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yarikopticyarikoptic
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RF patching so we can run 'script patches' and also apply direct patches
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‎.codespellrc

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[codespell]
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skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
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# Ignore diff/git format-patch headings which could include truncated lines
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ignore-regex = ^@@ -[0-9].*@@.*
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ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
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builtin = clear,rare,en-GB_to_en-US
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# this overloads default dictionaries and I have not yet figured out

‎tools/bids-2.0/README.md

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@@ -2,3 +2,19 @@ This directory to contain various little helpers which would script desired
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automated changes (where possible) for migrating specification (not datasets)
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to BIDS 2.0. Ideally scripts should have some header pointing to the
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underlying issue they are addressing.
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## `apply_all`
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`apply_all` script goes through `patches/` in a (numeric) sorted order
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and applies those "patches".
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"patches" could be of two types:
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- an executable -- a script to be executed which introduces the changes.
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- `.patch` - a regular patch which needs to be applied using `patch -p1`
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Typically for the same leading index (e.g. `01`) there would be a script and
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then a patch to possibly manually tune up remaining changes.
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`apply_all` could also take an index -- then it would stop applying patches
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having applied patches up to that index.

‎tools/bids-2.0/apply_all

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#!/bin/bash
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set -eu
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# hardcoding for now - relative path from the top
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rpath=tools/bids-2.0
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path="$(dirname "$0")"
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cd "$path/../.." # go to the top of bids-specification
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apply_until=${1:-}
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# harmonize appearance
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if [ -n "$apply_until" ] ; then
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apply_until=$(printf "%02d" "$apply_until")
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fi
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"$path/rename_participants_to_subjects"
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/bin/ls "$rpath"/patches/[0-9]* | sort -n | while read p; do
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if [ "${p##*.}" == "patch" ]; then
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echo "I: apply $p"
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patch -p1 < $p
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elif [ -x "$p" ] ; then
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echo "I: run $p"
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$p
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else
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echo "E: Do not know how to handle patch $p" >&2
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exit 1
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fi
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done

‎tools/bids-2.0/rename_participants_to_subjects renamed to ‎tools/bids-2.0/patches/01-01-rename_participants_to_subjects

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‎tools/bids-2.0/patches/01-02-rename_participants_to_subjects-fixup.patch

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From 087982854fd000f6cb9d321faf25c68e4a2f1b1c Mon Sep 17 00:00:00 2001
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From: Yaroslav Halchenko <[email protected]>
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Date: Fri, 12 Apr 2024 15:54:31 -0400
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Subject: [PATCH] Post fixes to apply_all to fix some indentations due to
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participant -> subject
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---
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src/appendices/coordinate-systems.md | 6 +++---
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src/schema/README.md | 4 ++--
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2 files changed, 5 insertions(+), 5 deletions(-)
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diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md
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index 9eb57359..9cb031b0 100644
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--- a/src/appendices/coordinate-systems.md
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+++ b/src/appendices/coordinate-systems.md
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@@ -233,10 +233,10 @@ described in [Common file level metadata fields][common file level metadata fiel
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In the case of multiple study templates, additional names may need to be defined.
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-| **Coordinate System** | **Description** |
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-| --------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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+| **Coordinate System** | **Description** |
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+| --------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| individual | Subject specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, subject-specific file to be fully defined. In context of surfaces this space has been referred to as `fsnative`. |
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-| study | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. |
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+| study | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. |
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### Non-template coordinate system identifiers
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diff --git a/src/schema/README.md b/src/schema/README.md
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index 0a6d7a3c..7587f01d 100644
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--- a/src/schema/README.md
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+++ b/src/schema/README.md
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@@ -243,7 +243,7 @@ and provide the *namespace* in which expressions are evaluated.
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The following operators should be defined by an interpreter:
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| Operator | Definition | Example |
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-| ----------- | ------------------------------------------------------------- | --------------------------------------------- |
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+| ----------- | ------------------------------------------------------------- |-----------------------------------------------|
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| `==` | equality | `suffix == "T1w"` |
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| `!=` | inequality | `entities.task != "rest"` |
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| `<`/`>` | less-than / greater-than | `sidecar.EchoTime < 0.5` |
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@@ -253,7 +253,7 @@ The following operators should be defined by an interpreter:
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| `&&` | conjunction, true if both RHS and LHS are true | `"Units" in sidecar && sidecar.Units == "mm"` |
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| `\|\|` | disjunction, true if either RHS or LHS is true | `a < mn \|\| a > mx` |
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| `.` | object query, returns value of subfield | `sidecar.Units` |
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-| `[]` | array/string index, returns value of Nth element (0-indexed) | `columns.subject_label[0]` |
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+| `[]` | array/string index, returns value of Nth element (0-indexed) | `columns.subject_label[0]` |
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| `+` | numeric addition / string concatenation | `x + 1`, `stem + "suffix"` |
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| `-`/`*`/`/` | numeric operators (division coerces to float) | `length(array) - 2`, `x * 2`, `1 / 2 == 0.5` |
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--
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2.43.0

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