Merge branch 'master' of https://github.com/xraypy/xraylarch

installers/GetLarch.bat

@@ -19,7 +19,7 @@ echo ## basic mamba installed, running updates
 set PATH=%prefix%;%prefix%\bin;%prefix%\condabin;%prefix%\Scripts;%PATH%
 
 echo ## Installing basic python scipy packages
-call %prefix%\Scripts\mamba install -yc conda-forge python==3.11.5 numpy scipy matplotlib h5py scikit-image scikit-learn pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy
+call %prefix%\Scripts\mamba install -yc conda-forge python==3.12.7 numpy scipy matplotlib h5py scikit-image scikit-learn pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy
 
 echo ## Installing xraylarch and dependencies from PyPI
 call %prefix%\Scripts\pip install xraylarch[larix]

installers/GetLarch.sh

@@ -8,19 +8,15 @@ prefix=$HOME/xraylarch
 larchurl='xraylarch[larix]'
 
 uname=`uname`
-if [ $uname == Darwin ]; then
-    uname=MacOSX
-fi
-
 condaurl="https://github.com/conda-forge/miniforge/releases/latest/download"
 
 condafile="Miniforge3-$uname-x86_64.sh"
-condafile="Mambaforge-$uname-x86_64.sh"
 
 logfile=GetLarch.log
 
 ## set list of conda packages to install from conda-forge
-cforge_pkgs="python=>3.12.3 numpy scipy matplotlib h5py scikit-image scikit-learn pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy"
+cforge_pkgs="python=>3.12.7 numpy scipy matplotlib h5py scikit-image scikit-learn pandas jupyter plotly wxpython fabio pyfai pymatgen mkl_fft tomopy"
+
 
 unset CONDA_EXE CONDA_PYTHON_EXE CONDA_PREFIX PROJ_LIB
 

installers/conda_constructor/construct.yaml

@@ -1,5 +1,5 @@
 name:  xraylarch
-version: 2023-10
+version: 2025-01
 
 channels:
     - https://conda.anaconda.org/conda-forge/
@@ -18,15 +18,15 @@ post_install: post_install_posix.sh [linux or osx]
 post_install: post_install_windows.bat [win]
 
 specs:
-    - python==3.11.5
+    - python==3.12.8
     - conda
     - mamba
     - openssl
     - setuptools>=61.0
     - pip
     - requests
-    - numpy>=1.24
-    - scipy>=1.9
+    - numpy>=1.25
+    - scipy>=1.13
     - matplotlib>=3.6
     - h5py>=3.7
     - sqlalchemy>=2.0

larch/io/columnfile.py

@@ -103,19 +103,26 @@ def getfloats(txt, allow_times=True):
       The `allow_times` will try to support common date-time strings
       using the dateutil module, returning a numerical value as the
       Unix timestamp, using
-          time.mktime(dateutil.parser.parse(word).timetuple())
+          dateutil.parser.parse(word).timestamp()
     """
-    words = [w.strip() for w in txt.replace(',', ' ').split()]
-    mktime = time.mktime
+    t = txt[:].strip()
+    if t[0] in ('#', ';', '!', '<', '*', '%'):
+        return [None]
+
+    for delim in ('\t', ',', ';'):
+        if t.count(delim) > 0:
+            t = t.replace(delim, ' ')
+    words = [w.strip() for w in t.split()]
     for i, w in enumerate(words):
         val = None
         try:
             val = float(w)
         except ValueError:
-            try:
-                val = mktime(dateparse(w).timetuple())
-            except ValueError:
-                pass
+            if allow_times:
+                try:
+                    val = dateparse(w).timestamp()
+                except ValueError:
+                    pass
         words[i] = val
     return words
 
@@ -278,7 +285,7 @@ def read_ascii(filename, labels=None, simple_labels=False,
     Examples:
 
         >>> feo_data = read_ascii('feo_rt1.dat')
-        >>> show(g)a
+        >>> show(g)
         == Group ascii_file feo_rt1.dat: 0 methods, 8 attributes ==
         array_labels: ['energy', 'xmu', 'i0']
         attrs: <Group header attributes from feo_rt1.dat>

larch/version.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 """Version information"""
 
-__release_version__ = '0.9.81'
-__date__    = '2024-September-20'
+__release_version__ = '2024.12.0'
+__date__    = '2024-December-20'
 __authors__ = "M. Newville, M. Rovezzi, M. Koker, B. Ravel, and others"
 
 from ._version import __version__, __version_tuple__

larch/wxlib/cif_browser.py

@@ -557,6 +557,17 @@ def onGetFeff(self, event=None):
         fefftext = cif2feffinp(cif.ciftext, catom, edge=edge, cluster_size=csize,
                                absorber_site=site_index, version8=version8,
                                with_h=with_h, extra_titles=etitles)
+        # hack for larixite 2024.10.0,
+        # but also, here we really want to force the print and control flags
+        flines = fefftext.split('\n')
+        for i, l in enumerate(flines):
+            x = l.strip()
+            if x.startswith('PRINT'):
+                flines[i] = 'PRINT     1      0     0     0     0      3'
+            elif x.startswith('CONTROL'):
+                flines[i] = 'CONTROL   1      1     1     1     1      1'
+
+        fefftext = '\n'.join(flines)
 
         self.wids['feff_runfolder'].SetValue(folder)
         self.wids['feff_text'].SetValue(fefftext)

larch/wxlib/parameter.py

@@ -103,6 +103,7 @@ def __init__(self, parent, param,  name_size=None, prefix=None,
                                    maxval=param.max,
                                    action=self.onValue,
                                    act_on_losefocus=True,
+                                   bell_on_invalid=False,
                                    gformat=True,
                                    size=(float_size, -1))
             self.widgets.append(self.value)
@@ -325,6 +326,7 @@ def __init__(self, parent, param, precision=4, vary=None,
 
         self.wids.val  = FloatCtrl(panel, value=param.value, size=(100, -1),
                                    precision=precision,
+                                   bell_on_invalid=False,
                                    minval=minval, maxval=maxval)
         self.wids.min  = FloatCtrl(panel, value=minval, size=(100, -1))
         self.wids.max  = FloatCtrl(panel, value=maxval, size=(100, -1))
@@ -392,6 +394,7 @@ def __init__(self, parent, param, size=(80, -1), show_name=False,
 
         self.wids.val = FloatCtrl(self, value=param.value,
                                   minval=param.min, maxval=param.max,
+                                  bell_on_invalid=False,
                                   precision=precision, size=size)
 
         self.wids.name = None

larch/wxxas/prepeak_panel.py

@@ -302,26 +302,27 @@ def build(self):
 
         sview.SetFont(self.font_fixedwidth)
 
-        xw = (175, 85, 85, 130, 130, 130)
+        xw = (170, 75, 75, 110, 115, 115, 100)
         if uname=='darwin':
-            xw = (160, 75, 75, 110, 110, 120)
+            xw = (150, 70, 70, 90, 95, 95, 95)
 
 
         sview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectFit)
         sview.AppendTextColumn('Label',  width=xw[0])
-        sview.AppendTextColumn('N_data', width=xw[1])
-        sview.AppendTextColumn('N_vary', width=xw[2])
+        sview.AppendTextColumn('Ndata', width=xw[1])
+        sview.AppendTextColumn('Nvary', width=xw[2])
         sview.AppendTextColumn('\u03c7\u00B2', width=xw[3])
         sview.AppendTextColumn('reduced \u03c7\u00B2', width=xw[4])
         sview.AppendTextColumn('Akaike Info', width=xw[5])
+        sview.AppendTextColumn('R^2', width=xw[6])
 
         for col in range(sview.ColumnCount):
             this = sview.Columns[col]
             this.Sortable = True
             this.Alignment = wx.ALIGN_RIGHT if col > 0 else wx.ALIGN_LEFT
             this.Renderer.Alignment = this.Alignment
 
-        sview.SetMinSize((750, 150))
+        sview.SetMinSize((775, 150))
 
         irow += 1
         sizer.Add(sview, (irow, 0), (1, 5), LEFT)
@@ -357,7 +358,7 @@ def build(self):
             this.Alignment = wx.ALIGN_RIGHT if col in (1, 2) else wx.ALIGN_LEFT
             this.Renderer.Alignment = this.Alignment
 
-        pview.SetMinSize((750, 200))
+        pview.SetMinSize((775, 200))
         pview.Bind(dv.EVT_DATAVIEW_SELECTION_CHANGED, self.onSelectParameter)
 
         irow += 1
@@ -466,7 +467,7 @@ def onSaveAllStats(self, evt=None):
 
         labels = [('Data Set' + ' '*25)[:25], 'Group name', 'n_data',
                  'n_varys', 'chi-square', 'reduced_chi-square',
-                 'akaike_info', 'bayesian_info']
+                 'akaike_info', 'bayesian_info', 'R^2']
 
         for pname in param_names:
             labels.append(pname)
@@ -485,7 +486,7 @@ def onSaveAllStats(self, evt=None):
                 label = (label + ' '*25)[:25]
             dat = [label, dgroup.groupname,
                    '%d' % result.ndata, '%d' % result.nvarys]
-            for attr in ('chisqr', 'redchi', 'aic', 'bic'):
+            for attr in ('chisqr', 'redchi', 'aic', 'bic', 'rsquared'):
                 dat.append(gformat(getattr(result, attr), 11))
             for pname in param_names:
                 val = stderr = 0
@@ -636,16 +637,18 @@ def show_results(self, datagroup=None, form=None, show_plot=False, larch_eval=No
 
         datagroup = self.datagroup
         self.peakfit_history = getattr(self.datagroup.prepeaks, 'fit_history', [])
-
         # cur = self.get_fitresult()
         wids = self.wids
         wids['stats'].DeleteAllItems()
         for i, res in enumerate(self.peakfit_history):
             args = [res.label]
-            for attr in ('ndata', 'nvarys', 'chisqr', 'redchi', 'aic'):
+            for attr in ('ndata', 'nvarys', 'chisqr', 'redchi',
+                        'aic', 'rsquared'):
                 val = getattr(res.result, attr)
                 if isinstance(val, int):
                     val = '%d' % val
+                elif attr == 'rsquared':
+                    val = f"{val:.5f}"
                 else:
                     val = gformat(val, 10)
                 args.append(val)
@@ -1044,6 +1047,7 @@ def fill_model_params(self, prefix, params):
             pname = prefix + pname
             if pname in parwids:
                 wids = parwids[pname]
+                wids.value.SetValue(par.value)
                 if wids.minval is not None:
                     wids.minval.SetValue(par.min)
                 if wids.maxval is not None:
@@ -1053,7 +1057,7 @@ def fill_model_params(self, prefix, params):
                     varstr = 'constrain'
                 if wids.vary is not None:
                     wids.vary.SetStringSelection(varstr)
-                wids.value.SetValue(par.value)
+
 
     def onPlotModel(self, evt=None):
         dgroup = self.controller.get_group()

larch/wxxas/xas_dialogs.py

@@ -580,8 +580,10 @@ def __init__(self, parent, controller, **kws):
         wids['xanes_step'] = FloatCtrl(panel, value=xanes_step,  **opts)
         wids['exafs_step'] = FloatCtrl(panel, value=0.05,  **opts)
 
+        wids['method'] = Choice(panel, choices=('spline', 'boxcar', 'centroid'),
+                                 size=(80, -1), action=self.on_rebin)
         for wname, wid in wids.items():
-            if wname != 'grouplist':
+            if wname not in ('grouplist', 'method'):
                 wid.SetAction(partial(self.on_rebin, name=wname))
 
         #wids['apply'] = Button(panel, 'Save / Overwrite', size=(150, -1),
@@ -592,7 +594,7 @@ def __init__(self, parent, controller, **kws):
                                  action=self.on_saveas)
         SetTip(wids['save_as'], 'Save corrected data as new group')
 
-        wids['save_as_name'] = wx.TextCtrl(panel, -1, self.dgroup.filename + '_rebin',
+        wids['save_as_name'] = wx.TextCtrl(panel, -1, self.dgroup.filename + '_rebin_s',
                                            size=(250, -1))
 
         def add_text(text, dcol=1, newrow=True):
@@ -629,6 +631,9 @@ def add_text(text, dcol=1, newrow=True):
         panel.Add(wids['exafs_step'])
         add_text('1/\u212B', newrow=False)
 
+        add_text('Smoothing Method: ', dcol=2)
+        panel.Add(wids['method'])
+
         # panel.Add(wids['apply'], dcol=2, newrow=True)
         panel.Add(wids['save_as'],  dcol=2, newrow=True)
         panel.Add(wids['save_as_name'], dcol=3)
@@ -664,8 +669,10 @@ def on_rebin(self, event=None, name=None, value=None):
             val = wids['exafs1'].GetValue()
             wids['xanes2'].SetValue(ktoe(val), act=False)
 
+        method = wids['method'].GetStringSelection().lower()
         e0 = wids['e0'].GetValue()
         args = dict(group=self.dgroup.groupname, e0=e0,
+                    method=method,
                     pre1=wids['pre1'].GetValue(),
                     pre2=wids['pre2'].GetValue(),
                     pre_step=wids['pre_step'].GetValue(),
@@ -677,9 +684,10 @@ def on_rebin(self, event=None, name=None, value=None):
         # do rebin:
         cmd = """rebin_xafs({group}, e0={e0:f}, pre1={pre1:f}, pre2={pre2:f},
         pre_step={pre_step:f}, xanes_step={xanes_step:f}, exafs1={exafs1:f},
-        exafs2={exafs2:f}, exafs_kstep={exafs_kstep:f})""".format(**args)
+        exafs2={exafs2:f}, exafs_kstep={exafs_kstep:f}, method='{method}')""".format(**args)
         self.cmd = cmd
         self.controller.larch.eval(cmd)
+        wids['save_as_name'].SetValue(f'{self.dgroup.filename}_rebin_{method[:3]}')
 
         if hasattr(self.dgroup, 'rebinned'):
             xnew = self.dgroup.rebinned.energy

larch/wxxas/xasgui.py

@@ -1449,7 +1449,7 @@ def onReadSpecfile_OK(self, script, path, scanlist, config=None):
                 mscript = '\n'.join(["{ngroup} = deepcopy({group})",
                                      yplotline,
                                     "{ngroup}.mu = {ngroup}.yplot",
-                                     "{ngroup}.plot_ylabel = '{ylabel}'"])
+                                    "{ngroup}.plot_ylabel = '{ylabel}'"])
                 i0 = '1.0'
                 if multi_i0  < len(config['array_labels']):
                     i0 = config['array_labels'][multi_i0]
@@ -1700,7 +1700,7 @@ def install_multichans(config):
                     yplotline = line.replace("{group}", "{ngroup}")
             mscript = ["{ngroup} = deepcopy({group})",
                        yplotline,
-                      "{ngroup}.{yarray} = {ngroup}.yplot[:]",
+                      "{ngroup}.mu = {ngroup}.{yarray} = {ngroup}.yplot[:]",
                       "{ngroup}.plot_ylabel = '{ylabel}'" ]
             if dtype == 'xydata':
                 mscript.append("{ngroup}.scale = ptp({ngroup}.y+1.e-15)")

larch/xafs/pre_edge.py

@@ -37,6 +37,7 @@ def find_e0(energy, mu=None, group=None, _larch=None):
     energy, mu, group = parse_group_args(energy, members=('energy', 'mu'),
                                          defaults=(mu,), group=group,
                                          fcn_name='find_e0')
+    energy, mu = remove_nans2(energy, mu)
     # first find e0 without smoothing, then refine with smoothing
     e1, ie0, estep1 = _finde0(energy, mu, estep=None, use_smooth=False)
     istart = max(3, ie0-75)

larch/xafs/rebin_xafs.py

@@ -1,5 +1,6 @@
 import numpy as np
 from scipy.interpolate import CubicSpline
+
 from larch import Group, Make_CallArgs, parse_group_args
 from larch.math import (index_of, interp1d,
                         remove_dups, remove_nans, remove_nans2)
@@ -70,7 +71,8 @@ def rebin_xafs(energy, mu=None, group=None, e0=None, pre1=None, pre2=-30,
     exafs1       end of XANES region, start of EXAFS region [15]
     exafs2       end of EXAFS region [last energy point]
     exafs_kstep  k-step for EXAFS region [0.05]
-    method       one of 'boxcar', 'centroid', 'spline' ['spline']
+    method       one of 'spline, 'boxcar', 'centroid' ['spline']
+
 
     Returns
     -------
@@ -101,7 +103,8 @@ def rebin_xafs(energy, mu=None, group=None, e0=None, pre1=None, pre2=-30,
        array.  For each new energy bin, the new value is selected from the
        data in the segment as either
          a) linear interpolation if there are fewer than 3 points in the segment.
-         b) mean value ('boxcar')
+         b) spline interpolation ('spline')
+         c) mean value ('boxcar')
          c) centroid ('centroid')
 
     """

setup.cfg

@@ -35,13 +35,13 @@ include_package_data = True
 python_requires = >=3.9
 setup_requires = setuptools_scm
 install_requires =
-    numpy>=1.22,<2
-    scipy>=1.7
+    numpy>=1.25
+    scipy>=1.13
     lmfit>=1.3.1
-    asteval>=1.0.2
+    asteval>=1.0.4
     uncertainties>=3.2.1
     pyshortcuts>=1.9.5
-    xraydb>=4.5.3
+    xraydb>=4.5.5
     larixite
     silx>=0.15.2
     matplotlib>=3.5