Update tests and rename oft_io script to convert_hist

src/python/OpenFUSIONToolkit/io.py

@@ -239,8 +239,17 @@ def save_to_hdf5(self,filename):
     def get(self, keyname, value=None):
         return self._data.get(keyname,value)
 
+    def keys(self):
+        return self._data.keys()
+
+    def items(self):
+        return self._data.items()
+
     def __getitem__(self, key):
         return self._data[key]
+
+    def __iter__(self):
+        return iter(self._data)
 
     def __repr__(self):
         r'''Print information about the file'''

src/tests/physics/test_ThinCurr.py

@@ -5,8 +5,9 @@
 import numpy as np
 test_dir = os.path.abspath(os.path.dirname(__file__))
 sys.path.append(os.path.abspath(os.path.join(test_dir, '..')))
+sys.path.append(os.path.abspath(os.path.join(test_dir, '..','..','python')))
 from oft_testing import run_OFT
-from oft_io import oft_histfile
+from OpenFUSIONToolkit.io import histfile
 
 mu0 = np.pi*4.E-7
 
@@ -195,9 +196,9 @@ def validate_fr(fr_real, fr_imag, tols=(1.E-4, 1.E-4)):
     """
     Helper function to validate frequency-response results against test case.
     """
-    hist_file = oft_histfile('thincurr_fr.dat')
-    fr_run_real = [hist_file.data[field][0] for field in hist_file.field_tags]
-    fr_run_imag = [hist_file.data[field][1] for field in hist_file.field_tags]
+    hist_file = histfile('thincurr_fr.dat')
+    fr_run_real = [hist_file[field][0] for field in hist_file]
+    fr_run_imag = [hist_file[field][1] for field in hist_file]
     if not len(fr_run_real) == len(fr_real):
         print("FAILED: Number of sensors does not match")
         return False
@@ -220,8 +221,8 @@ def validate_td(sigs_final, tols=(1.E-8, 1.E-3)):
     """
     Helper function to validate time-dependent results against test case.
     """
-    hist_file = oft_histfile('floops.hist')
-    td_sigs_final = [hist_file.data[field][-1] for field in hist_file.field_tags]
+    hist_file = histfile('floops.hist')
+    td_sigs_final = [hist_file[field][-1] for field in hist_file]
     if not len(td_sigs_final) == len(sigs_final):
         print("FAILED: Number of sensors does not match")
         return False

src/utilities/CMakeLists.txt

@@ -1,21 +1,17 @@
 # Python modules
 set( OFT_PY_HELPER_MODS
-  oft_io.py
   oft_mpl.py
   tokamaker_fit.py
 )
 foreach( file ${OFT_PY_HELPER_MODS} )
   install(FILES ${file} DESTINATION python COMPONENT app)
 endforeach()
 
-# Needed for testing
-if( OFT_BUILD_TESTS )
-  file( COPY oft_io.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/../tests )
-endif()
-
 # Scripts
 install(PROGRAMS build_xdmf.py DESTINATION python COMPONENT app)
 set( OFT_PYTHON_BINS build_xdmf.py ${OFT_PYTHON_BINS} CACHE INTERNAL "package_python_binaries" )
+install(PROGRAMS convert_hist.py DESTINATION python COMPONENT app)
+set( OFT_PYTHON_BINS convert_hist.py ${OFT_PYTHON_BINS} CACHE INTERNAL "package_python_binaries" )
 install(PROGRAMS convert_cubit.py DESTINATION python COMPONENT app)
 set( OFT_PYTHON_BINS convert_cubit.py ${OFT_PYTHON_BINS} CACHE INTERNAL "package_python_binaries" )
 install(PROGRAMS scripts/plot_mug_hist.py DESTINATION python COMPONENT app)

src/utilities/scripts/plot_mug_hist.py

@@ -3,7 +3,7 @@
 import sys
 import numpy
 import matplotlib.pyplot as plt
-import oft_io
+from OpenFUSIONToolkit.io import histfile
 import oft_mpl
 
 mu0 = numpy.pi*(4.E-7)
@@ -58,7 +58,7 @@ def get_gr(time, total_energy, hist_file):
 for (i, file) in enumerate(files):
     # Read fields from MUG history file
     print('Reading file: "{0}"'.format(file))
-    dump = oft_io.oft_histfile(file)
+    dump = histfile(file)
     ts = numpy.r_[dump.data['ts']]
     time = numpy.r_[dump.data['time']]*1.E3
     dt = time[1:-1] - time[0:-2]