# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1712826108 0
# Node ID 2ceaa943a2ad49b2780a468d2a76b8df316f50f3
# Parent  f802cd616862e37264595b9f11c2f3e773a67193
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8

diff -r f802cd616862 -r 2ceaa943a2ad common.py
--- a/common.py	Mon Mar 04 11:43:09 2024 +0000
+++ b/common.py	Thu Apr 11 09:01:48 2024 +0000
@@ -7,14 +7,14 @@
 
 
 def get_group(athena_group: AthenaGroup, key: str = None) -> Group:
-    group_keys = list(athena_group._athena_groups.keys())
+    group_keys = list(athena_group.keys())
     if key is None:
         key = group_keys[0]
     else:
         key = key.replace("-", "_")
 
     try:
-        return extract_athenagroup(athena_group._athena_groups[key])
+        return extract_athenagroup(athena_group.groups[key])
     except KeyError as e:
         raise KeyError(f"{key} not in {group_keys}") from e
 
@@ -28,7 +28,7 @@
         do_fft=False,
     )
     all_groups = {}
-    for key in athena_group._athena_groups.keys():
+    for key in athena_group.keys():
         print(f"\nExtracting group {key}")
         group = get_group(athena_group, key)
         pre_edge_with_defaults(group=group)
@@ -52,13 +52,22 @@
     return group
 
 
-def pre_edge_with_defaults(group: Group, settings: dict = None):
+def pre_edge_with_defaults(
+    group: Group, settings: dict = None, ref_channel: str = None
+):
     merged_settings = {}
-    try:
-        bkg_parameters = group.athena_params.bkg
-    except AttributeError as e:
-        print(f"Cannot load group.athena_params.bkg from group:\n{e}")
-        bkg_parameters = None
+    if ref_channel is not None:
+        print(f"Performing pre-edge with reference channel {ref_channel}")
+        ref = getattr(group, ref_channel.lower())
+        group.e0 = None
+        pre_edge(energy=group.energy, mu=ref, group=group)
+        bkg_parameters = group.pre_edge_details
+    else:
+        try:
+            bkg_parameters = group.athena_params.bkg
+        except AttributeError as e:
+            print(f"Cannot load group.athena_params.bkg from group:\n{e}")
+            bkg_parameters = None
 
     keys = (
         ("e0", "e0", None),
@@ -73,7 +82,11 @@
     )
     for key, parameters_key, default in keys:
         extract_attribute(
-            merged_settings, key, bkg_parameters, parameters_key, default
+            merged_settings=merged_settings,
+            key=key,
+            parameters_group=bkg_parameters,
+            parameters_key=parameters_key,
+            default=default,
         )
 
     if settings:
@@ -116,7 +129,11 @@
     )
     for key, parameters_key, default in keys:
         extract_attribute(
-            merged_settings, key, fft_parameters, parameters_key, default
+            merged_settings=merged_settings,
+            key=key,
+            parameters_group=fft_parameters,
+            parameters_key=parameters_key,
+            default=default,
         )
 
     if settings:
diff -r f802cd616862 -r 2ceaa943a2ad larch_artemis.xml
--- a/larch_artemis.xml	Mon Mar 04 11:43:09 2024 +0000
+++ b/larch_artemis.xml	Thu Apr 11 09:01:48 2024 +0000
@@ -2,7 +2,7 @@
     <description>generate Artemis projects from XAFS data</description>
     <macros>
         <!-- version of underlying tool (PEP 440) -->
-        <token name="@TOOL_VERSION@">0.9.74</token>
+        <token name="@TOOL_VERSION@">0.9.75</token>
         <!-- version of this tool wrapper (integer) -->
         <token name="@WRAPPER_VERSION@">0</token>
         <!-- citation should be updated with every underlying tool version -->
diff -r f802cd616862 -r 2ceaa943a2ad test-data/fit_report.txt
--- a/test-data/fit_report.txt	Mon Mar 04 11:43:09 2024 +0000
+++ b/test-data/fit_report.txt	Thu Apr 11 09:01:48 2024 +0000
@@ -1,50 +1,53 @@
 =================== FEFFIT RESULTS ====================
 \[\[Statistics\]\]
-   nvarys, npts       =  6, 104
-   n_independent      =  12\.205
-   chi_square         =  [\d\.]{9}
-   reduced chi_square =  [\d\.]{9}
-   r-factor           =  [\d\.]{9}
-   Akaike info crit   =  [\d\.]{9}
-   Bayesian info crit =  [\d\.]{9}
-
-\[\[Data\]\]
-   fit space          = 'r'
-   r-range            = 1\.400, 3\.000
-   k-range            = 3\.000, 14\.000
-   k window, dk       = 'hanning', 1\.000
-   paths used in fit  = \['feff/feff0001\.dat', 'feff/feff0002\.dat', 'feff/feff0003\.dat', 'feff/feff0004\.dat'\]
-   k-weight           = 2
-   epsilon_k          = Array\(mean=5\.1913e-4, std=4\.5676e-4\)
-   epsilon_r          = [\d\.]{9}
-   n_independent      = 12\.205
+  n_function_calls     = 4\d\d
+  n_variables          = 6
+  n_data_points        = 104
+  n_independent        = 12\.2045080
+  chi_square           = [\d\.]{10}
+  reduced chi_square   = [\d\.]{10}
+  r-factor             = [\d\.]{10}
+  Akaike info crit     = [\d\.]{10}
+  Bayesian info crit   = [\d\.]{10}
 
 \[\[Variables\]\]
-   alpha          = [-\s][\d\.]{9} \+/- [\d\.]{9}   \(init=  1\.0000e-7\)
-   amp            = [-\s][\d\.]{9} \+/- [\d\.]{9}   \(init=  1\.0000000\)
-   enot           = [-\s][\d\.]{9} \+/- [\d\.]{9}   \(init=  1\.0000e-7\)
-   ss             = [-\s][\d\.]{9} \+/- [\d\.]{9}   \(init=  0\.0030000\)
-   ss2            = [-\s][\d\.]{9} \+/- [\d\.]{9}   \(init=  0\.0030000\)
-   ss3            = [-\s][\d\.]{9} \+/- [\d\.]{9}  = 'ss2'
-   ssfe           = [-\s][\d\.]{9} \+/- [\d\.]{9}   \(init=  0\.0030000\)
+  alpha                = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 1\.0000e-7\)
+  amp                  = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 1\.0000000\)
+  enot                 = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 1\.0000e-7\)
+  ss                   = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 0\.0030000\)
+  ss2                  = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 0\.0030000\)
+  ss3                  = [-\s][\d\.]{9} \+/- [\d\.]{9}  = 'ss2'
+  ssfe                 = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 0\.0030000\)
 
-\[\[Correlations\]\]    \(unreported correlations are <  0\.100\)
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
-   \w+, \w+\s+= [\s\-]0\.\d{3}
+\[\[Correlations\]\] \(unreported correlations are <  0\.100\)
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
 
 
+\[\[Dataset\]\]
+  unique_id            = 'dm7xe57x'
+  fit space            = 'r'
+  r-range              = 1\.400, 3\.000
+  k-range              = 3\.000, 14\.000
+  k window, dk         = 'hanning', 1\.000
+  paths used in fit    = \['feff/feff0001\.dat', 'feff/feff0002\.dat', 'feff/feff0003\.dat', 'feff/feff0004\.dat'\]
+  k-weight             = 2
+  epsilon_k            = Array\(mean=5\.1913e-4, std=4\.5676e-4\)
+  epsilon_r            = [\d\.]{9}
+  n_independent        = 12\.205
+
 \[\[Paths\]\]
  = Path 'S1' = Rh K Edge
     feffdat file = feff/feff0001\.dat, from feff run 'feff'