gin commit from Ivory

New files: 8

.gitignore

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+.DS_Store

EEG for MNE/104.edf

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+/annex/objects/MD5-s28445376--c7489fc7a5953a50b4ae9cb7212df170

EEG for MNE/LED_28_06_2012_104.eeg

@@ -0,0 +1 @@
+/annex/objects/MD5-s27015720--bfc7ac8e710c6d38633820aa761faa26

EEG for MNE/LED_28_06_2012_104.vhdr

@@ -0,0 +1,103 @@
+Brain Vision Data Exchange Header File Version 1.0
+; Data created by the Vision Recorder
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=LED_28_06_2012_104.eeg
+MarkerFile=LED_28_06_2012_104.vmrk
+DataFormat=BINARY
+; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
+DataOrientation=MULTIPLEXED
+NumberOfChannels=19
+; Sampling interval in microseconds
+SamplingInterval=1000
+
+[Binary Infos]
+BinaryFormat=INT_16
+
+[Channel Infos]
+; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
+; <Resolution in "Unit">,<Unit>, Future extensions..
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in channel names are coded as "\1".
+Ch1=Fp1,,0.1,µV
+Ch2=Fp2,,0.1,µV
+Ch3=F3,,0.1,µV
+Ch4=F4,,0.1,µV
+Ch5=C3,,0.1,µV
+Ch6=C4,,0.1,µV
+Ch7=P3,,0.1,µV
+Ch8=P4,,0.1,µV
+Ch9=O1,,0.1,µV
+Ch10=O2,,0.1,µV
+Ch11=F7,,0.1,µV
+Ch12=F8,,0.1,µV
+Ch13=T3,,0.1,µV
+Ch14=T4,,0.1,µV
+Ch15=T5,,0.1,µV
+Ch16=T6,,0.1,µV
+Ch17=Fz,,0.1,µV
+Ch18=Cz,,0.1,µV
+Ch19=Pz,,0.1,µV
+
+[Comment]
+
+A m p l i f i e r  S e t u p
+============================
+Number of channels: 19
+Sampling Rate [Hz]: 1000
+Sampling Interval [µS]: 1000
+
+Channels
+--------
+#     Name      Phys. Chn.    Resolution / Unit   Low Cutoff [s]   High Cutoff [Hz]   Notch [Hz]    Series Res. [kOhm] Gradient         Offset
+1     Fp1         1                0.1 µV             10              250              Off                0                 
+2     Fp2         2                0.1 µV             10              250              Off                0                 
+3     F3          3                0.1 µV             10              250              Off                0                 
+4     F4          4                0.1 µV             10              250              Off                0                 
+5     C3          5                0.1 µV             10              250              Off                0                 
+6     C4          6                0.1 µV             10              250              Off                0                 
+7     P3          7                0.1 µV             10              250              Off                0                 
+8     P4          8                0.1 µV             10              250              Off                0                 
+9     O1          9                0.1 µV             10              250              Off                0                 
+10    O2          10               0.1 µV             10              250              Off                0                 
+11    F7          11               0.1 µV             10              250              Off                0                 
+12    F8          12               0.1 µV             10              250              Off                0                 
+13    T3          13               0.1 µV             10              250              Off                0                 
+14    T4          14               0.1 µV             10              250              Off                0                 
+15    T5          15               0.1 µV             10              250              Off                0                 
+16    T6          16               0.1 µV             10              250              Off                0                 
+17    Fz          17               0.1 µV             10              250              Off                0                 
+18    Cz          18               0.1 µV             10              250              Off                0                 
+19    Pz          19               0.1 µV             10              250              Off                0                 
+
+S o f t w a r e  F i l t e r s
+==============================
+Disabled
+
+
+Data Electrodes Selected Impedance Measurement Range: 0 - 5 kOhm
+Ground Electrode Selected Impedance Measurement Range: 0 - 10 kOhm
+Reference Electrode Selected Impedance Measurement Range: 0 - 10 kOhm
+Impedance [kOhm] at 14:52:52 :
+Fp1:          1
+Fp2:          1
+F3:           1
+F4:           1
+C3:           1
+C4:           1
+P3:           3
+P4:           1
+O1:           7
+O2:           3
+F7:           1
+F8:           3
+T3:           1
+T4:           2
+T5:           2
+T6:           1
+Fz:           1
+Cz:           2
+Pz:           1
+Ref:          3
+Gnd:         30

EEG for MNE/LED_28_06_2012_104.vmrk

@@ -0,0 +1,693 @@
+Brain Vision Data Exchange Marker File, Version 1.0
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=LED_28_06_2012_104.eeg
+
+[Marker Infos]
+; Each entry: Mk<Marker number>=<Type>,<Description>,<Position in data points>,
+; <Size in data points>, <Channel number (0 = marker is related to all channels)>
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in type or description text are coded as "\1".
+Mk1=New Segment,,1,1,0,20120628145438837393
+Mk2=Stimulus,S  6,3638,1,0
+Mk3=Stimulus,S  2,4683,1,0
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+Mk6=Stimulus,S  4,7675,1,0
+Mk7=Stimulus,S  4,8672,1,0
+Mk8=Stimulus,S  4,9669,1,0
+Mk9=Stimulus,S  4,10666,1,0
+Mk10=Stimulus,S  2,11663,1,0
+Mk11=Stimulus,S  4,12660,1,0
+Mk12=Stimulus,S  4,13657,1,0
+Mk13=Stimulus,S  4,14654,1,0
+Mk14=Stimulus,S  4,15651,1,0
+Mk15=Stimulus,S  4,16648,1,0
+Mk16=Stimulus,S  4,17645,1,0
+Mk17=Stimulus,S  2,18642,1,0
+Mk18=Stimulus,S  4,19639,1,0
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+Mk674=Stimulus,S  4,696322,1,0
+Mk675=Stimulus,S  4,697319,1,0
+Mk676=Stimulus,S  2,698316,1,0
+Mk677=Stimulus,S  4,699313,1,0
+Mk678=Stimulus,S  4,700310,1,0
+Mk679=Stimulus,S  4,701307,1,0
+Mk680=Stimulus,S  4,702304,1,0
+Mk681=Stimulus,S  4,703301,1,0
+Mk682=Stimulus,S  3,704141,1,0

mnetonix/bvtonix.py

@@ -0,0 +1,27 @@
+import os
+import sys
+import mne
+import mnetonix as m2n
+
+
+def main():
+    if len(sys.argv) < 2:
+        print("Please provide BrainVision vhdr filename as argument")
+        sys.exit(1)
+
+    bvfname = sys.argv[1]
+    locname = None
+    if len(sys.argv) > 2:
+        locname = sys.argv[2]
+        locname = os.path.abspath(locname)
+    root, ext = os.path.splitext(bvfname)
+    nfname = root + os.path.extsep + "nix"
+    print(f"Converting '{bvfname}' to NIX")
+    bvf = mne.io.read_raw_brainvision(bvfname)
+
+    m2n.write_raw_mne(nfname, bvf)
+    bvf.close()
+
+
+if __name__ == "__main__":
+    main()

mnetonix/edftonix.py

@@ -0,0 +1,28 @@
+import os
+import sys
+import mne
+import mnetonix as m2n
+
+
+def main():
+    if len(sys.argv) < 2:
+        print("Please provide an EDF filename as argument")
+        sys.exit(1)
+
+    efname = sys.argv[1]
+    locname = None
+    if len(sys.argv) > 2:
+        locname = sys.argv[2]
+        locname = os.path.abspath(locname)
+    root, ext = os.path.splitext(efname)
+    nfname = root + os.path.extsep + "nix"
+    print(f"Converting '{efname}' to NIX")
+    # stim_channel=False marks the last channel as "EDF Annotations"
+    ef = mne.io.read_raw_edf(efname, montage=locname,
+                             preload=True, stim_channel=False)
+    m2n.write_raw_mne(nfname, ef)
+    ef.close()
+
+
+if __name__ == "__main__":
+    main()

edftonix.py

@@ -1,9 +1,6 @@
-import os
-import sys
 from collections.abc import Iterable
 import matplotlib.pyplot as plt
 import numpy as np
-import mne
 import nixio as nix
 
 
@@ -22,6 +19,8 @@ def plot_channel(data_array, index):
 
 
 def create_md_tree(section, values):
+    if values is None:
+        return
     for k, v in values.items():
         if v is None:
             continue
@@ -52,31 +51,16 @@ def create_md_tree(section, values):
         section.create_property(k, v)
 
 
-def main():
-    if len(sys.argv) < 2:
-        print("Please provide an EDF filename as argument")
-        sys.exit(1)
-
-    efname = sys.argv[1]
-    locname = None
-    if len(sys.argv) > 2:
-        locname = sys.argv[2]
-        locname = os.path.abspath(locname)
-    root, ext = os.path.splitext(efname)
-    nfname = root + os.path.extsep + "nix"
-    print(f"Converting '{efname}' to NIX")
-    # stim_channel=False marks the last channel as "EDF Annotations"
-    ef = mne.io.read_raw_edf(efname, montage=locname,
-                             preload=True, stim_channel=False)
-    efinfo = ef.info
-    extrainfo = ef._raw_extras
+def write_raw_mne(nfname, mneraw):
+    mneinfo = mneraw.info
+    extrainfo = mneraw._raw_extras
 
     # data and times
-    data = ef.get_data()
-    time = ef.times
+    data = mneraw.get_data()
+    time = mneraw.times
 
-    nchan = efinfo["nchan"]
-    print(f"Found {nchan} channels with {ef.n_times} samples per channel")
+    nchan = mneinfo["nchan"]
+    print(f"Found {nchan} channels with {mneraw.n_times} samples per channel")
 
     # Create NIX file
     nf = nix.File(nfname, nix.FileMode.Overwrite)
@@ -90,8 +74,8 @@ def main():
     for dimlen in data.shape:
         if dimlen == nchan:
             # channel labels: SetDimension
-            da.append_set_dimension(labels=ef.ch_names)
-        elif dimlen == ef.n_times:
+            da.append_set_dimension(labels=mneraw.ch_names)
+        elif dimlen == mneraw.n_times:
             # times: RangeDimension
             # NOTE: EDF always uses seconds
             da.append_range_dimension(ticks=time, label="time", unit="s")
@@ -99,23 +83,18 @@ def main():
     # Write metadata to NIX
     # info dictionary
     infomd = nf.create_section("Info", "File metadata")
-    create_md_tree(infomd, efinfo)
+    create_md_tree(infomd, mneinfo)
     # extras
     if len(extrainfo) > 1:
         for idx, emd_i in enumerate(extrainfo):
             extrasmd = nf.create_section(f"Extras-{idx}",
                                          "Raw Extras metadata")
             create_md_tree(extrasmd, emd_i)
-    else:
+    elif extrainfo:
         extrasmd = nf.create_section("Extras", "Raw Extras metadata")
         create_md_tree(extrasmd, extrainfo[0])
 
     # all done
     nf.close()
-    ef.close()
     print(f"Created NIX file at '{nfname}'")
     print("Done")
-
-
-if __name__ == "__main__":
-    main()