def build(subject_id, valid_epochs):
psg_array = PSGService.load_cropped_array(subject_id)
labels = []
for epoch in valid_epochs:
value = np.interp(epoch.timestamp, psg_array[:, 0], psg_array[:, 1])
labels.append(value)
return np.array(labels)
def test_crop(self):
subject_id = 'subjectA'
crop_interval = Interval(start_time=50, end_time=101)
data = [
StageItem(epoch=Epoch(timestamp=10, index=2), stage=SleepStage.n1),
StageItem(epoch=Epoch(timestamp=50, index=3), stage=SleepStage.n2),
StageItem(epoch=Epoch(timestamp=100, index=4),
stage=SleepStage.n3),
StageItem(epoch=Epoch(timestamp=170, index=5),
stage=SleepStage.rem)
]
expected_data = [
StageItem(epoch=Epoch(timestamp=50, index=3), stage=SleepStage.n2),
StageItem(epoch=Epoch(timestamp=100, index=4),
stage=SleepStage.n3),
]
input_raw_data_collection = PSGRawDataCollection(subject_id=subject_id,
data=data)
returned_psg_raw_collection = PSGService.crop(
input_raw_data_collection, crop_interval)
self.assertEqual(subject_id, returned_psg_raw_collection.subject_id)
TestHelper.assert_models_equal(self, expected_data[0],
returned_psg_raw_collection.data[0])
TestHelper.assert_models_equal(self, expected_data[1],
returned_psg_raw_collection.data[1])
def crop_all(subject_id):
# psg_raw_collection = PSGService.read_raw(subject_id) # Used to extract PSG details from the reports
psg_raw_collection = PSGService.read_precleaned(
subject_id) # Loads already extracted PSG data
motion_collection = MotionService.load_raw(subject_id)
heart_rate_collection = HeartRateService.load_raw(subject_id)
valid_interval = RawDataProcessor.get_intersecting_interval(
[psg_raw_collection, motion_collection, heart_rate_collection])
psg_raw_collection = PSGService.crop(psg_raw_collection,
valid_interval)
motion_collection = MotionService.crop(motion_collection,
valid_interval)
heart_rate_collection = HeartRateService.crop(heart_rate_collection,
valid_interval)
PSGService.write(psg_raw_collection)
MotionService.write(motion_collection)
HeartRateService.write(heart_rate_collection)
ActivityCountService.build_activity_counts_without_matlab(
subject_id, motion_collection.data
) # Builds activity counts with python, not MATLAB
def test_write(self, mock_np):
subject_id = 'subjectA'
mock_np.array.return_value = returned_array = np.array([[1, 2], [3,
4]])
list_data = [[10, 1], [50, 2], [100, 3], [170, 5]]
data = [
StageItem(epoch=Epoch(timestamp=10, index=2), stage=SleepStage.n1),
StageItem(epoch=Epoch(timestamp=50, index=3), stage=SleepStage.n2),
StageItem(epoch=Epoch(timestamp=100, index=4),
stage=SleepStage.n3),
StageItem(epoch=Epoch(timestamp=170, index=5),
stage=SleepStage.rem)
]
psg_raw_data_collection = PSGRawDataCollection(subject_id=subject_id,
data=data)
psg_output_path = Constants.CROPPED_FILE_PATH.joinpath(
"subjectA_cleaned_psg.out")
PSGService.write(psg_raw_data_collection)
mock_np.array.assert_called_once_with(list_data)
mock_np.savetxt.assert_called_once_with(psg_output_path,
returned_array,
fmt='%f')
def get_valid_epochs(subject_id):
psg_collection = PSGService.load_cropped(subject_id)
motion_collection = MotionService.load_cropped(subject_id)
heart_rate_collection = HeartRateService.load_cropped(subject_id)
start_time = psg_collection.data[0].epoch.timestamp
motion_epoch_dictionary = RawDataProcessor.get_valid_epoch_dictionary(
motion_collection.timestamps, start_time)
hr_epoch_dictionary = RawDataProcessor.get_valid_epoch_dictionary(
heart_rate_collection.timestamps, start_time)
valid_epochs = []
for stage_item in psg_collection.data:
epoch = stage_item.epoch
if epoch.timestamp in motion_epoch_dictionary and epoch.timestamp in hr_epoch_dictionary \
and stage_item.stage != SleepStage.unscored:
valid_epochs.append(epoch)
return valid_epochs
def test_load_cropped_array(self, mock_pd):
subject_id = 'subject100'
cropped_psg_path = Constants.CROPPED_FILE_PATH.joinpath(
subject_id + "_cleaned_psg.out")
mock_pd.read_csv.return_value.values = np.array([[1, 2], [4, 5],
[10, 1]])
psg_collection = PSGService.load_cropped(subject_id)
mock_pd.read_csv.assert_called_once_with(str(cropped_psg_path),
delimiter=' ')
TestHelper.assert_models_equal(
self,
StageItem(epoch=Epoch(timestamp=1, index=0), stage=SleepStage.n2),
psg_collection.data[0])
TestHelper.assert_models_equal(
self,
StageItem(epoch=Epoch(timestamp=4, index=1), stage=SleepStage.rem),
psg_collection.data[1])
TestHelper.assert_models_equal(
self,
StageItem(epoch=Epoch(timestamp=10, index=2), stage=SleepStage.n1),
psg_collection.data[2])