diff --git a/bob/rppg/base/script/compute_performance.py b/bob/rppg/base/script/compute_performance.py
index 4e3ad221e83b101e1b4907fd6871145052b2b8c9..b268692f456a28cb4ac6763183e61d946c7c5228 100644
--- a/bob/rppg/base/script/compute_performance.py
+++ b/bob/rppg/base/script/compute_performance.py
@@ -1,11 +1,12 @@
#!/usr/bin/env python
# encoding: utf-8
-"""Generate resutls from heart rate computation (%(version)s)
+"""Generate results from heart rate computation (%(version)s)
Usage:
- %(prog)s (hci | cohface) [--protocol=<string>] [--subset=<string> ...]
- [--verbose ...] [--plot] [--outdir=<path>] [--indir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--verbose ...] [--plot] [--resultdir=<path>] [--hrdir=<path>]
[--overwrite]
%(prog)s (--help | -h)
@@ -17,24 +18,20 @@ Options:
-V, --version Show version
-v, --verbose Increases the verbosity (may appear multiple times)
-P, --plot Set this flag if you'd like to see some plots.
- -p, --protocol=<string> Protocol [default: all].
+ -p, --protocol=<string> Protocol [default: all].[default: all]
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -i, --indir=<path> The path to the saved heart rate values on your disk.
- -o, --outdir=<path> The path to the output directory where the results
- will be stored [default: performances].
+ -i, --hrdir=<path> The path to the saved heart rate values on your disk [default: hr].
+ -o, --resultdir=<path> The path to the output directory where the results
+ will be stored [default: results].
-O, --overwrite By default, we don't overwrite existing files.
Set this flag if you want to overwrite existing files.
Examples:
- To run the results generation for the cohface database
+ To run the results generation
- $ %(prog)s cohface -v
-
- You can change the output directory using the `-o' flag:
-
- $ %(prog)s hci -v -o /path/to/result/directory
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -50,6 +47,9 @@ logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ..utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -67,45 +67,28 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ hrdir = get_parameter(args, configuration, 'hrdir', 'hr')
+ resultdir = get_parameter(args, configuration, 'resultdir', 'results')
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
set_verbosity_level(logger, args['--verbose'])
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ # TODO: find a way to check protocol names - Guillaume HEUSCH, 22-06-2018
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# errors
errors = []
@@ -118,20 +101,19 @@ def main(user_input=None):
################
### LET'S GO ###
################
- outdir = args['--outdir']
# if output dir exists and not overwriting, stop
- if os.path.exists(outdir) and not args['--overwrite']:
- logger.info("Skipping output `%s': already exists, use --overwrite to force an overwrite", outdir)
+ if os.path.exists(resultdir) and not overwrite:
+ logger.info("Skipping output `%s': already exists, use --overwrite to force an overwrite", resultdir)
sys.exit()
else:
- bob.io.base.create_directories_safe(outdir)
+ bob.io.base.create_directories_safe(resultdir)
for obj in objects:
# load the heart rate
logger.debug("Loading computed heart rate from `%s'...", obj.path)
- hr_file = obj.make_path(args['--indir'], '.hdf5')
+ hr_file = obj.make_path(hrdir, '.hdf5')
try:
hr = bob.io.base.load(hr_file)
except (IOError, RuntimeError) as e:
@@ -169,7 +151,7 @@ def main(user_input=None):
logger.info(pearson_text)
# statistics in a text file
- stats_filename = os.path.join(outdir, 'stats.txt')
+ stats_filename = os.path.join(resultdir, 'stats.txt')
stats_file = open(stats_filename, 'w')
stats_file.write(rmse_text + "\n")
stats_file.write(mean_err_percent_text + "\n")
@@ -185,7 +167,7 @@ def main(user_input=None):
pyplot.xlabel('Ground truth [bpm]')
pyplot.ylabel('Estimated heart-rate [bpm]')
ax.set_title('Scatter plot')
- scatter_file = os.path.join(outdir, 'scatter.png')
+ scatter_file = os.path.join(resultdir, 'scatter.png')
pyplot.savefig(scatter_file)
# histogram of error
@@ -193,7 +175,7 @@ def main(user_input=None):
ax2 = f2.add_subplot(1,1,1)
ax2.hist(errors, bins=50, )
ax2.set_title('Distribution of the error')
- distribution_file = os.path.join(outdir, 'error_distribution.png')
+ distribution_file = os.path.join(resultdir, 'error_distribution.png')
pyplot.savefig(distribution_file)
# distribution of HR
@@ -204,7 +186,7 @@ def main(user_input=None):
pyplot.hist(inferred, label='Estimated HR', color='b', **histoargs)
pyplot.ylabel("Test set")
- if bool(args['--plot']):
+ if plot:
pyplot.show()
return 0
diff --git a/bob/rppg/base/script/frequency_analysis.py b/bob/rppg/base/script/frequency_analysis.py
index 223871d8b5427e696a35342e33647b443f74f4de..0b32c287a3200ba67dbf2fc8a8f178f87e747e15 100644
--- a/bob/rppg/base/script/frequency_analysis.py
+++ b/bob/rppg/base/script/frequency_analysis.py
@@ -1,11 +1,12 @@
#!/usr/bin/env python
# encoding: utf-8
-"""Frequency analysis of the filtered color signals to get the heart-rate (%(version)s)
+"""Frequency analysis of the pulse signal to get the heart-rate (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--verbose ...] [--plot] [--indir=<path>] [--outdir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--verbose ...] [--plot] [--pulsedir=<path>] [--hrdir=<path>]
[--framerate=<int>] [--nsegments=<int>] [--nfft=<int>]
[--overwrite]
@@ -19,13 +20,13 @@ Options:
-V, --version Show version
-P, --plot Set this flag if you'd like to follow-up the algorithm
execution graphically. We'll plot some interactions.
- -p, --protocol=<string> Protocol [default: all].
+ -p, --protocol=<string> Protocol [default: all].[default: all]
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -i, --indir=<path> The path to the saved filtered signals on your disk
- [default: filtered].
- -o, --outdir=<path> The path to the output directory where the resulting
- color signals will be stored [default: heart-rate].
+ -i, --pulsedir=<path> The path to the saved filtered signals on your disk
+ [default: pulse].
+ -o, --hrdir=<path> The path to the output directory where the resulting
+ color signals will be stored [default: hr].
-O, --overwrite By default, we don't overwrite existing files. The
processing will skip those so as to go faster. If you
still would like me to overwrite them, set this flag.
@@ -58,6 +59,9 @@ logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ..utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -75,45 +79,31 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ pulsedir = get_parameter(args, configuration, 'pulsedir', 'pulse')
+ hrdir = get_parameter(args, configuration, 'hrdir', 'hr')
+ framerate = get_parameter(args, configuration, 'framerate', 61)
+ nsegments = get_parameter(args, configuration, 'nsegments', 12)
+ nfft = get_parameter(args, configuration, 'nfft', 8192)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+
+ # TODO: find a way to check protocol names - Guillaume HEUSCH, 22-06-2018
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
################
### LET'S GO ###
@@ -121,39 +111,38 @@ def main(user_input=None):
for obj in objects:
# expected output file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(hrdir, '.hdf5')
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load the filtered color signals of shape (3, nb_frames)
logger.info("Frequency analysis of color signals from `%s'...", obj.path)
- filtered_file = obj.make_path(args['--indir'], '.hdf5')
+ filtered_file = obj.make_path(pulsedir, '.hdf5')
try:
signal = bob.io.base.load(filtered_file)
except (IOError, RuntimeError) as e:
logger.warn("Skipping file `%s' (no color signals file available)", obj.path)
continue
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
pyplot.plot(range(signal.shape[0]), signal, 'g')
pyplot.title('Filtered green signal')
pyplot.show()
# find the segment length, such that we have 8 50% overlapping segments (Matlab's default)
- segment_length = (2*signal.shape[0]) // (int(args['--nsegments']) + 1)
+ segment_length = (2*signal.shape[0]) // (nsegments + 1)
# the number of points for FFT should be larger than the segment length ...
- if int(args['--nfft']) < segment_length:
+ if nfft < segment_length:
logger.warn("Skipping file `%s' (nfft < nperseg)", obj.path)
continue
- nfft = int(args['--nfft'])
from scipy.signal import welch
- green_f, green_psd = welch(signal, int(args['--framerate']), nperseg=segment_length, nfft=nfft)
+ green_f, green_psd = welch(signal, framerate, nperseg=segment_length, nfft=nfft)
# find the max of the frequency spectrum in the range of interest
first = numpy.where(green_f > 0.7)[0]
@@ -166,7 +155,7 @@ def main(user_input=None):
hr = f_max*60.0
logger.info("Heart rate = {0}".format(hr))
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
pyplot.semilogy(green_f, green_psd, 'g')
xmax, xmin, ymax, ymin = pyplot.axis()
diff --git a/bob/rppg/base/utils.py b/bob/rppg/base/utils.py
index 9b64fae8388a04d066d79c4ae7248b896ab8c3bf..9250c421169f4fe4e75d67a732eb63707bcd3d37 100644
--- a/bob/rppg/base/utils.py
+++ b/bob/rppg/base/utils.py
@@ -99,3 +99,67 @@ def build_bandpass_filter(fs, order, plot=False):
pyplot.show()
return b
+
+
+def get_parameter(args, configuration, keyword, default):
+ """ Get the right value for a parameter
+
+ The parameters are either defined in a separate configuration file
+ or given directly via command-line. Note that the command-line
+ has priority over the configuration file.
+
+ As a convention, parameters made with more than one word
+ are provided with an underscore in the configuration file, and with an
+ hyphen in the command-line:
+
+ - configuration: batch_size=64
+ - command line: --batch-size=64
+
+ Parameters
+ ----------
+ args: dictionary
+ The arguments as parsed from the command line.
+ configuration: object
+ The arguments given by the configuration file.
+ keyword: string
+ the keyword for the parameter to process (in the "configuration" style)
+ default:
+ The default value of the parameter
+
+ Returns
+ -------
+ arg:
+ The right value for the given keyword argument
+
+ """
+
+ # get the keyword in a "docopt" friendly format
+ args_kw = '--' + keyword.replace('_', '-')
+
+ # get the type of this argument
+ _type = type(default)
+
+ # get the default value
+ arg_default = default
+
+ # get the argument in the configuration file
+ if hasattr(configuration, keyword):
+ arg_config = getattr(configuration, keyword)
+ else:
+ arg_config = None
+
+ # get the argument from the command-line
+ if default is not None:
+ arg_command = _type(args[args_kw])
+ else:
+ arg_command = default
+
+ # if the argument was not specified in the config file
+ if not hasattr(configuration, keyword):
+ return arg_command
+ else:
+ if (arg_command == arg_default):
+ return arg_config
+ else:
+ return arg_command
+
diff --git a/bob/rppg/chrom/script/extract_pulse.py b/bob/rppg/chrom/script/extract_pulse.py
index dc0dbe4e682a7ccf1f3aeee363c5402931f3901b..26e0fcb8ebd7fa2785aa0e82f8ae62376d7c43d7 100644
--- a/bob/rppg/chrom/script/extract_pulse.py
+++ b/bob/rppg/chrom/script/extract_pulse.py
@@ -4,8 +4,9 @@
"""Pulse extraction using CHROM algorithm (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--dbdir=<path>] [--outdir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--pulsedir=<path>]
[--start=<int>] [--end=<int>] [--motion=<float>]
[--threshold=<float>] [--skininit]
[--framerate=<int>] [--order=<int>]
@@ -22,9 +23,7 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -d, --dbdir=<path> The path to the database on your disk. If not set,
- defaults to Idiap standard locations.
- -o, --outdir=<path> The path to the directory where signal extracted
+ -o, --pulsedir=<path> The path to the directory where signal extracted
from the face area will be stored [default: pulse]
--start=<int> Starting frame index [default: 0].
--end=<int> End frame index [default: 0].
@@ -48,9 +47,9 @@ Options:
Example:
- To run the pulse extraction for the cohface database
+ To run the pulse extraction
- $ %(prog)s cohface -v
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -66,6 +65,9 @@ logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ...base.utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -93,45 +95,35 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ pulsedir = get_parameter(args, configuration, 'pulsedir', 'pulse')
+ start = get_parameter(args, configuration, 'start', 0)
+ end = get_parameter(args, configuration, 'end', 0)
+ motion = get_parameter(args, configuration, 'motion', 0.0)
+ threshold = get_parameter(args, configuration, 'threshold', 0.5)
+ skininit = get_parameter(args, configuration, 'skininit', False)
+ framerate = get_parameter(args, configuration, 'framerate', 61)
+ order = get_parameter(args, configuration, 'order', 128)
+ window = get_parameter(args, configuration, 'window', 0)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
- set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--dbdir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--dbdir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--dbdir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--dbdir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ set_verbosity_level(logger, verbosity_level)
+
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# if we are on a grid environment, just find what I have to process.
sge = False
@@ -146,33 +138,33 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
sys.exit()
# build the bandpass filter one and for all
- bandpass_filter = build_bandpass_filter(float(args['--framerate']), int(args['--order']), bool(args['--plot']))
+ bandpass_filter = build_bandpass_filter(framerate, order, plot)
# does the actual work - for every video in the available dataset,
# extract the signals and dumps the results to the corresponding directory
for obj in objects:
# expected output file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(pulsedir, '.hdf5')
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load video
- video = obj.load_video(dbdir)
+ video = obj.load_video(configuration.dbdir)
logger.info("Processing input video from `%s'...", video.filename)
# indices where to start and to end the processing
logger.debug("Sequence length = {0}".format(len(video)))
- start_index = int(args['--start'])
- end_index = int(args['--end'])
+ start_index = start
+ end_index = end
if (end_index == 0):
end_index = len(video)
if end_index > len(video):
@@ -185,7 +177,7 @@ def main(user_input=None):
nb_frames = end_index - start_index
# the grayscale difference between two consecutive frames (for stable frame selection)
- if bool(args['--motion']):
+ if motion:
diff_motion = numpy.zeros((nb_frames-1, 1), dtype='float64')
# load the result of face detection
@@ -211,24 +203,24 @@ def main(user_input=None):
bbox, quality = bob.ip.facedetect.detect_single_face(frame)
# motion difference (if asked for)
- if float(args['--motion']) > 0 and (i < (len(video) - 1)) and (counter > 0):
+ if motion > 0 and (i < (len(video) - 1)) and (counter > 0):
current = crop_face(frame, bbox, bbox.size[1])
diff_motion[counter-1] = compute_gray_diff(face, current)
face = crop_face(frame, bbox, bbox.size[1])
- if bool(args['--plot']) and args['--verbose'] >= 2:
+ if plot and verbosity_level >= 2:
from matplotlib import pyplot
pyplot.imshow(numpy.rollaxis(numpy.rollaxis(face, 2),2))
pyplot.show()
# skin filter
- if counter == 0 or bool(args['--skininit']):
+ if counter == 0 or skininit:
skin_filter.estimate_gaussian_parameters(face)
logger.debug("Skin color parameters:\nmean\n{0}\ncovariance\n{1}".format(skin_filter.mean, skin_filter.covariance))
- skin_mask = skin_filter.get_skin_mask(face, float(args['--threshold']))
+ skin_mask = skin_filter.get_skin_mask(face, threshold)
- if bool(args['--plot']) and args['--verbose'] >= 2:
+ if plot and verbosity_level >= 2:
from matplotlib import pyplot
skin_mask_image = numpy.copy(face)
skin_mask_image[:, skin_mask] = 255
@@ -260,14 +252,14 @@ def main(user_input=None):
break
# select the most stable number of consecutive frames, if asked for
- if float(args['--motion']) > 0:
- n_stable_frames_to_keep = int(float(args['--motion']) * nb_frames)
+ if motion > 0:
+ n_stable_frames_to_keep = int(motion * nb_frames)
logger.info("Number of stable frames kept for motion -> {0}".format(n_stable_frames_to_keep))
index = select_stable_frames(diff_motion, n_stable_frames_to_keep)
logger.info("Stable segment -> {0} - {1}".format(index, index + n_stable_frames_to_keep))
chrom = chrom[index:(index + n_stable_frames_to_keep),:]
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(2, sharex=True)
axarr[0].plot(range(chrom.shape[0]), chrom[:, 0], 'k')
@@ -283,7 +275,7 @@ def main(user_input=None):
x_bandpassed = filtfilt(bandpass_filter, numpy.array([1]), chrom[:, 0])
y_bandpassed = filtfilt(bandpass_filter, numpy.array([1]), chrom[:, 1])
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(2, sharex=True)
axarr[0].plot(range(x_bandpassed.shape[0]), x_bandpassed, 'k')
@@ -297,8 +289,8 @@ def main(user_input=None):
pulse = x_bandpassed - alpha * y_bandpassed
# overlap-add if window_size != 0
- if int(args['--window']) > 0:
- window_size = int(args['--window'])
+ if window > 0:
+ window_size = window
window_stride = window_size / 2
for w in range(0, (len(pulse)-window_size), window_stride):
pulse[w:w+window_size] = 0.0
@@ -309,7 +301,7 @@ def main(user_input=None):
sw *= numpy.hanning(window_size)
pulse[w:w+window_size] += sw
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(1)
pyplot.plot(range(pulse.shape[0]), pulse, 'k')
diff --git a/bob/rppg/chrom/script/extract_pulse_from_mask.py b/bob/rppg/chrom/script/extract_pulse_from_mask.py
index 0ae3748474c4ef850b6f31ce86614b474223cadd..15cfac0259bccde1a355efec6059daca51f50493 100644
--- a/bob/rppg/chrom/script/extract_pulse_from_mask.py
+++ b/bob/rppg/chrom/script/extract_pulse_from_mask.py
@@ -4,8 +4,9 @@
"""Pulse extraction using CHROM algorithm (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--dbdir=<path>] [--pulsedir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--pulsedir=<path>]
[--npoints=<int>] [--indent=<int>] [--quality=<float>] [--distance=<int>]
[--framerate=<int>] [--order=<int>] [--window=<int>]
[--overwrite] [--verbose ...] [--plot] [--gridcount]
@@ -20,10 +21,8 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -d, --dbdir=<path> The path to the database on your disk. If not set,
- defaults to Idiap standard locations.
- -f, --pulsedir=<path> The path to the directory where signal extracted
- from the face area will be stored [default: face]
+ -o, --pulsedir=<path> The path to the directory where signal extracted
+ from the face area will be stored [default: pulse].
-n, --npoints=<int> Number of good features to track [default: 40]
-i, --indent=<int> Indent (in percent of the face width) to apply to
keypoints to get the mask [default: 10]
@@ -46,9 +45,9 @@ Options:
Example:
- To run the pulse extractor for the cohface database
+ To run the pulse extraction
- $ %(prog)s cohface -v
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -64,6 +63,9 @@ logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ...base.utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -97,46 +99,35 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ pulsedir = get_parameter(args, configuration, 'pulsedir', 'pulse')
+ npoints = get_parameter(args, configuration, 'npoints', 40)
+ indent = get_parameter(args, configuration, 'indent', 10)
+ quality = get_parameter(args, configuration, 'quality', 0.01)
+ distance = get_parameter(args, configuration, 'distance', 10)
+ framerate = get_parameter(args, configuration, 'framerate', 61)
+ order = get_parameter(args, configuration, 'order', 128)
+ window = get_parameter(args, configuration, 'window', 0)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
- set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ set_verbosity_level(logger, verbosity_level)
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
+
# if we are on a grid environment, just find what I have to process.
sge = False
try:
@@ -150,27 +141,27 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
sys.exit()
# build the bandpass filter one and for all
- bandpass_filter = build_bandpass_filter(float(args['--framerate']), int(args['--order']), bool(args['--plot']))
+ bandpass_filter = build_bandpass_filter(framerate, order, plot)
# does the actual work - for every video in the available dataset,
# extract the signals and dumps the results to the corresponding directory
for obj in objects:
# expected output file
- output = obj.make_path(args['--pulsedir'], '.hdf5')
+ output = obj.make_path(pulsedir, '.hdf5')
# if output exists and not overwriting, skip this file
- if (os.path.exists(output)) and not args['--overwrite']:
+ if (os.path.exists(output)) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load video
- video = obj.load_video(dbdir)
+ video = obj.load_video(configuration.dbdir)
logger.info("Processing input video from `%s'...", video.filename)
# number of frames
@@ -194,7 +185,7 @@ def main(user_input=None):
# -> detect the face
# -> get "good features" inside the face
kpts = obj.load_drmf_keypoints()
- mask_points, mask = kp66_to_mask(frame, kpts, int(args['--indent']), bool(args['--plot']))
+ mask_points, mask = kp66_to_mask(frame, kpts, int(indent), plot)
try:
bbox = bounding_boxes[i]
@@ -204,8 +195,7 @@ def main(user_input=None):
# define the face width for the whole sequence
facewidth = bbox.size[1]
face = crop_face(frame, bbox, facewidth)
- good_features = get_good_features_to_track(face,int(args['--npoints']),
- float(args['--quality']), int(args['--distance']), bool(args['--plot']))
+ good_features = get_good_features_to_track(face,npoints, quality, distance, plot)
else:
# subsequent frames:
# -> crop the face with the bounding_boxes of the previous frame (so
@@ -215,7 +205,7 @@ def main(user_input=None):
# current corners
# -> apply this transformation to the mask
face = crop_face(frame, prev_bb, facewidth)
- good_features = track_features(prev_face, face, prev_features, bool(args['--plot']))
+ good_features = track_features(prev_face, face, prev_features, plot)
project = find_transformation(prev_features, good_features)
if project is None:
logger.warn("Sequence {0}, frame {1} : No projection was found"
@@ -235,9 +225,7 @@ def main(user_input=None):
prev_bb = bb
prev_face = crop_face(frame, prev_bb, facewidth)
- prev_features = get_good_features_to_track(face, int(args['--npoints']),
- float(args['--quality']), int(args['--distance']),
- bool(args['--plot']))
+ prev_features = get_good_features_to_track(face, npoints, quality, distance, plot)
if prev_features is None:
logger.warn("Sequence {0}, frame {1} No features to track"
" detected in the current frame, using the previous ones"
@@ -246,7 +234,7 @@ def main(user_input=None):
# get the mask
face_mask = get_mask(frame, mask_points)
- if bool(args['--plot']) and args['--verbose'] >= 2:
+ if plot and verbosity_level >= 2:
from matplotlib import pyplot
mask_image = numpy.copy(frame)
mask_image[:, face_mask] = 255
@@ -267,7 +255,7 @@ def main(user_input=None):
x_bandpassed = filtfilt(bandpass_filter, numpy.array([1]), chrom[:, 0])
y_bandpassed = filtfilt(bandpass_filter, numpy.array([1]), chrom[:, 1])
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(2, sharex=True)
axarr[0].plot(range(x_bandpassed.shape[0]), x_bandpassed, 'k')
@@ -281,8 +269,8 @@ def main(user_input=None):
pulse = x_bandpassed - alpha * y_bandpassed
# overlap-add if window_size != 0
- if int(args['--window']) > 0:
- window_size = int(args['--window'])
+ if int(window) > 0:
+ window_size = int(window)
window_stride = window_size / 2
for w in range(0, (len(pulse)-window_size), window_stride):
pulse[w:w+window_size] = 0.0
@@ -293,7 +281,7 @@ def main(user_input=None):
sw *= numpy.hanning(window_size)
pulse[w:w+window_size] += sw
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(1)
pyplot.plot(range(pulse.shape[0]), pulse, 'k')
diff --git a/bob/rppg/cvpr14/extract_utils.py b/bob/rppg/cvpr14/extract_utils.py
index 56c9664ca012c07d12daf2cc61649640558dfa6b..0015fa3c638370b5f22fce67476a9b2698002e22 100644
--- a/bob/rppg/cvpr14/extract_utils.py
+++ b/bob/rppg/cvpr14/extract_utils.py
@@ -19,9 +19,9 @@ def kp66_to_mask(image, keypoints, indent=10, plot=False):
Note also that this function is explicitly made for the
keypoints set generated by the Matlab software downloaded
from http://ibug.doc.ic.ac.uk/resources/drmf-matlab-code-cvpr-2013/
-
- If you decide to use another keypoint detector, you may need to
- rewrite a function to build the mask from your keypoints.
+
+ Update: this function also works when using
+ :py:class:`bob.ip.dlib.DlibLandmarkExtraction`
Parameters
----------
@@ -48,7 +48,7 @@ def kp66_to_mask(image, keypoints, indent=10, plot=False):
The points corresponding to vertices of the mask.
"""
- assert keypoints.shape[0] == 66, "You should provide a set 66 keypoints"
+ assert keypoints.shape[0] == 66 or keypoints.shape[0] == 68, "You should provide a set of 66 (DRMF) or 68 (dlib ) keypoints"
if plot:
imkey = numpy.copy(image)
@@ -104,6 +104,7 @@ def get_mask(image, mask_points):
It turns mask points into a region of interest and returns the
corresponding boolean array, of the same size as the image.
+
Taken from https://github.com/jdoepfert/roipoly.py/blob/master/roipoly.py
Parameters
diff --git a/bob/rppg/cvpr14/script/extract_signals.py b/bob/rppg/cvpr14/script/extract_face_and_bg_signals.py
similarity index 69%
rename from bob/rppg/cvpr14/script/extract_signals.py
rename to bob/rppg/cvpr14/script/extract_face_and_bg_signals.py
index 6b8bf5da8fe332a9eff9f0e8b9d784b3cbad55cc..51f5d18c809e51008aa6db0a6377f0da811f86c3 100644
--- a/bob/rppg/cvpr14/script/extract_signals.py
+++ b/bob/rppg/cvpr14/script/extract_face_and_bg_signals.py
@@ -1,14 +1,14 @@
#!/usr/bin/env python
# encoding: utf-8
-"""Extract mean green color on face and background regions
+"""Extract pulses according to Li's CVPR 2014 algorithm
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--dbdir=<path>] [--facedir=<path>] [--bgdir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--facedir=<path>] [--bgdir=<path>]
[--npoints=<int>] [--indent=<int>] [--quality=<float>] [--distance=<int>]
- [--wholeface]
- [--overwrite] [--verbose ...] [--plot] [--gridcount]
+ [--wholeface] [--overwrite] [--verbose ...] [--plot] [--gridcount]
%(prog)s (--help | -h)
%(prog)s (--version | -V)
@@ -19,9 +19,7 @@ Options:
-V, --version Show version
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
- all the data sets will be loaded.
- -d, --dbdir=<path> The path to the database on your disk. If not set,
- defaults to Idiap standard locations.
+ all the sets will be loaded.
-f, --facedir=<path> The path to the directory where signal extracted
from the face area will be stored [default: face]
-b, --bgdir=<path> The path to the directory where signal extracted
@@ -45,9 +43,9 @@ Options:
Example:
- To run the signal extractor for the cohface database
+ To run the pulse extractor:
- $ %(prog)s cohface -v
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -59,12 +57,14 @@ import os
import sys
import pkg_resources
-from bob.core.log import set_verbosity_level
from bob.core.log import setup
logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ...base.utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -94,46 +94,34 @@ def main(user_input=None):
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
- set_verbosity_level(logger, args['--verbose'])
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ facedir = get_parameter(args, configuration, 'facedir', 'face')
+ bgdir = get_parameter(args, configuration, 'bgdir', 'bg')
+ npoints = get_parameter(args, configuration, 'npoints', 40)
+ indent = get_parameter(args, configuration, 'indent', 10)
+ quality = get_parameter(args, configuration, 'quality', 0.01)
+ distance = get_parameter(args, configuration, 'distance', 10)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ wholeface = get_parameter(args, configuration, 'wholeface', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
- # TODO: change that to configuration file - Guillaume HEUSCH, 19-06-2018
+ # if the user wants more verbosity, lowers the logging level
+ from bob.core.log import set_verbosity_level
+ set_verbosity_level(logger, verbosity_level)
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--dbdir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--dbdir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--dbdir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--dbdir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ # TODO: find a way to check protocol names - Guillaume HEUSCH, 22-06-2018
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# if we are on a grid environment, just find what I have to process.
sge = False
@@ -148,7 +136,7 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
sys.exit()
@@ -157,16 +145,16 @@ def main(user_input=None):
for obj in objects:
# expected output file
- output_face = obj.make_path(args['--facedir'], '.hdf5')
- output_bg = obj.make_path(args['--bgdir'], '.hdf5')
+ output_face = obj.make_path(facedir, '.hdf5')
+ output_bg = obj.make_path(bgdir, '.hdf5')
# if output exists and not overwriting, skip this file
- if (os.path.exists(output_face) and os.path.exists(output_bg)) and not args['--overwrite']:
+ if (os.path.exists(output_face) and os.path.exists(output_bg)) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output_face)
continue
# load video
- video = obj.load_video(dbdir)
+ video = obj.load_video(configuration.dbdir)
logger.info("Processing input video from `%s'...", video.filename)
# load the result of face detection
@@ -187,9 +175,9 @@ def main(user_input=None):
# -> infer the mask from the keypoints
# -> detect the face
# -> get "good features" inside the face
- if not bool(args['--wholeface']):
+ if not wholeface:
kpts = obj.load_drmf_keypoints()
- mask_points, mask = kp66_to_mask(frame, kpts, int(args['--indent']), bool(args['--plot']))
+ mask_points, mask = kp66_to_mask(frame, kpts, indent, plot)
try:
bbox = bounding_boxes[i]
@@ -200,9 +188,8 @@ def main(user_input=None):
facewidth = bbox.size[1]
face = crop_face(frame, bbox, facewidth)
- if not bool(args['--wholeface']):
- good_features = get_good_features_to_track(face,int(args['--npoints']),
- float(args['--quality']), int(args['--distance']), bool(args['--plot']))
+ if not wholeface:
+ good_features = get_good_features_to_track(face, npoints, quality, distance, plot)
else:
# subsequent frames:
# -> crop the face with the bounding_boxes of the previous frame (so
@@ -212,8 +199,8 @@ def main(user_input=None):
# current corners
# -> apply this transformation to the mask
face = crop_face(frame, prev_bb, facewidth)
- if not bool(args['--wholeface']):
- good_features = track_features(prev_face, face, prev_features, bool(args['--plot']))
+ if not wholeface:
+ good_features = track_features(prev_face, face, prev_features, plot)
project = find_transformation(prev_features, good_features)
if project is None:
logger.warn("Sequence {0}, frame {1} : No projection was found"
@@ -233,11 +220,9 @@ def main(user_input=None):
prev_bb = bb
- if not bool(args['--wholeface']):
+ if not wholeface:
prev_face = crop_face(frame, prev_bb, facewidth)
- prev_features = get_good_features_to_track(face, int(args['--npoints']),
- float(args['--quality']), int(args['--distance']),
- bool(args['--plot']))
+ prev_features = get_good_features_to_track(face, npoints, quality, distance, plot)
if prev_features is None:
logger.warn("Sequence {0}, frame {1} No features to track"
" detected in the current frame, using the previous ones"
@@ -246,14 +231,14 @@ def main(user_input=None):
# get the bottom face region average colors
face_mask = get_mask(frame, mask_points)
- face_color[i] = compute_average_colors_mask(frame, face_mask, bool(args['--plot']))
+ face_color[i] = compute_average_colors_mask(frame, face_mask, plot)
else:
- face_color[i] = compute_average_colors_wholeface(face, bool(args['--plot']))
+ face_color[i] = compute_average_colors_wholeface(face, plot)
# get the background region average colors
bg_mask = numpy.zeros((frame.shape[1], frame.shape[2]), dtype=bool)
bg_mask[:100, :100] = True
- bg_color[i] = compute_average_colors_mask(frame, bg_mask, bool(args['--plot']))
+ bg_color[i] = compute_average_colors_mask(frame, bg_mask, plot)
# saves the data into an HDF5 file with a '.hdf5' extension
out_facedir = os.path.dirname(output_face)
diff --git a/bob/rppg/cvpr14/script/filter.py b/bob/rppg/cvpr14/script/filter.py
index d4a165c296e9665856173dc6ab4d0a118306b3a7..1ff143d6bd524ed40949309e531e3bd8e2402ccd 100644
--- a/bob/rppg/cvpr14/script/filter.py
+++ b/bob/rppg/cvpr14/script/filter.py
@@ -1,12 +1,13 @@
#!/usr/bin/env python
# encoding: utf-8
-"""Filtering of color signal (%(version)s)
+"""Filtering (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--verbose ...] [--plot] [--indir=<path>] [--outdir=<path>]
- [--lambda=<int>] [--window=<int>] [--framerate=<int>] [--order=<int>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--verbose ...] [--plot] [--motiondir=<path>] [--pulsedir=<path>]
+ [--Lambda=<int>] [--window=<int>] [--framerate=<int>] [--order=<int>]
[--overwrite] [--gridcount]
%(prog)s (--help | -h)
@@ -22,11 +23,11 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -i, --indir=<path> The path to the saved signals to be filtered on
+ -i, --motiondir=<path> The path to the saved signals to be filtered on
your disk [default: motion].
- -o, --outdir=<path> The path to the output directory where the resulting
+ -o, --pulsedir=<path> The path to the output directory where the resulting
color signals will be stored [default: filtered].
- --lambda=<int> Lambda parameter for detrending (see article) [default: 300]
+ --Lambda=<int> Lambda parameter for detrending (see article) [default: 300]
--window=<int> Moving window length [default: 23]
-f, --framerate=<int> Frame-rate of the video sequence [default: 61]
--order=<int> Bandpass filter order [default: 128]
@@ -37,13 +38,9 @@ Options:
Examples:
- To run the filters on the cohface database
+ To run the filters
- $ %(prog)s cohface -v
-
- You can change the output directory using the `-o' flag:
-
- $ %(prog)s hci -v -o /path/to/result/directory
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -67,6 +64,8 @@ logger = bob.core.log.setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -75,6 +74,7 @@ import bob.io.base
from ..filter_utils import detrend
from ..filter_utils import average
from ...base.utils import build_bandpass_filter
+from ...base.utils import get_parameter
def main(user_input=None):
@@ -88,45 +88,33 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Filtering for signals (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ motiondir = get_parameter(args, configuration, 'motiondir', 'motion')
+ pulsedir = get_parameter(args, configuration, 'pulsedir', 'pulse')
+ Lambda = get_parameter(args, configuration, 'Lambda', 300)
+ window = get_parameter(args, configuration, 'window', 23)
+ framerate = get_parameter(args, configuration, 'framerate', 61)
+ order = get_parameter(args, configuration, 'order', 128)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
- set_verbosity_level(logger, args['--verbose'])
+ set_verbosity_level(logger, verbosity_level)
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ # TODO: find a way to check protocol names - Guillaume HEUSCH, 22-06-2018
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# if we are on a grid environment, just find what I have to process.
sge = False
@@ -141,12 +129,12 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
sys.exit()
# build the bandpass filter one and for all
- b = build_bandpass_filter(float(args['--framerate']), int(args['--order']), bool(args['--plot']))
+ b = build_bandpass_filter(framerate, order, plot)
################
### LET'S GO ###
@@ -154,16 +142,16 @@ def main(user_input=None):
for obj in objects:
# expected output file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(pulsedir, '.hdf5')
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load the corrected color signals of shape (3, nb_frames)
logger.info("Filtering in signal from `%s'...", obj.path)
- motion_file = obj.make_path(args['--indir'], '.hdf5')
+ motion_file = obj.make_path(motiondir, '.hdf5')
try:
motion_corrected_signal = bob.io.base.load(motion_file)
except (IOError, RuntimeError) as e:
@@ -177,15 +165,15 @@ def main(user_input=None):
continue
# detrend
- green_detrend = detrend(motion_corrected_signal, int(args['--lambda']))
+ green_detrend = detrend(motion_corrected_signal, Lambda)
# average
- green_averaged = average(green_detrend, int(args['--window']))
+ green_averaged = average(green_detrend, window)
# bandpass
from scipy.signal import filtfilt
green_bandpassed = filtfilt(b, numpy.array([1]), green_averaged)
# plot the result
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, ax = pyplot.subplots(4, sharex=True)
ax[0].plot(range(motion_corrected_signal.shape[0]), motion_corrected_signal, 'g')
@@ -201,8 +189,8 @@ def main(user_input=None):
output_data = numpy.copy(green_bandpassed)
# saves the data into an HDF5 file with a '.hdf5' extension
- outdir = os.path.dirname(output)
- if not os.path.exists(outdir): bob.io.base.create_directories_safe(outdir)
+ pulse_outdir = os.path.dirname(output)
+ if not os.path.exists(pulse_outdir): bob.io.base.create_directories_safe(pulse_outdir)
bob.io.base.save(output_data, output)
logger.info("Output file saved to `%s'...", output)
diff --git a/bob/rppg/cvpr14/script/illumination_rectification.py b/bob/rppg/cvpr14/script/illumination_rectification.py
index 25470a38a059cd35308b546d2b94d52da42a35dd..38049ce1cedc9258f051b1cec8cae9963de1609a 100644
--- a/bob/rppg/cvpr14/script/illumination_rectification.py
+++ b/bob/rppg/cvpr14/script/illumination_rectification.py
@@ -1,14 +1,15 @@
#!/usr/bin/env python
# encoding: utf-8
-"""Illumination rectification for database videos (%(version)s)
+"""Illumination rectification (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--verbose ...] [--plot]
- [--facedir=<path>][--bgdir=<path>] [--outdir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--facedir=<path>][--bgdir=<path>] [--illumdir=<path>]
[--start=<int>] [--end=<int>] [--step=<float>]
[--length=<int>] [--overwrite] [--gridcount]
+ [--verbose ...] [--plot]
%(prog)s (--help | -h)
%(prog)s (--version | -V)
@@ -27,7 +28,7 @@ Options:
green color on the face region [default: face].
-b, --bgdir=<path> The path to the directory containing the average
green color on the background [default: background]
- -o, --outdir=<path> The path to the output directory where the resulting
+ -o, --illumdir=<path> The path to the output directory where the resulting
corrected signal will be stored [default: illumination]
-s, --start=<int> Index of the starting frame [default: 0].
-e, --end=<int> Index of the ending frame. If set to zero, the
@@ -41,13 +42,9 @@ Options:
Examples:
- To run the illumination rectification on the hci database
-
- $ %(prog)s hci -v
-
- You can change the output directory using the `-o' flag:
+ To run the illumination rectification
- $ %(prog)s hci -v -o /path/to/result/directory
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -65,11 +62,14 @@ logger = bob.core.log.setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
import bob.io.base
+from ...base.utils import get_parameter
from ..illum_utils import rectify_illumination
def main(user_input=None):
@@ -84,46 +84,34 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Illumination rectification for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ facedir = get_parameter(args, configuration, 'facedir', 'face')
+ bgdir = get_parameter(args, configuration, 'bgdir', 'bg')
+ illumdir = get_parameter(args, configuration, 'illumdir', 'illumination')
+ start = get_parameter(args, configuration, 'start', 0)
+ end = get_parameter(args, configuration, 'end', 0)
+ step = get_parameter(args, configuration, 'step', 0.05)
+ length = get_parameter(args, configuration, 'length', 1)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
- set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--facedir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--facedir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--facedir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--facedir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ set_verbosity_level(logger, verbosity_level)
+ # TODO: find a way to check protocol names - Guillaume HEUSCH, 22-06-2018
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# if we are on a grid environment, just find what I have to process.
sge = False
@@ -138,7 +126,7 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
sys.exit()
@@ -148,16 +136,16 @@ def main(user_input=None):
for obj in objects:
# expected output file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(illumdir, '.hdf5')
logger.debug("expected output file -> {0}".format(output))
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load the color signal of the face
- face_file = obj.make_path(args['--facedir'], '.hdf5')
+ face_file = obj.make_path(facedir, '.hdf5')
try:
face = bob.io.base.load(face_file)
except (IOError, RuntimeError) as e:
@@ -165,7 +153,7 @@ def main(user_input=None):
continue
# load the color signal of the background
- bg_file = obj.make_path(args['--bgdir'], '.hdf5')
+ bg_file = obj.make_path(bgdir, '.hdf5')
try:
bg = bob.io.base.load(bg_file)
except (IOError, RuntimeError) as e:
@@ -174,8 +162,8 @@ def main(user_input=None):
# indices where to start and to end the processing
logger.debug("Sequence length = {0}".format(face.shape[0]))
- start_index = int(args['--start'])
- end_index = int(args['--end'])
+ start_index = start
+ end_index = end
if (end_index == 0):
end_index = face.shape[0]
if end_index > face.shape[0]:
@@ -190,9 +178,9 @@ def main(user_input=None):
logger.debug("Processing %d frames...", face.shape[0])
# apply NLMS filtering
- corrected_green = rectify_illumination(face, bg, float(args['--step']), int(args['--length']))
+ corrected_green = rectify_illumination(face, bg, step, length)
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(3, sharex=True)
axarr[0].plot(range(face.shape[0]), face, 'g')
@@ -204,8 +192,8 @@ def main(user_input=None):
pyplot.show()
# saves the data into an HDF5 file with a '.hdf5' extension
- outdir = os.path.dirname(output)
- if not os.path.exists(outdir): bob.io.base.create_directories_safe(outdir)
+ outputdir = os.path.dirname(output)
+ if not os.path.exists(outputdir): bob.io.base.create_directories_safe(outputdir)
bob.io.base.save(corrected_green, output)
logger.info("Output file saved to `%s'...", output)
diff --git a/bob/rppg/cvpr14/script/motion_elimination.py b/bob/rppg/cvpr14/script/motion_elimination.py
index 374c76d5ea70fd4b6001601036f495d8a0ea133a..5e2f938a27f7621bccf71a2691970beb8a6c4765 100644
--- a/bob/rppg/cvpr14/script/motion_elimination.py
+++ b/bob/rppg/cvpr14/script/motion_elimination.py
@@ -1,11 +1,12 @@
#!/usr/bin/env python
# encoding: utf-8
-"""Non Rigid Motion Elimination for color signals (%(version)s)
+"""Non Rigid Motion Elimination (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--verbose ...] [--plot] [--indir=<path>] [--outdir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--verbose ...] [--plot] [--illumdir=<path>] [--motiondir=<path>]
[--seglength=<int>] [--save-threshold=<path>] [--load-threshold=<path>]
[--cutoff=<float>] [--cvpr14] [--overwrite]
@@ -22,9 +23,9 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -i, --indir=<path> The path to the saved illumination corrected signal
+ -i, --illumdir=<path> The path to the saved illumination corrected signal
on your disk [default: illumination].
- -o, --outdir=<path> The path to the output directory where the resulting
+ -o, --motiondir=<path> The path to the output directory where the resulting
motion corrected signals will be stored
[default: motion].
-L, --seglength=<int> The length of the segments [default: 61]
@@ -43,17 +44,9 @@ Options:
Examples:
- To run the motion elimination for the cohface database
+ To run the motion elimination
- $ %(prog)s cohface -v
-
- To just run a preliminary benchmark tests on the first 10 videos, do:
-
- $ %(prog)s cohface -v -l 10
-
- You can change the output directory using the `-o' flag:
-
- $ %(prog)s hci -v -o /path/to/result/directory
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -69,11 +62,14 @@ logger = bob.core.log.setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
import bob.io.base
+from ...base.utils import get_parameter
from ..motion_utils import build_segments
from ..motion_utils import prune_segments
from ..motion_utils import build_final_signal
@@ -91,55 +87,44 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Non-rigid motion elimination for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ illumdir = get_parameter(args, configuration, 'illumdir', 'illumination')
+ motiondir = get_parameter(args, configuration, 'motiondir', 'motion')
+ seglength = get_parameter(args, configuration, 'seglength', 61)
+ cutoff = get_parameter(args, configuration, 'cutoff', 0.05)
+ save_threshold = get_parameter(args, configuration, 'save-threshold', 'threshold.txt')
+ load_threshold = get_parameter(args, configuration, 'load-threshold', '')
+ cvpr14 = get_parameter(args, configuration, 'cvpr14', False)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
+ print(load_threshold)
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
set_verbosity_level(logger, args['--verbose'])
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ # TODO: find a way to check protocol names - Guillaume HEUSCH, 22-06-2018
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# determine the threshold for the standard deviation to be applied to the segments
# this part is not executed if a threshold is provided
- if (args['--load-threshold']) == 'None':
+ if load_threshold == 'None':
all_stds = []
for obj in objects:
# load the llumination corrected signal
logger.debug("Computing standard deviations in color signals from `%s'...", obj.path)
- illum_file = obj.make_path(args['--indir'], '.hdf5')
+ illum_file = obj.make_path(illumdir, '.hdf5')
try:
color = bob.io.base.load(illum_file)
except (IOError, RuntimeError) as e:
@@ -152,7 +137,7 @@ def main(user_input=None):
continue
# get the standard deviation in the segments
- green_segments, __ = build_segments(color, int(args['--seglength']))
+ green_segments, __ = build_segments(color, seglength)
std_green = numpy.std(green_segments, 1, ddof=1)
all_stds.extend(std_green.tolist())
@@ -160,34 +145,34 @@ def main(user_input=None):
# sort the std and find the 5% at the top to get the threshold
sorted_stds = sorted(all_stds, reverse=True)
- cut_index = int(float(args['--cutoff']) * len(all_stds)) + 1
+ cut_index = int(cutoff * len(all_stds)) + 1
threshold = sorted_stds[cut_index]
- logger.info("The threshold was {0} (removing {1} percent of the largest segments)".format(threshold, 100*float(args['--cutoff'])))
+ logger.info("The threshold was {0} (removing {1} percent of the largest segments)".format(threshold, 100*cutoff))
# write threshold to file
- f = open(args['--save-threshold'], 'w')
+ f = open(save_threshold, 'w')
f.write(str(threshold))
f.close()
else:
# load threshold
- f = open(args['--load-threshold'], 'r')
+ f = open(load_threshold, 'r')
threshold = float(f.readline().rstrip())
# cut segments where the std is too large
for obj in objects:
# expected output file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(motiondir, '.hdf5')
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load the color signals
logger.debug("Eliminating motion in color signals from `%s'...", obj.path)
- illum_file = obj.make_path(args['--indir'], '.hdf5')
+ illum_file = obj.make_path(illumdir, '.hdf5')
try:
color = bob.io.base.load(illum_file)
except (IOError, RuntimeError) as e:
@@ -201,7 +186,7 @@ def main(user_input=None):
continue
# divide the signals into segments
- green_segments, end_index = build_segments(color, int(args['--seglength']))
+ green_segments, end_index = build_segments(color, seglength)
# remove segments with high variability
pruned_segments, gaps, cut_index = prune_segments(green_segments, threshold)
@@ -209,12 +194,12 @@ def main(user_input=None):
if pruned_segments.shape[0] == 0:
logger.warn("All segments have been discared in {0}".format(obj.path))
continue
- if bool(args['--cvpr14']):
+ if cvpr14:
corrected_green = build_final_signal_cvpr14(pruned_segments, gaps)
else:
corrected_green = build_final_signal(pruned_segments, gaps)
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(2, sharex=True)
axarr[0].plot(range(end_index), color[:end_index], 'g')
@@ -229,8 +214,8 @@ def main(user_input=None):
pyplot.show()
# saves the data into an HDF5 file with a '.hdf5' extension
- outdir = os.path.dirname(output)
- if not os.path.exists(outdir): bob.io.base.create_directories_safe(outdir)
+ outputdir = os.path.dirname(output)
+ if not os.path.exists(outputdir): bob.io.base.create_directories_safe(outputdir)
bob.io.base.save(corrected_green, output)
logger.info("Output file saved to `%s'...", output)
diff --git a/bob/rppg/cvpr14/script/video2skin.py b/bob/rppg/cvpr14/script/video2skin.py
index 6b8037512c992276981363cf2a24bd63b9b0f2c9..3a951e06c004e3018a6a30d05dae11ccb9930a59 100644
--- a/bob/rppg/cvpr14/script/video2skin.py
+++ b/bob/rppg/cvpr14/script/video2skin.py
@@ -4,9 +4,9 @@
"""Skin color extraction for database videos (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
+ %(prog)s <configuration> [--protocol=<string>] [--subset=<string> ...]
[--verbose ...] [--plot]
- [--dbdir=<path>] [--outdir=<path>]
+ [--skindir=<path>]
[--overwrite] [--threshold=<float>] [--skininit]
[--gridcount]
@@ -23,9 +23,7 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -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].
+ -o, --skindir=<path> Where the skin color will be stored [default: skin].
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
@@ -38,17 +36,7 @@ Options:
Examples:
- To run the skin color extraction on the hci database
-
- $ %(prog)s hci -v
-
- To just run a preliminary benchmark tests on the first 10 videos, do:
-
- $ %(prog)s cohface -v -l 10
-
- You can change the output directory using the `-f' r `-b' flags (see help):
-
- $ %(prog)s hci -v -f /path/to/result/face-directory
+ To run the skin color extraction
See '%(prog)s --help' for more information.
@@ -60,7 +48,6 @@ import os
import sys
import pkg_resources
-from bob.core.log import set_verbosity_level
from bob.core.log import setup
logger = setup("bob.rppg.base")
@@ -72,6 +59,9 @@ import numpy
import bob.io.base
import bob.ip.skincolorfilter
+from bob.extension.config import load
+from ...base.utils import get_parameter
+
from ...base.utils import crop_face
from ..extract_utils import compute_average_colors_mask
@@ -87,44 +77,34 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ skindir = get_parameter(args, configuration, 'skindir', 'skin')
+ threshold = get_parameter(args, configuration, 'threshold', 0.5)
+ skininit = get_parameter(args, configuration, 'skininit', False)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
+ print(protocol)
+ print(type(protocol))
+
# if the user wants more verbosity, lowers the logging level
- set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ from bob.core.log import set_verbosity_level
+ set_verbosity_level(logger, verbosity_level)
+
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
+
+ print(objects)
# if we are on a grid environment, just find what I have to process.
sge = False
@@ -139,7 +119,7 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
sys.exit()
@@ -149,15 +129,15 @@ def main(user_input=None):
for obj in objects:
# expected output face file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(skindir, '.hdf5')
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load the video sequence into a reader
- video = obj.load_video(dbdir)
+ video = obj.load_video(configuration.dbdir)
logger.info("Processing input video from `%s'...", video.filename)
logger.debug("Sequence length = {0}".format(video.number_of_frames))
@@ -180,12 +160,12 @@ def main(user_input=None):
face = crop_face(frame, bounding_boxes[i], facewidth)
# skin filter
- if i == 0 or bool(args['--skininit']):
+ if i == 0 or bool(skininit):
skin_filter.estimate_gaussian_parameters(face)
logger.debug("Skin color parameters:\nmean\n{0}\ncovariance\n{1}".format(skin_filter.mean, skin_filter.covariance))
- skin_mask = skin_filter.get_skin_mask(face, float(args['--threshold']))
+ skin_mask = skin_filter.get_skin_mask(face, threshold)
- if bool(args['--plot']) and i == 0:
+ if plot and i == 0:
from matplotlib import pyplot
skin_mask_image = numpy.copy(face)
skin_mask_image[:, skin_mask] = 255
@@ -201,7 +181,7 @@ def main(user_input=None):
else:
skin_colors[i] = skin_colors[i-1]
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
f, axarr = pyplot.subplots(3, sharex=True)
diff --git a/bob/rppg/ssr/script/spatial_subspace_rotation.py b/bob/rppg/ssr/script/spatial_subspace_rotation.py
index c74d23b3d85cbedbb4771d047c9c77fbaf41402f..f906bf25e1b69167793e828e18b8adcd8d3e4d34 100644
--- a/bob/rppg/ssr/script/spatial_subspace_rotation.py
+++ b/bob/rppg/ssr/script/spatial_subspace_rotation.py
@@ -4,9 +4,10 @@
"""Pulse extraction using 2SR algorithm (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
[--verbose ...] [--plot]
- [--dbdir=<path>] [--outdir=<path>]
+ [--pulsedir=<path>]
[--threshold=<float>] [--skininit]
[--stride=<int>] [--start=<int>] [--end=<int>]
[--overwrite] [--gridcount]
@@ -24,9 +25,7 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -D, --dbdir=<path> The path to the database on your disk. If not set,
- defaults to Idiap standard locations.
- -o, --outdir=<path> The path to the output directory where the resulting
+ -o, --pulsedir=<path> The path to the output directory where the resulting
pulse signal will be stored [default: pulse].
--threshold=<float> Threshold on the skin probability map [default: 0.5].
--skininit If you want to reinitialize the skin model at each frame.
@@ -42,13 +41,9 @@ Options:
Examples:
- To run the spatial subspace rotation on the hci database
+ To run the spatial subspace rotation algorithm
- $ %(prog)s hci -v
-
- You can change the output directory using the `-o' flag:
-
- $ %(prog)s hci -v -o /path/to/result/directory
+ $ %(prog)s config.py -v
See '%(prog)s --help' for more information.
@@ -65,6 +60,9 @@ logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ...base.utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -89,45 +87,32 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ pulsedir = get_parameter(args, configuration, 'pulsedir', 'pulse')
+ start = get_parameter(args, configuration, 'start', 0)
+ end = get_parameter(args, configuration, 'end', 0)
+ threshold = get_parameter(args, configuration, 'threshold', 0.5)
+ skininit = get_parameter(args, configuration, 'skininit', False)
+ stride = get_parameter(args, configuration, 'stride', 61)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
- set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--dbdir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--dbdir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--dbdir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--dbdir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ set_verbosity_level(logger, verbosity_level)
+
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
# if we are on a grid environment, just find what I have to process.
sge = False
@@ -142,28 +127,28 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
# does the actual work
for obj in objects:
# expected output file
- output = obj.make_path(args['--outdir'], '.hdf5')
+ output = obj.make_path(pulsedir, '.hdf5')
# if output exists and not overwriting, skip this file
- if os.path.exists(output) and not args['--overwrite']:
+ if os.path.exists(output) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load the video sequence into a reader
- video = obj.load_video(dbdir)
+ video = obj.load_video(configuration.dbdir)
logger.info("Processing input video from `%s'...", video.filename)
# indices where to start and to end the processing
logger.debug("Sequence length = {0}".format(len(video)))
- start_index = int(args['--start'])
- end_index = int(args['--end'])
+ start_index = int(start)
+ end_index = int(end)
if (end_index == 0):
end_index = len(video)
if end_index > len(video):
@@ -178,7 +163,7 @@ def main(user_input=None):
bounding_boxes = obj.load_face_detection()
# the temporal stride
- temporal_stride = int(args['--stride'])
+ temporal_stride = int(stride)
# the result -> the pulse signal
output_data = numpy.zeros(nb_final_frames, dtype='float64')
@@ -201,18 +186,14 @@ def main(user_input=None):
try:
if counter == 0:
# init skin parameters in any cases if it's the first frame
- skin_pixels = get_skin_pixels(frame, i,
- True, float(args['--threshold']), bounding_boxes)
+ skin_pixels = get_skin_pixels(frame, i, True, threshold, bounding_boxes)
else:
- skin_pixels = get_skin_pixels(frame, i,
- bool(args['--skininit']), float(args['--threshold']), bounding_boxes)
+ skin_pixels = get_skin_pixels(frame, i, skininit, threshold, bounding_boxes)
except NameError:
if counter == 0:
- skin_pixels = get_skin_pixels(frame, i,
- bool(args['--skininit']), float(args['--threshold']))
+ skin_pixels = get_skin_pixels(frame, i, skininit, threshold)
else:
- skin_pixels = get_skin_pixels(frame, i,
- bool(args['--skininit']), float(args['--threshold']))
+ skin_pixels = get_skin_pixels(frame, i, skininit, threshold)
logger.debug("There are {0} skin pixels in this frame".format(skin_pixels.shape[1]))
# no skin pixels detected, generally due to no face detection
@@ -223,11 +204,9 @@ def main(user_input=None):
while skin_pixels.shape[1] <= 0:
try:
- skin_pixels = get_skin_pixels(video[i-k], (i-k),
- bool(args['--skininit']), float(args['--threshold']), bounding_boxes, skin_frame=frame)
+ skin_pixels = get_skin_pixels(video[i-k], (i-k), skininit, threshold, bounding_boxes, skin_frame=frame)
except NameError:
- skin_pixels = get_skin_pixels(video[i-k], (i-k),
- bool(args['--skininit']), float(args['--threshold']), skin_frame=frame)
+ skin_pixels = get_skin_pixels(video[i-k], (i-k), skininit, threshold, skin_frame=frame)
k += 1
logger.warn("got skin pixels in frame {0}".format(i-k))
@@ -235,15 +214,14 @@ def main(user_input=None):
# build c matrix and get eigenvectors and eigenvalues
eigenvalues[:, counter], eigenvectors[:, :, counter] = get_eigen(skin_pixels)
-
# plot the cluster of skin pixels and eigenvectors (see Figure 1)
- if bool(args['--plot']) and args['--verbose'] >= 2:
+ if plot and verbosity_level >= 2:
plot_eigenvectors(skin_pixels, eigenvectors[:, :, counter])
# build P and add it to the pulse signal
if counter >= temporal_stride:
tau = counter - temporal_stride
- p = build_P(counter, int(args['--stride']), eigenvectors, eigenvalues)
+ p = build_P(counter, stride, eigenvectors, eigenvalues)
output_data[tau:counter] += (p - numpy.mean(p))
counter += 1
@@ -252,7 +230,7 @@ def main(user_input=None):
break
# plot the pulse signal
- if bool(args['--plot']):
+ if plot:
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
diff --git a/bob/rppg/ssr/script/ssr_from_mask.py b/bob/rppg/ssr/script/ssr_from_mask.py
index 944926a7a784c531154186880efec90060f2ddda..12fce13eec0c8889fd241b8f6a5d25f7a47138ad 100644
--- a/bob/rppg/ssr/script/ssr_from_mask.py
+++ b/bob/rppg/ssr/script/ssr_from_mask.py
@@ -4,8 +4,9 @@
"""Pulse extractor using 2SR algorithm (%(version)s)
Usage:
- %(prog)s (cohface | hci) [--protocol=<string>] [--subset=<string> ...]
- [--dbdir=<path>] [--pulsedir=<path>]
+ %(prog)s <configuration>
+ [--protocol=<string>] [--subset=<string> ...]
+ [--pulsedir=<path>]
[--npoints=<int>] [--indent=<int>] [--quality=<float>] [--distance=<int>]
[--stride=<int>]
[--overwrite] [--verbose ...] [--plot] [--gridcount]
@@ -20,10 +21,8 @@ Options:
-p, --protocol=<string> Protocol [default: all].
-s, --subset=<string> Data subset to load. If nothing is provided
all the data sets will be loaded.
- -d, --dbdir=<path> The path to the database on your disk. If not set,
- defaults to Idiap standard locations.
-o, --pulsedir=<path> The path to the directory where signal extracted
- from the face area will be stored [default: face]
+ from the face area will be stored [default: pulse]
-n, --npoints=<int> Number of good features to track [default: 40]
-i, --indent=<int> Indent (in percent of the face width) to apply to
keypoints to get the mask [default: 10]
@@ -31,7 +30,7 @@ Options:
[default: 0.01]
-e, --distance=<int> Minimum distance between detected good features to
track [default: 10]
- --stride=<int> Temporal stride [default: 20]
+ --stride=<int> Temporal stride [default: 61]
-O, --overwrite By default, we don't overwrite existing files. The
processing will skip those so as to go faster. If you
still would like me to overwrite them, set this flag.
@@ -43,9 +42,10 @@ Options:
Example:
- To run the pulse extractor for the cohface database
+ To run the spatial subspace rotation algorithm
+
+ $ %(prog)s config.py -v
- $ %(prog)s cohface -v
See '%(prog)s --help' for more information.
@@ -61,6 +61,9 @@ logger = setup("bob.rppg.base")
from docopt import docopt
+from bob.extension.config import load
+from ...base.utils import get_parameter
+
version = pkg_resources.require('bob.rppg.base')[0].version
import numpy
@@ -94,46 +97,34 @@ def main(user_input=None):
completions = dict(prog=prog, version=version,)
args = docopt(__doc__ % completions, argv=arguments, version='Signal extractor for videos (%s)' % version,)
+
+ # load configuration file
+ configuration = load([os.path.join(args['<configuration>'])])
+
+ # get various parameters, either from config file or command-line
+ protocol = get_parameter(args, configuration, 'protocol', 'all')
+ subset = get_parameter(args, configuration, 'subset', None)
+ pulsedir = get_parameter(args, configuration, 'pulsedir', 'pulse')
+ npoints = get_parameter(args, configuration, 'npoints', 40)
+ indent = get_parameter(args, configuration, 'indent', 10)
+ quality = get_parameter(args, configuration, 'quality', 0.01)
+ distance = get_parameter(args, configuration, 'distance', 10)
+ stride = get_parameter(args, configuration, 'stride', 61)
+ overwrite = get_parameter(args, configuration, 'overwrite', False)
+ plot = get_parameter(args, configuration, 'plot', False)
+ gridcount = get_parameter(args, configuration, 'gridcount', False)
+ verbosity_level = get_parameter(args, configuration, 'verbose', 0)
+
# if the user wants more verbosity, lowers the logging level
from bob.core.log import set_verbosity_level
- set_verbosity_level(logger, args['--verbose'])
-
- # chooses the database driver to use
- if args['cohface']:
- import bob.db.cohface
- if os.path.isdir(bob.db.cohface.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.cohface.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.cohface.Database(dbdir)
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'clean') or (args['--protocol'] == 'natural')):
- logger.warning("Protocol should be either 'clean', 'natural' or 'all' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
-
- elif args['hci']:
- import bob.db.hci_tagging
- import bob.db.hci_tagging.driver
- if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
- logger.debug("Using Idiap default location for the DB")
- dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
- elif args['--indir'] is not None:
- logger.debug("Using provided location for the DB")
- dbdir = args['--indir']
- else:
- logger.warn("Could not find the database directory, please provide one")
- sys.exit()
- db = bob.db.hci_tagging.Database()
- if not((args['--protocol'] == 'all') or (args['--protocol'] == 'cvpr14')):
- logger.warning("Protocol should be either 'all' or 'cvpr14' (and not {0})".format(args['--protocol']))
- sys.exit()
- objects = db.objects(args['--protocol'], args['--subset'])
+ set_verbosity_level(logger, verbosity_level)
+ if hasattr(configuration, 'database'):
+ objects = configuration.database.objects(protocol, subset)
+ else:
+ logger.error("Please provide a database in your configuration file !")
+ sys.exit()
+
# if we are on a grid environment, just find what I have to process.
sge = False
try:
@@ -147,26 +138,26 @@ def main(user_input=None):
raise RuntimeError("Grid request for job {} on a setup with {} jobs".format(pos, len(objects)))
objects = [objects[pos]]
- if args['--gridcount']:
+ if gridcount:
print(len(objects))
# the temporal stride
- temporal_stride = int(args['--stride'])
+ temporal_stride = stride
# does the actual work - for every video in the available dataset,
# extract the signals and dumps the results to the corresponding directory
for obj in objects:
# expected output file
- output = obj.make_path(args['--pulsedir'], '.hdf5')
+ output = obj.make_path(pulsedir, '.hdf5')
# if output exists and not overwriting, skip this file
- if (os.path.exists(output)) and not args['--overwrite']:
+ if (os.path.exists(output)) and not overwrite:
logger.info("Skipping output file `%s': already exists, use --overwrite to force an overwrite", output)
continue
# load video
- video = obj.load_video(dbdir)
+ video = obj.load_video(configuration.dbdir)
logger.info("Processing input video from `%s'...", video.filename)
nb_final_frames = len(video)
@@ -191,7 +182,7 @@ def main(user_input=None):
# -> detect the face
# -> get "good features" inside the face
kpts = obj.load_drmf_keypoints()
- mask_points, mask = kp66_to_mask(frame, kpts, int(args['--indent']), bool(args['--plot']))
+ mask_points, mask = kp66_to_mask(frame, kpts, indent, plot)
try:
bbox = bounding_boxes[i]
@@ -201,9 +192,7 @@ def main(user_input=None):
# define the face width for the whole sequence
facewidth = bbox.size[1]
face = crop_face(frame, bbox, facewidth)
-
- good_features = get_good_features_to_track(face,int(args['--npoints']),
- float(args['--quality']), int(args['--distance']), bool(args['--plot']))
+ good_features = get_good_features_to_track(face,npoints, quality, distance, plot)
else:
# subsequent frames:
# -> crop the face with the bounding_boxes of the previous frame (so
@@ -213,7 +202,7 @@ def main(user_input=None):
# current corners
# -> apply this transformation to the mask
face = crop_face(frame, prev_bb, facewidth)
- good_features = track_features(prev_face, face, prev_features, bool(args['--plot']))
+ good_features = track_features(prev_face, face, prev_features, plot)
project = find_transformation(prev_features, good_features)
if project is None:
logger.warn("Sequence {0}, frame {1} : No projection was found"
@@ -234,9 +223,7 @@ def main(user_input=None):
prev_face = crop_face(frame, prev_bb, facewidth)
- prev_features = get_good_features_to_track(face, int(args['--npoints']),
- float(args['--quality']), int(args['--distance']),
- bool(args['--plot']))
+ prev_features = get_good_features_to_track(face, npoints, quality, distance, plot)
if prev_features is None:
logger.warn("Sequence {0}, frame {1} No features to track"
" detected in the current frame, using the previous ones"
@@ -246,7 +233,7 @@ def main(user_input=None):
# get the bottom face region
face_mask = get_mask(frame, mask_points)
- if bool(args['--plot']):
+ if plot:
from matplotlib import pyplot
mask_image = numpy.copy(frame)
mask_image[:, face_mask] = 255
@@ -262,17 +249,17 @@ def main(user_input=None):
eigenvalues[:, i], eigenvectors[:, :, i] = get_eigen(skin_pixels)
# plot the cluster of skin pixels and eigenvectors (see Figure 1)
- if bool(args['--plot']) and args['--verbose'] >= 2:
+ if plot and verbosity_level >= 2:
plot_eigenvectors(skin_pixels, eigenvectors[:, :, i])
# build P and add it to the pulse signal
if i >= temporal_stride:
tau = i - temporal_stride
- p = build_P(i, int(args['--stride']), eigenvectors, eigenvalues)
+ p = build_P(i, int(stride), eigenvectors, eigenvalues)
output_data[tau:i] += (p - numpy.mean(p))
# plot the pulse signal
- if bool(args['--plot']):
+ if plot:
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 321013fe20128294bd3fc366237983b47903327c..6266b6a65121db6b99e0cd4ecfebe838c27e929b 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -7,17 +7,17 @@ package:
build:
entry_points:
- - 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
- - cvpr14_motion.py = bob.rppg.cvpr14.script.motion_elimination:main
- - cvpr14_filter.py = bob.rppg.cvpr14.script.filter:main
- - chrom_pulse.py = bob.rppg.chrom.script.extract_pulse:main
- - chrom_pulse_from_mask.py = bob.rppg.chrom.script.extract_pulse_from_mask:main
- - ssr_pulse.py = bob.rppg.ssr.script.spatial_subspace_rotation:main
- - ssr_pulse_from_mask.py = bob.rppg.ssr.script.ssr_from_mask:main
- - rppg_get_heart_rate.py = bob.rppg.base.script.frequency_analysis:main
- - rppg_compute_performance.py = bob.rppg.base.script.compute_performance:main
+ - bob_rppg_cvpr14_extract_face_and_bg_signals.py = bob.rppg.cvpr14.script.extract_face_and_bg_signals:main
+ - bob_rppg_cvpr14_video2skin.py = bob.rppg.cvpr14.script.video2skin:main
+ - bob_rppg_cvpr14_illumination.py = bob.rppg.cvpr14.script.illumination_rectification:main
+ - bob_rppg_cvpr14_motion.py = bob.rppg.cvpr14.script.motion_elimination:main
+ - bob_rppg_cvpr14_filter.py = bob.rppg.cvpr14.script.filter:main
+ - bob_rppg_chrom_pulse.py = bob.rppg.chrom.script.extract_pulse:main
+ - bob_rppg_chrom_pulse_from_mask.py = bob.rppg.chrom.script.extract_pulse_from_mask:main
+ - bob_rppg_ssr_pulse.py = bob.rppg.ssr.script.spatial_subspace_rotation:main
+ - bob_rppg_ssr_pulse_from_mask.py = bob.rppg.ssr.script.ssr_from_mask:main
+ - bob_rppg_base_get_heart_rate.py = bob.rppg.base.script.frequency_analysis:main
+ - bob_rppg_base_compute_performance.py = bob.rppg.base.script.compute_performance:main
number: {{ environ.get('BOB_BUILD_NUMBER', 0) }}
run_exports:
- {{ pin_subpackage(name) }}
@@ -57,17 +57,17 @@ test:
imports:
- {{ name }}
commands:
- - cvpr14_extract_signals.py --help
- - cvpr14_video2skin.py --help
- - cvpr14_illumination.py --help
- - cvpr14_motion.py --help
- - cvpr14_filter.py --help
- - chrom_pulse.py --help
- - chrom_pulse_from_mask.py --help
- - ssr_pulse.py --help
- - ssr_pulse_from_mask.py --help
- - rppg_get_heart_rate.py --help
- - rppg_compute_performance.py --help
+ - bob_rppg_cvpr14_extract_face_and_bg_signals.py --help
+ - bob_rppg_cvpr14_video2skin.py --help
+ - bob_rppg_cvpr14_illumination.py --help
+ - bob_rppg_cvpr14_motion.py --help
+ - bob_rppg_cvpr14_filter.py --help
+ - bob_rppg_chrom_pulse.py --help
+ - bob_rppg_chrom_pulse_from_mask.py --help
+ - bob_rppg_ssr_pulse.py --help
+ - bob_rppg_ssr_pulse_from_mask.py --help
+ - bob_rppg_base_get_heart_rate.py --help
+ - bob_rppg_base_compute_performance.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
diff --git a/doc/conf.py b/doc/conf.py
index f0edcfc68d724415bf879de7ab75b744454afc03..a209f39a6fc35a956b53d00b97efe86a4881325e 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -240,7 +240,6 @@ if os.path.exists(sphinx_requirements):
else:
intersphinx_mapping = link_documentation()
-
# We want to remove all private (i.e. _. or __.__) members
# that are not in the list of accepted functions
accepted_private_functions = ['__array__']
diff --git a/doc/extra-intersphinx.txt b/doc/extra-intersphinx.txt
index de1df192e062468ec5114891de0e674749011bf0..355bc942582d6c197cf1446693a111863a96fab0 100644
--- a/doc/extra-intersphinx.txt
+++ b/doc/extra-intersphinx.txt
@@ -1 +1,2 @@
bob.ip.skincolorfilter
+bob.ip.dlib
diff --git a/doc/guide_chrom.rst b/doc/guide_chrom.rst
index 076c777de762c3657327fa92cb152991c9b504ee..8d2714467d9f766aa90cafa0e1f61bdd76430752 100644
--- a/doc/guide_chrom.rst
+++ b/doc/guide_chrom.rst
@@ -39,28 +39,66 @@ The mean skin color value is then computed, and projected onto the XY chrominanc
colorspace. The signals in this colorspace are filtered using a bandpass filter
before the final pulse signal is built.
-
To extract the pulse signal from video sequences, do the following::
- $ ./bin/chrom_pulse.py cohface -vv
+ $ ./bin/bob_rppg_chrom_pulse.py config.py -vv
To see the full options, including parameters and protocols, type::
- $ ./bin/chrom_pulse.py --help
+ $ ./bin/bob_rppg_chrom_pulse.py --help
+
+As you can see, the script takes a configuration file as argument. This
+configuration file is required to at least specify the database, but can also
+be used to provide various parameters. A full example of configuration is
+given below.
+
+.. code-block:: python
+
+ import os, sys
+
+ # DATABASE
+ import bob.db.hci_tagging
+ import bob.db.hci_tagging.driver
+ if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
+ dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
+ if dbdir == '':
+ print("You should provide a directory where the DB is located")
+ sys.exit()
+ database = bob.db.hci_tagging.Database()
+ protocol = 'cvpr14'
+ framerate = 61
+
+ basedir = 'chrom-hci-cvpr14/'
+
+ # EXTRACT PULSE
+ pulsedir = basedir + 'pulse'
+ start = 306
+ end = 2136
+ motion = 0
+ threshold = 0.1
+ skininit = True
+ order = 128
+ window = 0
+
+ # FREQUENCY ANALYSIS
+ hrdir = basedir + 'hr'
+ nsegments = 12
+ nfft = 2048
+
+ # RESULTS
+ resultdir = basedir + 'results'
-The output of this step normally goes into a directory (you can override on
-the options for this application) named ``pulse``.
.. note::
The execution of this script is very slow - mainly due to the face detection.
You can speed it up using the gridtk_ (especially, if you're at Idiap). For example::
- $ ./bin/jman sub -t 3490 -- ./bin/chrom_pulse.py cohface
+ $ ./bin/jman sub -t 3490 -- ./bin/bob_rppg_chrom_pulse.py cohface
The number of jobs (i.e. 3490) is given by typing::
- $ ./bin/chrom_pulse.py cohface --gridcount
+ $ ./bin/bob_rppg_chrom_pulse.py cohface --gridcount
.. _gridtk: https://pypi.python.org/pypi/gridtk
diff --git a/doc/guide_cvpr14.rst b/doc/guide_cvpr14.rst
index 4278ec7deafadd676a1f7990a3a906055cde202a..5dd152d4944e64e6aa89ccedd6e6a35f61b35688 100644
--- a/doc/guide_cvpr14.rst
+++ b/doc/guide_cvpr14.rst
@@ -22,41 +22,69 @@ The algorithm to retrieve the pulse signal can be divided into several steps:
3. Eliminating non-rigid motion.
4. Filtering
+All the scripts rely on the usage of a configuration file, which specify the
+database interface, the path where the raw data (i.e. video sequences) are stored
+and various parameters.
+
+Below you can find a (minmal) example of a configuration file.
+
+.. code-block:: python
+
+ import os, sys
+ import bob.db.hci_tagging
+ import bob.db.hci_tagging.driver
+
+ if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
+ dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
+
+ if dbdir == '':
+ print("You should provide a directory where the DB is located")
+ sys.exit()
+
+ database = bob.db.hci_tagging.Database()
+ protocol = 'cvpr14'
+
+As you can see, here you should **at least** have the `database` and
+the `dbdir` parameters set.
+
Step 1: Extract signals from video sequences
--------------------------------------------
This scripts first load previously detected facial keypoints to build the mask
covering the bottom region of the face (note that the keypoints are not
-provided, but could be obtained using bob.ip.flandmark for instance). Once the
+provided, but could be obtained using `bob.ip.dlib
+<https://gitlab.idiap.ch/bob/bob.ip.dlib>`_ for instance. Once the
mask has been built, it is tracked across the whole sequence using the
methodology described in [li-cvpr-2014]_. The face is
detected using :py:func:`bob.ip.facedetect.detect_single_face`, and the
-tracking makes usage of openCV (version 2).
+tracking makes usage of OpenCV.
To extract the mean green colors the face region and of
-the background across the video sequences of the COHFACE
-database, do the following::
+the background across the video sequences of the defined database
+in the configuration file, do the following::
- $ ./bin/cvpr14_extract_signals.py cohface -vv
+ $ ./bin/bob_rppg_cvpr14_extract_face_and_bg_signals.py config.py -vv
To see the full options, including parameters and protocols, type::
- $ ./bin/cvpr14_extract_signals.py --help
+ $ ./bin/bob_rppg_cvpr14_extract_face_and_bg_signals.py --help
-The output of this step normally goes into directories (you can override on
-the options for this application) named ``face`` and ``background``.
+Note that you can either pass parameters through command-line, or
+by specififing them in the configuration file. Be aware that
+the command-line overrides the configuration file though.
.. note::
The execution of this script is very slow - mainly due to the face detection.
- You can speed it up using the gridtk_ (especially, if you're at Idiap). For example::
+ You can speed it up using the gridtk_ toolbox (especially, if you're at Idiap).
+ For example::
- $ ./bin/jman sub -t 3490 -- ./bin/cvpr14_extract_signals.py cohface
+ $ ./bin/jman sub -t 3490 -- ./bin/bob_rppg_cvpr14_extract_face_and_bg_signals. config.py
The number of jobs (i.e. 3490) is given by typing::
- $ ./bin/cvpr14_extract_signals.py cohface --gridcount
+ $ ./bin/bob_rppg_cvpr14_extract_face_and_bg_signals.py cohface --gridcount
Step 2: Illumination Rectification
@@ -68,10 +96,10 @@ Normalized Linear Mean Square and is then removed from the face signal. To get
the rectified green signal of the face area, you should execute the following
script::
- $ ./bin/cvpr14_illumination.py cohface -v
+ $ ./bin/bob_rppg_cvpr14_illumination.py config.py -v
-This script takes as input the result directories (normally named) ``face`` and
-``background`` and outputs data to a directory named ``illumination``.
+Again, parameters can be passed either through the configuration file or
+the command-line
Step 3: Non rigid Motion Elimination
@@ -85,13 +113,8 @@ channel on all the segment of all sequences. By default, the threshold is set su
of all the segments will be retained. To get the signals where large motion has
been eliminated, execute the following commands::
- $ ./bin/cvpr14_motion.py cohface --save-threshold threshold.txt -vv
- $ ./bin/cvpr14_motion.py cohface --load-threshold threshold.txt -vv
-
-This script takes as input the result directory (normally named)
-``illumination`` and outputs data to a directory called
-``motion``. The first call computes the threshold while the second
-one actually discards segments and builds the corrected signals.
+ $ ./bin/bob_rppg_cvpr14_motion.py cohface --save-threshold threshold.txt -vv
+ $ ./bin/bob_rppg_cvpr14_motion.py cohface --load-threshold threshold.txt -vv
Step 4: Filtering
@@ -106,10 +129,70 @@ window. Finally, a bandpass filter is applied to restrict the
frequencies to the range corresponding to a plausible heart-rate. To filter the
signal, you should execute the following command::
- $ ./bin/cvpr14_filter.py cohface -vv
+ $ ./bin/bob_rppg_cvpr14_filter.py cohface -vv
+
+A Full Configuration File Example
+---------------------------------
+
+.. note::
+
+ This configuration file can (and probably should) be used with all the
+ scripts mentioned above
+
+.. code-block:: python
+
+ import os, sys
+
+ import bob.db.hci_tagging
+ import bob.db.hci_tagging.driver
+
+ # DATABASE
+ if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
+ dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
+ if dbdir == '':
+ print("You should provide a directory where the DB is located")
+ sys.exit()
+ database = bob.db.hci_tagging.Database()
+ protocol = 'cvpr14'
+
+ basedir = 'li-hci-cvpr14/'
+
+ # EXTRACT FACE AND BACKGROUND
+ facedir = basedir + 'face'
+ bgdir = basedir + 'bg'
+ npoints = 200
+ indent = 10
+ quality = 0.01
+ distance = 10
+ verbose = 2
+
+ # ILLUMINATION CORRECTION
+ illumdir = basedir + 'illumination'
+ start = 306
+ end = 2136
+ step = 0.05
+ length = 3
+
+ # MOTION ELIMINATION
+ motiondir = basedir + 'motion'
+ seglength = 61
+ cutoff = 0.05
+
+ # FILTERING
+ pulsedir = basedir + 'pulse'
+ Lambda = 300
+ window = 21
+ framerate = 61
+ order = 128
+
+ # FREQUENCY ANALYSIS
+ hrdir = basedir + 'hr'
+ nsegments = 16
+ nfft = 8192
+
+ # RESULTS
+ resultdir = basedir + 'results'
-This script normally takes data from a directory called ``motion-eliminated``
-and outputs data to a directory called ``filtered``.
.. _gridtk: https://pypi.python.org/pypi/gridtk
diff --git a/doc/guide_performance.rst b/doc/guide_performance.rst
index b8984e6b65a5034d995f72dd9dcb9978cb585607..87133712de288fb5c97a53cd35565c326418e6f6 100644
--- a/doc/guide_performance.rst
+++ b/doc/guide_performance.rst
@@ -13,12 +13,7 @@ signal. The Welch's algorithm is applied to find the power spectrum of the
signal, and the heart rate is found using peak detection in the frequency range
of interest. To obtain the heart-rate, you should do the following::
- $ ./bin/rppg_frequency_analysis.py hci -vv
-
-This script normally takes data from a directory called ``pulse``
-and outputs data to a directory called ``heart-rate``. This output represents
-the end of the processing chain and contains the estimated heart-rate for every
-video sequence in the dataset.
+ $ ./bin/bob_rppg_base_get_heart_rate.py config.py -v
Generating performance measures
@@ -27,7 +22,35 @@ Generating performance measures
In order to get some insights on how good the computed heart-rates match the
ground truth, you should execute the following script::
- $ ./bin/rppg_compute_performance.py hci --indir heart-rate -v -P
+ $ ./bin/bob_rppg_base_compute_performance.py config.py -v
This will output and save various statistics (Root Mean Square Error,
-Pearson correlation) as well as figures (error distribution, scatter plot)
+Pearson correlation) as well as figures (error distribution, scatter plot).
+
+
+Again, these scripts rely on the use of configuration
+files. An minimal example is given below:
+
+.. code-block:: python
+
+ import os, sys
+
+ import bob.db.hci_tagging
+ import bob.db.hci_tagging.driver
+
+ # DATABASE
+ if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
+ dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
+ if dbdir == '':
+ print("You should provide a directory where the DB is located")
+ sys.exit()
+ database = bob.db.hci_tagging.Database()
+ protocol = 'cvpr14'
+
+ basedir = 'li-hci-cvpr14/'
+
+ # FREQUENCY ANALYSIS
+ hrdir = basedir + 'hr'
+ nsegments = 16
+ nfft = 8192
+
diff --git a/doc/guide_ssr.rst b/doc/guide_ssr.rst
index c3f5269848a3e98ae278d583791653368e0eb7cb..d4237ab135d80218f4583f89a996d9e19a5f8ef0 100644
--- a/doc/guide_ssr.rst
+++ b/doc/guide_ssr.rst
@@ -33,24 +33,64 @@ from each frame image. Hence, a skin color filter (:py:mod:`bob.ip.skincolorfilt
is applied to retrieve a mask containing skin pixels.
After having applied the skin color filter, the full algorithm is applied,
-as described in Algorithm 1 in the paper. To get the pulse signal, do
-the following::
+as described in Algorithm 1 in the paper. To get the pulse signals for
+all video in a database, do the following::
- $ ./bin/ssr_pulse.py cohface
+ $ ./bin/bob_rppg_ssr_pulse.py config.py -v
-The result of this script will be the pulse signal.
-The output of this step normally goes into a directory named ``pulse``.
+To see the full options, including parameters and protocols, type::
+
+ $ ./bin/bob_rppg_ssr_pulse.py --help
+
+As you can see, the script takes a configuration file as argument. This
+configuration file is required to at least specify the database, but can also
+be used to provide various parameters. A full example of configuration is
+given below.
+
+.. code-block:: python
+
+ import os, sys
+ import bob.db.hci_tagging
+ import bob.db.hci_tagging.driver
+
+ if os.path.isdir(bob.db.hci_tagging.driver.DATABASE_LOCATION):
+ dbdir = bob.db.hci_tagging.driver.DATABASE_LOCATION
+
+ if dbdir == '':
+ print("You should provide a directory where the DB is located")
+ sys.exit()
+
+ database = bob.db.hci_tagging.Database()
+ protocol = 'cvpr14'
+
+ basedir = 'ssr-hci-cvpr14/'
+
+ # EXTRACT PULSE
+ pulsedir = basedir + 'pulse'
+ start = 306
+ end = 2136
+ threshold = 0.1
+ skininit = True
+ stride = 30
+
+ # FREQUENCY ANALYSIS
+ hrdir = basedir + 'hr'
+ nsegments = 8
+ nfft = 4096
+
+ # RESULTS
+ resultdir = basedir + 'results'
.. note::
The execution of this script is very slow - mainly due to the face detection.
You can speed it up using the gridtk_ (especially, if you're at Idiap). For example::
- $ ./bin/jman sub -t 3490 -- ./bin/ssr_pulse.py cohface
+ $ ./bin/jman sub -t 3490 -- ./bin/bob_rppg_ssr_pulse.py cohface
The number of jobs (i.e. 3490) is given by typing::
- $ ./bin/ssr_pulse.py cohface --gridcount
+ $ ./bin/bob_rppg_ssr_pulse.py cohface --gridcount
.. _gridtk: https://pypi.python.org/pypi/gridtk
diff --git a/doc/index.rst b/doc/index.rst
index 7138c4a395db09460db6303474589083800b8d64..c027caaa3d6abf6953ce6c888ca3c9faffdca63f 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -19,12 +19,15 @@ This module contains the implementation of different remote photoplesthymography
* 2SR [wang-tbe-2015]_.
Also, we provide scripts to infer the heart-rate from the pulse signals, and
-to evaluate global performance on two different databases: Manhob HCI-Tagging
-(http://mahnob-db.eu/hci-tagging/) and COHFACE (http://www.idiap.ch/dataset/cohface).
+to evaluate global performance on a database.
+
+Note that this package was first meant to be used with the Manhob HCI-Tagging
+(http://mahnob-db.eu/hci-tagging/) and COHFACE (http://www.idiap.ch/dataset/cohface)
+databases, but could easily be extended to other datasets.
.. warning::
- You should download the databases before trying to run anything below!
+ You should download the aforementioned databases before trying to run anything below!
Documentation
-------------
diff --git a/scripts-article/README.rst b/scripts-article/README.rst
deleted file mode 100644
index 7c0ae97dc9982e5cc25e71c308a091f762159f8f..0000000000000000000000000000000000000000
--- a/scripts-article/README.rst
+++ /dev/null
@@ -1,35 +0,0 @@
-Scripts for generating article results
---------------------------------------
-
-In this folder, you can find the scripts that have been used to generate the
-results in the article. They assume that the path to the database is either
-'hci' or 'cohface' in the package root folder (this could be a symlink
-though)::
-
- chrom-cohface-clean-natural.py --> Table 7 column 2
- chrom-cohface-clean.py --> Table 5, line 2
- chrom-cohface-complete-face.py --> Table 8, column 1, line 2
- chrom-cohface-complete-mask.py --> Table 8, column 3, line 2
- chrom-cohface-complete-skin.py --> Table 8, column 2, line 2
- chrom-hci-cvpr14.py --> Table 2, column 2
- chrom-hci-protocols.py --> Table 4, line 2
- chrom-xdb-cohface-hci.py --> Table 6, line 2, column 2
- chrom-xdb-hci-cohface.py --> Table 6, line 1, column 2
- li-cohface-clean-natural.py --> Table 7, column 1
- li-cohface-clean.py --> Table 5, line 1
- li-cohface-complete-mask.py --> Table 8, line 1, column 3
- li-cohface-complete-skin.py --> Table 8, line 1, column 2
- li-cohface-complete-wholeface.py --> Table 8, line 1, column 1
- li-hci-cvpr14.py --> Table 2, column 1
- li-hci-protocols.py --> Table 4, line 1
- li-xdb-cohface-hci.py --> Table 6, column 1, line 2
- li-xdb-hci-cohface.py --> Table 6, column 1, line 1
- ssr-cohface-clean-natural.py --> Table 7, column 3
- ssr-cohface-clean.py --> Table 5, line 3
- ssr-hci-cvpr14.py --> Table 2, column 3
- ssr-hci-protocols.py --> Table 4, line 3
- ssr-xdb-cohface-hci.py --> Table 6, column 3, line 2
- ssr-xdb-hci-cohface.py --> Table 6, column 3, line 1
- ssr-cohface-complete-face.py --> Table 8, line 3, column 1
- ssr-cohface-complete-skin.py --> Table 8, line 3, column 2
- ssr-cohface-complete-mask.py --> Table 8, line 3, column 3
diff --git a/scripts-article/chrom-cohface-clean-natural.py b/scripts-article/chrom-cohface-clean-natural.py
deleted file mode 100644
index de63b1a9effca690e8f9aacffb07ffeff38c45ad..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-cohface-clean-natural.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/chrom-cohface-clean-natural/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.2
-order = 32
-window = 0
-
-n_segments = 8
-nfft = 1024
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py cohface --protocol natural --subset test --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --window ' + str(window) + ' --skininit -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol natural --subset test --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol natural --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-cohface-clean.py b/scripts-article/chrom-cohface-clean.py
deleted file mode 100644
index c3d5a97730ef3a090db4a3ff5e989c73f93137c6..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-cohface-clean.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join('experiments/paper/chrom-cohface-clean/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.2
-order = 32
-window = 0
-
-n_segments = 8
-nfft = 1024
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py cohface --protocol clean --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --window ' + str(window) + ' --skininit -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol clean --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-cohface-complete-face.py b/scripts-article/chrom-cohface-complete-face.py
deleted file mode 100644
index 0529e2c279aea33e1a36d0b5a967dfadf9120c46..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-cohface-complete-face.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join('experiments/paper/chrom-cohface-complete-face/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-skin_threshold = 0.0
-
-# parameters
-order = 128
-window = 0
-
-n_segments = 8
-nfft = 512
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py cohface --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --order ' + str(order) + ' --window ' + str(window) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-cohface-complete-mask.py b/scripts-article/chrom-cohface-complete-mask.py
deleted file mode 100644
index 41df2512570e7d00e9bbbf06f18d77b7e296f4a3..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-cohface-complete-mask.py
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/chrom-cohface-complete-mask/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-npoints = 40
-indent = 15
-
-order = 128
-window = 256
-
-n_segments = 8
-nfft = 512
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n\n')
-f.write('indent = ' + str(indent) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse_from_mask.py cohface --dbdir cohface --pulsedir ' + str(pulse_dir) + ' --framerate ' + str(framerate) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' --order ' + str(order) + ' --window ' + str(window) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-cohface-complete-skin.py b/scripts-article/chrom-cohface-complete-skin.py
deleted file mode 100644
index 1d4bff4cf032c70e8f8e27bd8b2a34547bcf26d6..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-cohface-complete-skin.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join('experiments/paper/chrom-cohface-complete-skin/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.3
-order = 64
-window = 0
-
-n_segments = 8
-nfft = 512
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py cohface --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --order ' + str(order) + ' --window ' + str(window) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-hci-cvpr14.py b/scripts-article/chrom-hci-cvpr14.py
deleted file mode 100644
index a3a9aebae41b1de41855c21c9729e303212e9c23..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-hci-cvpr14.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/chrom-hci-cvpr14/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir = base_expe_dir + 'results'
-
-framerate = 61
-
-# parameters
-skin_threshold = 0.1
-order = 32
-window = 0
-
-n_segments = 12
-nfft = 2048
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py hci --protocol cvpr14 --dbdir hci --bboxdir bounding-boxes --outdir ' + str(pulse_dir) + ' --start 306 --end 2136 --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --window ' + str(window) + ' --skininit -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --protocol cvpr14 --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --protocol cvpr14 --indir ' + hr_dir + ' --outdir ' + results_dir + ' -v')
diff --git a/scripts-article/chrom-hci-protocols.py b/scripts-article/chrom-hci-protocols.py
deleted file mode 100644
index fada77704af2bc240be29e93d3974bf0cea41b56..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-hci-protocols.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/chrom-hci-protocols/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 61
-
-# parameters
-skin_threshold = 0.3
-order = 32
-window = 32
-
-n_segments = 8
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py hci --dbdir hci --bboxdir bounding-boxes --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --window ' + str(window) + ' --skininit -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-xdb-cohface-hci.py b/scripts-article/chrom-xdb-cohface-hci.py
deleted file mode 100644
index 8e5cdf3865d23330fbd4489e1edf63124329ba95..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-xdb-cohface-hci.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/chrom-xdb-cohface-hci/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 61
-
-# parameters
-skin_threshold = 0.2
-order = 32
-window = 0
-
-n_segments = 8
-nfft = 1024
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py hci --subset test --dbdir hci --bboxdir bounding-boxes --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --window ' + str(window) + ' --skininit -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --subset test --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/chrom-xdb-hci-cohface.py b/scripts-article/chrom-xdb-hci-cohface.py
deleted file mode 100644
index 2adc4e64ff24d9bd8463e251f2d68db77b78b3b1..0000000000000000000000000000000000000000
--- a/scripts-article/chrom-xdb-hci-cohface.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/chrom-xdb-hci-cohface/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.3
-order = 32
-window = 32
-
-n_segments = 8
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('window = ' + str(window) + '\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'chrom_pulse.py cohface --protocol clean --subset test --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --framerate ' + str(framerate) + ' --window ' + str(window) + ' --skininit -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol clean --subset test --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-cohface-clean-natural.py b/scripts-article/li-cohface-clean-natural.py
deleted file mode 100644
index 093f27b9e40379cf957ec0080967b5552d6cdd31..0000000000000000000000000000000000000000
--- a/scripts-article/li-cohface-clean-natural.py
+++ /dev/null
@@ -1,97 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-### WARNING ###
-# be sure to first run li-cohface-clean.py to get the threshold file
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-cohface-clean-natural/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-npoints = 100
-indent = 10
-
-adaptation = 0.01
-filter_length = 5
-
-segment_length = 40
-cutoff = 0.02
-threshold_file = 'experiments/paper/li-cohface-clean/illumination/threshold.txt'
-
-Lambda = 300
-window = 3
-order = 32
-
-n_segments = 4
-nfft = 4096
-
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py cohface --protocol natural --subset test --dbdir cohface --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py cohface --protocol natural --subset test --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py cohface --protocol natural --subset test --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' +str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py cohface --protocol natural --subset test --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol natural --subset test --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol natural --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-cohface-clean.py b/scripts-article/li-cohface-clean.py
deleted file mode 100644
index d91e56a48ec82e660342798ccb8a99c73344345e..0000000000000000000000000000000000000000
--- a/scripts-article/li-cohface-clean.py
+++ /dev/null
@@ -1,97 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-cohface-clean/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-threshold_file = illumination_dir + '/threshold.txt'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-npoints = 100
-indent = 10
-
-adaptation = 0.01
-filter_length = 5
-
-segment_length = 40
-cutoff = 0.02
-
-Lambda = 300
-window = 3
-order = 32
-
-n_segments = 4
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py cohface --protocol clean --dbdir cohface --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py cohface --protocol clean --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> determine the threshold
-os.system(bin_folder + 'cvpr14_motion.py cohface --protocol clean --subset train --subset dev --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --save-threshold ' + threshold_file + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py cohface --protocol clean --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' +str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py cohface --protocol clean --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol clean --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-cohface-complete-face.py b/scripts-article/li-cohface-complete-face.py
deleted file mode 100644
index 7f4c518fc3659b755a9a1dbacb739759937a338a..0000000000000000000000000000000000000000
--- a/scripts-article/li-cohface-complete-face.py
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-cohface-complete-wholeface/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-threshold_file = illumination_dir + '/threshold.txt'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-#parameters
-adaptation = 0.01
-filter_length = 5
-
-segment_length = 40
-cutoff = 0.1
-
-Lambda = 100
-window = 3
-order = 64
-
-n_segments = 4
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py cohface --dbdir cohface --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --wholeface -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py cohface --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> determine the threshold
-os.system(bin_folder + 'cvpr14_motion.py cohface --subset train --subset dev --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --save-threshold ' + threshold_file + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py cohface --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' +str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py cohface --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-cohface-complete-mask.py b/scripts-article/li-cohface-complete-mask.py
deleted file mode 100644
index 28f70935ec86ba91b9152523f357264019778f36..0000000000000000000000000000000000000000
--- a/scripts-article/li-cohface-complete-mask.py
+++ /dev/null
@@ -1,97 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-cohface-complete-mask/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-threshold_file = illumination_dir + '/threshold.txt'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-npoints = 200
-indent = 10
-
-adaptation = 0.01
-filter_length = 5
-
-segment_length = 40
-cutoff = 0.02
-
-Lambda = 300
-window = 3
-order = 32
-
-n_segments = 4
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py cohface --subset train --subset dev --dbdir cohface --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py cohface --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> determine the threshold
-os.system(bin_folder + 'cvpr14_motion.py cohface --subset train --subset dev --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --save-threshold ' + threshold_file + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py cohface --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' +str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py cohface --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-cohface-complete-skin.py b/scripts-article/li-cohface-complete-skin.py
deleted file mode 100644
index d271a03889085015af550cedc60cc01ba466d949..0000000000000000000000000000000000000000
--- a/scripts-article/li-cohface-complete-skin.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-cohface-complete-skin/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-threshold_file = illumination_dir + '/threshold.txt'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-#parameters
-skin_threshold = 0.8
-
-adaptation = 0.01
-filter_length = 3
-
-segment_length = 40
-cutoff = 0.1
-
-Lambda = 100
-window = 3
-order = 128
-
-n_segments = 8
-nfft = 512
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_video2skin.py cohface --dbdir cohface --outdir ' + str(facedir) + ' --threshold ' + str(skin_threshold) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py cohface --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> determine the threshold
-os.system(bin_folder + 'cvpr14_motion.py cohface --subset train --subset dev --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --save-threshold ' + threshold_file + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py cohface --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' +str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py cohface --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-hci-cvpr14.py b/scripts-article/li-hci-cvpr14.py
deleted file mode 100644
index 03b2950d0b84698eed372cd197d2e16460f3d67e..0000000000000000000000000000000000000000
--- a/scripts-article/li-hci-cvpr14.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-hci-cvpr14/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-threshold_file = illumination_dir + '/threshold.txt'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir = base_expe_dir + 'results'
-
-# fixed parameter
-framerate = 61
-
-# parameters
-npoints = 200
-indent = 10
-
-adaptation = 0.05
-filter_length = 3
-
-segment_length = 61
-cutoff = 0.05
-
-Lambda = 300
-window = 21
-order = 128
-
-n_segments = 16
-nfft = 8192
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py hci --protocol cvpr14 --dbdir hci, --bboxdir bounding-boxes --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py hci --protocol cvpr14 --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' --start 306 --end 2136 -v')
-
-# motion elimination -> determine the threshold
-os.system(bin_folder + 'cvpr14_motion.py hci --protocol cvpr14 --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --save-threshold ' + threshold_file + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py hci --protocol cvpr14 --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength 61 --cutoff 0.05 --load-threshold ' + threshold_file + ' -v')
-
-# filter
-os.system(bin_folder + 'cvpr14_filter.py hci --protocol cvpr14 --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --protocol cvpr14 --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --protocol cvpr14 --indir ' + hr_dir + ' --outdir ' + results_dir + ' -v')
diff --git a/scripts-article/li-hci-protocols.py b/scripts-article/li-hci-protocols.py
deleted file mode 100644
index 053f0c93cc3dfb785693bb0b1e9d4fae648052c0..0000000000000000000000000000000000000000
--- a/scripts-article/li-hci-protocols.py
+++ /dev/null
@@ -1,97 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-hci-protocols/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-threshold_file = illumination_dir + '/threshold.txt'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 61
-
-# parameters
-npoints = 400
-indent = 10
-
-adaptation = 0.05
-filter_length = 3
-
-segment_length = 30
-cutoff = 0.1
-
-Lambda = 500
-window = 23
-order = 96
-
-n_segments = 12
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py hci --dbdir hci, --bboxdir bounding-boxes --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py hci --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> determine the threshold
-os.system(bin_folder + 'cvpr14_motion.py hci --subset train --subset dev --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --save-threshold ' + threshold_file + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py hci --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength 61 --cutoff 0.05 --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py hci --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-xdb-cohface-hci.py b/scripts-article/li-xdb-cohface-hci.py
deleted file mode 100644
index 6d0f58cd6ce52f109c31a75801047e9918d8b789..0000000000000000000000000000000000000000
--- a/scripts-article/li-xdb-cohface-hci.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-### WARNING ###
-# be sure to run li-cohface-clean.py first to get the threshold file
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-xdb-cohface-hci/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 61
-
-# parameters
-npoints = 100
-indent = 10
-
-adaptation = 0.01
-filter_length = 5
-
-segment_length = 120 # 2 times the framerate, as for COHFACE training set
-cutoff = 0.02
-threshold_file = 'experiments/paper/li-cohface-clean/illumination/threshold.txt'
-
-Lambda = 300
-window = 9
-order = 96
-
-n_segments = 4
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py hci --dbdir hci --subset test --bboxdir bounding-boxes --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) ' --indent ' + str(indent))
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py hci --subset test --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py hci --subset test --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py hci --subset test --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --subset test --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/li-xdb-hci-cohface.py b/scripts-article/li-xdb-hci-cohface.py
deleted file mode 100644
index 71a34e1b81a1f824c840972455883c233e661aac..0000000000000000000000000000000000000000
--- a/scripts-article/li-xdb-hci-cohface.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-### WARNING ###
-# be sure to first run li-hci-protocols.py to get the required threshold file
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/li-xdb-hci-cohface/')
-facedir = base_expe_dir + 'face'
-bgdir = base_expe_dir + 'bg'
-illumination_dir = base_expe_dir + 'illumination'
-motion_dir = base_expe_dir + 'motion'
-filtered_dir = base_expe_dir + 'filtered'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-npoints = 400
-indent = 10
-
-adaptation = 0.05
-filter_length = 3
-
-segment_length = 10 # half of the frame rate
-cutoff = 0.1
-threshold_file = 'experiments/paper/li-hci-protocols/illumination/threshold.txt'
-
-Lambda = 500
-window = 23
-order = 96
-
-n_segments = 12
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n')
-f.write('indent [%] = ' + str(indent) + '\n\n')
-f.write('adaptation step = ' + str(adaptation) + '\n')
-f.write('filter length = ' + str(filter_length) + '\n\n')
-f.write('segment length [frames] = ' + str(segment_length) + '\n')
-f.write('cutoff [% / 100] = ' + str(cutoff) + '\n\n')
-f.write('lambda = ' + str(Lambda) + '\n')
-f.write('window = ' + str(window) + '\n')
-f.write('order = ' + str(order) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# signals extraction
-os.system(bin_folder + 'cvpr14_extract_signals.py cohface --protocol clean --subset test --dbdir cohface --facedir ' + str(facedir) + ' --bgdir ' + str(bgdir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' -v')
-
-# illumination correction
-os.system(bin_folder + 'cvpr14_illumination.py cohface --protocol clean --subset test --facedir ' + facedir + ' --bgdir ' + bgdir + ' --outdir ' + illumination_dir + ' --step ' + str(adaptation) + ' --length ' + str(filter_length) + ' -v')
-
-# motion elimination -> remove segments
-os.system(bin_folder + 'cvpr14_motion.py cohface --protocol clean --subset test --indir ' + illumination_dir + ' --outdir ' + motion_dir + ' --seglength ' + str(segment_length) + ' --cutoff ' + str(cutoff) + ' --load-threshold ' + threshold_file + ' -v')
-
-# filtering
-os.system(bin_folder + 'cvpr14_filter.py cohface --protocol clean --subset test --indir ' + motion_dir + ' --outdir ' + filtered_dir + ' --lambda ' + str(Lambda) + ' --window ' + str(window) + ' --order ' + str(order) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol clean --subset test --indir ' + filtered_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-cohface-clean-natural.py b/scripts-article/ssr-cohface-clean-natural.py
deleted file mode 100644
index f3c1f4eea4947f299a36d4d2d909fa307d517754..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-cohface-clean-natural.py
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-cohface-clean-natural/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.8
-stride = 80
-
-n_segments = 8
-nfft = 2048
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py cohface --protocol natural --subset test --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol natural --subset test --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' + str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol natural --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-cohface-clean.py b/scripts-article/ssr-cohface-clean.py
deleted file mode 100644
index 3a4802fde74e9f7f469fac9c56bf45fddf279983..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-cohface-clean.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-cohface-clean/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.8
-stride = 80
-
-n_segments = 8
-nfft = 2048
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py cohface --protocol clean --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol clean --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' + str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-cohface-complete-face.py b/scripts-article/ssr-cohface-complete-face.py
deleted file mode 100644
index 560c58a6f4e7e1c50c1885536d03929d6327e0bb..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-cohface-complete-face.py
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join('experiments/paper/ssr-cohface-complete-face/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-skin_threshold = 0.0
-
-# parameters
-stride = 10
-
-n_segments = 16
-nfft = 512
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py cohface --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-cohface-complete-mask.py b/scripts-article/ssr-cohface-complete-mask.py
deleted file mode 100644
index a283a5b30fe2a4ca0e9c9c59e7ac56f4790663da..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-cohface-complete-mask.py
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-cohface-complete-mask/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-npoints = 100
-indent = 10
-
-stride = 10
-
-n_segments = 8
-nfft = 1024
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('npoints = ' + str(npoints) + '\n\n')
-f.write('indent = ' + str(indent) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse_from_mask.py cohface --dbdir cohface --pulsedir ' + str(pulse_dir) + ' --npoints ' + str(npoints) + ' --indent ' + str(indent) + ' --stride ' + str(stride) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-cohface-complete-skin.py b/scripts-article/ssr-cohface-complete-skin.py
deleted file mode 100644
index a3f8244884c1f47cf78d86a7b9568509cb99ae3d..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-cohface-complete-skin.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join('experiments/paper/ssr-cohface-complete-skin/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.6
-stride = 10
-
-n_segments = 8
-nfft = 512
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py cohface --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py cohface --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-hci-cvpr14.py b/scripts-article/ssr-hci-cvpr14.py
deleted file mode 100644
index 694d4a57d246531568c8e24a11b43dd451bfb971..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-hci-cvpr14.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-hci-cvpr14/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir = base_expe_dir + 'results'
-
-framerate = 61
-
-# parameters
-skin_threshold = 0.1
-stride = 30
-
-n_segments = 8
-nfft = 4096
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py hci --protocol cvpr14 --dbdir hci --bboxdir bounding-boxes --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' --start 306 --end 2136 -v --skininit')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --protocol cvpr14 --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --protocol cvpr14 --indir ' + hr_dir + ' --outdir ' + results_dir + ' -v')
diff --git a/scripts-article/ssr-hci-protocols.py b/scripts-article/ssr-hci-protocols.py
deleted file mode 100644
index 0eff543e7735f95f4fb2de3883fc79a1cb7c20a3..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-hci-protocols.py
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-hci-protocols/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 61
-
-# parameters
-skin_threshold = 0.1
-stride = 30
-
-n_segments = 8
-nfft = 8192
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py hci --dbdir hci --bboxdir bounding-boxes --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v --skininit')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset train --subset dev --indir ' + hr_dir + ' --outdir ' + results_dir_train + ' -v')
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-xdb-cohface-hci.py b/scripts-article/ssr-xdb-cohface-hci.py
deleted file mode 100644
index e2fbb0ff27f83c822c630b0bef487d1f768426b8..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-xdb-cohface-hci.py
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-xdb-cohface-hci/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 61
-
-# parameters
-skin_threshold = 0.8
-stride = 80
-
-n_segments = 8
-nfft = 2048
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-# pulse extraction
-os.system(bin_folder + 'ssr_pulse.py hci --subset test --dbdir hci --bboxdir bounding-boxes --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py hci --subset test --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' + str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py hci --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/scripts-article/ssr-xdb-hci-cohface.py b/scripts-article/ssr-xdb-hci-cohface.py
deleted file mode 100644
index 4eb84414a067fc17e96a9fda27d7652bf02b8a24..0000000000000000000000000000000000000000
--- a/scripts-article/ssr-xdb-hci-cohface.py
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/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/>.
-
-import os, sys
-
-# directories and file
-current_folder = os.path.dirname(os.path.abspath(__file__))
-root_folder = os.path.dirname(current_folder)
-bin_folder = os.path.join(root_folder, 'bin/')
-
-base_expe_dir = os.path.join(root_folder, 'experiments/paper/ssr-xdb-hci-cohface/')
-pulse_dir = base_expe_dir + 'pulse'
-hr_dir = base_expe_dir + 'hr'
-results_dir_train = base_expe_dir + 'results-train'
-results_dir_test = base_expe_dir + 'results-test'
-
-framerate = 20
-
-# parameters
-skin_threshold = 0.1
-stride = 30
-
-n_segments = 8
-nfft = 8192
-
-# write a file with the parameters - useful to keep track sometimes ..
-param_file = base_expe_dir + '/parameters.txt'
-if not os.path.isdir(base_expe_dir):
- os.makedirs(base_expe_dir)
-
-f = open(param_file, 'w')
-f.write('skin threshold = ' + str(skin_threshold) + '\n\n')
-f.write('stride = ' + str(stride) + '\n\n')
-f.write('Welch segments = ' + str(n_segments) + '\n')
-f.write('npoints FFT = ' + str(nfft) + '\n')
-f.close()
-
-os.system(bin_folder + 'ssr_pulse.py cohface --protocol clean --subset test --dbdir cohface --outdir ' + str(pulse_dir) + ' --threshold ' + str(skin_threshold) + ' --stride ' + str(stride) + ' -v --skininit')
-
-# computing heart-rate
-os.system(bin_folder + 'rppg_get_heart_rate.py cohface --protocol clean --subset test --indir ' + pulse_dir + ' --outdir ' + hr_dir + ' --framerate ' + str(framerate) + ' --nsegments ' +str(n_segments) + ' --nfft ' + str(nfft) + ' -v')
-
-# computing performance
-os.system(bin_folder + 'rppg_compute_performance.py cohface --protocol clean --subset test --indir ' + hr_dir + ' --outdir ' + results_dir_test + ' -v')
diff --git a/setup.py b/setup.py
index 9615800068d88cbd8103f87d939c579113188266..ccc68f9a88c4bd2009212d530231c88e863d73f3 100644
--- a/setup.py
+++ b/setup.py
@@ -32,17 +32,17 @@ setup(
entry_points={
'console_scripts': [
- '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',
- 'cvpr14_motion.py = bob.rppg.cvpr14.script.motion_elimination:main',
- 'cvpr14_filter.py = bob.rppg.cvpr14.script.filter:main',
- 'chrom_pulse.py = bob.rppg.chrom.script.extract_pulse:main',
- 'chrom_pulse_from_mask.py = bob.rppg.chrom.script.extract_pulse_from_mask:main',
- 'ssr_pulse.py = bob.rppg.ssr.script.spatial_subspace_rotation:main',
- 'ssr_pulse_from_mask.py = bob.rppg.ssr.script.ssr_from_mask:main',
- 'rppg_get_heart_rate.py = bob.rppg.base.script.frequency_analysis:main',
- 'rppg_compute_performance.py = bob.rppg.base.script.compute_performance:main'
+ 'bob_rppg_cvpr14_extract_face_and_bg_signals.py = bob.rppg.cvpr14.script.extract_face_and_bg_signals:main',
+ 'bob_rppg_cvpr14_video2skin.py = bob.rppg.cvpr14.script.video2skin:main',
+ 'bob_rppg_cvpr14_illumination.py = bob.rppg.cvpr14.script.illumination_rectification:main',
+ 'bob_rppg_cvpr14_motion.py = bob.rppg.cvpr14.script.motion_elimination:main',
+ 'bob_rppg_cvpr14_filter.py = bob.rppg.cvpr14.script.filter:main',
+ 'bob_rppg_chrom_pulse.py = bob.rppg.chrom.script.extract_pulse:main',
+ 'bob_rppg_chrom_pulse_from_mask.py = bob.rppg.chrom.script.extract_pulse_from_mask:main',
+ 'bob_rppg_ssr_pulse.py = bob.rppg.ssr.script.spatial_subspace_rotation:main',
+ 'bob_rppg_ssr_pulse_from_mask.py = bob.rppg.ssr.script.ssr_from_mask:main',
+ 'bob_rppg_base_get_heart_rate.py = bob.rppg.base.script.frequency_analysis:main',
+ 'bob_rppg_base_compute_performance.py = bob.rppg.base.script.compute_performance:main',
],
},