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Commit c24fafdf authored by Amir MOHAMMADI's avatar Amir MOHAMMADI
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Merge branch 'touches' into 'master' 

Remove bob vuln metrics and evaluate commands

See merge request !47
parents 861911a5 cd1fedfe
Pipeline #21369 passed with stages
in 9 minutes and 57 seconds
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bob/pad/base/script/pad_commands.py
View file @ c24fafdf
......@@ -88,7 +88,7 @@ def evaluate(ctx, scores, evaluation, **kwargs):
common_options.MULTI_METRICS_HELP.format(
names='FtA, APCER, BPCER, FAR, FRR, ACER',
criteria=CRITERIA, score_format=SCORE_FORMAT,
command='bob measure multi-metrics'),
command='bob pad multi-metrics'),
criteria=CRITERIA)
def multi_metrics(ctx, scores, evaluation, protocols_number, **kwargs):
ctx.meta['min_arg'] = protocols_number * (2 if evaluation else 1)
......
bob/pad/base/script/vuln_commands.py
View file @ c24fafdf
......@@ -2,17 +2,12 @@
"""
import os
import logging
import numpy
import click
import pkg_resources
from click_plugins import with_plugins
from click.types import FLOAT
from bob.measure.script import common_options
from bob.extension.scripts.click_helper import (verbosity_option,
open_file_mode_option,
bool_option,
AliasedGroup, list_float_option)
from bob.extension.scripts.click_helper import (
verbosity_option, bool_option, list_float_option)
from bob.core import random
from bob.io.base import create_directories_safe
from bob.bio.base.score import load
......@@ -23,15 +18,15 @@ NUM_ZEIMPOSTORS = 5000
NUM_PA = 5000
def hlines_at_option(dflt=' ', **kwargs):
'''Get option to draw const FNMRlines'''
return list_float_option(
name='hlines-at', short_name='hla',
desc='If given, draw horizontal lines at the given axis positions. '
'Your values must be separated with a comma (,) without space. '
'This option works in ROC and DET curves.',
nitems=None, dflt=dflt, **kwargs
)
def fnmr_at_option(dflt=' ', **kwargs):
'''Get option to draw const FNMR lines'''
return list_float_option(
name='fnmr', short_name='fnmr',
desc='If given, draw horizontal lines at the given FNMR position. '
'Your values must be separated with a comma (,) without space. '
'This option works in ROC and DET curves.',
nitems=None, dflt=dflt, **kwargs
)
def gen_score_distr(mean_gen, mean_zei, mean_pa, sigma_gen=1, sigma_zei=1,
......@@ -49,7 +44,6 @@ def gen_score_distr(mean_gen, mean_zei, mean_pa, sigma_gen=1, sigma_zei=1,
return genuine_scores, zei_scores, pa_scores
def write_scores_to_file(neg, pos, filename, attack=False):
"""Writes score distributions into 4-column score files. For the format of
the 4-column score files, please refer to Bob's documentation.
......@@ -65,14 +59,13 @@ def write_scores_to_file(neg, pos, filename, attack=False):
"""
create_directories_safe(os.path.dirname(filename))
with open(filename, 'wt') as f:
for i in pos:
f.write('x x foo %f\n' % i)
for i in neg:
if attack:
f.write('x attack foo %f\n' % i)
else:
f.write('x y foo %f\n' % i)
for i in pos:
f.write('x x foo %f\n' % i)
for i in neg:
if attack:
f.write('x attack foo %f\n' % i)
else:
f.write('x y foo %f\n' % i)
@click.command()
......@@ -108,7 +101,6 @@ def gen(outdir, mean_gen, mean_zei, mean_pa):
attack=True)
@click.command()
@common_options.scores_argument(min_arg=2, nargs=-1)
@common_options.output_plot_file_option(default_out='vuln_roc.pdf')
......@@ -128,7 +120,7 @@ def gen(outdir, mean_gen, mean_zei, mean_pa):
@click.option('--real-data/--no-real-data', default=True, show_default=True,
help='If False, will annotate the plots hypothetically, instead '
'of with real data values of the calculated error rates.')
@hlines_at_option()
@fnmr_at_option()
@click.pass_context
def roc(ctx, scores, real_data, **kwargs):
"""Plot ROC
......@@ -167,7 +159,7 @@ def roc(ctx, scores, real_data, **kwargs):
@click.option('--real-data/--no-real-data', default=True, show_default=True,
help='If False, will annotate the plots hypothetically, instead '
'of with real data values of the calculated error rates.')
@hlines_at_option()
@fnmr_at_option()
@click.pass_context
def det(ctx, scores, real_data, **kwargs):
"""Plot DET
......@@ -189,7 +181,6 @@ def det(ctx, scores, real_data, **kwargs):
process.run()
@click.command()
@common_options.scores_argument(min_arg=2, force_eval=True, nargs=-1)
@common_options.output_plot_file_option(default_out='vuln_epc.pdf')
......@@ -234,7 +225,6 @@ def epc(ctx, scores, **kwargs):
process.run()
@click.command()
@common_options.scores_argument(min_arg=2, force_eval=True, nargs=-1)
@common_options.output_plot_file_option(default_out='vuln_epsc.pdf')
......@@ -270,43 +260,42 @@ def epc(ctx, scores, **kwargs):
@click.pass_context
def epsc(ctx, scores, criteria, var_param, fixed_param, three_d, sampling,
**kwargs):
"""Plot EPSC (expected performance spoofing curve):
You need to provide 4 score
files for each biometric system in this order:
"""Plot EPSC (expected performance spoofing curve):
\b
* licit development scores
* licit evaluation scores
* spoof development scores
* spoof evaluation scores
You need to provide 4 score
files for each biometric system in this order:
See :ref:`bob.pad.base.vulnerability` in the documentation for a guide on
vulnerability analysis.
\b
* licit development scores
* licit evaluation scores
* spoof development scores
* spoof evaluation scores
Note that when using 3D plots with option ``--three-d``, you cannot plot
both WER and IAPMR on the same figure (which is possible in 2D).
See :ref:`bob.pad.base.vulnerability` in the documentation for a guide on
vulnerability analysis.
Examples:
$ bob vuln epsc -v -o my_epsc.pdf dev-scores1 eval-scores1
Note that when using 3D plots with option ``--three-d``, you cannot plot
both WER and IAPMR on the same figure (which is possible in 2D).
$ bob vuln epsc -v -D {licit,spoof}/scores-{dev,eval}
"""
if three_d:
if (ctx.meta['wer'] and ctx.meta['iapmr']):
raise click.BadParameter('Cannot plot both WER and IAPMR in 3D')
ctx.meta['sampling'] = sampling
process = figure.Epsc3D(
ctx, scores, True, load.split,
criteria, var_param, fixed_param
)
else:
process = figure.Epsc(
ctx, scores, True, load.split,
criteria, var_param, fixed_param
)
process.run()
Examples:
$ bob vuln epsc -v -o my_epsc.pdf dev-scores1 eval-scores1
$ bob vuln epsc -v -D {licit,spoof}/scores-{dev,eval}
"""
if three_d:
if (ctx.meta['wer'] and ctx.meta['iapmr']):
raise click.BadParameter('Cannot plot both WER and IAPMR in 3D')
ctx.meta['sampling'] = sampling
process = figure.Epsc3D(
ctx, scores, True, load.split,
criteria, var_param, fixed_param
)
else:
process = figure.Epsc(
ctx, scores, True, load.split,
criteria, var_param, fixed_param
)
process.run()
@click.command()
......@@ -366,38 +355,6 @@ def hist(ctx, scores, evaluation, **kwargs):
process.run()
@click.command(context_settings=dict(token_normalize_func=lambda x: x.lower()))
@common_options.scores_argument(min_arg=2, force_eval=True, nargs=-1)
@common_options.table_option()
@common_options.criterion_option(lcriteria=['eer', 'min-hter'])
@common_options.thresholds_option()
@open_file_mode_option()
@common_options.output_log_metric_option()
@common_options.legends_option()
@verbosity_option()
@click.pass_context
def metrics(ctx, scores, **kwargs):
"""Generate table of metrics for vulnerability PAD
You need to provide 4 scores
files for each vuln system in this order:
\b
* licit development scores
* licit evaluation scores
* spoof development scores
* spoof evaluation scores
Examples:
$ bob vuln vuln_metrics -v {licit,spoof}/scores-{dev,eval}
"""
process = figure.Metrics(ctx, scores, True, load.split)
process.run()
@click.command()
@common_options.scores_argument(min_arg=2, force_eval=True, nargs=-1)
@common_options.output_plot_file_option(default_out='fmr_iapmr.pdf')
......@@ -416,52 +373,10 @@ def metrics(ctx, scores, **kwargs):
@common_options.semilogx_option()
@click.pass_context
def fmr_iapmr(ctx, scores, **kwargs):
"""Plot FMR vs IAPMR
You need to provide 4 scores
files for each vuln system in this order:
\b
* licit development scores
* licit evaluation scores
* spoof development scores
* spoof evaluation scores
Examples:
$ bob vuln fmr_iapmr -v dev-scores eval-scores
"""Plot FMR vs IAPMR
$ bob vuln fmr_iapmr -v {licit,spoof}/scores-{dev,eval}
"""
process = figure.FmrIapmr(ctx, scores, True, load.split)
process.run()
@click.command()
@common_options.scores_argument(min_arg=2, force_eval=True, nargs=-1)
@common_options.legends_option()
@common_options.sep_dev_eval_option()
@common_options.table_option()
@common_options.output_log_metric_option()
@common_options.output_plot_file_option(default_out='vuln_eval.pdf')
@common_options.points_curve_option()
@common_options.lines_at_option()
@common_options.const_layout_option()
@common_options.figsize_option(dflt=None)
@common_options.style_option()
@common_options.linestyles_option()
@verbosity_option()
@click.pass_context
def evaluate(ctx, scores, **kwargs):
'''Runs error analysis on score sets for vulnerability studies
\b
1. Computes bob vuln vuln_metrics
2. Plots EPC, EPSC, vulnerability histograms, fmr vs IAPMR to a multi-page
PDF file
You need to provide 4 score files for each biometric system in this order:
You need to provide 4 scores
files for each vuln system in this order:
\b
* licit development scores
......@@ -470,31 +385,9 @@ def evaluate(ctx, scores, **kwargs):
* spoof evaluation scores
Examples:
$ bob vuln evaluate -o my_epsc.pdf dev-scores1 eval-scores1
$ bob vuln fmr_iapmr -v dev-scores eval-scores
$ bob vuln evaluate -D {licit,spoof}/scores-{dev,eval}
'''
# first time erase if existing file
click.echo("Computing vuln metrics...")
ctx.invoke(metrics, scores=scores, evaluation=True)
if 'log' in ctx.meta and ctx.meta['log'] is not None:
click.echo("[metrics] => %s" % ctx.meta['log'])
# avoid closing pdf file before all figures are plotted
ctx.meta['closef'] = False
click.echo("Computing histograms...")
ctx.meta['criterion'] = 'eer' # no criterion passed in evaluate
ctx.forward(hist) # use class defaults plot settings
click.echo("Computing DET...")
ctx.forward(det) # use class defaults plot settings
click.echo("Computing ROC...")
ctx.forward(roc) # use class defaults plot settings
click.echo("Computing EPC...")
ctx.forward(epc) # use class defaults plot settings
click.echo("Computing EPSC...")
ctx.forward(epsc) # use class defaults plot settings
click.echo("Computing FMR vs IAPMR...")
ctx.meta['closef'] = True
ctx.forward(fmr_iapmr) # use class defaults plot settings
click.echo("Vuln successfully completed!")
click.echo("[plots] => %s" % (ctx.meta['output']))
$ bob vuln fmr_iapmr -v {licit,spoof}/scores-{dev,eval}
"""
process = figure.FmrIapmr(ctx, scores, True, load.split)
process.run()
bob/pad/base/script/vuln_figure.py
View file @ c24fafdf
'''Runs error analysis on score sets, outputs metrics and plots'''
import math
import click
import numpy as np
import matplotlib.pyplot as mpl
import bob.measure.script.figure as measure_figure
import bob.bio.base.script.figure as bio_figure
from tabulate import tabulate
from bob.measure.utils import get_fta_list
from bob.measure import (
frr_threshold, far_threshold, eer_threshold, min_hter_threshold, farfrr,
epc, ppndf, min_weighted_error_rate_threshold
frr_threshold, far_threshold, farfrr,
ppndf, min_weighted_error_rate_threshold
)
from bob.measure.plot import (det, det_axis, roc_for_far, log_values, epc)
from bob.measure import plot
from . import error_utils
class Metrics(measure_figure.Metrics):
def __init__(self, ctx, scores, evaluation, func_load):
super(Metrics, self).__init__(ctx, scores, evaluation, func_load)
''' Compute metrics from score files'''
def compute(self, idx, input_scores, input_names):
''' Compute metrics for the given criteria'''
# extract pos and negative and remove NaNs
neg_list, pos_list, _ = get_fta_list(input_scores)
dev_neg, dev_pos = neg_list[0], pos_list[0]
criter = self._criterion or 'eer'
threshold = error_utils.calc_threshold(criter, dev_neg, dev_pos) \
if self._thres is None else self._thres[idx]
far, frr = farfrr(neg_list[1], pos_list[1], threshold)
iapmr, _ = farfrr(neg_list[3], pos_list[1], threshold)
title = self._legends[idx] if self._legends is not None else None
headers = ['' or title, '%s (threshold=%.2g)' %
(criter.upper(), threshold)]
rows = []
rows.append(['FMR (%)', '{:>5.1f}%'.format(100 * far)])
rows.append(['FNMR (%)', '{:>5.1f}%'.format(frr * 100)])
rows.append(['HTER (%)', '{:>5.1f}%'.format(50 * (far + frr))])
rows.append(['IAPMR (%)', '{:>5.1f}%'.format(100 * iapmr)])
click.echo(
tabulate(rows, headers, self._tablefmt),
file=self.log_file
)
def _iapmr_dot(threshold, iapmr, real_data, **kwargs):
# plot a dot on threshold versus IAPMR line and show IAPMR as a number
axlim = mpl.axis()
......@@ -185,7 +152,7 @@ class Epc(PadPlot):
mpl.gcf().clear()
mpl.grid()
epc(
plot.epc(
licit_dev_neg, licit_dev_pos, licit_eval_neg, licit_eval_pos,
self._points,
color='C0', linestyle=self._linestyles[idx],
......@@ -228,7 +195,6 @@ class Epc(PadPlot):
ax1.tick_params(axis='y', colors='C0')
ax1.spines['left'].set_color('C0')
title = self._legends[idx] if self._legends is not None else self._title
if title.replace(' ', ''):
mpl.title(title)
......@@ -448,7 +414,7 @@ class BaseVulnDetRoc(PadPlot):
super(BaseVulnDetRoc, self).__init__(
ctx, scores, evaluation, func_load)
self._no_spoof = no_spoof
self._hlines_at = ctx.meta.get('hlines_at', [])
self._fnmrs_at = ctx.meta.get('fnmr', [])
self._real_data = True if real_data is None else real_data
self._legend_loc = None
......@@ -469,7 +435,7 @@ class BaseVulnDetRoc(PadPlot):
if not self._no_spoof and spoof_neg is not None:
ax1 = mpl.gca()
ax2 = ax1.twiny()
ax2.set_xlabel('IAPMR', color='C3')
ax2.set_xlabel('IAPMR (%)', color='C3')
ax2.set_xticklabels(ax2.get_xticks())
ax2.tick_params(axis='x', colors='C3')
ax2.xaxis.label.set_color('C3')
......@@ -487,10 +453,10 @@ class BaseVulnDetRoc(PadPlot):
)
mpl.sca(ax1)
if self._hlines_at is None:
if self._fnmrs_at is None:
return
for line in self._hlines_at:
for line in self._fnmrs_at:
thres_baseline = frr_threshold(licit_neg, licit_pos, line)
axlim = mpl.axis()
......@@ -547,7 +513,6 @@ class BaseVulnDetRoc(PadPlot):
label=label_spoof
) # FAR point, spoof scenario
def end_process(self):
''' Set title, legend, axis labels, grid colors, save figures and
close pdf is needed '''
......@@ -594,9 +559,9 @@ class DetVuln(BaseVulnDetRoc):
def __init__(self, ctx, scores, evaluation, func_load, real_data,
no_spoof):
super(DetVuln, self).__init__(ctx, scores, evaluation, func_load,
real_data, no_spoof)
self._x_label = self._x_label or "FMR"
self._y_label = self._y_label or "FNMR"
real_data, no_spoof)
self._x_label = self._x_label or "FMR (%)"
self._y_label = self._y_label or "FNMR (%)"
add = ''
if not self._no_spoof:
add = " and overlaid SPOOF scenario"
......@@ -605,16 +570,16 @@ class DetVuln(BaseVulnDetRoc):
def _set_axis(self):
if self._axlim is not None and None not in self._axlim:
det_axis(self._axlim)
plot.det_axis(self._axlim)
else:
det_axis([0.01, 99, 0.01, 99])
plot.det_axis([0.01, 99, 0.01, 99])
def _get_farfrr(self, x, y, thres):
points = farfrr(x, y, thres)
return points, [ppndf(i) for i in points]
def _plot(self, x, y, points, **kwargs):
det(
plot.det(
x, y, points,
color=kwargs.get('color'),
linestyle=kwargs.get('linestyle'),
......@@ -639,9 +604,9 @@ class RocVuln(BaseVulnDetRoc):
self._legend_loc = self._legend_loc or best_legend
def _plot(self, x, y, points, **kwargs):
roc_for_far(
plot.roc_for_far(
x, y,
far_values=log_values(self._min_dig or -4),
far_values=plot.log_values(self._min_dig or -4),
CAR=self._semilogx,
color=kwargs.get('color'), linestyle=kwargs.get('linestyle'),
label=kwargs.get('label')
......@@ -694,8 +659,8 @@ class FmrIapmr(PadPlot):
title = self._title if self._title is not None else "FMR vs IAPMR"
if title.replace(' ', ''):
mpl.title(title)
mpl.xlabel(self._x_label or "FMR (%)")
mpl.ylabel(self._y_label or "IAPMR (%)")
mpl.xlabel(self._x_label or "FMR")
mpl.ylabel(self._y_label or "IAPMR")
mpl.grid(True, color=self._grid_color)
if self._disp_legend:
mpl.legend(loc=self._legend_loc)
......
bob/pad/base/test/test_commands.py
View file @ c24fafdf
import sys
import click
from click.testing import CliRunner
import pkg_resources
from ..script import (pad_commands, vuln_commands)
def test_det_pad():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -19,7 +16,6 @@ def test_det_pad():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_det_vuln():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -31,7 +27,7 @@ def test_det_vuln():
'data/spoof/scores-eval')
runner = CliRunner()
with runner.isolated_filesystem():
result = runner.invoke(vuln_commands.det, ['-hla', '0.2',
result = runner.invoke(vuln_commands.det, ['-fnmr', '0.2',
'-o',
'DET.pdf',
licit_dev, licit_test,
......@@ -39,7 +35,6 @@ def test_det_vuln():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_fmr_iapmr_vuln():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -64,7 +59,6 @@ def test_fmr_iapmr_vuln():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_hist_pad():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -96,7 +90,6 @@ def test_hist_pad():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_hist_vuln():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -123,28 +116,6 @@ def test_hist_vuln():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_metrics_vuln():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
licit_test = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-eval')
spoof_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/spoof/scores-dev')
spoof_test = pkg_resources.resource_filename('bob.pad.base.test',
'data/spoof/scores-eval')
runner = CliRunner()
with runner.isolated_filesystem():
result = runner.invoke(
vuln_commands.metrics,
['--criterion', 'eer', licit_dev, licit_test,
spoof_dev, spoof_test]
)
assert result.exit_code == 0, (result.exit_code, result.output)
def test_metrics_pad():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -159,7 +130,6 @@ def test_metrics_pad():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_epc_vuln():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
......@@ -199,7 +169,7 @@ def test_epsc_vuln():
['--output', 'epsc.pdf',
licit_dev, licit_test,
spoof_dev, spoof_test])
assert result.exit_code == 0, (result.exit_code, result.output)
assert result.exit_code == 0, (result.exit_code, result.output, result.exception)
result = runner.invoke(vuln_commands.epsc,
['--output', 'epsc.pdf', '-I',
......@@ -221,8 +191,7 @@ def test_epsc_vuln():
assert result.exit_code == 0, (result.exit_code, result.output)
def test_evaluate_vuln():
def test_evaluate_pad():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
licit_test = pkg_resources.resource_filename('bob.pad.base.test',
......@@ -236,20 +205,3 @@ def test_evaluate_vuln():
result = runner.invoke(pad_commands.evaluate,
[licit_dev, licit_test, spoof_dev, spoof_test])
assert result.exit_code == 0, (result.exit_code, result.output)
def test_evaluate_vuln():
licit_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-dev')
licit_test = pkg_resources.resource_filename('bob.pad.base.test',
'data/licit/scores-eval')
spoof_dev = pkg_resources.resource_filename('bob.pad.base.test',
'data/spoof/scores-dev')
spoof_test = pkg_resources.resource_filename('bob.pad.base.test',