Merge pull request #199 from jhlegarreta/enh/download-pet-sub02

ENH: Fetch `sub-02` data for PET notebook

Author: jhlegarreta

scripts/fetch_pet_nb_gin_data.sh

@@ -3,30 +3,49 @@
 DEST_DIR=$1
 
 # Define variables
-LIST_URL="gin.g-node.org/jhlegarreta/tests-nifreeze/raw/AddPETData"
+LIST_URL="gin.g-node.org/nipreps-data/tests-nifreeze/raw/master"
 
 FOLDER="pet_data"
-SUB_LABEL="sub-01"
+SRC_SUB_LABELS=("sub-01")
+MTN_SUB_LABELS=("sub-02")
+SUB_LABELS=("${SRC_SUB_LABELS[@]}" "${MTN_SUB_LABELS[@]}")
 SESSION_LABEL="ses-baseline"
 ANAT_LABEL="anat"
 PET_LABEL="pet"
-ANAT_FNAMES=("sub-01_ses-baseline_T1w.nii")
-PET_FNAMES=("sub-01_ses-baseline_pet.json" "sub-01_ses-baseline_pet.nii.gz" "sub-01_ses-baseline_recording-manual_blood.json" "sub-01_ses-baseline_recording-manual_blood.tsv")
+ANAT_FNAMES_CMN_SSTR=("ses-baseline_T1w.nii")
+PET_FNAMES_CMN_SSTR=("ses-baseline_pet.json" "ses-baseline_pet.nii.gz" "ses-baseline_recording-manual_blood.json" "ses-baseline_recording-manual_blood.tsv")
+MOTION_FNAMES_CMN_SSTR=("ses-baseline_ground_truth_motion.csv")
+UNDERSCORE="_"
 
 # Create target directory structure
-mkdir -p "${DEST_DIR}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${ANAT_LABEL}"
-mkdir -p "${DEST_DIR}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${PET_LABEL}"
+for sub_id in "${SUB_LABELS[@]}"; do
+    mkdir -p "${DEST_DIR}/${FOLDER}/${sub_id}/${SESSION_LABEL}/${ANAT_LABEL}"
+    mkdir -p "${DEST_DIR}/${FOLDER}/${sub_id}/${SESSION_LABEL}/${PET_LABEL}"
+done
 
 # Download anatomical files
-for fname in "${ANAT_FNAMES[@]}"; do
-    url="${LIST_URL}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${ANAT_LABEL}/${fname}"
-    wget -nv -O "${DEST_DIR}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${ANAT_LABEL}/${fname}" "${url}"
+for sub_id in "${SUB_LABELS[@]}"; do
+    fname="${ANAT_FNAMES_CMN_SSTR[@]/#/${sub_id}${UNDERSCORE}}"
+    url="${LIST_URL}/${FOLDER}/${sub_id}/${SESSION_LABEL}/${ANAT_LABEL}/${fname}"
+    wget -nv -O "${DEST_DIR}/${FOLDER}/${sub_id}/${SESSION_LABEL}/${ANAT_LABEL}/${fname}" "${url}"
 done
 
 # Download PET files
-for fname in "${PET_FNAMES[@]}"; do
-    url="${LIST_URL}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${PET_LABEL}/${fname}"
-    wget -nv -O "${DEST_DIR}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${PET_LABEL}/${fname}" "${url}"
+for sub_id in "${SUB_LABELS[@]}"; do
+    fnames=("${PET_FNAMES_CMN_SSTR[@]/#/${sub_id}${UNDERSCORE}}")
+    for fname in "${fnames[@]}"; do
+      url="${LIST_URL}/${FOLDER}/${sub_id}/${SESSION_LABEL}/${PET_LABEL}/${fname}"
+      wget -nv -O "${DEST_DIR}/${FOLDER}/${sub_id}/${SESSION_LABEL}/${PET_LABEL}/${fname}" "${url}"
+    done
+done
+
+# Download motion files
+for sub_id in "${MTN_SUB_LABELS[@]}"; do
+    fnames=("${MOTION_FNAMES_CMN_SSTR[@]/#/${sub_id}${UNDERSCORE}}")
+    for fname in "${fnames[@]}"; do
+      url="${LIST_URL}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${PET_LABEL}/${fname}"
+      wget -nv -O "${DEST_DIR}/${FOLDER}/${SUB_LABEL}/${SESSION_LABEL}/${PET_LABEL}/${fname}" "${url}"
+    done
 done
 
 echo "PET data successfully downloaded to the '${DEST_DIR}/${FOLDER}' directory."