Merge branch 'xraypy:master' into struct2xas

doc/larch.bib

@@ -1,4 +1,3 @@
-
 @string{jacs = "Journal of the American Chemical Society"}
 @string{jsr   = "Journal of Synchrotron Radiation"}
 @string{prb  = "Physical Review B"}
@@ -18,6 +17,31 @@ @string{xbible
                   Techniques of {EXAFS}, {SEXAFS}, and {XANES}}"}
 
 
+@article{XDI2016,
+   author = {B. Ravel and M. Newville},
+   title = {XAFS Data Interchange: A single spectrum XAFS data file format },
+   journal = {Journal of Physics: Conference Series},
+   year    = "2016",
+   volume  = "712",
+   pages   = "012148",
+   doi     = {10.1088/1742-6596/712/1/012148},
+}
+
+
+@article{XASDataFormats,
+   author = {Ravel, B. and Hester, J. R. and Sole, V. A. and Newville, M.},
+   title = {Towards data format standardization for X-ray absorption spectroscopy},
+   journal = jsr,
+   year = {2012},
+   volume = {19},
+   number = {6},
+   pages = {869-874},
+   month = {Nov},
+   note = {International Workshop on Improving Data Quality and Quantity for XAFS
+           Experiments, Tsukuba, JAPAN, APR 12-13, 2011},
+   doi= {10.1107/S0909049512036886},
+}
+
 
 @article{larch2013,
    author  = {M. Newville},
@@ -39,7 +63,8 @@ @Misc{ixasportal
   title =  {International X-ray Absorption Society},
   key  =  {IXAS},
   year = 2012,
-  url = {{https://www.ixasportal.net/}}}
+  url = {{https://xrayabsorption.org}}}
+
 
 @article{ATOMS,
   author = {B. Ravel},
@@ -723,12 +748,12 @@ @article{Hall:es0164
 }
 
 @InBook{HallWestbrook,
-  author = 	 {Hall, S. R. and Westbrook, J. D.},
-  title = 	 {International Tables for Crystallography},
-  chapter = 	 {2.2},
-  publisher = 	 {IUCr},
-  year = 	 2005,
-  volume = 	 {G}
+  author =       {Hall, S. R. and Westbrook, J. D.},
+  title =        {International Tables for Crystallography},
+  chapter =      {2.2},
+  publisher =    {IUCr},
+  year =         2005,
+  volume =       {G}
 }
 
 
@@ -760,35 +785,35 @@ @article{PhysRevLett.27.1204
 
 @Misc{data_format_working_group,
   key = "XAS Data Format Working Group",
-  title = 	 {Data Format Working Group Wiki},
+  title =        {Data Format Working Group Wiki},
   url = {{https://github.com/XraySpectroscopy/Data-Format-Working-Group/wiki}},
-  year = 	 2012}
+  year =         2012}
 
 @Misc{hdf_group,
 key = {HDF GROUP},
   title = {HDF GROUP - HDF5},
   url = {{https://www.hdfgroup.org/HDF5/}},
-  year = 	 2012}
+  year =         2012}
 
 
 @Misc{sqlite,
-  author = 	 {Hipp, D. R.},
-  title = 	 {SQLite},
+  author =       {Hipp, D. R.},
+  title =        {SQLite},
   url = {{https://www.sqlite.org}},
-  year = 	 2012}
+  year =         2012}
 
 @Misc{xasformat_mailing_list,
   key = {XAS Data Format Working Group},
-  title = 	 "XASFORMAT mailing list",
+  title =        "XASFORMAT mailing list",
   url = {{https://millenia.cars.aps.anl.gov/mailman/listinfo/xasformat}},
-  year = 	 2012}
+  year =         2012}
 
 
 @Misc{lytle_database,
-  author = 	 {Lytle, F. and Boyanov, B. and Segre, S.},
-  title = 	 {Farrel Lytle XAFS Database},
+  author =       {Lytle, F. and Boyanov, B. and Segre, S.},
+  title =        {Farrel Lytle XAFS Database},
   url = {{https://ixs.iit.edu/database}},
-  year = 	 1995
+  year =         1995
 }
 
 

larch/apps.py

@@ -75,15 +75,16 @@ def create_shortcut(self):
         make_shortcut(script, name=self.name, icon=icon,
                       terminal=self.terminal, folder='Larch')
 
-APPS = (LarchApp('Larch CLI', 'larch', terminal=True),
-        LarchApp('Larch GUI', 'larch --wxgui'),
-        LarchApp('XAS Viewer',  'xas_viewer',  icon='onecone'),
+APPS = (LarchApp('Larch CLI',  'larch', terminal=True),
+        LarchApp('Larch GUI',  'larch --wxgui'),
+        LarchApp('XAS Viewer', 'xas_viewer',  icon='onecone'),
+        LarchApp('Larix',       'xas_viewer',  icon='onecone'),
         LarchApp('GSE MapViewer', 'gse_mapviewer',  icon='gse_xrfmap'),
-        LarchApp('XRF Display',  'xrfdisplay',  icon='ptable'),
+        LarchApp('XRF Viewer',  'larch_xrf',  icon='ptable'),
+        LarchApp('XRD1D Viewer', 'larch_xrd1d')
         # LarchApp('GSE DTCorrect', 'gse_dtcorrect'),
         # LarchApp('Dioptas', 'dioptas_larch', icon='dioptas'),
         # LarchApp('2D XRD Viewer', 'xrd2d_viewer'),
-        # LarchApp('1D XRD Viewer', 'xrd1d_viewer')
         )
 
 
@@ -99,7 +100,6 @@ def make_desktop_shortcuts():
     updater.create_shortcut()
 
 
-
 def make_cli(description='run larch program', filedesc='data file'):
     usage = "usage: %prog [options] file"
     parser = ArgumentParser(description=description)
@@ -140,7 +140,7 @@ def run_xas_viewer():
     kwargs = make_cli(description="Larch's XAS Viewer and Analysis Program")
     XASViewer(check_version=True, **kwargs).MainLoop()
 
-def run_xrfdisplay():
+def run_larch_xrf():
     """ XRF Display"""
     set_locale()
     use_mpl_wxagg()
@@ -151,7 +151,7 @@ def run_xrfdisplay():
                     filedesc='MCA File (.mca)')
     XRFApp(**kwargs).MainLoop()
 
-def run_xrfdisplay_epics():
+def run_epics_xrf():
     """XRF Display for Epics Detectors"""
     set_locale()
     use_mpl_wxagg()
@@ -160,12 +160,12 @@ def run_xrfdisplay_epics():
     from larch.epics import EpicsXRFApp
     EpicsXRFApp().MainLoop()
 
-def run_xrd1d_viewer():
+def run_larch_xrd1d():
     """XRD Display for 1D patternss"""
     set_locale()
     use_mpl_wxagg()
-    from larch.wxxrd import XRD1DViewer
-    XRD1DViewer().MainLoop()
+    from larch.wxxrd import XRD1DApp
+    XRD1DApp().MainLoop()
 
 def run_xrd2d_viewer():
     """XRD Display for 2D patternss"""

larch/io/__init__.py

@@ -44,6 +44,7 @@
                               is_specfile)
 from .stepscan_file import read_stepscan
 
+from .nexus_xas import NXxasFile
 
 def read_tiff(fname, _larch=None, *args, **kws):
     """read image data from a TIFF file as an array"""