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/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
     ----------
-
     scores :
         :py:class:`numpy.ndarray` : array
 
@@ -37,7 +35,6 @@ def get_fta(scores):
 
     Parameters
     ----------
-
     scores :
         Tuple of (``positive``, ``negative``) :py:class:`numpy.ndarray`.
 
@@ -61,7 +58,6 @@ def get_thres(criter, neg, pos, far=None):
 
     Parameters
     ----------
-
     criter :
         Criterion (`eer` or `hter`)
     neg : :py:class:`numpy.ndarray`:
@@ -71,10 +67,8 @@ def get_thres(criter, neg, pos, far=None):
 
     Returns
     -------
-
     :py:obj:`float`
         threshold
-
     """
     if criter == 'eer':
         from . import eer_threshold
@@ -84,13 +78,12 @@ def get_thres(criter, neg, pos, far=None):
         return min_hter_threshold(neg, pos)
     elif criter == 'far':
         if far is None:
-            raise click.UsageError("FAR value must be provided through "
-                                   "``--far-value`` option.")
+            raise ValueError("FAR value must be provided through "
+                             "``--far-value`` option.")
         from . import far_threshold
         return far_threshold(neg, pos, far)
-
     else:
-        raise click.UsageError("Incorrect plotting criterion: ``%s``" % criter)
+        raise ValueError("Incorrect plotting criterion: ``%s``" % criter)
 
 def get_colors(n):
     """get_colors
@@ -98,13 +91,11 @@ def get_colors(n):
 
     Parameters
     ----------
-
     n : :obj:`int`
         Number of colors to output
 
     Returns
     -------
-
     :any:`list`
         list of colors
     """

doc/py_api.rst

@@ -127,3 +127,5 @@ Details
 .. automodule:: bob.measure.utils
 .. automodule:: bob.measure.script.figure
 .. automodule:: bob.measure.script.commands
+.. automodule:: bob.measure.script.gen
+.. automodule:: bob.measure.script.common_options