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Lucas-McLucas-Mc
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Improves EDF speed / fixes bugs
1 parent 8269d41 commit 20dda53

11 files changed

+278
-250
lines changed

‎docs/conf.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ def __getattr__(cls, name):
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return MagicMock()
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MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot', 'pandas', 'scipy',
33-
'sklearn', 'sklearn.preprocessing', 'mne']
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'sklearn', 'sklearn.preprocessing']
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sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
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# -- General configuration ------------------------------------------------

‎requirements.txt

Lines changed: 0 additions & 1 deletion
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@@ -5,7 +5,6 @@ idna==2.9
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joblib==0.14.1
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kiwisolver==1.2.0
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matplotlib==3.2.1
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mne==0.20.5
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nose==1.3.7
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numpy==1.18.5
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pandas==1.0.3

‎sample-data/SC4001E0-PSG.edf

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‎sample-data/SC4001E0_PSG.dat

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‎sample-data/SC4001E0_PSG.hea

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‎sample-data/wave_4.dat

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‎sample-data/wave_4.edf

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‎sample-data/wave_4.hea

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,8 @@
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wave_4 7 1 3659 0:00 01/01/2001
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wave_4.dat 16x1000 1(1)/uV 15 0 5393 -12624 0 ECG
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wave_4.dat 16x100 2(1)/mg 13 0 1371 18209 0 Accelerometer_X
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wave_4.dat 16x100 2(1)/mg 13 0 1273 29556 0 Accelerometer_Y
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wave_4.dat 16x100 2(1)/mg 13 0 -473 -31584 0 Accelerometer_Z
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wave_4.dat 16 1(1) 15 0 32766 -29151 0 Marker
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wave_4.dat 16x5 1(-32767)/ms 15 0 -32768 13833 0 HRV
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wave_4.dat 16 -19.3447902992(3064)/degC 11 2048 2461 27731 0 DEV_Temperature

‎setup.py

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -63,7 +63,6 @@
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'joblib>=0.11',
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'kiwisolver>=1.1.0',
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'matplotlib>=2.0.0',
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'mne>=0.18.0',
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'numpy>=1.10.1',
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'pandas>=0.17.0',
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'pyparsing>=2.0.4',

‎tests/test_record.py

Lines changed: 17 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -256,7 +256,7 @@ def test_2f(self):
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"""
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# Uniform sample rates
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record_MIT = wfdb.rdrecord('sample-data/n16').__dict__
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record_EDF = wfdb.rdrecord('sample-data/n16.edf').__dict__
259+
record_EDF = wfdb.edf2mit('sample-data/n16.edf').__dict__
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261261
fields = list(record_MIT.keys())
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# Original MIT format method of checksum is outdated, sometimes
@@ -270,8 +270,13 @@ def test_2f(self):
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for field in fields:
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# Signal value will be slightly off due to C to Python type conversion
272272
if field == 'p_signal':
273-
true_array = np.array(record_MIT[field])
274-
pred_array = np.array(record_EDF[field])
273+
true_array = np.array(record_MIT[field]).flatten()
274+
pred_array = np.array(record_EDF[field]).flatten()
275+
# Prevent divide by zero warning
276+
for i,v in enumerate(true_array):
277+
if v == 0:
278+
true_array[i] = 1
279+
pred_array[i] = 1
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sig_diff = np.abs((pred_array - true_array) / true_array)
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sig_diff[sig_diff == -np.inf] = 0
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sig_diff[sig_diff == np.inf] = 0
@@ -299,8 +304,8 @@ def test_2g(self):
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"""
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# Non-uniform sample rates
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record_MIT = wfdb.rdrecord('sample-data/SC4001E0_PSG').__dict__
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record_EDF = wfdb.rdrecord('sample-data/SC4001E0-PSG.edf').__dict__
307+
record_MIT = wfdb.rdrecord('sample-data/wave_4').__dict__
308+
record_EDF = wfdb.edf2mit('sample-data/wave_4.edf').__dict__
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305310
fields = list(record_MIT.keys())
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# Original MIT format method of checksum is outdated, sometimes
@@ -309,19 +314,18 @@ def test_2g(self):
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# Original MIT format units are less comprehensive since they
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# default to mV if unknown.. therefore added more default labels
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fields.remove('units')
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# Initial value of signal will be off due to resampling done by
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# MNE in the EDF reading phase
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fields.remove('init_value')
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# Samples per frame will be off due to resampling done by MNE in
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# the EDF reading phase... I should probably fix this later
317-
fields.remove('samps_per_frame')
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319318
test_results = []
320319
for field in fields:
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# Signal value will be slightly off due to C to Python type conversion
322321
if field == 'p_signal':
323-
true_array = np.array(record_MIT[field])
324-
pred_array = np.array(record_EDF[field])
322+
true_array = np.array(record_MIT[field]).flatten()
323+
pred_array = np.array(record_EDF[field]).flatten()
324+
# Prevent divide by zero warning
325+
for i,v in enumerate(true_array):
326+
if v == 0:
327+
true_array[i] = 1
328+
pred_array[i] = 1
325329
sig_diff = np.abs((pred_array - true_array) / true_array)
326330
sig_diff[sig_diff == -np.inf] = 0
327331
sig_diff[sig_diff == np.inf] = 0

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