Convert SVG figures from Nature Publishing Group to CellPress style, generate high quality raster and aggregated pdfs

figure_convert_NPG2CellPress.sh

CURRENT_DATE=20181212
NUMBER_MAIN_FIGURES=5
NUMBER_SUPP_FIGURES=11
ROOT_DIR=/home/path/to/paper/figures

cd $ROOT_DIR
mkdir -p cropped_unlabeled_pngs

# Cell Press format convertion
## supplementary Figure to FigureS
echo "Supplementary Figure to FigureS"
for FIGURE in $(eval echo "{1..$NUMBER_SUPP_FIGURES}")
do
    echo "Supplementary Figure: " $FIGURE
    sed -i "s/Supplementary Figure /Figure S/g" FigureS${FIGURE}.svg
done
## lowercase to uppercase panel letters
echo "Uppercase panel letters"
A='>(\w)<'
B='>\U\1<'
for FIGURE in $(eval echo "{1..$NUMBER_MAIN_FIGURES}")
do
    echo "Main Figure: " $FIGURE
    sed -ri "s/$A/$B/g" Figure${FIGURE}.svg
done
for FIGURE in $(eval echo "{1..$NUMBER_SUPP_FIGURES}")
do
    echo "Supplementary Figure: " $FIGURE
    sed -ri "s/$A/$B/g" FigureS${FIGURE}.svg
done


# Usual stuff
echo "Figures in A4 format"
for FIGURE in $(eval echo "{1..$NUMBER_MAIN_FIGURES}")
do
    echo "Main Figure: " $FIGURE
    inkscape --export-pdf=Figure${FIGURE}.pdf Figure${FIGURE}.svg
done
for FIGURE in $(eval echo "{1..$NUMBER_SUPP_FIGURES}")
do
    echo "Supplementary Figure: " $FIGURE
    inkscape --export-pdf=FigureS${FIGURE}.pdf FigureS${FIGURE}.svg
done

pdfunite $(eval echo Figure"{1..$NUMBER_MAIN_FIGURES}".pdf) MainFigures.${CURRENT_DATE}.pdf
pdfunite $(eval echo FigureS"{1..$NUMBER_SUPP_FIGURES}".pdf) SupplementaryFigures.${CURRENT_DATE}.pdf
pdfunite MainFigures.${CURRENT_DATE}.pdf SupplementaryFigures.${CURRENT_DATE}.pdf AllFigures.${CURRENT_DATE}.pdf

echo "Trimmed figures"
for FIGURE in $(eval echo "{1..$NUMBER_MAIN_FIGURES}")
do
    echo "Main Figure: " $FIGURE
    sed "s/Figure $FIGURE//g" Figure${FIGURE}.svg > Figure${FIGURE}.trimmed.svg
    inkscape --export-area-drawing --export-pdf=Figure${FIGURE}.trimmed.pdf --export-margin=5 Figure${FIGURE}.trimmed.svg
    inkscape --export-area-drawing --export-png=cropped_unlabeled_pngs/Figure${FIGURE}.cropped_unlabeled.png --export-background=white --export-dpi=300 --export-margin=5 Figure${FIGURE}.trimmed.svg
done
for FIGURE in $(eval echo "{1..$NUMBER_SUPP_FIGURES}")
do
    echo "Supplementary Figure: " $FIGURE
    sed "s/Figure S$FIGURE//g" FigureS${FIGURE}.svg > FigureS${FIGURE}.trimmed.svg
    inkscape --export-area-drawing --export-pdf=FigureS${FIGURE}.trimmed.pdf --export-margin=5 FigureS${FIGURE}.trimmed.svg
    inkscape --export-area-drawing --export-png=cropped_unlabeled_pngs/FigureS${FIGURE}.cropped_unlabeled.png --export-background=white --export-dpi=300 --export-margin=5 FigureS${FIGURE}.trimmed.svg
done

pdfunite $(eval echo Figure"{1..$NUMBER_MAIN_FIGURES}".trimmed.pdf) MainFigures.${CURRENT_DATE}.cropped_unlabeled.pdf
pdfunite $(eval echo FigureS"{1..$NUMBER_SUPP_FIGURES}".trimmed.pdf) SupplementaryFigures.${CURRENT_DATE}.cropped_unlabeled.pdf
pdfunite MainFigures.${CURRENT_DATE}.cropped_unlabeled.pdf SupplementaryFigures.${CURRENT_DATE}.cropped_unlabeled.pdf AllFigures.${CURRENT_DATE}.cropped_unlabeled.pdf

rm $(eval echo Figure"{1..$NUMBER_MAIN_FIGURES}".trimmed.svg)
rm $(eval echo Figure"{1..$NUMBER_MAIN_FIGURES}".trimmed.pdf)
rm $(eval echo FigureS"{1..$NUMBER_SUPP_FIGURES}".trimmed.svg)
rm $(eval echo FigureS"{1..$NUMBER_SUPP_FIGURES}".trimmed.pdf)