Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] BEP 020 Eye Tracking #1128

Open
wants to merge 193 commits into
base: master
Choose a base branch
from
Open
Changes from 1 commit
Commits
Show all changes
193 commits
Select commit Hold shift + click to select a range
a73a9ea
create branch bep020
chloepasturel Oct 1, 2021
b43e979
Add datatype metadata and suffixes for eye tracking
chloepasturel Oct 1, 2021
ac14d18
bep020 md
greckla Nov 29, 2021
3316ef5
Update 10-eye-tracking.md
greckla Nov 29, 2021
033a948
minor update md
greckla Nov 29, 2021
971ac2a
minor updates md 2
greckla Nov 29, 2021
6236f83
final changes and working version with mkdocs
Dec 1, 2021
1d71719
add forgotten example
Dec 1, 2021
131b75d
final changes
Dec 1, 2021
b7f4d5d
latest changes
Jun 15, 2022
5aa62f7
Update 10-eye-tracking.md
mszinte Jun 16, 2022
686a5f3
Apply suggestions from code review
Remi-Gau Nov 12, 2022
4a46c9f
Merge branch 'master' into bep020
Remi-Gau Nov 12, 2022
0388cc1
fix bad latin
Remi-Gau Nov 12, 2022
e4f72c9
md lint
Remi-Gau Nov 12, 2022
19d4b6c
fix yml
Remi-Gau Nov 12, 2022
7b6721d
md lint
Remi-Gau Nov 12, 2022
6a71758
lint yml
Remi-Gau Nov 12, 2022
7941bab
add semantic line breaks
Remi-Gau Nov 12, 2022
f1c255b
move suffix
Remi-Gau Nov 12, 2022
2ffe348
rm CogPOID and CogAtlas yml
Remi-Gau Nov 12, 2022
e7658c9
move some metadata
Remi-Gau Nov 12, 2022
3d2bf96
move more metadata
Remi-Gau Nov 12, 2022
0369d4e
move more metadata
Remi-Gau Nov 12, 2022
53e80f1
rely on task.yml for events
Remi-Gau Nov 12, 2022
9f87572
change extension to tsv
Remi-Gau Nov 12, 2022
d19eaf8
fix schema
Remi-Gau Nov 12, 2022
d222325
fix links
Remi-Gau Nov 12, 2022
7c3a071
fix typos
Remi-Gau Nov 12, 2022
53d7894
fix link
Remi-Gau Nov 12, 2022
0cd1366
most of the change but mkserve not working yet
Dec 5, 2022
108c18c
some more change still not working
Dec 6, 2022
df50fd8
change in mkdocs.yml based on commments
Dec 6, 2022
c90de08
run pre-commit and fix yml
Remi-Gau Dec 6, 2022
e01eed1
Merge branch 'master' into bep020
Remi-Gau Dec 6, 2022
5cc22ba
add eyetrack modality object
Remi-Gau Dec 6, 2022
647af5e
format markdown
Remi-Gau Dec 6, 2022
77bf482
format markdown
Remi-Gau Dec 6, 2022
141e480
space missing in tabular_data/eyetrack.yaml
Dec 7, 2022
8c7618f
merging
Dec 7, 2022
d678149
fixing conflict for real
Dec 7, 2022
01332e5
automatic changes by pre-commit
Dec 7, 2022
b89469e
instru
Dec 7, 2022
8fc5f0f
pre-commit stuff
Dec 7, 2022
6fce90b
correct error of manipulation of logo.eps
Dec 7, 2022
0009d63
some test
Dec 7, 2022
dc793a3
some test
Dec 7, 2022
a5f7cfc
some test
Dec 7, 2022
2f81069
some test
Dec 7, 2022
63352df
changes of columns names
Dec 7, 2022
564a206
Update src/modality-specific-files/eye-tracking.md
mszinte Dec 8, 2022
d6e8aed
change in metadata
Dec 8, 2022
42f4527
Merge branch 'bep020' of https://github.com/mszinte/bids-specificatio…
Dec 8, 2022
7ca6a42
test new changes with pre-commit
Dec 8, 2022
7d435de
correct error in eyetrack.md
Dec 8, 2022
ea1d18f
add RecordTimeStart and RecordTimeEnd
Dec 8, 2022
49ec9e9
cahnge eye_sample to eye_timestamp
Dec 8, 2022
7fb149c
correct error example json
Dec 8, 2022
7a55abd
error in datasets links
Dec 8, 2022
e3f74f8
last round of review on main doc
Dec 8, 2022
9df5c68
slight modif of SAOI
Dec 8, 2022
c45f480
slight modif of main md
Dec 8, 2022
edc7c6f
correction of space
Dec 8, 2022
518d8f6
try without modality
Dec 8, 2022
8549d0e
Update src/modality-specific-files/eye-tracking.md
mszinte Dec 8, 2022
f194526
put back mkdocs.yaml with unsorted modality specific files
Dec 8, 2022
0e0f800
Update src/modality-specific-files/eye-tracking.md
mszinte Dec 8, 2022
15f817e
Update src/schema/objects/metadata.yaml
mszinte Dec 8, 2022
171eff9
Update src/schema/objects/metadata.yaml
mszinte Dec 8, 2022
d0c919a
Update src/schema/objects/metadata.yaml
mszinte Dec 8, 2022
39deaae
change after review of tsalo
Dec 8, 2022
b621542
Merge branch 'bep020' of https://github.com/mszinte/bids-specificatio…
Dec 8, 2022
c76af5b
put back /tool/filetree_exampl.ipynb
Dec 8, 2022
70c5edb
instru
Dec 8, 2022
9f223a1
change on metadata based on tsalo comments
Dec 8, 2022
a9bfaaf
change to desambiguate the columns in case of two eyes recording
Dec 16, 2022
4c8327b
change to account for the BEP020
Dec 16, 2022
c6a8354
change of json example in reply to https://github.com/bids-standard/b…
Dec 16, 2022
81d960e
change RecordTimeStart and RecordTimeEnd to StartTime_eyetrack (with …
Dec 16, 2022
1796cec
take out Scree settings from metadata as they were put in the main br…
Dec 16, 2022
457e339
Merge branch 'master' into bep020
mszinte Dec 16, 2022
a0410f8
insist on calibration in the text
Dec 16, 2022
e4c8ad8
add eyetrack suffix to timeseries suffixes in task.yaml in order to a…
Dec 16, 2022
f063523
point 2 on suggestion https://github.com/bids-standard/bids-specifica…
Dec 16, 2022
720311c
Merge remote-tracking branch 'upstream/master' into bep020
Remi-Gau Dec 24, 2022
7868f57
fix markdown
Remi-Gau Dec 24, 2022
8269cd3
fix markdown
Remi-Gau Dec 24, 2022
c4c342b
Merge branch 'master' into bep020
Remi-Gau Apr 5, 2023
752e38d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 5, 2023
893911c
Merge branch 'master' into bep020
Remi-Gau May 23, 2023
d802ab2
Merge branch 'master' into bep020
Remi-Gau Jun 6, 2023
af48333
Merge remote-tracking branch 'upstream/master' into bep20
Remi-Gau Jun 12, 2023
37f7cd1
codespell fixes
Remi-Gau Jun 12, 2023
9ecb9ea
schema fix
Remi-Gau Jun 12, 2023
e286064
change to follow recommandations of https://doi.org/10.3758/s13428-02…
Jun 28, 2023
e513efa
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 28, 2023
a414937
Merge branch 'master' into bep020
Remi-Gau Jun 28, 2023
6f535cb
split metadata
Remi-Gau Jun 29, 2023
3ac5ca5
fix metadata
Remi-Gau Jun 29, 2023
a31fbdd
format
Remi-Gau Jun 29, 2023
17f296d
fix typo
Remi-Gau Jul 3, 2023
691ec27
update example
Remi-Gau Jul 3, 2023
a4af030
make gunzip optional
Remi-Gau Jul 3, 2023
c9787a8
Merge branch 'master' into bep020
Remi-Gau Jul 4, 2023
a0acebe
add required events.json metadata
Remi-Gau Jul 5, 2023
f96f383
fix list
Remi-Gau Jul 6, 2023
08250d3
fix list
Remi-Gau Jul 6, 2023
95d6dbf
Merge branch 'master' into bep020
Remi-Gau Sep 7, 2023
2169021
Update eye-tracking.md
mszinte Oct 5, 2023
9314fc0
Changes for metadata
julia-pfarr Oct 5, 2023
8e01771
Merge pull request #1 from julia-pfarr/julia
julia-pfarr Oct 5, 2023
1aeeff5
Merge pull request #5 from julia-pfarr/bep020
julia-pfarr Oct 26, 2023
2b85072
change unit of ScreenSize in example events.json
julia-pfarr Oct 26, 2023
754f1c0
Merge pull request #6 from julia-pfarr/bep020
julia-pfarr Nov 9, 2023
205a35f
Update src/modality-specific-files/eye-tracking.md
Remi-Gau Nov 20, 2023
cda8874
Apply suggestions from code review
Remi-Gau Nov 28, 2023
8be9429
Update src/schema/objects/columns.yaml
Remi-Gau Nov 28, 2023
e6ef2d6
Update src/schema/objects/columns.yaml
Remi-Gau Nov 28, 2023
84b869a
Update metadata.yaml
mszinte Nov 30, 2023
0ca61b4
Merge branch 'master' into bep020
Remi-Gau Nov 30, 2023
53fcd97
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 30, 2023
4c7a30f
Update src/schema/objects/metadata.yaml
Remi-Gau Nov 30, 2023
6c2b2f5
fix issues in mkdocs.yml
Remi-Gau Nov 30, 2023
79fd36b
hasty copy paste
Remi-Gau Nov 30, 2023
edc81bc
fix time stamp
Remi-Gau Nov 30, 2023
fcaaeaa
add placeholder for eventual publication
sappelhoff Nov 30, 2023
0bb5e41
Update metadata.yaml
mszinte Nov 30, 2023
c2ca15b
Update src/modality-specific-files/eye-tracking.md
mszinte Nov 30, 2023
632eca2
Update src/modality-specific-files/eye-tracking.md
mszinte Dec 7, 2023
75c0baa
Update src/modality-specific-files/near-infrared-spectroscopy.md
Remi-Gau Feb 29, 2024
05c8227
enh: a proposal for the new ``RecordingType`` (-> ``PhysioType``) idea
oesteban Feb 29, 2024
cbd2da7
enh: add eyetracking examples
oesteban Feb 29, 2024
8f90b33
enh: revise metadata specifications
oesteban Feb 29, 2024
a1126da
fix: remove duplicated metadata entry
oesteban Feb 29, 2024
e728546
restore eyetrack sidecars
oesteban Feb 29, 2024
87e93c1
Merge pull request #8 from oesteban/bep020-proposal
oesteban Feb 29, 2024
ef49458
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 29, 2024
1d05d11
fix: pacify codespell
oesteban Feb 29, 2024
2920134
fix: pacify markdown linter
oesteban Feb 29, 2024
3636333
fix: attempt to get line numbers on tsv files
oesteban Feb 29, 2024
aeac149
fix: attempt 2 to get line numbers on tsv files
oesteban Feb 29, 2024
9df5c4e
Update src/modality-specific-files/eye-tracking.md
oesteban Mar 1, 2024
b7d19b2
fix: address several issues, add example datasets, pacify remark
oesteban Mar 1, 2024
8b2e7e5
enh: better ordering, clearer definitions
oesteban Mar 1, 2024
6968915
sty: pacify remark
oesteban Mar 1, 2024
b56d7e0
enh: change zero-based to one-base indexes, more consistent with BIDS
oesteban Mar 1, 2024
a618326
fix: remove redirected URL
oesteban Mar 1, 2024
57b1737
Merge branch 'master' into bep020
oesteban Mar 1, 2024
12b1abc
enh: add columns definition for physioevents and improve eyetracker e…
oesteban Mar 1, 2024
c8d8fc3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 1, 2024
01f820d
fix: length of new message column description
oesteban Mar 1, 2024
61a1f31
fix: improved definition of ForeignIndexColumn
oesteban Mar 1, 2024
ea5cc44
Merge branch 'master' into bep020
oesteban Mar 2, 2024
1e188a0
enh: clearly state specific physio types at the outset
oesteban Mar 2, 2024
366cbc9
enh: improving and adding example file trees
oesteban Mar 2, 2024
3b71c1f
fix: normalize file tree macros and repare syntax of some
oesteban Mar 2, 2024
e209833
fix: typos and readability improvements
oesteban Mar 2, 2024
e9fcd85
review and slight text modification
Mar 21, 2024
6f0d8fb
Merge branch 'master' into bep020
Remi-Gau Mar 21, 2024
d16fd64
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 21, 2024
5ef41f4
Merge remote-tracking branch 'upstream/master' into bep020
oesteban Mar 22, 2024
311b645
fix: revert boilerplate about publication
oesteban Mar 22, 2024
90b9fba
enh: drop "old" eyetrack
oesteban Mar 22, 2024
51d7ae9
fix: ``"cyclopean"`` value for ``RecordedEye`` metadata
oesteban Mar 22, 2024
239f93c
fix: deduplicate example datasets, and move eyetrack's ones into an a…
oesteban Mar 22, 2024
f34589c
fix: missing setting eyetrack tabular data allowed to add columns
oesteban Mar 22, 2024
3606735
enh: deep reorganization of the section
oesteban Mar 24, 2024
4aed597
fix: pacify linter
oesteban Mar 24, 2024
3bbe59c
Update src/modality-specific-files/physiological-and-other-continuous…
oesteban Mar 25, 2024
3beafc6
enh: move escalating events' metadata to REQUIRED into task data section
oesteban Mar 25, 2024
8c95b8c
Merge remote-tracking branch 'upstream/master' into bep020
oesteban Apr 11, 2024
96d984e
Merge branch 'master' into bep020
oesteban May 29, 2024
f57f393
fix unit
Remi-Gau Jul 28, 2024
8b6d458
use levels to describe metadata
Remi-Gau Jul 28, 2024
6aeb1c2
Merge remote-tracking branch 'upstream/master' into pr/mszinte/1128
Remi-Gau Jul 28, 2024
e92027c
fix typo
Remi-Gau Jul 28, 2024
26c463a
minor schema fix
Remi-Gau Jul 28, 2024
a6a1c9d
Merge branch 'master' into bep020
Remi-Gau Sep 5, 2024
0ad7fb1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 5, 2024
a5ea212
fix
Remi-Gau Sep 5, 2024
6e787b6
enh: add @Sourav-Kulkarni's suggestions about eye-tracker/screen dist…
oesteban Oct 3, 2024
9e697d2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 3, 2024
09b40d7
enh: address @qian-chu's review comment about documenting timestamp
oesteban Oct 3, 2024
cce40a0
enh: address @Remi-Gau's comment on column order
oesteban Oct 3, 2024
19dab86
Update src/modality-specific-files/physiological-recordings.md
oesteban Dec 18, 2024
e222088
Update src/modality-specific-files/physiological-recordings.md
oesteban Dec 18, 2024
edaeace
Update src/modality-specific-files/physiological-recordings.md
mszinte Dec 19, 2024
a4671fb
fix: address issue of ``EnvironmentCoordinates``
oesteban Jan 15, 2025
9a6c10e
enh: add note about the type of pupil size being recorded
oesteban Jan 15, 2025
c040159
enh: document all four columns of physio.json file
oesteban Jan 15, 2025
e3c698c
Update src/schema/objects/metadata.yaml
oesteban Jan 15, 2025
97688ec
Merge remote-tracking branch 'upstream/master' into bep020
oesteban Jan 16, 2025
3198a73
fix: remove backtick breaking yaml file
oesteban Jan 16, 2025
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
change after review of tsalo
  • Loading branch information
mszinte committed Dec 8, 2022
commit 39deaaeb5dbf6b37e4144c8941aa092d9eac0d1c
19 changes: 14 additions & 5 deletions src/schema/objects/metadata.yaml
Original file line number Diff line number Diff line change
@@ -213,7 +213,7 @@ AverageCalibrationError:
description: |
Average calibration error in visual degree.
type: number
unit: visual degree
unit: degree
B0FieldIdentifier:
name: B0FieldIdentifier
display_name: B0 Field Identifier
@@ -382,9 +382,9 @@ CalibrationList:
This list includes the calibration type, recorded eye,
maximal calibration error, average calibration error,
and time relative to the first event of the event file.
type: object
type: array
items:
type: object
type: array
CalibrationPosition:
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

assumes the same position for all calibrations / validations

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

can you elaborate on the problem?

name: CalibrationPosition
display_name: Calibration Position
@@ -395,7 +395,11 @@ CalibrationPosition:
anyOf:
mszinte marked this conversation as resolved.
Show resolved Hide resolved
- type: array
oesteban marked this conversation as resolved.
Show resolved Hide resolved
items:
type: number
type: array
minItems: 2
maxItems: 2
items:
type: number
CalibrationType:
name: CalibrationType
display_name: Calibration Type
@@ -2017,8 +2021,9 @@ MaximalCalibrationError:
name: MaximalCalibrationError
display_name: Maximal Calibration Error
description: |
Maximal calibration error in visual degree.
Maximal calibration error in degree.
type: number
mszinte marked this conversation as resolved.
Show resolved Hide resolved
unit: degree
Remi-Gau marked this conversation as resolved.
Show resolved Hide resolved
MeasurementToolMetadata:
name: MeasurementToolMetadata
display_name: Measurement Tool Metadata
@@ -2810,6 +2815,10 @@ SampleCoordinateUnits:
description: |
Unit of individual samples (`"pixel"`, `"mm"` or `"cm"`) .
type: string
mszinte marked this conversation as resolved.
Show resolved Hide resolved
enum:
- pixel
- mm
- cm
SampleEmbedding:
name: SampleEmbedding
display_name: Sample Embedding
140 changes: 14 additions & 126 deletions tools/filetree_example.ipynb
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -11,24 +11,9 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"```Text\n",
"├─ sub-01_part-mag_T1w.nii.gz \n",
"├─ sub-01_part-mag_T1w.json \n",
"├─ sub-01_part-phase_T1w.nii.gz comments can be added here\n",
"└─ sub-01_part-phase_T1w.json but padding them could be optimised\n",
"```\n",
"\n"
]
}
],
"outputs": [],
"source": [
"directory_list = {\n",
" \"sub-01_part-mag_T1w.nii.gz\" : \"\", # leave this value empty for files\n",
@@ -44,27 +29,9 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"```Text\n",
"├─ sub-01/\n",
"│ ├─ sub-01_part-mag_T1w.nii.gz \n",
"│ ├─ sub-01_part-mag_T1w.json \n",
"│ ├─ sub-01_part-phase_T1w.nii.gz \n",
"│ └─ sub-01_part-phase_T1w.json \n",
"└─ sub-02/\n",
" └─ sub-02_part-mag_T1w.nii.gz \n",
"```\n",
"\n"
]
}
],
"outputs": [],
"source": [
"directory_dict = {\n",
" \"sub-01\": { # use nested dictionaries to represent directories\n",
@@ -85,26 +52,9 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"```Text\n",
"└─ sub-01/\n",
" └─ anat/\n",
" ├─ sub-01_part-mag_T1w.nii.gz \n",
" ├─ sub-01_part-mag_T1w.json \n",
" ├─ sub-01_part-phase_T1w.nii.gz \n",
" └─ sub-01_part-phase_T1w.json \n",
"```\n",
"\n"
]
}
],
"outputs": [],
"source": [
"nested_directory_dict = {\n",
" \"sub-01\" : {\n",
@@ -124,32 +74,9 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"```Text\n",
"└─ my_processed_data/\n",
" ├─ code/\n",
" │ ├─ processing_pipeline-1.0.0.img \n",
" │ ├─ hpc_submitter.sh \n",
" │ └─ ... \n",
" ├─ sourcedata/\n",
" │ ├─ sub-01/\n",
" │ ├─ sub-02/\n",
" │ └─ ... \n",
" ├─ sub-01/\n",
" ├─ sub-02/\n",
" └─ ... \n",
"```\n",
"\n"
]
}
],
"outputs": [],
"source": [
"directory = { \n",
" \"my_processed_data\": {\n",
@@ -176,33 +103,9 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"```Text\n",
"├─ dataset_description.json \n",
"├─ sub-01/\n",
"│ ├─ sessions.tsv \n",
"│ ├─ ses-01/\n",
"│ │ └─ anat/\n",
"│ │ ├─ sub-01_part-mag_T1w.nii.gz \n",
"│ │ ├─ sub-01_part-mag_T1w.json \n",
"│ │ ├─ sub-01_part-phase_T1w.nii.gz \n",
"│ │ └─ sub-01_part-phase_T1w.json \n",
"│ └─ scans.tsv \n",
"└─ ses-02/\n",
" └─ func/\n",
" └─ sub-01_bold.nii.gz \n",
"```\n",
"\n"
]
}
],
"outputs": [],
"source": [
"# you can also represent files and directories on the same level\n",
"\n",
@@ -234,24 +137,9 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"```Text\n",
"└─ sub-<label>/\n",
" └─ <datatype>/\n",
" ├─ <matches>_eyetrack.json \n",
" └─ <matches>_eyetrack.tsv \n",
"```\n",
"\n"
]
}
],
"outputs": [],
"source": [
"# example for bep020 with matching tree\n",
"directory = {\n",
@@ -295,7 +183,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.2"
"version": "3.9.13"
}
},
"nbformat": 4,