Merge branch 'moving' into 'theo'

Moving biometrics-related functionality to bob.bio.base

See merge request !49

bob/measure/__init__.py

@@ -7,9 +7,7 @@ from . import version
 from .version import module as __version__
 
 from . import plot
-from . import load
 from . import calibration
-from . import openbr
 import numpy
 
 def mse (estimation, target):
@@ -134,9 +132,7 @@ def recognition_rate(cmc_scores, threshold = None, rank = 1):
   The input has a specific format, which is a list of two-element tuples.  Each
   of the tuples contains the negative :math:`\\{S_p^-\\}` and the positive
   :math:`\\{S_p^+\\}` scores for one probe item :math:`p`, or ``None`` in case
-  of open set recognition.  To read the lists from score files in 4 or 5 column
-  format, please use the :py:func:`bob.measure.load.cmc_four_column` or
-  :py:func:`bob.measure.load.cmc_five_column` function.
+  of open set recognition.
 
   If ``threshold`` is set to ``None``, the rank 1 recognition rate is defined
   as the number of test items, for which the highest positive
@@ -172,9 +168,9 @@ def recognition_rate(cmc_scores, threshold = None, rank = 1):
   Parameters:
 
     cmc_scores (:py:class:`list`): A list in the format ``[(negatives,
-      positives), ...]`` containing the CMC scores loaded with one of the
-      functions (:py:func:`bob.measure.load.cmc_four_column` or
-      :py:func:`bob.measure.load.cmc_five_column`).
+      positives), ...]`` containing the CMC scores (i.e. :py:class:`list`: 
+      A list of tuples, where each tuple contains the
+      ``negative`` and ``positive`` scores for one probe of the database).
 
       Each pair contains the ``negative`` and the ``positive`` scores for **one
       probe item**.  Each pair can contain up to one empty array (or ``None``),
@@ -258,9 +254,7 @@ def cmc(cmc_scores):
 
   The input has a specific format, which is a list of two-element tuples. Each
   of the tuples contains the negative and the positive scores for one probe
-  item.  To read the lists from score files in 4 or 5 column format, please use
-  the :py:func:`bob.measure.load.cmc_four_column` or
-  :py:func:`bob.measure.load.cmc_five_column` function.
+  item.
 
   For each probe item the probability that the rank :math:`r` of the positive
   score is calculated.  The rank is computed as the number of negative scores
@@ -281,10 +275,7 @@ def cmc(cmc_scores):
 
   cmc_scores : :py:class:`list`
     A list in the format ``[(negatives, positives), ...]`` containing the CMC
-    scores loaded with one of the functions
-    :py:func:`bob.measure.load.cmc_four_column`,
-    :py:func:`bob.measure.load.cmc_five_column`, or
-    :py:func:`bob.measure.load.cmc`.
+    scores.
 
     Each pair contains the ``negative`` and the ``positive`` scores for **one
     probe item**.  Each pair can contain up to one empty array (or ``None``),
@@ -345,9 +336,7 @@ def detection_identification_rate(cmc_scores, threshold, rank = 1):
   Parameters:
 
     cmc_scores (:py:class:`list`): A list in the format ``[(negatives,
-      positives), ...]`` containing the CMC scores loaded with one of the
-      functions (:py:func:`bob.measure.load.cmc_four_column` or
-      :py:func:`bob.measure.load.cmc_five_column`).
+      positives), ...]`` containing the CMC.
 
       Each pair contains the ``negative`` and the ``positive`` scores for **one
       probe item**.  Each pair can contain up to one empty array (or ``None``),
@@ -406,9 +395,9 @@ def false_alarm_rate(cmc_scores, threshold):
   Parameters:
 
     cmc_scores (:py:class:`list`): A list in the format ``[(negatives,
-      positives), ...]`` containing the CMC scores loaded with one of the
-      functions (:py:func:`bob.measure.load.cmc_four_column` or
-      :py:func:`bob.measure.load.cmc_five_column`).
+      positives), ...]`` containing the CMC scores (i.e. :py:class:`list`: 
+      A list of tuples, where each tuple contains the
+      ``negative`` and ``positive`` scores for one probe of the database).
 
       Each pair contains the ``negative`` and the ``positive`` scores for **one
       probe item**.  Each pair can contain up to one empty array (or ``None``),

bob/measure/data/compute_perf.output.txt

-Failure To Acquire (FTA) in the development set is: 0.000%
-Failure To Acquire (FTA) in the test set is: 0.000%
-[Min. criterion: EER] Threshold on Development set: -4.830500e-03
-       | Development     | Test           
--------+-----------------+------------------
-  FMR  | 6.731% (35/520) | 2.500% (13/520)
-  FNMR | 6.667% (26/390) | 6.154% (24/390)
-  FAR  | 6.731%          | 2.500%         
-  FRR  | 6.667%          | 6.154%         
-  HTER | 6.699%          | 4.327%         
-[Min. criterion: Min. HTER] Threshold on Development set: 3.430500e-03
-       | Development     | Test           
--------+-----------------+------------------
-  FMR  | 4.231% (22/520) | 1.731% (9/520) 
-  FNMR | 7.949% (31/390) | 7.692% (30/390)
-  FAR  | 4.231%          | 1.731%         
-  FRR  | 7.949%          | 7.692%         
-  HTER | 6.090%          | 4.712%         

bob/measure/data/scores-cmc-4col-open-set-one-error.txt

-1 1 probe_1 1
-1 1 probe_2 1
-1 2 probe_3 0
-1 2 probe_4 0
-1 2 probe_5 0
-1 3 probe_6 0
-1 3 probe_7 0
-1 4 probe_8 0
-1 5 probe_9 0
-2 1 probe_1 0
-2 1 probe_2 0
-2 2 probe_3 1
-2 2 probe_4 1
-2 2 probe_5 1
-2 3 probe_6 0
-2 3 probe_7 0
-2 4 probe_8 0
-2 5 probe_9 0
-3 1 probe_1 0
-3 1 probe_2 0
-3 2 probe_3 0
-3 2 probe_4 0
-3 2 probe_5 0
-3 3 probe_6 1
-3 3 probe_7 -0.1
-3 4 probe_8 0
-3 5 probe_9 0

bob/measure/data/scores-cmc-4col-open-set-two-errors.txt

-1 1 probe_1 1
-1 1 probe_2 1
-1 2 probe_3 0
-1 2 probe_4 0
-1 2 probe_5 0
-1 3 probe_6 0
-1 3 probe_7 0
-1 4 probe_8 0
-1 5 probe_9 0
-2 1 probe_1 0
-2 1 probe_2 0
-2 2 probe_3 1
-2 2 probe_4 1
-2 2 probe_5 1
-2 3 probe_6 0
-2 3 probe_7 0
-2 4 probe_8 0
-2 5 probe_9 0
-3 1 probe_1 0
-3 1 probe_2 0
-3 2 probe_3 0
-3 2 probe_4 0
-3 2 probe_5 0
-3 3 probe_6 1
-3 3 probe_7 -0.1
-3 4 probe_8 0
-3 5 probe_9 10

bob/measure/data/scores-cmc-4col-open-set.txt

-1 1 probe_1 1
-1 1 probe_2 1
-1 2 probe_3 0
-1 2 probe_4 0
-1 2 probe_5 0
-1 3 probe_6 0
-1 3 probe_7 0
-1 4 probe_8 0
-1 5 probe_9 0
-2 1 probe_1 0
-2 1 probe_2 0
-2 2 probe_3 1
-2 2 probe_4 1
-2 2 probe_5 1
-2 3 probe_6 0
-2 3 probe_7 0
-2 4 probe_8 0
-2 5 probe_9 0
-3 1 probe_1 0
-3 1 probe_2 0
-3 2 probe_3 0
-3 2 probe_4 0
-3 2 probe_5 0
-3 3 probe_6 1
-3 3 probe_7 1
-3 4 probe_8 0
-3 5 probe_9 0

bob/measure/data/scores.mask

-S2
-unknown-gallery.lst
-unknown-probe.lst
-MB 100 20 xV4
-
\ No newline at end of file

bob/measure/plot.py

@@ -451,13 +451,9 @@ def det_axis(v, **kwargs):
 def cmc(cmc_scores, logx=True, **kwargs):
   """Plots the (cumulative) match characteristics and returns the maximum rank.
 
-  This function plots a CMC curve using the given CMC scores, which can be read
-  from the our score files using the
-  :py:func:`bob.measure.load.cmc_four_column` or
-  :py:func:`bob.measure.load.cmc_five_column` methods.  The structure of the
-  ``cmc_scores`` parameter is relatively complex.  It contains a list of pairs
-  of lists.  For each probe object, a pair of list negative and positive scores
-  is required.
+  This function plots a CMC curve using the given CMC scores (:py:class:`list`: 
+      A list of tuples, where each tuple contains the
+      ``negative`` and ``positive`` scores for one probe of the database).
 
 
   Parameters:

conda/meta.yaml

@@ -6,11 +6,6 @@ package:
   version: {{ environ.get('BOB_PACKAGE_VERSION', '0.0.1') }}
 
 build:
-  entry_points:
-    - bob_compute_perf.py = bob.measure.script.compute_perf:main
-    - bob_eval_threshold.py = bob.measure.script.eval_threshold:main
-    - bob_apply_threshold.py = bob.measure.script.apply_threshold:main
-    - bob_plot_cmc.py = bob.measure.script.plot_cmc:main
   number: {{ environ.get('BOB_BUILD_NUMBER', 0) }}
   run_exports:
     - {{ pin_subpackage(name) }}
@@ -51,10 +46,6 @@ test:
   imports:
     - {{ name }}
   commands:
-    - bob_compute_perf.py --help
-    - bob_eval_threshold.py --help
-    - bob_apply_threshold.py --help
-    - bob_plot_cmc.py --help
     - nosetests --with-coverage --cover-package={{ name }} -sv {{ name }}
     - sphinx-build -aEW {{ project_dir }}/doc {{ project_dir }}/sphinx
     - sphinx-build -aEb doctest {{ project_dir }}/doc sphinx

doc/py_api.rst

@@ -64,21 +64,6 @@ Generic
    bob.measure.rmse
    bob.measure.get_config
 
-Loading data
-------------
-
-.. autosummary::
-   bob.measure.load.open_file
-   bob.measure.load.scores
-   bob.measure.load.split
-   bob.measure.load.cmc
-   bob.measure.load.four_column
-   bob.measure.load.split_four_column
-   bob.measure.load.cmc_four_column
-   bob.measure.load.five_column
-   bob.measure.load.split_five_column
-   bob.measure.load.cmc_five_column
-
 Calibration
 -----------
 
@@ -98,19 +83,10 @@ Plotting
    bob.measure.plot.cmc
    bob.measure.plot.detection_identification_curve
 
-OpenBR conversions
-------------------
-
-.. autosummary::
-   bob.measure.openbr.write_matrix
-   bob.measure.openbr.write_score_file
-
 
 Details
 -------
 
 .. automodule:: bob.measure
-.. automodule:: bob.measure.load
 .. automodule:: bob.measure.calibration
 .. automodule:: bob.measure.plot
-.. automodule:: bob.measure.openbr