Commit 48d71d49 authored by André Anjos's avatar André Anjos 💬
Browse files

[tests] More

parent 4ab8f319
......@@ -4,7 +4,123 @@
# Wed 30 Sep 2015 12:13:47 CEST
import os
import bob
import numpy
import bob.db.base
import bob.io.base
def bdf_load_signal(fn, name='EXG3', start=None, end=None):
"""Loads a signal named ``name`` from the BDF filenamed ``fn``
Parameters:
fn (path): The full path to the file to read
name (str): The name of the channel to read.
start (int, option): Start time in seconds
end (int, optional): End time in seconds
List of physiological channels used (there are more available, but contain no
meaningful data) on the Mahnob HCI-Tagging database:
These are the 32 electrodes from the EEG cap (measurements in uV; for full
positioning details, see the full database description report, available on
the database website):
* AF3
* AF4
* C3
* C4
* CP1
* CP2
* CP5
* CP6
* Cz
* F3
* F4
* F7
* F8
* FC1
* FC2
* FC5
* FC6
* Fp1
* Fp2
* Fz
* O1
* O2
* Oz
* P3
* P4
* P7
* P8
* PO3
* PO4
* Pz
* T7
* T8
These are ECG sensors (measurements in uV):
* EXG1: Upper right corner of chest, under clavicle bone
* EXG2: Upper left corner of chest, under clavicle bone
* EXG3: Left side of abdomen (very clean)
Other sensors:
* GSR1: Galvanic skin response (in Ohm)
* Resp: Respiration belt (in uV)
* Status: Status channel containing markers (Boolean)
* Temp: Skin temperature on the left pinky (Celsius)
"""
import edflib
e = edflib.EdfReader(fn)
# get the status information, so we how the video is synchronized
status_index = e.getSignalTextLabels().index('Status')
sample_frequency = e.samplefrequency(status_index)
status_size = e.samples_in_file(status_index)
status = numpy.zeros((status_size,), dtype='float64')
e.readsignal(status_index, 0, status_size, status)
status = status.round().astype('int')
nz_status = status.nonzero()[0]
# because we're interested in the video bits, make sure to get data
# from that period only
video_start = nz_status[0]
video_end = nz_status[-1]
# retrieve information from this rather chaotic API
index = e.getSignalTextLabels().index(name)
sample_frequency = e.samplefrequency(index)
video_start_seconds = video_start/sample_frequency
if start is not None:
start += video_start_seconds
start *= sample_frequency
if start < video_start: start = video_start
start = int(start)
else:
start = video_start
if end is not None:
end += video_start_seconds
end *= sample_frequency
if end > video_end: end = video_end
end = int(end)
else:
end = video_end
# now read the data into a numpy array (read everything or libedf crashes)
container = numpy.zeros((end-start,), dtype='float64')
e.readsignal(index, start, end-start, container)
return container, sample_frequency
class File(object):
""" Generic file container for HCI-Tagging files
......@@ -26,7 +142,7 @@ class File(object):
self.basedir = basedir
self.stem = bdf
self.video_stem = video
self.duration = duration
self.duration = int(duration)
def __repr__(self):
......@@ -80,5 +196,5 @@ class File(object):
"""
path = self.make_path(directory, extension)
bob.db.utils.makedirs_safe(os.path.dirname(path))
bob.io.save(data, path)
bob.db.base.utils.makedirs_safe(os.path.dirname(path))
bob.io.base.save(data, path)
......@@ -39,6 +39,25 @@ class HCITaggingTest(unittest.TestCase):
self.assertEqual(len(self.db.objects()), 3490)
@db_available
def test02_can_read_bdf(self):
from .models import bdf_load_signal
for obj in self.db.objects():
path = obj.make_path(DATABASE_LOCATION, '.bdf')
self.assertTrue(os.path.exists(path))
signal, freq = bdf_load_signal(path)
time = len(signal)/freq
# correlation between video data and physiological signal
if abs(time-obj.duration) > 2:
print('Physiological signal (%d seconds) is very different in size from estimated video duration (%d seconds) on sample `%s/%s\'' % (time, obj.duration, obj.basedir, obj.stem))
class CmdLineTest(unittest.TestCase):
"""Makes sure our command-line is working properly."""
......
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