diff --git a/slideMacro b/slideMacro index 2d4b1f0..4e214c4 100755 --- a/slideMacro +++ b/slideMacro @@ -30,7 +30,7 @@ SCRIPTNAME=$(basename $0) DESCRIPTIONSHORT="Create scaled *.macro.png from a virtual slide." DEPENDENCIES=("convert") SUPPORTED_FORMATS=("TIFF" "Aperio" "Hamamatsu" "iScan" "iScanHT" "Leica") -DEFAULT_MACROSUFFIX=".macro" +DEFAULT_MACROSUFFIX="" DEFAULT_MACRO_THUMBSIZE="" #"2000x2000" # Maximum size of macro image DEFAULT_IM_ARGS="" # convert arguments # -verbose DEFAULT_SLURMARGS="--time 00:05:00 --mem=8G" # Maximum values: rt=runtime HH:MM:SS vmem=GB @@ -271,7 +271,7 @@ getMacroLeica(){ getMacroHamamatsu(){ LAYER=5 # 5 determined from example file (http://openslide.cs.cmu.edu/download/openslide-testdata/) # convert -quiet $IM_ARGS "$FILEFULL[$LAYER]" -resize "${DEFAULT_MACRO_THUMBSIZE}>" -fuzz 1% -transparent "#ECECEC" "$MACRO" - convert -quiet $IM_ARGS "$FILEFULL[$LAYER]" -resize "${DEFAULT_MACRO_THUMBSIZE}>" -fuzz 1% "$MACRO" + convert -quiet $IM_ARGS "$FILEFULL[$LAYER]" "$MACRO" } getMacroiScan(){ LAYER=7 # 7 determined from example file (http://openslide.cs.cmu.edu/download/openslide-testdata/)