def __init__(self, properties):
                     values = np.array(hist['values'])
                 else:
                     # Load the values from a file
-                    values = np.genfromtxt(hist['values']['filename'], delimiter=',')
+                    filename = hist['values']['filename']
+                    if not isabs(filename):
+                        filename = join(directory, filename)
+                    values = np.genfromtxt(filename, delimiter=',')
 
                 time_history = TimeHistory(
                     time=Q_(values[:, time_col], time_units),

pyked/tests/test_validation.py

@@ -363,7 +363,7 @@ def properties(self, request):
 
     @pytest.mark.parametrize("properties", [
         'testfile_st.yaml', 'testfile_st2.yaml', 'testfile_rcm.yaml', 'testfile_required.yaml',
-        'testfile_uncertainty.yaml', 'testfile_rcm2.yaml',
+        'testfile_uncertainty.yaml', 'testfile_rcm2.yaml', 'testfile_rcm3.yaml'
     ], indirect=['properties'])
     def test_valid_yaml(self, properties):
         """Ensure ChemKED YAML is validated

pyked/tests/testfile_rcm3.yaml

@@ -0,0 +1,66 @@
+---
+file-authors:
+  - name: Kyle E Niemeyer
+    ORCID: 0000-0003-4425-7097
+file-version: 0
+chemked-version: 0.0.1
+reference:
+  doi: 10.1002/kin.20180
+  authors:
+    - name: Gaurav Mittal
+    - name: Chih-Jen Sung
+      ORCID: 0000-0003-2046-8076
+    - name: Richard A Yetter
+  journal: International Journal of Chemical Kinetics
+  year: 2006
+  volume: 38
+  pages: 516-529
+  detail: Fig. 6, open circle
+experiment-type: ignition delay
+apparatus:
+  kind: rapid compression machine
+  institution: Case Western Reserve University
+  facility: CWRU RCM
+datapoints:
+  - temperature:
+      - 297.4 kelvin
+    ignition-delay:
+      - 1.0 ms
+    pressure:
+      - 958.0 torr
+    composition:
+      kind: mole fraction
+      species:
+        - species-name: H2
+          InChI: 1S/H2/h1H
+          amount:
+            - 0.12500
+        - species-name: O2
+          InChI: 1S/O2/c1-2
+          amount:
+            - 0.06250
+        - species-name: N2
+          InChI: 1S/N2/c1-2
+          amount:
+            - 0.18125
+        - species-name: Ar
+          InChI: 1S/Ar
+          amount:
+            - 0.63125
+    ignition-type:
+      target: pressure
+      type: d/dt max
+    rcm-data:
+      compression-time:
+        - 38.0 ms
+    time-histories:
+      - type: volume
+        time:
+          units: s
+          column: 0
+        quantity:
+          units: cm3
+          column: 1
+        values:
+          filename: rcm_history.csv 
+...

pyked/validation.py

@@ -251,15 +251,21 @@ def _validate_isvalid_history(self, isvalid_history, field, value):
             self._error(field, 'incompatible units; should be consistent '
                         'with ' + property_units['time'])
 
-        # Check that the values have the right number of columns
-        n_cols = len(value['values'][0])
-        max_cols = max(value['time']['column'],
-                       value['quantity']['column'],
-                       value.get('uncertainty', {}).get('column', 0)) + 1
-        if n_cols > max_cols:
-            self._error(field, 'too many columns in the values')
-        elif n_cols < max_cols:
-            self._error(field, 'not enough columns in the values')
+        try:
+            if 'filename' not in value['values'].keys():
+                self._error(field, 'must include filename or list of values')
+            # If reading from a file, the file will not be validated.
+            # A file can have an arbitrary number of columns, and the columns
+            # to be used are specified.
+        except AttributeError:
+            n_cols = len(value['values'][0])
+            max_cols = max(value['time']['column'],
+                           value['quantity']['column'],
+                           value.get('uncertainty', {}).get('column', 0)) + 1
+            if n_cols > max_cols:
+                self._error(field, 'too many columns in the values')
+            elif n_cols < max_cols:
+                self._error(field, 'not enough columns in the values')
 
     def _validate_isvalid_quantity(self, isvalid_quantity, field, value):
         """Checks for valid given value and appropriate units.