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

examples/feffit/doc_feffit1.out

@@ -11,7 +11,7 @@
    Bayesian info crit = 41.4428977
 
 [[Dataset]]
-   dataset unique_id  = 'dgpiqpwi'
+   unique_id          = 'dc5vezx7'
    fit space          = 'r'
    r-range            = 1.400, 3.000
    k-range            = 3.000, 17.000

examples/feffit/doc_feffit2.out

@@ -11,7 +11,7 @@
    Bayesian info crit = 12.5185008
 
 [[Dataset]]
-   dataset unique_id  = 'do2js2h5'
+   unique_id          = 'ds3qtgjs'
    fit space          = 'r'
    r-range            = 1.400, 3.500
    k-range            = 3.000, 17.000

examples/feffit/doc_feffit3.out

@@ -11,7 +11,7 @@
    Bayesian info crit = 243.985673
 
 [[Datasets (3)]]
-   dataset unique_id  = 'd3hdjp7v'
+   unique_id          = 'd3hdjp7v'
    fit space          = 'r'
    r-range            = 1.400, 3.400
    k-range            = 3.000, 17.000
@@ -21,7 +21,7 @@
    epsilon_k          = Array(mean=0.0011450, std=9.5319e-4)
    epsilon_r          = 0.0384855
    n_independent      = 18.825
-   dataset unique_id  = 'd3s3lmwo'
+   unique_id          = 'd3s3lmwo'
    fit space          = 'r'
    r-range            = 1.400, 3.400
    k-range            = 3.000, 17.000
@@ -31,7 +31,7 @@
    epsilon_k          = Array(mean=0.0010796, std=0.0010404)
    epsilon_r          = 0.0362874
    n_independent      = 18.825
-   dataset unique_id  = 'dcultf7u'
+   unique_id          = 'dcultf7u'
    fit space          = 'r'
    r-range            = 1.400, 3.400
    k-range            = 3.000, 17.000

installers/conda_constructor/construct.yaml

@@ -41,6 +41,7 @@ specs:
     - pyyaml
     - toml
     - sphinx
+    - notebook<7
     - dill
     - psycopg2
     - patchelf         # [linux]

larch/io/athena_project.py

@@ -111,7 +111,7 @@ def make_athena_args(group, hashkey=None, **kws):
                  ('bkg_rbkg', '1.0'), ('bkg_slope', '0'),
                  ('bkg_pre1', '-150'), ('bkg_pre2', '-30'),
                  ('bkg_nor1', '150'), ('bkg_nor2', '800'),
-                 ('bkg_nnorm', '1'),
+                 ('bkg_nnorm', '1'), ('bkg_nvict', '0'),
                  ('prjrecord', 'athena.prj, 1'),  ('chi_column', ''),
                  ('chi_string', ''), ('collided', '0'), ('columns', ''),
                  ('daq', ''), ('denominator', '1'), ('display', '0'),
@@ -166,7 +166,7 @@ def make_athena_args(group, hashkey=None, **kws):
             args[aname] = val
 
     bkg_map = dict(nnorm='nnorm', nor1='norm1', nor2='norm2', pre1='pre1',
-                   pre2='pre2')
+                   pre2='pre2', nvict='nvict')
 
     if hasattr(group, 'pre_edge_details'):
         for aname, lname in bkg_map.items():
@@ -231,6 +231,7 @@ def format_array(arr):
 
 def clean_bkg_params(grp):
     grp.nnorm = getattr(grp, 'nnorm', 2)
+    grp.nvict = getattr(grp, 'nvict', 0)
     grp.e0   = getattr(grp, 'e0', -1)
     grp.rbkg = getattr(grp, 'rbkg', 1)
     grp.pre1 = getattr(grp, 'pre1', -150)
@@ -834,6 +835,7 @@ def read(self, filename=None, match=None, do_preedge=True, do_bkg=False,
                          pre1=float(pars.pre1), pre2=float(pars.pre2),
                          norm1=float(pars.nor1), norm2=float(pars.nor2),
                          nnorm=float(pars.nnorm),
+                         nvict=float(pars.nvict),
                          make_flat=bool(pars.flatten))
                 if do_bkg and hasattr(pars, 'rbkg'):
                     autobk(this, e0=float(pars.e0), rbkg=float(pars.rbkg),

larch/plot/plotly_xafsplots.py

@@ -68,7 +68,7 @@ def get_display(win=1, *args, **kws):
                 )
 
 def set_label_weight(label, w):
-    return label.replace('__W__', '{0:g}'.format(w))
+    return label.replace('_w_', '{0:g}'.format(w))
 
 # common XAFS plot labels
 def chirlab(kweight, show_mag=True, show_real=False, show_imag=False):
@@ -105,17 +105,17 @@ def chirlab(kweight, show_mag=True, show_real=False, show_imag=False):
                    chie    = r'$\chi(E)$',
                    chie0   = r'$\chi(E)$',
                    chie1   = r'$E\chi(E) \rm\, (eV)$',
-                   chiew   = r'$E^{__W__}\chi(E) \rm\,(eV^{__W__})$',
-                   chikw   = r'$k^{{__W__}}\chi(k) \rm\,(\unicode{x212B}^{{-__W__}})$',
+                   chiew   = r'$E^{{_w_}\chi(E) \rm\,(eV^{_w_})$',
+                   chikw   = r'$k^{{_w_}}\chi(k) \rm\,(\unicode{x212B}^{{-_w_}})$',
                    chi0    = r'$\chi(k)$',
                    chi1    = r'$k\chi(k) \rm\,(\unicode{x212B}^{-1})$',
                    chi2    = r'$k^2\chi(k) \rm\,(\unicode{x212B}^{-2})$',
                    chi3    = r'$k^3\chi(k) \rm\,(\unicode{x212B}^{-3})$',
-                   chir    = r'$\chi(R) \rm\,(\unicode{x212B}^{{-__W__}})$',
-                   chirmag = r'$|\chi(R)| \rm\,(\unicode{x212B}^{{-__W__}})$',
-                   chirre  = r'${{\rm Re}}[\chi(R)] \rm\,(\unicode{x212B}^{{-__W__}})$',
-                   chirim  = r'${{\rm Im}}[\chi(R)] \rm\,(\unicode{x212B}^{{-__W__}})$',
-                   chirpha = r'${{\rm Phase}}[\chi(R)] \rm\,(\unicode{x212B}^{{-__W__}})$',
+                   chir    = r'$\chi(R) \rm\,(\unicode{x212B}^{{-_w_}})$',
+                   chirmag = r'$|\chi(R)| \rm\,(\unicode{x212B}^{{-_w_}})$',
+                   chirre  = r'${{\rm Re}}[\chi(R)] \rm\,(\unicode{x212B}^{{-_w_}})$',
+                   chirim  = r'${{\rm Im}}[\chi(R)] \rm\,(\unicode{x212B}^{{-_w_}})$',
+                   chirpha = r'${{\rm Phase}}[\chi(R)] \rm\,(\unicode{x212B}^{{-_w_}})$',
                    e0color = '#B2B282',
                    chirlab = chirlab)
 
@@ -625,9 +625,7 @@ def plot_chik(dgroup, kweight=None, kmax=None, show_window=True,
 
     if kmax is not None:
         fig.set_xrange(0, kmax)
-    ylabel = plotlabels.chi0
-    if kweight > 0:
-        ylabel = set_label_weight(plotlabels.chikw, kweight)
+    ylabel = set_label_weight(plotlabels.chikw, kweight)
     fig.set_style(title=title, xaxis_title=plotlabels.k,
                   yaxis_title=ylabel)
 
@@ -924,17 +922,12 @@ def plot_path_k(dataset, ipath=0, kmin=0, kmax=None, offset=0, label=None,
 
     chi_kw = offset + path.chi * path.k**kweight
 
-    fig = PlotlyFigure(two_yaxis=False)
-    fig.add_plot(path.k, chi_kw, label=label)
-
-    if kmin is not None or kmax is not None:
-        fig.set_xrange(kmin, kmax)
-
-    ylabel = set_label_weight(plotlabels.chikw, kweight)
-    fig.set_style(title=title, xaxis_title=plotlabels.k,
-                  yaxis_title=ylabel)
-    fig.show()
-    return fig
+    _plot(path.k, chi_kw, label=label, xmin=kmin, xmax=kmax,
+          xlabel=plotlabels.k,
+          ylabel=set_label_weight(plotlabels.chikw, kweight),
+          win=win, new=new, delay_draw=delay_draw, _larch=_larch, **kws)
+    if delay_draw:
+        redraw(win=win, xmin=kmin, xmax=kmax, _larch=_larch)
 #enddef
 
 def plot_path_r(dataset, ipath, rmax=None, offset=0, label=None,
@@ -967,28 +960,28 @@ def plot_path_r(dataset, ipath, rmax=None, offset=0, label=None,
     if label is None:
         label = 'path %i' % (1+ipath)
     #endif
-    kweight = dataset.transform.kweight
+    kweight =dataset.transform.kweight
+    ylabel = plotlabels.chirlab(kweight, show_mag=show_mag,
+                                show_real=show_real, show_imag=show_imag)
 
-    fig = PlotlyFigure(two_yaxis=False)
+    opts = dict(xlabel=plotlabels.r, ylabel=ylabel, xmax=rmax, new=new,
+                delay_draw=True, _larch=_larch)
+
+    opts.update(kws)
     if show_mag:
-        fig.add_plot(path.r, offset+path.chir_mag, label=f'|{label}|')
-
+        _plot(path.r,  offset+path.chir_mag, label=label, **opts)
+        opts['new'] = False
+    #endif
     if show_real:
-        fig.add_plot(path.r, offset+path.chir_re, label=f'Re[{label}]')        
-
+        _plot(path.r,  offset+path.chir_re, label=label, **opts)
+        opts['new'] = False
+    #endif
     if show_imag:
-        fig.add_plot(path.r,  offset+path.chir_im, label=f'Im[{label}]')
-
-    if rmax is not None:
-        fig.set_xrange(0, rmax)
-
-    ylabel = plotlabels.chirlab(kweight, show_mag=show_mag,
-                                show_real=show_real, show_imag=show_imag)
-    fig.set_style(title=title, xaxis_title=plotlabels.r,
-                  yaxis_title=ylabel)
-    fig.show()
-    return fig
-
+        _plot(path.r,  offset+path.chir_im, label=label, **opts)
+        opts['new'] = False
+    #endif
+    redraw(win=win, xmax=rmax, _larch=_larch)
+#enddef
 
 def plot_paths_k(dataset, offset=-1, kmin=0, kmax=None, title=None,
                  new=True, delay_draw=False, win=1, _larch=None, **kws):
@@ -1018,22 +1011,18 @@ def plot_paths_k(dataset, offset=-1, kmin=0, kmax=None, title=None,
 
     title = _get_title(dataset, title=title)
 
-    fig = PlotlyFigure(two_yaxis=False)
-    fig.add_plot(model.k, model_chi_kw, label='sum')
-
-    for ipath, path in enumerate(dataset.pathlist):
-        label = 'path %i' % (1+ipath)
-        chi_kw = offset + path.chi * path.k**kweight
-        fig.add_plot(path.k, chi_kw+(ipath+1)*offset, label=label)
-
-    if kmin is not None or kmax is not None:
-        fig.set_xrange(kmin, kmax)
-
-    ylabel = set_label_weight(plotlabels.chikw, kweight)
-    fig.set_style(title=title, xaxis_title=plotlabels.k,
-                  yaxis_title=ylabel)
-    fig.show()
-    return fig
+    _plot(model.k, model_chi_kw, title=title, label='sum', new=new,
+          xlabel=plotlabels.r, ylabel=plotlabels.chikw.format(kweight),
+          xmin=kmin, xmax=kmax, win=win, delay_draw=True,_larch=_larch,
+          **kws)
+
+    for ipath in range(len(dataset.pathlist)):
+        plot_path_k(dataset, ipath, offset=(ipath+1)*offset,
+                    kmin=kmin, kmax=kmax, new=False, delay_draw=True,
+                    win=win, _larch=_larch)
+    #endfor
+    redraw(win=win, xmin=kmin, xmax=kmax, _larch=_larch)
+#enddef
 
 def plot_paths_r(dataset, offset=-0.25, rmax=None, show_mag=True,
                  show_real=False, show_imag=False, title=None, new=True,
@@ -1064,35 +1053,29 @@ def plot_paths_r(dataset, offset=-0.25, rmax=None, show_mag=True,
     ylabel = plotlabels.chirlab(kweight, show_mag=show_mag,
                                 show_real=show_real, show_imag=show_imag)
     title = _get_title(dataset, title=title)
-
-
-    fig = PlotlyFigure(two_yaxis=False)
+    opts = dict(xlabel=plotlabels.r, ylabel=ylabel, xmax=rmax, new=new,
+                delay_draw=True, title=title, _larch=_larch)
+    opts.update(kws)
     if show_mag:
-        fig.add_plot(model.r,  model.chir_mag, label='|sum|')
+        _plot(model.r,  model.chir_mag, label='|sum|', **opts)
+        opts['new'] = False
+    #endif
     if show_real:
-        fig.add_plot(model.r,  model.chir_re, label='Re[sum]')
+        _plot(model.r,  model.chir_re, label='Re[sum]', **opts)
+        opts['new'] = False
+    #endif
     if show_imag:
-        fig.add_plot(model.r,  model.chir_im, label='Im[sum]')
-
-    for ipath, path in enumerate(dataset.pathlist):
-        label = 'path %i' % (1+ipath)
-        off = (ipath+1)*offset
-        if show_mag:
-            fig.add_plot(path.r, off+path.chir_mag, label=f'|{label}|')
-        if show_real:
-            fig.add_plot(path.r, off+path.chir_re, label=f'Re[{label}]')        
-        if show_imag:
-            fig.add_plot(path.r, off+path.chir_im, label=f'Im[{label}]')
-
-    if rmax is not None:
-        fig.set_xrange(0, rmax)
+        _plot(model.r,  model.chir_im, label='Im[sum]', **opts)
+        opts['new'] = False
+    #endif
 
-    ylabel = plotlabels.chirlab(kweight, show_mag=show_mag,
-                                show_real=show_real, show_imag=show_imag)
-    fig.set_style(title=title, xaxis_title=plotlabels.r,
-                  yaxis_title=ylabel)
-    fig.show()
-    return fig
+    for ipath in range(len(dataset.pathlist)):
+        plot_path_r(dataset, ipath, offset=(ipath+1)*offset,
+                    show_mag=show_mag, show_real=show_real,
+                    show_imag=show_imag, **opts)
+    #endfor
+    redraw(win=win, xmax=rmax,_larch=_larch)
+#enddef
 
 
 def extend_plotrange(x, y, xmin=None, xmax=None, extend=0.10):