[MAINT] reuse pybids synthetic dataset

tests/conftest.py

@@ -7,14 +7,13 @@
 import numpy as np
 import pandas as pd
 import pytest
-from bids.tests import get_test_data_path
 
 from bidsmreye.quality_control import compute_displacement, compute_robust_outliers
 
 
 @pytest.fixture
-def pybids_test_dataset() -> Path:
-    return Path(get_test_data_path()) / "synthetic" / "derivatives" / "fmriprep"
+def pybids_test_dataset(data_dir) -> Path:
+    return data_dir / "synthetic" / "derivatives" / "fmriprep"
 
 
 @pytest.fixture

tests/data/synthetic/T1w.json

@@ -0,0 +1,5 @@
+{
+    "RepetitionTime": 2.5,
+    "EchoTime": 0.0029,
+    "FlipAngle": 8
+}

tests/data/synthetic/code/create_synthetic_ds.sh

@@ -0,0 +1,79 @@
+#!/bin/bash
+
+# small bash script to create a synthetic BIDS data set
+
+# defines where the BIDS data set will be created
+start_dir=$(pwd)
+raw_dir=${start_dir}/../
+
+subject_list='01 02 03 04 05'
+session_list='01'
+
+create_raw_dwi() {
+
+	target_dir=$1
+	subject=$2
+	ses=$3
+
+	this_dir=${target_dir}/sub-${subject}/ses-${ses}/dwi
+
+	mkdir -p "${this_dir}"
+
+	suffix='_dwi'
+	source_image=${target_dir}/../images/4d.nii.gz
+	filename=${this_dir}/sub-${subject}_ses-${ses}${suffix}.nii.gz
+	cp "${source_image}" "${filename}"
+
+	source_bval=${start_dir}/dwi.bval
+	filename=${this_dir}/sub-${subject}_ses-${ses}${suffix}.bval
+	cp "${source_bval}" "${filename}"
+
+	source_bvec=${start_dir}/dwi.bvec
+	filename=${this_dir}/sub-${subject}_ses-${ses}${suffix}.bvec
+	cp "${source_bvec}" "${filename}"
+
+}
+
+create_raw_fmap() {
+
+	target_dir=$1
+	subject=$2
+	ses=$3
+
+	this_dir=${target_dir}/sub-${subject}/ses-${ses}/fmap
+
+	mkdir -p ${this_dir}
+
+	source_image=${target_dir}/../images/3d.nii.gz
+
+	fmap_suffix_list='_phasediff _magnitude1 _magnitude2'
+
+	for suffix in ${fmap_suffix_list}; do
+		cp "${source_image}" "${this_dir}/sub-${subject}_ses-${ses}${suffix}.nii.gz"
+	done
+
+	RepetitionTime=0.4
+	EchoTime1=00519
+	EchoTime2=0.00765
+	FlipAngle=60
+	template='{"FlipAngle":%f, "RepetitionTime":%f, "EchoTime1":%f, "EchoTime2":%f, "IntendedFor": ["%s", "%s"], "PhaseEncodingDirection": "j-"}'
+
+	suffix='_bold'
+
+	task_name='nback'
+	IntendedFor1="$(echo ses-${ses}/func/sub-${subject}_ses-${ses}_task-${task_name}_run-01${suffix}.nii.gz)"
+	IntendedFor2="$(echo ses-${ses}/func/sub-${subject}_ses-${ses}_task-${task_name}_run-02${suffix}.nii.gz)"
+	json_string=$(printf "$template" "$FlipAngle" "$RepetitionTime" "$EchoTime1" "$EchoTime2" "$IntendedFor1" "$IntendedFor2")
+	echo "$json_string" >${this_dir}/sub-${subject}_ses-${ses}_phasediff.json
+	echo "$json_string" >${this_dir}/sub-${subject}_ses-${ses}_phasediff.json
+
+}
+
+# RAW DATASET
+for subject in ${subject_list}; do
+	for ses in ${session_list}; do
+		create_raw_dwi ${raw_dir} ${subject} ${ses}
+		create_raw_fmap ${raw_dir} ${subject} ${ses}
+	done
+
+done

tests/data/synthetic/code/dwi.bval

@@ -0,0 +1 @@
+0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000

tests/data/synthetic/code/dwi.bvec

@@ -0,0 +1,3 @@
+0 0.99955850839614 0.01954407058656 0.00294903200119 0.57941150665283 -0.22696028649807 -0.88946276903152 0.81388407945632 0.25786191225051 0.94657051563262 0.48336026072502 0.31938299536705 0.42975607514381 -0.4763910472393 -0.59470033645629 -0.59882068634033 -0.83007228374481 0.88395410776138 0.2610293328762 0.09066703915596 -0.80151742696762 0.53270918130874 -0.79953873157501 0.94853943586349 0.26080328226089 -0.04598157480359 0.20106360316276 0.76368796825408 -0.13214653730392 -0.14714884757995 0.89985853433609 -0.57571458816528 -0.35732066631317 -0.33106037974357 -0.31264066696167 -0.96581315994262 -0.95102477073669 0.43446427583694 -0.75675719976425 0.73082029819488 -0.67709231376647 0.67937570810318 -0.13976696133613 -0.72053796052932 -0.07321017235517 0.5839369893074 -0.07184987515211 -0.55975395441055 0.82137787342071 0.36826944351196 -0.19602409005165 -0.73164790868759 0.43177768588066 0.52686661481857 -0.19931995868682 0.4891959130764 0.37798687815666 -0.70318156480789 0.26638954877853 -0.01923633553087 0.02821243368089 0.54735606908798 -0.30064421892166 0.73979389667511 0.28209447860717
+0 -0.02049821615219 0.98761302232742 0.52286034822464 -0.80844813585281 -0.65079009532928 -0.30648133158683 0.02310398034751 0.87089902162551 0.07609922438859 -0.81609696149826 -0.78027993440628 -0.53328257799148 -0.50823193788528 0.61257445812225 0.04065646231174 -0.53946721553802 0.02398272044956 -0.41599848866462 -0.91442102193832 0.48670825362205 0.79603910446167 0.26488894224166 -0.28364571928978 0.67999285459518 -0.03036121465265 -0.9791235923767 -0.642438352108 0.20882698893547 0.83522641658783 0.37077417969703 0.37174785137176 -0.00542591279372 -0.04497369006276 -0.27928236126899 -0.25846034288406 0.19096466898918 -0.89682209491729 0.62152820825576 0.30336225032806 -0.08724510669708 0.59735131263732 -0.82620531320571 0.31055691838264 0.72652155160903 -0.69059783220291 -0.48624488711357 -0.81753581762313 -0.42245289683342 -0.68479514122009 0.54096210002899 -0.67699402570724 0.76565784215927 0.5939724445343 -0.3681089580059 0.28870034217834 -0.87901186943054 -0.34432905912399 0.93346035480499 0.24267202615737 -0.96214282512664 -0.18922631442546 0.30678990483284 0.53955316543579 0.9575902223587
+0 0.02150822617113 -0.15568755567073 -0.85241317749023 -0.10341253876686 -0.72454214096069 -0.33900585770607 -0.58056783676147 -0.41838020086288 -0.31338959932327 0.31677860021591 0.53773391246795 0.72864228487014 -0.71746206283569 -0.52065771818161 0.79985052347183 -0.14126154780387 0.46695810556411 0.8710965514183 0.39447921514511 0.34739750623703 -0.28730210661888 0.53904712200164 -0.14077690243721 -0.68526721000671 0.99848085641861 -0.02984086796641 -0.06366975605487 -0.96898341178894 0.52985268831253 -0.22974103689193 0.72825574874877 -0.93396604061126 0.94253724813461 -0.90788620710372 -0.02007177658379 -0.24307298660278 0.0833735987544 -0.20253752171993 -0.61145150661468 -0.73070788383483 0.426168769598 -0.54575622081756 -0.61998349428176 -0.6832326054573 -0.42672303318977 -0.87086367607116 -0.13531495630741 0.38323882222175 -0.62883508205413 0.81788432598114 0.0798152834177 0.47679767012596 -0.60795408487319 0.90816700458526 -0.82300633192062 -0.29062712192535 -0.62207180261611 0.24018363654613 0.96991771459579 -0.27108195424079 0.81522691249847 0.90304642915725 -0.40197896957397 -0.05868147313594

tests/data/synthetic/dataset_description.json

@@ -0,0 +1,6 @@
+{
+	"Name": "Synthetic dataset for inclusion in BIDS-examples",
+	"BIDSVersion": "1.0.2",
+	"License": "PD",
+	"Authors": ["Markiewicz, C. J."]
+}

tests/data/synthetic/derivatives/fmriprep/dataset_description.json

@@ -0,0 +1,10 @@
+{
+	"PipelineDescription": {
+		"Name": "fmriprep"
+	},
+	"Name": "synthetic",
+	"BIDSVersion": "1.7.1",
+	"License": "PD",
+	"Authors": ["Markiewicz, C. J."],
+	"DatasetType": "derivative"
+}