Merge pull request #410 from htwangtw/read-spike

Add support for Spike2 files

Author: smoia

phys2bids/io.py

@@ -538,3 +538,88 @@ def load_gep(filename):
     timeseries = [t_ch, trigger]
     timeseries.extend(data)
     return BlueprintInput(timeseries, freq, names, units, 1)
+
+
+def load_smr(filename, chtrig=0):
+    """Load Spike2 smr file and populate object phys_input.
+
+    Parameters
+    ----------
+    filename: str
+        Path to the spike smr or smrx file.
+
+    chtrig : int
+        Index of trigger channel.
+
+    Returns
+    -------
+    BlueprintInput
+
+    Note
+    ----
+    Index of chtrig is 1-index (i.e. spike2 channel number).
+
+    See Also
+    --------
+    physio_obj.BlueprintInput
+    """
+    import sonpy
+
+    # taken from sonpy demo
+    read_data = {
+        sonpy.lib.DataType.Adc: sonpy.lib.SonFile.ReadInts,
+        sonpy.lib.DataType.EventFall: sonpy.lib.SonFile.ReadEvents,
+        sonpy.lib.DataType.EventRise: sonpy.lib.SonFile.ReadEvents,
+        sonpy.lib.DataType.EventBoth: sonpy.lib.SonFile.ReadEvents,
+        sonpy.lib.DataType.Marker: sonpy.lib.SonFile.ReadMarkers,
+        sonpy.lib.DataType.AdcMark: sonpy.lib.SonFile.ReadWaveMarks,
+        sonpy.lib.DataType.RealMark: sonpy.lib.SonFile.ReadRealMarks,
+        sonpy.lib.DataType.TextMark: sonpy.lib.SonFile.ReadTextMarks,
+        sonpy.lib.DataType.RealWave: sonpy.lib.SonFile.ReadFloats,
+    }
+
+    smrfile = sonpy.lib.SonFile(filename, True)
+    time_base = smrfile.GetTimeBase()
+    n_channels = smrfile.MaxChannels()
+    freq, names, units, timeseries = [], [], [], []
+    for i in range(n_channels):
+        current_channel = smrfile.ChannelType(i)
+        max_n_tick = smrfile.ChannelMaxTime(i)
+        if current_channel != sonpy.lib.DataType.Off and max_n_tick > 0:
+            max_n_tick = smrfile.ChannelMaxTime(i)
+            sample_rate = smrfile.GetIdealRate(i)
+            if current_channel == sonpy.lib.DataType.Adc:
+                divide = smrfile.ChannelDivide(i)
+            else:  # marker channels
+                divide = 1 / (time_base * sample_rate)
+            # conversion factor from CED spike2 doc
+            # http://ced.co.uk/img/Spike9.pdf
+            gain = smrfile.GetChannelScale(i) / 6553.6
+            offset = smrfile.GetChannelOffset(i)
+            name = smrfile.GetChannelTitle(chan=i)
+            unit = smrfile.GetChannelUnits(chan=i)
+
+            n_samples = int(np.floor((max_n_tick) / divide))
+            raw_signal = read_data[current_channel](
+                smrfile, chan=i, nMax=n_samples, tFrom=0, tUpto=max_n_tick
+            )
+
+            signal = np.array(raw_signal) * gain + offset
+
+            # save the data
+            freq.append(sample_rate)
+            names.append(name)
+            units.append(unit)
+            timeseries.append(signal)
+
+    # use the channel with highest sample rate to create time stamps
+    idx_max = np.argmax(freq)
+    n_timepoints = len(timeseries[idx_max])  # end point included
+    time = np.arange(n_timepoints) * freq[idx_max]
+
+    # prepend to the existing list
+    freq = [freq[idx_max]] + freq
+    timeseries = [time] + timeseries
+    units = ["s"] + units
+    names = ["time"] + names
+    return BlueprintInput(timeseries, freq, names, units, chtrig)

phys2bids/tests/conftest.py

@@ -138,3 +138,13 @@ def ge_badfiles(testpath):
     tmp = fetch_file("tdmyn", testpath, "PPGData_epiRT_columnscsv_00_00_000")
     tmp = fetch_file("b6skq", testpath, "PPGData_epiRT_columnstsv_00_00_000")
     return fetch_file("8235b", testpath, "PPGData_epiRT_string0000_00_00_000")
+
+
+@pytest.fixture
+def spike2_smrx_file(testpath):
+    return fetch_file("7x5qw", testpath, "Test_ppg_pulse_spike2.smrx")
+
+
+@pytest.fixture
+def spike2_smr_file(testpath):
+    return fetch_file("zdpfr", testpath, "Test_ppg_pulse_spike2.smr")

phys2bids/tests/test_io.py

@@ -1,5 +1,6 @@
 import math
 import os
+import sys
 
 import numpy as np
 import pytest
@@ -214,3 +215,37 @@ def test_load_gep_two_files_resp(ge_two_gep_files_resp, testpath):
     gep_data2 = np.loadtxt(os.path.join(testpath, "PPGData_epiRT_0000000000_00_00_000.gep"))
     assert np.array_equal(gep_data1, phys_obj.timeseries[2])
     assert np.array_equal(gep_data2, phys_obj.timeseries[3])
+
+
+@pytest.mark.skipif(
+    sys.version_info < (3, 7) or sys.version_info > (3, 9),
+    reason="Requires python between 3.7 and 3.9",
+)
+@pytest.mark.xfail(reason="We need to fix sonpy install")
+def test_load_smr(spike2_smr_file, spike2_smrx_file):
+    chtrig = 5
+
+    # 32-bit file
+    phys_obj = io.load_smr(spike2_smr_file, chtrig)
+    assert phys_obj.ch_name[0] == "time"
+    assert phys_obj.freq[0] == 1000.0
+    assert phys_obj.units[0] == "s"
+
+    # checks that the scanner strigger is in the right channel
+    # the marker channels are stored as binary
+    assert phys_obj.ch_name[chtrig] == "Scan Vol"
+    assert phys_obj.freq[chtrig] == 200.0
+    assert phys_obj.units[chtrig] == ""
+    assert len(phys_obj.timeseries[chtrig]) == 60
+
+    # 64-bit file should have the same
+    phys_obj = io.load_smr(spike2_smrx_file, chtrig)
+    assert phys_obj.ch_name[0] == "time"
+    assert phys_obj.freq[0] == 1000.0
+    assert phys_obj.units[0] == "s"
+    # checks that the scanner trigger is in the right channel
+    # the marker channels are stored as binary
+    assert phys_obj.ch_name[chtrig] == "Scan Vol"
+    assert phys_obj.freq[chtrig] == 200.0
+    assert phys_obj.units[chtrig] == ""
+    assert len(phys_obj.timeseries[chtrig]) == 60

setup.cfg

@@ -36,6 +36,8 @@ packages = find:
 include_package_data = True
 
 [options.extras_require]
+spike2 =
+    sonpy >=1.7.5;python_version=='3.7.*,3.8.*,3.9.*'
 acq =
     bioread >=1.0.5
 mat=
@@ -55,6 +57,7 @@ style =
 interfaces =
     %(acq)s
     %(mat)s
+    %(spike2)s
 test =
     pytest >=5.3
     pytest-cov