Created
August 6, 2024 20:34
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export roi
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| import org.apache.commons.io.FilenameUtils | |
| def name = FilenameUtils.getBaseName(getProjectEntry().getImageName()) | |
| def server = getCurrentServer() | |
| selectObjectsByClassification("flow") | |
| anns =[] | |
| def anns = getSelectedObjects() | |
| i=0 | |
| for (ann in anns) { | |
| def roi = ann.getROI() | |
| def requestROI = RegionRequest.createInstance(server.getPath(), 1, roi) | |
| def path = buildFilePath(PROJECT_BASE_DIR,"ROI",name+"_ROI"+i+".tif") | |
| writeImageRegion(server, requestROI, path) | |
| i=i+1 | |
| } | |
| print name + " done" | |
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| # Check if the number of arguments is correct | |
| if [ "$#" -ne 2 ]; then | |
| echo "Usage: $0 <input_folder> <output_folder>" | |
| exit 1 | |
| fi | |
| input_folder="$1" | |
| output_folder="$2" | |
| # Ensure the output folder exists | |
| mkdir -p "$output_folder" | |
| # Iterate over each file in the input folder | |
| for input_file in "$input_folder"/*; do | |
| # Get the base name of the file without the path | |
| file_name=$(basename -- "$input_file") | |
| # Construct the output file path | |
| output_file="$output_folder/$file_name" | |
| # Run the VIPS command | |
| vips im_vips2tiff $input_file $output_file:jpeg:95,tile,pyramid | |
| done |
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| #!/bin/bash | |
| # Check if the number of arguments is correct | |
| if [ "$#" -ne 2 ]; then | |
| echo "Usage: $0 <input_folder> <output_folder>" | |
| exit 1 | |
| fi | |
| input_folder="$1" | |
| output_folder="$2" | |
| # Ensure the output folder exists | |
| #mkdir -p "$output_folder" | |
| # Function to process a single image | |
| process_image() { | |
| input_file="$1" | |
| output_folder="$2" | |
| file_name=$(basename -- "$input_file") | |
| output_file="$output_folder/$file_name" | |
| vips im_vips2tiff $input_file $output_file:jpeg:95,tile,pyramid | |
| } | |
| # Export the function to make it available to parallel | |
| export -f process_image | |
| # Use find to get a list of input files and pass them to parallel for processing | |
| find "$input_folder" -type f -print0 | parallel -0 -j "$(nproc)" process_image {} $output_folder |
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