More contribution function comparisons to IDL functions (#290)

* move out env setup to make testing easier

* add another Fe IX G(T) comparison test

* numpy v2 compatibility

* add new Fe IX G(T) to examples page

examples/idl_comparisons/goft_comparison.py

@@ -61,15 +61,16 @@ def plot_idl_comparison(x, y_idl, y_python, fig, n_rows, i_row, quantity_name, t
 
 
 ################################################
-# Next, plot the comparison between the ionization fraction results
+# Next, plot the comparison between the contribution function results
 # for a selected number of ions. The regions highlighted in red denote
 # places where the contribution function is less than :math:`10^{-6}` times
-# the peak of the ionization fraction. In these regions, the comparison is
+# the peak of the contribution function. In these regions, the comparison is
 # between the two results is not as critical as the contribution function
 # is comparatively small in these regions.
 goft_files = [
     'goft_20_15_200.972',
     'goft_26_9_171.073',
+    'goft_26_9_188.496',
     'goft_26_11_188.497',
     'goft_26_14_197.862',
     'goft_26_16_262.984',
@@ -87,8 +88,16 @@ def plot_idl_comparison(x, y_idl, y_python, fig, n_rows, i_row, quantity_name, t
     idx = np.argmin(np.abs(transitions - idl_result['wavelength']))
     # NOTE: Multiply by 0.83 because the fiasco calculation does not include the n_H/n_e ratio
     goft = contribution_func[:, 0, idx] * 0.83
-    axes = plot_idl_comparison(ion.temperature, idl_result['contribution_function'], goft,
-                               fig, len(goft_files), 3*i, f'{ion.ion_name_roman}')
+    line_label = f'{ion.ion_name_roman} {idl_result["wavelength"]:latex_inline}'
+    axes = plot_idl_comparison(
+        ion.temperature,
+        idl_result['contribution_function'],
+        goft,
+        fig,
+        len(goft_files),
+        3*i,
+        line_label,
+    )
     axes[0].legend()
-    print(f'IDL code to produce {ion.ion_name_roman} contribution function result:')
+    print(f'IDL code to produce {line_label} contribution function result:')
     print(template_env.from_string(idl_result['idl_script']).render(**idl_result))

fiasco/tests/idl/conftest.py

@@ -1,7 +1,6 @@
-import os
 import pytest
 
-from astropy.utils.data import get_pkg_data_path
+from .helpers import setup_idl_environment
 
 
 @pytest.fixture(scope="session")
@@ -14,26 +13,4 @@ def idl_env(ascii_dbase_root, request):
     idl_codebase_root = request.config.getoption('--idl-codebase-root')
     if idl_executable is None or idl_codebase_root is None:
         return None
-    try:
-        import hissw
-    except ImportError:
-        return None
-    extra_paths = [d for d, _, _ in os.walk(idl_codebase_root)]
-    header = f'''
-    defsysv,'!xuvtop','{ascii_dbase_root}'
-    defsysv,'!abund_file',''
-    defsysv,'!ioneq_file',''
-    '''
-    extra_paths += [get_pkg_data_path('ssw_gen_functions', package='fiasco.tests.idl')]
-    env = hissw.Environment(
-        idl_only=True,
-        idl_home=idl_executable,
-        header=header,
-        extra_paths=extra_paths
-    )
-    try:
-        _ = env.run('print,!xuvtop')
-    except (hissw.util.SSWIDLError, hissw.util.IDLLicenseError):
-        return None
-    else:
-        return env
+    return setup_idl_environment(ascii_dbase_root, idl_codebase_root, idl_executable)

fiasco/tests/idl/helpers.py

@@ -1,11 +1,17 @@
 """
 Helpers for tests related to comparing with IDL output
 """
+import os
 import pathlib
 
 from astropy.utils.data import get_pkg_data_path
 
-__all__ = ['get_idl_test_output_filepath', 'read_idl_test_output', 'run_idl_script']
+__all__ = [
+    'get_idl_test_output_filepath',
+    'read_idl_test_output',
+    'setup_idl_environment',
+    'run_idl_script',
+]
 
 
 def get_idl_test_output_filepath(name, version):
@@ -24,6 +30,53 @@ def read_idl_test_output(name, version, keys=None):
     return output
 
 
+def setup_idl_environment(ascii_dbase_root,
+                          idl_codebase_root,
+                          idl_executable,
+                          ssw_gen_root=None):
+    """
+    Setup an IDL environment for CHIANTI
+
+    .. note:: If `hissw` is not installed or IDL or SSW are not installed, this
+              function will return None.
+
+    Parameters
+    ----------
+    ascii_dbase_root: path-like
+        Path to top of IDL database tree
+    idl_codebase_root: path-like
+        Path to top of CHIANTI IDL software tree
+    idl_executable: path-like
+        Path to IDL executable
+    """
+    try:
+        import hissw
+    except ImportError:
+        return None
+    extra_paths = [d for d, _, _ in os.walk(idl_codebase_root)]
+    header = f'''
+    defsysv,'!xuvtop','{ascii_dbase_root}'
+    defsysv,'!abund_file',''
+    defsysv,'!ioneq_file',''
+    '''
+    if ssw_gen_root is None:
+        extra_paths += [get_pkg_data_path('ssw_gen_functions', package='fiasco.tests.idl')]
+    else:
+        extra_paths += [d for d, _, _ in os.walk(ssw_gen_root)]
+    env = hissw.Environment(
+        idl_only=True,
+        idl_home=idl_executable,
+        header=header,
+        extra_paths=extra_paths
+    )
+    try:
+        _ = env.run('print,!xuvtop', verbose=False)
+    except (hissw.util.SSWIDLError, hissw.util.IDLLicenseError):
+        return None
+    else:
+        return env
+
+
 def run_idl_script(idl_env, script, input_args, save_vars, file_name, version, format_func=None, write_file=True):
     """
     Helper function for running CHIANTI IDL via hissw in tests

fiasco/tests/idl/test_idl_goft.py

@@ -14,18 +14,22 @@
 # by wavelength so I have to run the g_of_t function once with the GUI selector to work out
 # what integer index corresponds to which wavelength. For any additional test that is added to
 # the list below, this index will need to be computed and added to the list below.
+# NOTE: These indices will change with database version number so they'll need to be updated
+# or we will have to find a way to select them automatically.
 INDEX_WAVE_MAPPING = {
-    200.972*u.Angstrom: 297,
-    171.073*u.Angstrom: 13946,
-    188.497*u.Angstrom: 22527,
-    197.862*u.Angstrom: 27964,
-    262.984*u.Angstrom: 1415,
+    'Ca XV 200.972 Angstrom': 297,
+    'Fe IX 171.073 Angstrom': 13946,
+    'Fe IX 188.496 Angstrom': 18403,
+    'Fe XI 188.497 Angstrom': 22527,
+    'Fe XIV 197.862 Angstrom': 27964,
+    'Fe XVI 262.984 Angstrom': 1415,
 }
 
 
 @pytest.mark.parametrize(('ion_name', 'wavelength'), [
     ('Ca XV', 200.972*u.Angstrom),
     ('Fe IX', 171.073*u.Angstrom),
+    ('Fe IX', 188.496*u.Angstrom),
     ('Fe XI', 188.497*u.Angstrom),
     ('Fe XIV', 197.862*u.Angstrom),
     ('Fe XVI', 262.984*u.Angstrom),
@@ -54,7 +58,7 @@ def test_idl_compare_goft(idl_env, hdf5_dbase_root, dbase_version, ion_name, wav
         'iz': iz,
         'wavelength': wavelength,
         'wave_window': 1 * u.angstrom,
-        'index': INDEX_WAVE_MAPPING[wavelength],
+        'index': INDEX_WAVE_MAPPING[f'{ion_name} {wavelength}'],
         'density': 1e+10 * u.cm**(-3),
         'abundance': 'sun_coronal_1992_feldman_ext',
         'ioneq': 'chianti',

fiasco/util/setup_db.py

@@ -199,5 +199,5 @@ def build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=None, check_hash=F
             if 'ion_index' in hf:
                 del hf['ion_index']
             ion_list = list_ions(hdf5_dbase_root)
-            ds = hf.create_dataset('ion_index', data=np.array(ion_list).astype(np.string_))
+            ds = hf.create_dataset('ion_index', data=np.array(ion_list).astype(np.bytes_))
             ds.attrs['unit'] = 'SKIP'