fix install stuff

bob/rppg/chrom/extract_utils.py

@@ -12,9 +12,9 @@ def compute_mean_rgb(image, mask=None):
   
   Parameters
   ----------
-  image: 3d numpy array
+  image: numpy.ndarray 
     The image to process
-  mask: 2d boolen numpy array
+  mask: numpy.ndarray
     Mask of the size of the image, telling which pixels
     should be considered
 
@@ -40,9 +40,9 @@ def compute_gray_diff(previous, current):
   
   Parameters
   ----------
-  previous: 3d numpy array
+  previous: numpy.ndarray  
     The previous frame.
-  current: 3d numpy array
+  current: numpy.ndarray 
     The current frame.
  
   Returns
@@ -65,7 +65,7 @@ def select_stable_frames(diff, n):
 
   Parameters
   ----------
-  diff: 1d numpy array
+  diff: numpy.ndarray 
     The sum of absolute pixel intensity differences between 
     consecutive frames, across the whole sequence.
   n: int

bob/rppg/chrom/script/extract_pulse.py

 #!/usr/bin/env python
 # encoding: utf-8
 
-# Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/
-# Written by Guillaume Heusch <guillaume.heusch@idiap.ch>,
-# 
-# This file is part of bob.rpgg.base.
-# 
-# bob.rppg.base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License version 3 as
-# published by the Free Software Foundation.
-# 
-# bob.rppg.base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with bob.rppg.base. If not, see <http://www.gnu.org/licenses/>.
-
 """Pulse extraction for database videos (%(version)s)
 
 Usage:

bob/rppg/cvpr14/script/video2skin.py

 #!/usr/bin/env python
 # encoding: utf-8
 
-# Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/
-# Written by Guillaume Heusch <guillaume.heusch@idiap.ch>,
-# 
-# This file is part of bob.rpgg.base.
-# 
-# bob.rppg.base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License version 3 as
-# published by the Free Software Foundation.
-# 
-# bob.rppg.base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with bob.rppg.base. If not, see <http://www.gnu.org/licenses/>.
-
-'''Skin color extraction for database videos (%(version)s)
+"""Skin color extraction for database videos (%(version)s)
 
 Usage:
   %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...] 
            [--verbose ...] [--plot]
-           [--dbdir=<path>] [--outdir=<path>] [--limit=<int>]
+           [--dbdir=<path>] [--outdir=<path>] 
            [--overwrite] [--threshold=<float>] [--skininit]
            [--gridcount] 
 
@@ -43,7 +26,6 @@ Options:
   -D, --dbdir=<path>        The path to the database on your disk. If not set,
                             defaults to Idiap standard locations.
   -o, --outdir=<path>       Where the skin color will be stored [default: skin].
-  -l, --limit=<int>         Limits the processing to the first N videos of the
                             database (for testing purposes)
   -O, --overwrite           By default, we don't overwrite existing files. The
                             processing will skip those so as to go faster. If you
@@ -54,7 +36,6 @@ Options:
 
 
 
-
 Examples:
 
   To run the skin color extraction on the hci database
@@ -72,16 +53,16 @@ Examples:
 
 See '%(prog)s --help' for more information.
 
-'''
+"""
+from __future__ import print_function
 
 import os
 import sys
 import pkg_resources
 
-import logging
-__logging_format__='[%(levelname)s] %(message)s'
-logging.basicConfig(format=__logging_format__)
-logger = logging.getLogger("extract_log")
+from bob.core.log import set_verbosity_level
+from bob.core.log import setup
+logger = setup("bob.rppg.base")
 
 from docopt import docopt
 
@@ -103,19 +84,11 @@ def main(user_input=None):
       arguments = sys.argv[1:]
 
   prog = os.path.basename(sys.argv[0])
-  completions = dict(
-          prog=prog,
-          version=version,
-          )
-  args = docopt(
-      __doc__ % completions,
-      argv=arguments,
-      version='Skin color extraction for videos (%s)' % version,
-      )
+  completions = dict(prog=prog, version=version,)
+  args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
 
   # if the user wants more verbosity, lowers the logging level
-  if args['--verbose'] == 1: logging.getLogger().setLevel(logging.INFO)
-  elif args['--verbose'] >= 2: logging.getLogger().setLevel(logging.DEBUG)
+  set_verbosity_level(logger, args['--verbose'])
 
   # chooses the database driver to use
   if args['cohface']:
@@ -153,21 +126,22 @@ def main(user_input=None):
       sys.exit()
     objects = db.objects(args['--protocol'], args['--subset'])
 
-  # tells the number of grid objects, and exit
-  if args['--gridcount']:
-    print len(objects)
-    sys.exit()
-
   # if we are on a grid environment, just find what I have to process.
-  if os.environ.has_key('SGE_TASK_ID'):
+  sge = False
+  try:
+    sge = os.environ.has_key('SGE_TASK_ID') # python2
+  except AttributeError:
+    sge = 'SGE_TASK_ID' in os.environ # python3
+    
+  if sge:
     pos = int(os.environ['SGE_TASK_ID']) - 1
     if pos >= len(objects):
-      raise RuntimeError, "Grid request for job %d on a setup with %d jobs" % \
-          (pos, len(objects))
+      raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
     objects = [objects[pos]]
 
-  else: #maybe the user wants to limit the total amount of videos for testing
-    if args['--limit']: objects = objects[:int(args['--limit'])]
+  if args['--gridcount']:
+    print(len(objects))
+    sys.exit()
 
   # does the actual work - for every video in the available dataset,
   # extract the average color in both the mask area and in the backround,

setup.py

@@ -32,7 +32,6 @@ setup(
 
   entry_points={
     'console_scripts': [
-      'rppg_bbox.py = bob.rppg.base.script.extract_boundingboxes:main',
       'cvpr14_extract_signals.py = bob.rppg.cvpr14.script.extract_signals:main',
       'cvpr14_video2skin.py = bob.rppg.cvpr14.script.video2skin:main',
       'cvpr14_illumination.py = bob.rppg.cvpr14.script.illumination_rectification:main',