From 470d5b62ce2a27923d96bda69be03764870f1ad2 Mon Sep 17 00:00:00 2001 From: Agah Karakuzu Date: Mon, 16 Nov 2020 11:33:03 -0500 Subject: [PATCH 01/14] [ENH] Add flip entity - Modify `echo` entity respectively --- src/99-appendices/09-entities.md | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md index a605bec91e..0f975f872c 100644 --- a/src/99-appendices/09-entities.md +++ b/src/99-appendices/09-entities.md @@ -133,13 +133,26 @@ Full name: Echo Format: `echo-` -Definition: Multi-echo data MUST be split into one file per echo. -Each file shares the same name with the exception of the `_echo-` -key/value. +Definition: If constituents of an entity-linked file collection differ as a +function of `EchoTime` acquisition parameter, the `_echo-` key/value +pair MUST be used to distinguish individual files. Please note that the `` denotes the number/index (in the form of a nonnegative integer) of the echo not the echo time value which needs to be stored in the field `EchoTime` of the separate JSON file. +## flip + +Full name: Flip Angle + +Format: `flip-` + +Definition: If constituents of an entity-linked file collection differ as a +function of `FlipAngle` acquisition parameter, the `_flip-` key/value +pair MUST be used to distinguish individual files. +Please note that the `` denotes the number/index (in the form of a +nonnegative integer), not the `FlipAngle` value which needs to be +stored in the field `FlipAngle` of the separate JSON file. + ## recording Full name: Recording From 7ad14e8a6a799c0012cf0c6a2d17274b648f8267 Mon Sep 17 00:00:00 2001 From: Agah Karakuzu Date: Mon, 16 Nov 2020 12:29:27 -0500 Subject: [PATCH 02/14] revert entities.md and update the schema --- src/99-appendices/09-entities.md | 21 ++++----------------- src/schema/entities.yaml | 19 +++++++++++++++---- 2 files changed, 19 insertions(+), 21 deletions(-) diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md index 0f975f872c..73c3d5765d 100644 --- a/src/99-appendices/09-entities.md +++ b/src/99-appendices/09-entities.md @@ -133,26 +133,13 @@ Full name: Echo Format: `echo-` -Definition: If constituents of an entity-linked file collection differ as a -function of `EchoTime` acquisition parameter, the `_echo-` key/value -pair MUST be used to distinguish individual files. +Definition: Multi-echo data MUST be split into one file per echo. +Each file shares the same name with the exception of the `_echo-` +key/value. Please note that the `` denotes the number/index (in the form of a nonnegative integer) of the echo not the echo time value which needs to be stored in the field `EchoTime` of the separate JSON file. -## flip - -Full name: Flip Angle - -Format: `flip-` - -Definition: If constituents of an entity-linked file collection differ as a -function of `FlipAngle` acquisition parameter, the `_flip-` key/value -pair MUST be used to distinguish individual files. -Please note that the `` denotes the number/index (in the form of a -nonnegative integer), not the `FlipAngle` value which needs to be -stored in the field `FlipAngle` of the separate JSON file. - ## recording Full name: Recording @@ -203,4 +190,4 @@ Instead of a simple renaming, files should be read in and saved under their new names with dedicated tools like MNE, which will ensure that not only the file names, but also the internal file pointers will be updated. It is RECOMMENDED that .fif files with multiple parts use the -`split-` entity to indicate each part. +`split-` entity to indicate each part. \ No newline at end of file diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml index eecff7353c..296e6fbe86 100644 --- a/src/schema/entities.yaml +++ b/src/schema/entities.yaml @@ -102,13 +102,24 @@ echo: name: Echo entity: echo description: | - Multi-echo data MUST be split into one file per echo. - Each file shares the same name with the exception of the `_echo-` - key/value. + If constituents of an entity-linked file collection differ as a + function of `EchoTime` acquisition parameter, the `_echo-` key/value + pair MUST be used to distinguish individual files. Please note that the `` denotes the number/index (in the form of a nonnegative integer) of the echo not the echo time value which needs to be stored in the field `EchoTime` of the separate JSON file. format: index +flip: + name: Flip Angle + entity: flip + description: | + If constituents of an entity-linked file collection differ as a function of + `FlipAngle` acquisition parameter, the `_flip-` key/value pair MUST + be used to distinguish individual files. + Please note that the `` denotes the number/index (in the form of a + nonnegative integer), not the `FlipAngle` value which needs to be stored in + the field `FlipAngle` of the separate JSON file. + format: index recording: name: Recording entity: recording @@ -153,4 +164,4 @@ split: the file names, but also the internal file pointers will be updated. It is RECOMMENDED that .fif files with multiple parts use the `split-` entity to indicate each part. - format: index + format: index \ No newline at end of file From ef7440858df559269f20cc17c6645e7ece0439ea Mon Sep 17 00:00:00 2001 From: Agah Karakuzu Date: Mon, 16 Nov 2020 12:45:44 -0500 Subject: [PATCH 03/14] Use schema tools --- src/99-appendices/09-entities.md | 61 ++++++++++++++++++++------------ src/schema/entities.yaml | 4 +-- 2 files changed, 41 insertions(+), 24 deletions(-) diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md index 73c3d5765d..f2565ca848 100644 --- a/src/99-appendices/09-entities.md +++ b/src/99-appendices/09-entities.md @@ -17,7 +17,7 @@ each is given in the [Entity Table](04-entity-table.md). Full name: Subject -Format: `sub-