Various small changes after Amir review: add/remove command options, use...

Various small changes after Amir review: add/remove command options, use matplotlib 2.2.2 functionalities, fix doc

bob/measure/plot.py

@@ -260,7 +260,7 @@ def epc(dev_negatives, dev_positives, test_negatives, test_positives,
   return pyplot.plot(out[0, :], 100.0 * out[1, :], **kwargs)
 
 
-def det(negatives, positives, npoints=100, axisfontsize='x-small', **kwargs):
+def det(negatives, positives, npoints=100, **kwargs):
   """Plots Detection Error Trade-off (DET) curve as defined in the paper:
 
   Martin, A., Doddington, G., Kamm, T., Ordowski, M., & Przybocki, M. (1997).
@@ -381,9 +381,9 @@ def det(negatives, positives, npoints=100, axisfontsize='x-small', **kwargs):
   pticks = [ppndf(float(v)) for v in desiredTicks]
   ax = pyplot.gca()  # and finally we set our own tick marks
   ax.set_xticks(pticks)
-  ax.set_xticklabels(desiredLabels, size=axisfontsize)
+  ax.set_xticklabels(desiredLabels)
   ax.set_yticks(pticks)
-  ax.set_yticklabels(desiredLabels, size=axisfontsize)
+  ax.set_yticklabels(desiredLabels)
 
   return retval
 

bob/measure/script/commands.py

@@ -21,16 +21,14 @@ from bob.extension.scripts.click_helper import (verbosity_option,
 @verbosity_option()
 @click.pass_context
 def metrics(ctx, scores, evaluation, **kwargs):
-    """Prints a single output line that contains all info for a given
-    criterion (eer or hter).
+    """Prints a table that contains FtA, FAR, FRR, FMR, FMNR, HTER for a given
+    threshold criterion (eer or hter).
 
-    You need provide one or more development score file(s) for each experiment.
+    You need to provide one or more development score file(s) for each experiment.
     You can also provide evaluation files along with dev files. If only dev scores
     are provided, you must use flag `--no-evaluation`.
 
-    Resulting table format can be changer using the `--tablefmt`. Default
-    formats are `fancy_grid` when output in the terminal and `latex` when
-    written in a log file (see `--log`)
+    Resulting table format can be changed using the `--tablefmt`.
 
     Examples:
         $ bob measure metrics dev-scores
@@ -42,7 +40,6 @@ def metrics(ctx, scores, evaluation, **kwargs):
     process = figure.Metrics(ctx, scores, evaluation, load.split_files)
     process.run()
 
-
 @click.command()
 @common_options.scores_argument(nargs=-1)
 @common_options.title_option()
@@ -53,12 +50,14 @@ def metrics(ctx, scores, evaluation, **kwargs):
 @common_options.points_curve_option()
 @common_options.semilogx_option(True)
 @common_options.axes_val_option(dflt=[1e-4, 1, 1e-4, 1])
-@common_options.axis_fontsize_option()
 @common_options.x_rotation_option()
 @common_options.x_label_option()
 @common_options.y_label_option()
 @common_options.lines_at_option()
 @common_options.const_layout_option()
+@common_options.figsize_option()
+@common_options.style_option()
+@common_options.const_layout_option()
 @verbosity_option()
 @click.pass_context
 def roc(ctx, scores, evaluation, **kwargs):
@@ -67,7 +66,7 @@ def roc(ctx, scores, evaluation, **kwargs):
     false non match rate on the vertical axis.  The values for the axis will be
     computed using :py:func:`bob.measure.roc`.
 
-    You need provide one or more development score file(s) for each experiment.
+    You need to provide one or more development score file(s) for each experiment.
     You can also provide evaluation files along with dev files. If only dev scores
     are provided, you must use flag `--no-evaluation`.
 
@@ -82,7 +81,6 @@ def roc(ctx, scores, evaluation, **kwargs):
     process = figure.Roc(ctx, scores, evaluation, load.split_files)
     process.run()
 
-
 @click.command()
 @common_options.scores_argument(nargs=-1)
 @common_options.output_plot_file_option(default_out='det.pdf')
@@ -91,12 +89,14 @@ def roc(ctx, scores, evaluation, **kwargs):
 @common_options.sep_dev_eval_option()
 @common_options.eval_option()
 @common_options.axes_val_option(dflt=[0.01, 95, 0.01, 95])
-@common_options.axis_fontsize_option(dflt=6)
 @common_options.x_rotation_option(dflt=45)
 @common_options.x_label_option()
 @common_options.y_label_option()
 @common_options.points_curve_option()
 @common_options.const_layout_option()
+@common_options.figsize_option()
+@common_options.style_option()
+@common_options.const_layout_option()
 @verbosity_option()
 @click.pass_context
 def det(ctx, scores, evaluation, **kwargs):
@@ -104,7 +104,7 @@ def det(ctx, scores, evaluation, **kwargs):
     modified ROC curve which plots error rates on both axes
     (false positives on the x-axis and false negatives on the y-axis)
 
-    You need provide one or more development score file(s) for each experiment.
+    You need to provide one or more development score file(s) for each experiment.
     You can also provide evaluation files along with dev files. If only dev scores
     are provided, you must use flag `--no-evaluation`.
 
@@ -119,17 +119,18 @@ def det(ctx, scores, evaluation, **kwargs):
     process = figure.Det(ctx, scores, evaluation, load.split_files)
     process.run()
 
-
 @click.command()
 @common_options.scores_argument(eval_mandatory=True, nargs=-1)
 @common_options.output_plot_file_option(default_out='epc.pdf')
 @common_options.title_option()
 @common_options.titles_option()
 @common_options.points_curve_option()
-@common_options.axis_fontsize_option()
 @common_options.const_layout_option()
 @common_options.x_label_option()
 @common_options.y_label_option()
+@common_options.figsize_option()
+@common_options.style_option()
+@common_options.const_layout_option()
 @verbosity_option()
 @click.pass_context
 def epc(ctx, scores, **kwargs):
@@ -138,7 +139,7 @@ def epc(ctx, scores, **kwargs):
     a-priori on the development set and accounts for varying relative cost
     in [0; 1] of FPR and FNR when calculating the threshold.
 
-    You need provide one or more development score and eval file(s)
+    You need to provide one or more development score and eval file(s)
     for each experiment.
 
     Examples:
@@ -149,27 +150,28 @@ def epc(ctx, scores, **kwargs):
     process = figure.Epc(ctx, scores, True, load.split_files)
     process.run()
 
-
 @click.command()
 @common_options.scores_argument(nargs=-1)
 @common_options.output_plot_file_option(default_out='hist.pdf')
 @common_options.eval_option()
 @common_options.n_bins_option()
 @common_options.criterion_option()
-@common_options.axis_fontsize_option()
 @common_options.thresholds_option()
 @common_options.const_layout_option()
 @common_options.show_dev_option()
 @common_options.print_filenames_option()
 @common_options.title_option()
 @common_options.titles_option()
+@common_options.figsize_option()
+@common_options.style_option()
+@common_options.const_layout_option()
 @verbosity_option()
 @click.pass_context
 def hist(ctx, scores, evaluation, **kwargs):
     """ Plots histograms of positive and negatives along with threshold
     criterion.
 
-    You need provide one or more development score file(s) for each experiment.
+    You need to provide one or more development score file(s) for each experiment.
     You can also provide evaluation files along with dev files. If only dev scores
     are provided, you must use flag `--no-evaluation`.
 
@@ -189,7 +191,6 @@ def hist(ctx, scores, evaluation, **kwargs):
     process = figure.Hist(ctx, scores, evaluation, load.split_files)
     process.run()
 
-
 @click.command()
 @common_options.scores_argument(nargs=-1)
 @common_options.titles_option()
@@ -203,6 +204,9 @@ def hist(ctx, scores, evaluation, **kwargs):
 @common_options.n_bins_option()
 @common_options.lines_at_option()
 @common_options.const_layout_option()
+@common_options.figsize_option()
+@common_options.style_option()
+@common_options.const_layout_option()
 @verbosity_option()
 @click.pass_context
 def evaluate(ctx, scores, evaluation, **kwargs):
@@ -227,6 +231,11 @@ def evaluate(ctx, scores, evaluation, **kwargs):
     Examples:
         $ bob measure evaluate dev-scores
 
+        $ bob measure evaluate scores-dev1 scores-eval1 scores-dev2
+        scores-eval2
+
+        $ bob measure evaluate /path/to/sys-{1,2,3}/scores-{dev,eval}
+
         $ bob measure evaluate -l metrics.txt -o my_plots.pdf dev-scores eval-scores
     '''
     # first time erase if existing file
@@ -256,11 +265,10 @@ def evaluate(ctx, scores, evaluation, **kwargs):
     if evaluation:
         click.echo("Computing EPC...")
         ctx.forward(epc) # use class defaults plot settings
-        ctx.forward(epc)
     # the last one closes the file
     ctx.meta['closef'] = True
     click.echo("Computing score histograms...")
-    ctx.meta['criter'] = 'hter'  # no criterion passed in evaluate
+    ctx.meta['criter'] = 'eer'  # no criterion passed in evaluate
     ctx.forward(hist)
     click.echo("Evaluate successfully completed!")
     click.echo("[plots] => %s" % (ctx.meta['output']))

bob/measure/script/common_options.py

 '''Stores click common options for plots'''
 
-import math
 import pkg_resources  # to make sure bob gets imported properly
 import logging
 import click
-from click.types import INT, FLOAT, Choice, File
+from click.types import INT, FLOAT
 import matplotlib.pyplot as plt
 from matplotlib.backends.backend_pdf import PdfPages
-from bob.extension.scripts.click_helper import (verbosity_option, bool_option,
-                                                list_float_option)
+from bob.extension.scripts.click_helper import (bool_option, list_float_option)
 
-logger = logging.getLogger(__name__)
+LOGGER = logging.getLogger(__name__)
 
 def scores_argument(eval_mandatory=False, min_len=1, **kwargs):
     """Get the argument for scores, and add `dev-scores` and `eval-scores` in
@@ -18,7 +16,6 @@ def scores_argument(eval_mandatory=False, min_len=1, **kwargs):
 
     Parameters
     ----------
-
     eval_mandatory :
         If evaluation files are mandatory
     min_len :
@@ -27,7 +24,8 @@ def scores_argument(eval_mandatory=False, min_len=1, **kwargs):
 
     Returns
     -------
-        Click option
+     callable
+      A decorator to be used for adding score arguments for click commands
     """
     def custom_scores_argument(func):
         def callback(ctx, param, value):
@@ -129,23 +127,10 @@ def lines_at_option(**kwargs):
     '''Get option to draw const far line'''
     return list_float_option(
         name='lines-at', short_name='la',
-        desc='If given, draw a veritcal lines on ROC plots',
+        desc='If given, draw veritcal lines on ROC plots',
         nitems=None, dflt=None, **kwargs
     )
 
-def axis_fontsize_option(dflt=8, **kwargs):
-    '''Get option for axis font size'''
-    def custom_axis_fontsize_option(func):
-        def callback(ctx, param, value):
-            value = abs(value)
-            ctx.meta['fontsize'] = value
-            return value
-        return click.option(
-            '-F', '--fontsize', type=click.INT, default=dflt, show_default=True,
-            help='Axis fontsize',
-            callback=callback, **kwargs)(func)
-    return custom_axis_fontsize_option
-
 def x_rotation_option(dflt=0, **kwargs):
     '''Get option for rotartion of the x axis lables'''
     def custom_x_rotation_option(func):
@@ -159,7 +144,6 @@ def x_rotation_option(dflt=0, **kwargs):
             callback=callback, **kwargs)(func)
     return custom_x_rotation_option
 
-
 def cost_option(**kwargs):
     '''Get option to get cost for FAR'''
     def custom_cost_option(func):
@@ -174,18 +158,6 @@ def cost_option(**kwargs):
             callback=callback, **kwargs)(func)
     return custom_cost_option
 
-def n_sys_option(**kwargs):
-    '''Get the number of systems to be processed'''
-    def custom_n_sys_option(func):
-        def callback(ctx, param, value):
-            ctx.meta['n_sys'] = value
-            return value
-        return click.option(
-            '--n-sys', type=INT, default=1, show_default=True,
-            help='The number of systems to be processed',
-            callback=callback, is_eager=True , **kwargs)(func)
-    return custom_n_sys_option
-
 def points_curve_option(**kwargs):
     '''Get the number of points use to draw curves'''
     def custom_points_curve_option(func):
@@ -248,7 +220,7 @@ def output_plot_file_option(default_out='plots.pdf', **kwargs):
             print the path of the file in the log'''
             ctx.meta['output'] = value
             ctx.meta['PdfPages'] = PdfPages(value)
-            logger.debug("Plots will be output in %s", value)
+            LOGGER.debug("Plots will be output in %s", value)
             return value
         return click.option(
             '-o', '--output',
@@ -264,7 +236,7 @@ def output_plot_metric_option(**kwargs):
             ''' Save ouput file  and associated pdf in context list,
             print the path of the file in the log'''
             if value is not None:
-                logger.debug("Metrics will be output in %s", value)
+                LOGGER.debug("Metrics will be output in %s", value)
             ctx.meta['log'] = value
             return value
         return click.option(
@@ -279,7 +251,6 @@ def criterion_option(lcriteria=['eer', 'hter', 'far'], **kwargs):
 
     Parameters
     ----------
-
     lcriteria : :any:`list`
         List of possible criteria
     """
@@ -299,7 +270,6 @@ def criterion_option(lcriteria=['eer', 'hter', 'far'], **kwargs):
             callback=callback, is_eager=True ,**kwargs)(func)
     return custom_criterion_option
 
-
 def far_option(**kwargs):
     '''Get option to get far value'''
     def custom_far_option(func):
@@ -314,40 +284,6 @@ def far_option(**kwargs):
             callback=callback, show_default=True,**kwargs)(func)
     return custom_far_option
 
-def rank_option(**kwargs):
-    '''Get option for rank parameter'''
-    def custom_rank_option(func):
-        def callback(ctx, param, value):
-            value = 1 if value < 0 else value
-            ctx.meta['rank'] = value
-            return value
-        return click.option(
-            '--rank', type=click.INT, default=1,
-            help='Given threshold for metrics computations',
-            callback=callback, show_default=True,**kwargs)(func)
-    return custom_rank_option
-
-def label_option(name_option='x_label', **kwargs):
-    '''Get labels options based on the given name.
-
-    Parameters:
-    ----------
-    name_option: str, optional
-        Name of the label option (e.g. x-lable, y1-label)
-    '''
-    def custom_label_option(func):
-        def callback(ctx, param, value):
-            ''' Get and save labels list in the context list '''
-            ctx.meta[name_option.replace('-', '_')] = value if value is None else \
-                    [int(i) for i in value.split(',')]
-            return value
-        return click.option(
-            '--' + name_option,
-            help='The id of figures which should have x_label separated by '
-            'comma. For example ``--%s 1,2,4``.' % name_option,
-            callback=callback, **kwargs)(func)
-    return custom_label_option
-
 def figsize_option(**kwargs):
     '''Get option for matplotlib figsize'''
     def custom_figsize_option(func):

bob/measure/script/figure.py

@@ -4,7 +4,6 @@ from __future__ import division, print_function
 from abc import ABCMeta, abstractmethod
 import sys
 import ntpath
-import numpy
 import click
 import matplotlib
 import matplotlib.pyplot as mpl
@@ -36,29 +35,14 @@ class MeasureBase(object):
 
     Attributes
     ----------
-
-    _scores: :any:`list`:
-        List of input files (e.g. dev-{1, 2, 3}, {dev,eval}-scores1
-
-    _ctx : :py:class:`dict`
-        Click context dictionary.
-
-    _eval : :py:class:`bool`
-        True if eval data are used
-
-    _titles: :any:`list`
-        List of titles for each system (dev + (eval) scores)
-
     func_load:
         Function that is used to load the input files
-
     """
     __metaclass__ = ABCMeta #for python 2.7 compatibility
     def __init__(self, ctx, scores, eval, func_load):
         """
         Parameters
         ----------
-
         ctx : :py:class:`dict`
             Click context dictionary.
 
@@ -137,10 +121,8 @@ class MeasureBase(object):
 
         Parameters
         ----------
-
         idx : :obj:`int`
             index of the system
-
         dev_score:
             Development scores. Can be a tuple (neg, pos) of
             :py:class:`numpy.ndarray` (e.g.
@@ -173,7 +155,6 @@ class MeasureBase(object):
 
         Returns
         -------
-
             dev_scores: :any:`list`: A list that contains, for each required
             dev score file, the output of ``func_load``
             eval_scores: :any:`list`: A list that contains, for each required
@@ -210,8 +191,7 @@ class MeasureBase(object):
         '''Process score files and return neg/pos/fta for eval and dev'''
         dev_neg = dev_pos = dev_fta = eval_neg = eval_pos = eval_fta = None
         if dev_score[0] is not None:
-            dev_score, dev_fta = utils.get_fta(dev_score)
-            dev_neg, dev_pos = dev_score
+            (dev_neg, dev_pos), dev_fta = utils.get_fta(dev_score)
             if dev_neg is None:
                 raise click.UsageError("While loading dev-score file")
 
@@ -229,29 +209,8 @@ class Metrics(MeasureBase):
 
     Attributes
     ----------
-
-    _tablefmt: str
-        Table format
-
-    _criter: str
-        Criterion to compute threshold, see :py:func:`bob.measure.utils.get_thres`
-
-    _open_mode: str
-        Open mode of the output file (e.g. `w`, `a+`)
-
-    _thres: :any:`list`
-        If given, uses those threshold instead of computing them. Lenght of the
-        list must be the same as the number of systems.
-
-    _far: :obj:`float`
-        If given, uses this FAR to compute threshold
-
-    _log: str
-        Path to output log file
-
     log_file: str
         output stream
-
     '''
     def __init__(self, ctx, scores, evaluation, func_load):
         super(Metrics, self).__init__(ctx, scores, evaluation, func_load)
@@ -361,33 +320,11 @@ class Metrics(MeasureBase):
 class PlotBase(MeasureBase):
     ''' Base class for plots. Regroup several options and code
     shared by the different plots
-
-    Attributes
-    ----------
-
-    _output: str
-        Path to the output pdf file
-
-    _points: :obj:`int`
-        Number of points used to draw curves
-
-
-    _split: :obj:`bool`
-        If False, dev and eval curves will be printed on the some figure
-
-    _axlim: :any:`list`
-        Minimum/Maximum values for the X and Y axes
-
-    _x_rotation: :obj:`int`
-        Rotation of the X axis labels
-
-    _axisfontsize: :obj:`int`
-        Axis font size
     '''
     def __init__(self, ctx, scores, evaluation, func_load):
         super(PlotBase, self).__init__(ctx, scores, evaluation, func_load)
         self._output = None if 'output' not in ctx.meta else ctx.meta['output']
-        self._points = None if 'points' not in ctx.meta else ctx.meta['points']
+        self._points = 100 if 'points' not in ctx.meta else ctx.meta['points']
         self._split = None if 'split' not in ctx.meta else ctx.meta['split']
         self._axlim = None if 'axlim' not in ctx.meta else ctx.meta['axlim']
         self._clayout = None if 'clayout' not in ctx.meta else\
@@ -396,9 +333,8 @@ class PlotBase(MeasureBase):
         ctx.meta['show_fn']
         self._x_rotation = None if 'x_rotation' not in ctx.meta else \
                 ctx.meta['x_rotation']
-        self._axisfontsize = 6 if 'fontsize' not in ctx.meta else \
-                ctx.meta['fontsize']
-
+        if 'style' in ctx.meta:
+            mpl.style.use(ctx.meta['style'])
         self._nb_figs = 2 if self._eval and self._split else 1
         self._multi_plots = len(self.dev_scores) > 1
         self._colors = utils.get_colors(len(self.dev_scores))
@@ -422,14 +358,11 @@ class PlotBase(MeasureBase):
         self._ctx.meta else PdfPages(self._output)
 
         for i in range(self._nb_figs):
-            fig = mpl.figure(i + 1)
+            fs = None if 'figsize' not in self._ctx.meta else\
+                    self._ctx.meta['figsize']
+            fig = mpl.figure(i + 1, figsize=fs)
+            fig.set_constrained_layout(self._clayout)
             fig.clear()
-            if self._axisfontsize is not None:
-                mpl.rc('xtick', labelsize=self._axisfontsize)
-                mpl.rc('ytick', labelsize=self._axisfontsize)
-                mpl.rc('legend', fontsize=6)
-                mpl.rc('axes', labelsize=8)
-                #mpl.rcParams['figure.constrained_layout.use'] = self._clayout
 
     def end_process(self):
         ''' Set title, legend, axis labels, grid colors, save figures and
@@ -449,8 +382,6 @@ class PlotBase(MeasureBase):
                 mpl.grid(True, color=self._grid_color)
                 mpl.legend(loc='best')
                 self._set_axis()
-                #gives warning when applied with mpl
-                fig.set_tight_layout(True)
                 mpl.xticks(rotation=self._x_rotation)
                 self._pdf_page.savefig(fig)
 
@@ -472,22 +403,9 @@ class PlotBase(MeasureBase):
     def _set_axis(self):
         if self._axlim is not None and None not in self._axlim:
             mpl.axis(self._axlim)
-        else:
-            mpl.axes().autoscale()
 
 class Roc(PlotBase):
-    ''' Handles the plotting of ROC
-
-    Attributes
-    ----------
-
-    _semilogx: :obj:`bool`
-        If true, X-axis will be semilog10
-
-    _fmr_at: :obj:`float`
-        If not None, plot a vertical line at this value on the dev plot and
-        corresponding dots on the eval plot (if any).
-    '''
+    ''' Handles the plotting of ROC'''
     def __init__(self, ctx, scores, evaluation, func_load):
         super(Roc, self).__init__(ctx, scores, evaluation, func_load)
         self._semilogx = True if 'semilogx' not in ctx.meta else\
@@ -588,7 +506,7 @@ class Det(PlotBase):
             linestyle = '-' if not self._split else LINESTYLES[idx % 14]
             plot.det(
                 dev_neg, dev_pos, self._points, color=self._colors[idx],
-                linestyle=linestyle, axisfontsize=self._axisfontsize,
+                linestyle=linestyle,
                 label=self._label('development', dev_file, idx, **self._kwargs)
             )
             if self._split:
@@ -596,13 +514,13 @@ class Det(PlotBase):
             linestyle = '--' if not self._split else LINESTYLES[idx % 14]
             plot.det(
                 eval_neg, eval_pos, self._points, color=self._colors[idx],
-                linestyle=linestyle, axisfontsize=self._axisfontsize,
+                linestyle=linestyle,
                 label=self._label('eval', eval_file, idx, **self._kwargs)
             )
         else:
             plot.det(
                 dev_neg, dev_pos, self._points, color=self._colors[idx],
-                linestyle=LINESTYLES[idx % 14], axisfontsize=self._axisfontsize,
+                linestyle=LINESTYLES[idx % 14],
                 label=self._label('development', dev_file, idx, **self._kwargs)
             )
 
@@ -619,39 +537,26 @@ class Epc(PlotBase):
         if 'eval_scores_0' not in self._ctx.meta:
             raise click.UsageError("EPC requires dev and eval score files")
         self._title = self._title or 'EPC'
-        self._x_label = self._x_label or 'Cost'
-        self._y_label = self._y_label or 'Min. HTER (%)'
+        self._x_label = self._x_label or r'$\alpha$'
+        self._y_label = self._y_label or 'HTER (%)'
         self._eval = True #always eval data with EPC
         self._split = False
         self._nb_figs = 1
 
     def compute(self, idx, dev_score, dev_file, eval_score, eval_file=None):
-        ''' Plot EPC using
-        :py:func:`bob.measure.plot.epc`'''
+        ''' Plot EPC using :py:func:`bob.measure.plot.epc` '''
         dev_neg, dev_pos, _, eval_neg, eval_pos, _ =\
                 self._process_scores(dev_score, eval_score)
         plot.epc(
             dev_neg, dev_pos, eval_neg, eval_pos, self._points,
             color=self._colors[idx], linestyle=LINESTYLES[idx % 14],
-            label=self._label('curve', dev_file + "_" + eval_file, idx, **self._kwargs)
+            label=self._label(
+                'curve', dev_file + "_" + eval_file, idx, **self._kwargs
+            )
         )
 
 class Hist(PlotBase):
-    ''' Functional base class for histograms
-
-    Attributes
-    ----------
-
-    _nbins: :obj:`int`, str
-    Number of bins. Default: `auto`
-
-    _thres: :any:`list`
-        If given, uses those threshold instead of computing them. Lenght of the
-        list must be the same as the number of systems.
-
-    _criter: str
-        Criterion to compute threshold (eer or hter)
-    '''
+    ''' Functional base class for histograms'''
     def __init__(self, ctx, scores, evaluation, func_load):
         super(Hist, self).__init__(ctx, scores, evaluation, func_load)
         self._nbins = None if 'nbins' not in ctx.meta else ctx.meta['nbins']
@@ -710,7 +615,6 @@ class Hist(PlotBase):
             if not self._show_dev:
                 self._plot_legends()
 
-        fig.set_tight_layout(True)
         self._pdf_page.savefig(fig)
 
     def _get_title(self, idx, dev_file, eval_file):
@@ -739,7 +643,6 @@ class Hist(PlotBase):
             mpl.legend(lines, labels,
                        loc='best', fancybox=True, framealpha=0.5)
 
-
     def _get_neg_pos_thres(self, idx, dev_score, eval_score):
         dev_neg, dev_pos, _, eval_neg, eval_pos, _ = self._process_scores(
             dev_score, eval_score
@@ -752,7 +655,7 @@ class Hist(PlotBase):
 
     def _density_hist(self, scores, **kwargs):
         n, bins, patches = mpl.hist(
-            scores, normed=True, bins=self._nbins, **kwargs
+            scores, density=True, bins=self._nbins, **kwargs
         )
         return (n, bins, patches)
 
@@ -761,9 +664,8 @@ class Hist(PlotBase):
         kwargs.setdefault('color', 'C3')
         kwargs.setdefault('linestyle', '--')
         kwargs.setdefault('label', label)
-        _, _, ymax, ymin = mpl.axis()
         # plot a vertical threshold line
-        mpl.axvline(x=threshold, ymin=ymin, ymax=ymax, **kwargs)
+        mpl.axvline(x=threshold, ymin=0, ymax=1, **kwargs)
 
     def _setup_hist(self, neg, pos):
         ''' This function can be overwritten in derived classes'''

bob/measure/script/gen.py

@@ -16,11 +16,10 @@ NUM_NEG = 5000
 NUM_POS = 5000
 
 def gen_score_distr(mean_neg, mean_pos, sigma_neg=1, sigma_pos=1):
-        """Generate scores from normal distributions
+    """Generate scores from normal distributions
 
     Parameters
     ----------
-
     mean_neg : float
         Mean for negative scores
     mean_pos : float
@@ -32,10 +31,9 @@ def gen_score_distr(mean_neg, mean_pos, sigma_neg=1, sigma_pos=1):
 
     Returns
     -------
-
-    neg_scores : array_like
+    neg_scores : :any:`list`
         Negatives scores
-    pos_scores : array_like
+    pos_scores : :any:`list`
         Positive scores
     """
     mt = random.mt19937()  # initialise the random number generator
@@ -56,9 +54,9 @@ def write_scores_to_file(pos, neg, filename):
 
     Parameters
     ----------
-    pos : array_like
+    pos : :py:class:`numpy.ndarray`
         Scores for positive samples.
-    neg : array_like
+    neg : :py:class:`numpy.ndarray`
         Scores for negative samples.
     filename : str
         The path to write the score to.

bob/measure/script/measure.py

@@ -7,8 +7,8 @@ from click.types import INT, FLOAT, Choice, File
 
 
 @with_plugins(pkg_resources.iter_entry_points('bob.measure.cli'))
-@click.group(chain=True)
+@click.group()
 def measure():
-    """Entry for bob.measure commands."""
+    """Generic performance evaluation commands."""
     pass
 

bob/measure/utils.py

@@ -2,7 +2,6 @@
 
 import numpy
 import scipy.stats
-import click
 import bob.core
 
 def remove_nan(scores):
@@ -12,7 +11,6 @@ def remove_nan(scores):
 
     Parameters