Implement discrete xbob.io packaging

buildout.cfg

@@ -11,20 +11,20 @@ auto-checkout = *
 develop = src/xbob.extension
           src/xbob.blitz
           src/xbob.math
-          src/xbob.io
+          src/xbob.io.base
           .
 
 ; options for xbob.buildout extension
 debug = true
 verbose = true
-prefixes = /idiap/group/torch5spro/nightlies/last/bob/linux-x86_64-release
+prefixes = /idiap/group/torch5spro/releases/preview/install/linux-x86_64-release
            /Users/andre/work/bob/b/dbg/
 
 [sources]
 xbob.extension = git https://github.com/bioidiap/xbob.extension branch=prototype
 xbob.blitz = git https://github.com/bioidiap/xbob.blitz
 xbob.math = git https://github.com/bioidiap/xbob.math
-xbob.io = git https://github.com/bioidiap/xbob.io
+xbob.io.base = git https://github.com/bioidiap/xbob.io.base
 
 [scripts]
 recipe = xbob.buildout:scripts

doc/conf.py

@@ -59,12 +59,12 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'xbob.io'
+project = u'xbob.measure'
 import time
 copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
 
 # Grab the setup entry
-distribution = pkg_resources.require('xbob.io')[0]
+distribution = pkg_resources.require('xbob.measure')[0]
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -130,7 +130,7 @@ if sphinx.__version__ >= "1.0":
 #html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = 'xbob_io'
+#html_short_title = 'xbob_measure'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -188,7 +188,7 @@ html_favicon = 'img/favicon.ico'
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'xbob_io_doc'
+htmlhelp_basename = 'xbob_measure_doc'
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -202,7 +202,7 @@ latex_font_size = '10pt'
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'xbob_io.tex', u'Bob I/O Routines',
+  ('index', 'xbob_measure.tex', u'Bob Performance Measurement Routines',
    u'Biometrics Group, Idiap Research Institute', 'manual'),
 ]
 
@@ -242,7 +242,7 @@ rst_epilog = """
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'xbob_io', u'Bob I/O Routines Documentation', [u'Idiap Research Institute'], 1)
+    ('index', 'xbob_measure', u'Bob Performance Measurement Routines', [u'Idiap Research Institute'], 1)
 ]
 
 # Default processing flags for sphinx

setup.py

@@ -29,7 +29,7 @@ setup(
       'setuptools',
       'xbob.blitz',
       'xbob.math',
-      'xbob.io',
+      'xbob.io.base',
       'matplotlib',
     ],
 

xbob/measure/test_error.py

@@ -11,7 +11,7 @@
 import os
 import numpy
 import nose.tools
-import xbob.io
+import xbob.io.base
 
 from .version import externals
 from distutils.version import StrictVersion
@@ -26,7 +26,7 @@ def F(f):
 
 def save(fname, data):
   """Saves a single array into a file in the 'data' directory."""
-  xbob.io.Array(data).save(os.path.join('data', fname))
+  xbob.io.base.Array(data).save(os.path.join('data', fname))
 
 
 def test_basic_ratios():
@@ -36,8 +36,8 @@ def test_basic_ratios():
   # We test the basic functionaly on FAR and FRR calculation. The first
   # example is separable, with a separation threshold of about 3.0
 
-  positives = xbob.io.load(F('linsep-positives.hdf5'))
-  negatives = xbob.io.load(F('linsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('linsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('linsep-negatives.hdf5'))
 
   minimum = min(positives.min(), negatives.min())
   maximum = max(positives.max(), negatives.max())
@@ -92,8 +92,8 @@ def test_indexing():
 
   # This test verifies that the output of correctly_classified_positives() and
   # correctly_classified_negatives() makes sense.
-  positives = xbob.io.load(F('linsep-positives.hdf5'))
-  negatives = xbob.io.load(F('linsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('linsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('linsep-negatives.hdf5'))
 
   minimum = min(positives.min(), negatives.min())
   maximum = max(positives.max(), negatives.max())
@@ -126,8 +126,8 @@ def test_thresholding():
   # calculate the threshold that minimizes the EER.
 
   # This test set is not separable.
-  positives = xbob.io.load(F('nonsep-positives.hdf5'))
-  negatives = xbob.io.load(F('nonsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('nonsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('nonsep-negatives.hdf5'))
   threshold = eer_threshold(negatives, positives)
 
   # Of course we have to make sure that will set the EER correctly:
@@ -153,8 +153,8 @@ def test_thresholding():
   # trickier, as you have no points in the middle of the range to compare
   # things to. This is where the currently used recursive algorithm seems to
   # do better. Let's verify
-  positives = xbob.io.load(F('linsep-positives.hdf5'))
-  negatives = xbob.io.load(F('linsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('linsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('linsep-negatives.hdf5'))
   threshold = eer_threshold(negatives, positives)
   # the result here is 3.242 (which is what is expect ;-)
 
@@ -180,15 +180,15 @@ def test_plots():
   from . import eer_threshold, roc, precision_recall_curve, det, epc
 
   # This test set is not separable.
-  positives = xbob.io.load(F('nonsep-positives.hdf5'))
-  negatives = xbob.io.load(F('nonsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('nonsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('nonsep-negatives.hdf5'))
   threshold = eer_threshold(negatives, positives)
 
   # This example will test the ROC plot calculation functionality.
   xy = roc(negatives, positives, 100)
   # uncomment the next line to save a reference value
   # save('nonsep-roc.hdf5', xy)
-  xyref = xbob.io.load(F('nonsep-roc.hdf5'))
+  xyref = xbob.io.base.load(F('nonsep-roc.hdf5'))
   if HAVE_BOB_1_2_2: xyref = xyref[::-1,:]
   assert numpy.array_equal(xy, xyref)
 
@@ -196,14 +196,14 @@ def test_plots():
   xy = precision_recall_curve(negatives, positives, 100)
   # uncomment the next line to save a reference value
   # save('nonsep-roc.hdf5', xy)
-  xyref = xbob.io.load(F('nonsep-precisionrecall.hdf5'))
+  xyref = xbob.io.base.load(F('nonsep-precisionrecall.hdf5'))
   assert numpy.array_equal(xy, xyref)
 
   # This example will test the DET plot calculation functionality.
   det_xyzw = det(negatives, positives, 100)
   # uncomment the next line to save a reference value
   # save('nonsep-det.hdf5', det_xyzw)
-  det_xyzw_ref = xbob.io.load(F('nonsep-det.hdf5'))
+  det_xyzw_ref = xbob.io.base.load(F('nonsep-det.hdf5'))
   if HAVE_BOB_1_2_2: det_xyzw_ref = det_xyzw_ref[::-1,:]
   assert numpy.allclose(det_xyzw, det_xyzw_ref, atol=1e-15)
 
@@ -219,7 +219,7 @@ def test_plots():
       test_negatives, test_positives, 100)
   # uncomment the next line to save a reference value
   # save('nonsep-epc.hdf5', xy)
-  xyref = xbob.io.load(F('nonsep-epc.hdf5'))
+  xyref = xbob.io.base.load(F('nonsep-epc.hdf5'))
   assert numpy.allclose(xy, xyref, atol=1e-15)
 
 
@@ -231,8 +231,8 @@ def test_rocch():
   # calculate the threshold that minimizes the EER on the ROC Convex Hull
 
   # This test set is separable.
-  positives = xbob.io.load(F('linsep-positives.hdf5'))
-  negatives = xbob.io.load(F('linsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('linsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('linsep-negatives.hdf5'))
   # References obtained using Bosaris 1.06
   pmiss_pfa_ref = numpy.array([[1., 0., 0.], [0., 0., 1.]])
   if HAVE_BOB_1_2_2: pmiss_pfa_ref = pmiss_pfa_ref[::-1,:]
@@ -246,8 +246,8 @@ def test_rocch():
   assert abs(eer-eer_ref) < 1e-4
 
   # This test set is not separable.
-  positives = xbob.io.load(F('nonsep-positives.hdf5'))
-  negatives = xbob.io.load(F('nonsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('nonsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('nonsep-negatives.hdf5'))
   # References obtained using Bosaris 1.06
   pmiss_pfa_ref = numpy.array([[1., 0.68, 0.28, 0.1, 0.06, 0., 0.], [0, 0, 0.08, 0.12, 0.22, 0.48, 1.]])
   if HAVE_BOB_1_2_2: pmiss_pfa_ref = pmiss_pfa_ref[::-1,:]
@@ -297,8 +297,8 @@ def test_calibration():
 
   # Tests the cllr and min_cllr measures
   # This test set is separable.
-  positives = xbob.io.load(F('linsep-positives.hdf5'))
-  negatives = xbob.io.load(F('linsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('linsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('linsep-negatives.hdf5'))
 
   cllr = calibration.cllr(negatives, positives)
   min_cllr = calibration.min_cllr(negatives, positives)
@@ -309,8 +309,8 @@ def test_calibration():
   nose.tools.assert_almost_equal(min_cllr, 0.)
 
   # This test set is not separable.
-  positives = xbob.io.load(F('nonsep-positives.hdf5'))
-  negatives = xbob.io.load(F('nonsep-negatives.hdf5'))
+  positives = xbob.io.base.load(F('nonsep-positives.hdf5'))
+  negatives = xbob.io.base.load(F('nonsep-negatives.hdf5'))
 
   cllr = calibration.cllr(negatives, positives)
   min_cllr = calibration.min_cllr(negatives, positives)