[DATALAD] Recorded changes

README.md

@@ -2,3 +2,9 @@
 
 Gin: https://gin.g-node.org/TheChymera/mvmdna
 GitHub: https://github.com/TheChymera/mvmnda
+
+## Internal
+
+### Adding data
+
+Due to Git and Git-annex intricaciles, apparently “shared” mode causes issues, please put new data in `/mnt/DATA/data/studies/manish/incoming/mvmnda` on typhon.

rawdata/code/reposit.py

@@ -2,17 +2,21 @@ from datetime import datetime
 from dateutil import tz
 from pathlib import Path
 from neuroconv.converters import SpikeGLXConverterPipe
+import json
 
-folder_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/sub-pixelfiber/ses-01"
-#folder_path = "../../sourcedata/M387-2023-10-20_g0/M387-2023-10-20_g0_imec0/M387-2023-10-20_g0_tcat.imec0.ap.bin"
-#folder_path = "../../sourcedata/M387-2023-10-20_g0"
-converter = SpikeGLXConverterPipe(folder_path=folder_path)
+dir_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/Ach_DualPixel_7_14_23/Ach_DualPixel_7_14_23_g0"
+#dir_path = "/mnt/DATA/data/studies/manish/mvmnda/sourcedata/sub-pixelfiber/M387-2023-10-20_g0"
+#dir_path = "../../sourcedata/M387-2023-10-20_g0"
+converter = SpikeGLXConverterPipe(folder_path=dir_path)
 
 # Extract what metadata we can from the source files
 metadata = converter.get_metadata()
-# For data provenance we add the time zone information to the conversion
+
+# The following doesn't work as per the guide ( https://neuroconv.readthedocs.io/en/main/conversion_examples_gallery/recording/spikeglx.html#single-stream ), apparently no session_start_time is read in:
 #session_start_time = metadata["NWBFile"]["session_start_time"].replace(tzinfo=tz.gettz("US/Pacific"))
-#metadata["NWBFile"].update(session_start_time=session_start_time)
+# So we do:
+session_start_time = datetime.now(tz.tzlocal())
+metadata["NWBFile"].update(session_start_time=session_start_time)
 
 # Choose a path for saving the nwb file and run the conversion
 nwbfile_path = "/mnt/DATA/data/studies/manish/mvmnda/rawdata/my_spikeglx_session.nwb"

rawdata/dataset_description.json

@@ -0,0 +1,8 @@
+{
+  "author": [
+    "Alice A",
+    " Bob B",
+    "Alice A",
+    " Bob B"
+  ]
+}

rawdata/my_spikeglx_session.nwb

@@ -0,0 +1 @@
+../.git/annex/objects/0W/JZ/MD5E-s181840--ab0823394beae190d1921dfdbbb07ff8.nwb/MD5E-s181840--ab0823394beae190d1921dfdbbb07ff8.nwb

rawdata/participants.tsv

@@ -0,0 +1,2 @@
+subject_id
+sub-pixelfiber

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rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_ephys.json

@@ -0,0 +1,3 @@
+{
+  "PowerLineFrequency": 60
+}

rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_ephys.nwb

@@ -0,0 +1 @@
+../../../../.git/annex/objects/7P/mZ/MD5E-s189166911064--c8616e804722c783a2d6a548e0bdda3c.nwb/MD5E-s189166911064--c8616e804722c783a2d6a548e0bdda3c.nwb

rawdata/sub-pixelfiber/ses-01/ephys/sub-pixelfiber_ses-01_probes.tsv

@@ -0,0 +1,2 @@
+probe_id	type
+probe-None	Neuropixel

rawdata/sub-pixelfiber/sub-pixelfiber_sessions.tsv

@@ -0,0 +1,2 @@
+session_id
+ses-01

sourcedata/M387-2023-10-20_g0/M387-2023-10-20_g0_ct_offsets.txt

@@ -0,0 +1,4 @@
+smp_imap0:	0
+smp_nidq:	0
+sec_imap0:	0.000000
+sec_nidq:	0.000000

sourcedata/M387-2023-10-20_g0/M387-2023-10-20_g0_fyi.txt

@@ -0,0 +1,5 @@
+outpath_probe0=D:/NPX_Data/M387/M387-2023-10-20_g0/M387-2023-10-20_g0_imec0
+outpath_top=D:/NPX_Data/M387/M387-2023-10-20_g0
+supercat_element={D:/NPX_Data/M387,M387-2023-10-20_g0}
+sync_imec0=D:/NPX_Data/M387/M387-2023-10-20_g0/M387-2023-10-20_g0_imec0/M387-2023-10-20_g0_tcat.imec0.ap.xd_384_6_500.txt
+sync_ni=D:/NPX_Data/M387/M387-2023-10-20_g0/M387-2023-10-20_g0_tcat.nidq.xa_0_500.txt

sourcedata/M387-2023-10-20_g0/M387-2023-10-20_g0_imec0/M387-2023-10-20_g0_tcat.imec0.ap.bin

@@ -0,0 +1 @@
+../../../.git/annex/objects/Px/V2/MD5E-s28380712360--c7f100aa24922e58c75de1b4de6530f6.ap.bin/MD5E-s28380712360--c7f100aa24922e58c75de1b4de6530f6.ap.bin

sourcedata/M387-2023-10-20_g0/M387-2023-10-20_g0_imec0/M387-2023-10-20_g0_tcat.imec0.lf.bin

@@ -0,0 +1 @@
+../../../.git/annex/objects/3M/54/MD5E-s2365059620--093f01a35829e4f045abe67683fa57f9.lf.bin/MD5E-s2365059620--093f01a35829e4f045abe67683fa57f9.lf.bin

sourcedata/M387-2023-10-20_g0/M387-2023-10-20_g0_tcat.nidq.meta

@@ -0,0 +1,50 @@
+acqMnMaXaDw=0,0,8,1
+appVersion=20230323
+catGTCmdline0=<CatGT -dir=D:/NPX_Data/M387 -run=M387-2023-10-20 -g=0 -t=0 -prb_fld -t_miss_ok -ni -ap -prb=0 -gblcar -chnexcl={0;191} -xd=0,0,384,6,500>
+catGVals=0,0
+catNFiles=1
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+fileCreateTime=2023-10-30T10:02:07
+fileCreateTime_original=2023-10-20T16:48:50
+fileName=
+fileSHA1=0
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+fileTimeSecs=1228.594336
+firstSample=62458838
+gateMode=Immediate
+nDataDirs=1
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+niAiRangeMax=5
+niAiRangeMin=-5
+niAiTermination=Default
+niClockLine1=Internal
+niClockSource=PXI1Slot3_8ch_IntMax : 31250.000000
+niDev1=PXI1Slot3
+niDev1ProductName=PXI-6221
+niMAChans1=
+niMAGain=1
+niMNChans1=
+niMNGain=200
+niMaxInt=32768
+niMuxFactor=32
+niSampRate=31250
+niStartEnable=false
+niStartLine=PXI1Slot3/port0/line0
+niXAChans1=0:7
+niXDBytes1=1
+niXDChans1=0:7
+snsMnMaXaDw=0,0,8,1
+snsSaveChanSubset=all
+syncNiChan=0
+syncNiChanType=1
+syncNiThresh=1.1
+syncSourceIdx=3
+syncSourcePeriod=1
+trigMode=Immediate
+typeImEnabled=1
+typeNiEnabled=1
+typeObEnabled=0
+typeThis=nidq
+userNotes=
+~snsChanMap=(0,0,32,8,1)(XA0;0:0)(XA1;1:1)(XA2;2:2)(XA3;3:3)(XA4;4:4)(XA5;5:5)(XA6;6:6)(XA7;7:7)(XD0;8:8)
+~snsShankMap=(1,2,0)

sourcedata/NP2_kilosortChanMap.mat

@@ -0,0 +1 @@
+../.git/annex/objects/fz/kw/MD5E-s2045--c8420dc59e38229628261d833f637977.mat/MD5E-s2045--c8420dc59e38229628261d833f637977.mat

sourcedata/neuropixPhase3A_kilosortChanMap.mat

@@ -0,0 +1 @@
+../.git/annex/objects/Q2/kx/MD5E-s2001--bdc2ce603e81292c9d5e631a083d4ab5.mat/MD5E-s2001--bdc2ce603e81292c9d5e631a083d4ab5.mat

sourcedata/neuropixPhase3A_option4_kilosortChanMap.mat

@@ -0,0 +1 @@
+../.git/annex/objects/59/43/MD5E-s1592--0f991e2a0cda7da250578d5541d23947.mat/MD5E-s1592--0f991e2a0cda7da250578d5541d23947.mat

sourcedata/neuropixPhase3B1_kilosortChanMap.mat

@@ -0,0 +1 @@
+../.git/annex/objects/z8/4v/MD5E-s1996--9ac179ee20be8b80f783252a702846a6.mat/MD5E-s1996--9ac179ee20be8b80f783252a702846a6.mat

sourcedata/neuropixPhase3B2_kilosortChanMap.mat

@@ -0,0 +1 @@
+../.git/annex/objects/xZ/gx/MD5E-s2043--62616c6320caa746a4f1835e7772397c.mat/MD5E-s2043--62616c6320caa746a4f1835e7772397c.mat

sourcedata/sub-pixelfiber/ses-01/Ach_DualPixel_7_14_23_g0_imec0/Ach_DualPixel_7_14_23_g0_t0.imec0.ap.meta

@@ -1 +0,0 @@
-../../../../.git/annex/objects/wX/qj/SHA256E-s20242--9e568b8ea970491c5a342aeca3f07ba713058c4bbc86dc4827db2662c4785a6b.ap.meta/SHA256E-s20242--9e568b8ea970491c5a342aeca3f07ba713058c4bbc86dc4827db2662c4785a6b.ap.meta

sourcedata/sub-pixelfiber/ses-01/Ach_DualPixel_7_14_23_g0_imec0/Ach_DualPixel_7_14_23_g0_t0.imec0.lf.meta

@@ -1 +0,0 @@
-../../../../.git/annex/objects/vv/17/SHA256E-s20421--7957edc73e53160620dfe1b11318f6d64bc3cdbc7ee1ef0e6a51d32ef62d4ee8.lf.meta/SHA256E-s20421--7957edc73e53160620dfe1b11318f6d64bc3cdbc7ee1ef0e6a51d32ef62d4ee8.lf.meta