Merge pull request #548 from lmfit/html_repr

alternative html_repr

Author: newville

lmfit/minimizer.py

@@ -35,6 +35,7 @@
 
 from ._ampgo import ampgo
 from .parameter import Parameter, Parameters
+from .printfuncs import fitreport_html_table
 
 # check for EMCEE
 try:
@@ -349,6 +350,11 @@ def _calculate_statistics(self):
         self.aic = _neg2_log_likel + 2 * self.nvarys
         self.bic = _neg2_log_likel + np.log(self.ndata) * self.nvarys
 
+    def _repr_html_(self, show_correl=True, min_correl=0.1):
+        """Returns a HTML representation of parameters data."""
+        return fitreport_html_table(self, show_correl=show_correl,
+                                    min_correl=min_correl)
+
 
 class Minimizer(object):
     """A general minimizer for curve fitting and optimization."""

lmfit/model.py

@@ -15,7 +15,7 @@
 from .confidence import conf_interval
 from .jsonutils import HAS_DILL, decode4js, encode4js
 from .minimizer import validate_nan_policy, MinimizerResult
-from .printfuncs import ci_report, fit_report
+from .printfuncs import ci_report, fit_report, fitreport_html_table
 
 # Use pandas.isnull for aligning missing data if pandas is available.
 # otherwise use numpy.isnan
@@ -1565,6 +1565,13 @@ def fit_report(self, modelpars=None, show_correl=True,
         modname = self.model._reprstring(long=True)
         return '[[Model]]\n    %s\n%s\n' % (modname, report)
 
+    def _repr_html_(self, show_correl=True, min_correl=0.1):
+        """Returns a HTML representation of parameters data."""
+        report = fitreport_html_table(self, show_correl=show_correl,
+                                      min_correl=min_correl)
+        modname = self.model._reprstring(long=True)
+        return "<h2> Model</h2> %s %s" % (modname, report)
+
     def dumps(self, **kws):
         """Represent ModelResult as a JSON string.
 

lmfit/parameter.py

@@ -11,6 +11,7 @@
 import uncertainties
 
 from .jsonutils import decode4js, encode4js
+from .printfuncs import params_html_table
 
 SCIPY_FUNCTIONS = {'gamfcn': scipy.special.gamma}
 for name in ('erf', 'erfc', 'wofz'):
@@ -284,6 +285,10 @@ def pretty_print(self, oneline=False, colwidth=8, precision=4, fmt='g',
             print(line.format(name_len=name_len, n=colwidth, p=precision,
                               f=fmt, **pvalues))
 
+    def _repr_html_(self):
+        """Returns a HTML representation of parameters data."""
+        return params_html_table(self)
+
     def add(self, name, value=None, vary=True, min=-inf, max=inf, expr=None,
             brute_step=None):
         """Add a Parameter.

lmfit/printfuncs.py

@@ -10,8 +10,6 @@
 except ImportError:
     HAS_NUMDIFFTOOLS = False
 
-from .parameter import Parameters
-
 
 def alphanumeric_sort(s, _nsre=re.compile('([0-9]+)')):
     """Sort alphanumeric string."""
@@ -111,6 +109,7 @@ def fit_report(inpars, modelpars=None, show_correl=True, min_correl=0.1,
        Multi-line text of fit report.
 
     """
+    from .parameter import Parameters
     if isinstance(inpars, Parameters):
         result, params = None, inpars
     if hasattr(inpars, 'params'):
@@ -210,6 +209,105 @@ def fit_report(inpars, modelpars=None, show_correl=True, min_correl=0.1,
     return '\n'.join(buff)
 
 
+def fitreport_html_table(result, show_correl=True, min_correl=0.1):
+    """Report minimizer result as an html table"""
+    html = []
+    add = html.append
+
+    def stat_row(label, val, val2=''):
+        add('<tr><td>%s</td><td>%s</td><td>%s</td></tr>' % (label, val, val2))
+    add('<h2>Fit Statistics</h2>')
+    add('<table>')
+    stat_row('fitting method', result.method)
+    stat_row('# function evals', result.nfev)
+    stat_row('# data points', result.ndata)
+    stat_row('# variables', result.nvarys)
+    stat_row('chi-square', gformat(result.chisqr))
+    stat_row('reduced chi-square', gformat(result.redchi))
+    stat_row('Akaike info crit.', gformat(result.aic))
+    stat_row('Bayesian info crit.', gformat(result.bic))
+    add('</table>')
+    add('<h2>Variables</h2>')
+    add(result.params._repr_html_())
+    if show_correl:
+        correls = []
+        parnames = list(result.params.keys())
+        for i, name in enumerate(result.params):
+            par = result.params[name]
+            if not par.vary:
+                continue
+            if hasattr(par, 'correl') and par.correl is not None:
+                for name2 in parnames[i+1:]:
+                    if (name != name2 and name2 in par.correl and
+                            abs(par.correl[name2]) > min_correl):
+                        correls.append((name, name2, par.correl[name2]))
+        if len(correls) > 0:
+            sort_correls = sorted(correls, key=lambda val: abs(val[2]))
+            sort_correls.reverse()
+            extra = '(unreported correlations are < %.3f)' % (min_correl)
+            add('<h2>Correlations %s</h2>' % extra)
+            add('<table>')
+            for name1, name2, val in sort_correls:
+                stat_row(name1, name2, "%.4f" % val)
+            add('</table>')
+    return ''.join(html)
+
+
+def params_html_table(params):
+    """Returns a HTML representation of parameters data."""
+    has_err = any([p.stderr is not None for p in params.values()])
+    has_expr = any([p.expr is not None for p in params.values()])
+    has_brute = any([p.brute_step is not None for p in params.values()])
+
+    html = []
+    add = html.append
+
+    def cell(x, cat='td'):
+        return add('<%s> %s </%s>' % (cat, x, cat))
+
+    add('<table><tr>')
+    headers = ['name', 'value']
+    if has_err:
+        headers.extend(['standard error', 'relative error'])
+    headers.extend(['initial value', 'min', 'max', 'vary'])
+    if has_expr:
+        headers.append('expression')
+    if has_brute:
+        headers.append('brute step')
+    for h in headers:
+        cell(h, cat='th')
+    add('</tr>')
+
+    for p in params.values():
+        rows = [p.name, gformat(p.value)]
+        if has_err:
+            serr, perr = '', ''
+            if p.stderr is not None:
+                serr = gformat(p.stderr)
+                perr = '%.2f%%' % (100 * p.stderr / p.value)
+            rows.extend([serr, perr])
+        rows.extend((p.init_value, gformat(p.min), gformat(p.max),
+                     '%s' % p.vary))
+        if has_expr:
+            expr = ''
+            if p.expr is not None:
+                expr = p.expr
+            rows.append(expr)
+
+        if has_brute:
+            brute_step = 'None'
+            if p.brute_step is not None:
+                brute_step = gformat(p.brute_step)
+            rows.append(brute_step)
+
+        add('<tr>')
+        for r in rows:
+            cell(r)
+        add('</tr>')
+    add('</table>')
+    return ''.join(html)
+
+
 def report_errors(params, **kws):
     """Print a report for fitted params: see error_report()."""
     print(fit_report(params, **kws))

tests/test_fitreports.py

@@ -0,0 +1,75 @@
+import numpy as np
+
+from lmfit import Minimizer, Parameters, conf_interval, ci_report, fit_report
+from lmfit.models import GaussianModel
+from lmfit.lineshapes import gaussian
+
+np.random.seed(0)
+
+
+def test_reports_created():
+    """do a simple Model fit but with all the bells-and-whistles
+    and verify that the reports are created
+    """
+    x = np.linspace(0, 12, 601)
+    data = gaussian(x, amplitude=36.4, center=6.70, sigma=0.88)
+    data = data + np.random.normal(size=len(x), scale=3.2)
+    model = GaussianModel()
+    params = model.make_params(amplitude=50, center=5, sigma=2)
+
+    params['amplitude'].min = 0
+    params['sigma'].min = 0
+    params['sigma'].brute_step = 0.001
+
+    result = model.fit(data, params, x=x)
+
+    report = result.fit_report()
+    assert(len(report) > 500)
+
+    html_params = result.params._repr_html_()
+    assert(len(html_params) > 500)
+
+    html_report = result._repr_html_()
+    assert(len(html_report) > 1000)
+
+
+def test_ci_report():
+    """test confidence interval report"""
+
+    def residual(pars, x, data=None):
+        argu = (x*pars['decay'])**2
+        shift = pars['shift']
+        if abs(shift) > np.pi/2:
+            shift = shift - np.sign(shift)*np.pi
+        model = pars['amp']*np.sin(shift + x/pars['period']) * np.exp(-argu)
+        if data is None:
+            return model
+        return model - data
+
+    p_true = Parameters()
+    p_true.add('amp', value=14.0)
+    p_true.add('period', value=5.33)
+    p_true.add('shift', value=0.123)
+    p_true.add('decay', value=0.010)
+
+    n = 2500
+    xmin = 0.
+    xmax = 250.0
+    x = np.linspace(xmin, xmax, n)
+    data = residual(p_true, x) + np.random.normal(scale=0.7215, size=n)
+
+    fit_params = Parameters()
+    fit_params.add('amp', value=13.0)
+    fit_params.add('period', value=2)
+    fit_params.add('shift', value=0.0)
+    fit_params.add('decay', value=0.02)
+
+    mini = Minimizer(residual, fit_params, fcn_args=(x,),
+                     fcn_kws={'data': data})
+    out = mini.leastsq()
+    report = fit_report(out)
+    assert(len(report) > 500)
+
+    ci, tr = conf_interval(mini, out, trace=True)
+    report = ci_report(ci)
+    assert(len(report) > 250)