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[NeuralynxRawIO] Factor ncs blocks and repackage #905

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Merged
JuliaSprenger merged 89 commits into from
Nov 25, 2020
Merged

[NeuralynxRawIO] Factor ncs blocks and repackage #905

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0e1079e
Move constants into class so accessible for testing.
Oct 9, 2020
a00174f
Test of building NcsBlocks.
Oct 12, 2020
623e4f7
Handle old files with truncated frequency in header and test.
Oct 13, 2020
fa37c1c
Change interface on parse versus build.
Nov 7, 2020
ba90b78
Tests for PRE4 type and code corrections.
Nov 7, 2020
fe9648f
Fix initializer, update loop vars.
Oct 26, 2020
00ac190
Add additional tests on v5.5.1 with 2 blocks
Oct 26, 2020
3fd8256
Tests of block construction for incomplete blocks
Oct 26, 2020
b4b3272
Fix up single block case.
Oct 26, 2020
9e0c17c
Remove unneeded classes. Clean up style.
Nov 7, 2020
32d52c3
Add test of side effects of read_ncs_files
Oct 27, 2020
0baa2bd
Use NcsBlocksFactory and logical or.
Nov 7, 2020
76a577f
Fix off by one in range for list. Comments.
Oct 28, 2020
6d29d7b
Use standard time calculation for last time of block.
Oct 28, 2020
88436f6
Remove test with tolerance over whole length. Fix microsPerSampUsed a…
Oct 29, 2020
91c22a7
Tests of raw io for incomplete records multiple block case.
Oct 29, 2020
f56cd74
Update stop times to include time for samples in partially filled rec…
Oct 29, 2020
02e2c9b
PEP and style cleanup. Corrected gap comment.
Oct 29, 2020
d8d0ee2
Line shortening for PEP8.
Oct 29, 2020
09bc595
More PEP8 items.
Nov 7, 2020
f70da3f
Move constants into class so accessible for testing.
Nov 17, 2020
bb2a1f1
Test of building NcsBlocks.
Nov 17, 2020
5cf3880
Handle old files with truncated frequency in header and test.
Oct 13, 2020
dfcf977
Change interface on parse versus build.
Oct 16, 2020
3ee754a
Tests for PRE4 type and code corrections.
Oct 19, 2020
5eb1c23
Fix initializer, update loop vars.
Oct 26, 2020
ee5e8c6
Add additional tests on v5.5.1 with 2 blocks
Oct 26, 2020
90000f1
Tests of block construction for incomplete blocks
Oct 26, 2020
9e7633f
Fix up single block case.
Oct 26, 2020
2fbe5b8
Remove unneeded classes. Clean up style.
Oct 27, 2020
2e9e6d7
Use private dtype by new private name.
Oct 27, 2020
7b980c8
Add test of side effects of read_ncs_files
Oct 27, 2020
edc984d
Use NcsBlocksFactory and logical or.
Oct 27, 2020
5635177
Fix off by one in range for list. Comments.
Oct 28, 2020
2215a6f
Use standard time calculation for last time of block.
Oct 28, 2020
7b60634
Remove test with tolerance over whole length. Fix microsPerSampUsed a…
Oct 29, 2020
7a39f69
Tests of raw io for incomplete records multiple block case.
Oct 29, 2020
65f691f
PEP and style cleanup. Corrected gap comment.
Oct 29, 2020
484cd39
Line shortening for PEP8.
Oct 29, 2020
bf0709a
More PEP8 items.
Oct 29, 2020
3293377
Remove conflict markers.
Nov 17, 2020
cdcb110
More conflict resolution for rebase.
Nov 17, 2020
a556d20
Correct column error in data tested.
Nov 17, 2020
9ac215f
Update comment on PRE4 file limitations.
Oct 29, 2020
fe9ab5e
Tests for PRE4 file type in Cheetah v4.0.2.
Oct 29, 2020
99c96e8
PEP8 indent corrections.
Oct 29, 2020
8f02dd8
Small PEP8 correctin.
Oct 29, 2020
593b77a
Proper time opened header for BML and use of frequency.
Oct 30, 2020
45bef5c
Download files and activate tests for BML style files.
Oct 30, 2020
4e61fa9
record start and end times in NcsBlocks for verification later
Oct 30, 2020
20cfd07
Code to handle digitallynx with cheetah v1
Oct 30, 2020
79a9596
Fixes to handle split block.
Nov 2, 2020
b6bf030
Tests NcsBlockFactory with split blocks and unfilled records.
Nov 2, 2020
ad93089
Tests of data read in ncs files with partial records and split blocks.
Nov 2, 2020
3351e8f
Handle testing less data than available in all segments.
Nov 4, 2020
922e893
Read and test with partial blocks. Test all types in test_neuralyxio.
Nov 6, 2020
e42444a
Read and test with partial blocks. Test all types in test_neuralyxio.
Nov 17, 2020
4667c8f
PEP8 fix ups.
Nov 6, 2020
32ce51d
Language and function renaming.
Nov 6, 2020
5ccd4db
verify block function and test
Nov 9, 2020
4e1217f
Call renamed functions.
Nov 9, 2020
bd767ea
use _verifyBlockStructure to ensure same structure
Nov 9, 2020
699736f
Properly limit samples compared.
Nov 9, 2020
798b53f
Temporarily remove data test.
Nov 17, 2020
0fc8716
Remove duplication of some older tests.
Nov 10, 2020
1105bde
Comments on structure of segment defining fields.
Nov 11, 2020
b739375
Factor out NcsBlock object.
Nov 11, 2020
b395a26
Change factory methods to use NcsBlock.
Nov 11, 2020
4bc384f
Rewrite tests for NcsBlocks refactoring.
Nov 11, 2020
aa84538
More refactoring of NcsBlocks.
Nov 11, 2020
dbcb867
Gather all NcsBlocks first, then build segements.
Nov 13, 2020
2f4bb0f
change name to _scan_ncs_files rather than read
Nov 13, 2020
ca12653
Proper formatting of number of NcsBlock structures.
Nov 14, 2020
0561ffa
Move neuralynxrawio to subdirectory to factor our other classes.
Nov 14, 2020
fdd2e52
Eliminate WholeTimesPositionBlock as class.
Nov 16, 2020
7141334
Factor helper classes out in package.
Nov 17, 2020
7849078
PEP8 fix ups.
Nov 17, 2020
115da4c
More PEP8 fixups.
Nov 17, 2020
da2fb8a
Changes to address comments by Julia Sprenger
Nov 20, 2020
08ddf17
Fix up some PEP8 comments.
Nov 20, 2020
e418709
Roll back inadvertent commit of local gin repository.
Nov 20, 2020
c9a3194
Fixup improperly resolved conflicts.
Nov 21, 2020
146de1a
Explicit skip of troublesome test_keep_original_spike_times.
Nov 21, 2020
bde1c19
More PEP8 fixups.
Nov 21, 2020
7ef3578
Replace inadvertently deleted package file.
Nov 21, 2020
61da495
Repaired inadvertent modification of blocks variable in nixio
Nov 21, 2020
36fcbe0
Another conflict marker removed.
Nov 21, 2020
0ed5529
Take 6.3.2 io tests out.
Nov 21, 2020
49e32b9
Specify no entitites to test.
Nov 24, 2020
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2 changes: 1 addition & 1 deletion neo/io/neuralynxio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
"""

from neo.io.basefromrawio import BaseFromRaw
from neo.rawio.neuralynxrawio import NeuralynxRawIO
from neo.rawio.neuralynxrawio.neuralynxrawio import NeuralynxRawIO


class NeuralynxIO(NeuralynxRawIO, BaseFromRaw):
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2 changes: 1 addition & 1 deletion neo/rawio/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@
from neo.rawio.examplerawio import ExampleRawIO
from neo.rawio.intanrawio import IntanRawIO
from neo.rawio.micromedrawio import MicromedRawIO
from neo.rawio.neuralynxrawio import NeuralynxRawIO
from neo.rawio.neuralynxrawio.neuralynxrawio import NeuralynxRawIO
from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO
from neo.rawio.neuroscoperawio import NeuroScopeRawIO
from neo.rawio.nixrawio import NIXRawIO
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