Created
October 23, 2024 23:16
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#QuPath HPC project run
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| base_path = "B:/data/BE/cell_detect/acformer/" | |
| collected_data = NULL | |
| for (dataset in c("NU_dataset_rois","MDA1_dataset_rois","MDA2_dataset_rois")){ | |
| txt_path = paste(base_path,dataset ,"img_list.txt",sep="/") | |
| print(txt_path) | |
| txt_table = read.table(txt_path) | |
| txt_table[2] <- dataset | |
| if (is.null(collected_data)){ | |
| collected_data <- txt_table | |
| }else{ | |
| collected_data <- rbind(collected_data, txt_table ) | |
| } | |
| } | |
| write.csv(collected_data, paste0(base_path,"/img_list.csv")) | |
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| #!/bin/bash | |
| #!################################################################################ | |
| #!#### Modify the options in this section as appropriate ###### | |
| #!#### Change path to log files to your desired location ###### | |
| #!#### rds-cache path: /rsrch6/scratch/trans_mol_path/YOURNAME/aitil/logs/ ###### | |
| #!################################################################################ | |
| #BSUB -J qupath_export | |
| #BSUB -W 0:30 | |
| #BSUB -o /rsrch5/home/trans_mol_path/cercan/data/BE/cell_detect/acformer/NU_dataset_rois/scripts/logs/%J_%I_lsf.out | |
| #BSUB -e /rsrch5/home/trans_mol_path/cercan/data/BE/cell_detect/acformer/NU_dataset_rois/scripts/logs/%J_%I_lsf.err | |
| #BSUB -cwd /rsrch5/home/trans_mol_path/cercan/code/Barretts/CLAM/ | |
| #BSUB -q short | |
| #BSUB -n 4 | |
| #BSUB -M 2 | |
| #BSUB -R rusage[mem=64] | |
| #BSUB -B | |
| #BSUB -N | |
| #BSUB –u [email protected] | |
| #BSUB -J "patch[1-1484:1]" | |
| #!### you need to change the end index #### | |
| #!###### you need to change this part ##################### | |
| #cd /rsrch5/home/trans_mol_path/cercan/code/Barretts/CLAM/ | |
| #module load singularity/3.7.0 | |
| #module load cuda10.0/toolkit/10.0.130 | |
| # module load anaconda3/2023.07-2 | |
| # source activate clam_albm_tf | |
| QUPATH=/rsrch5/home/trans_mol_path/cercan/app/QuPath044/QuPath/bin/QuPath.sh | |
| base_folder=/rsrch5/home/trans_mol_path/cercan/data/BE/cell_detect/acformer/ | |
| csv_file=$base_folder/img_list.csv | |
| proj=$(awk -F',' "NR==$LSB_JOBINDEX {print \$2}" "$csv_file"| tr -d '[:space:]') | |
| img_name=$(awk -F',' "NR==$LSB_JOBINDEX {print \$1}" "$csv_file"| tr -d '[:space:]') | |
| project_file=$base_folder/$proj/project.qpproj | |
| scipt_path=$base_folder/NU_dataset_rois/scripts/export_tissue_tile_acformer.groovy | |
| echo "LSB_JOBINDEX : $LSB_JOBINDEX" | |
| echo "project_file : $project_file" | |
| echo "img_name : $img_name" | |
| echo "scipt_path : $scipt_path" | |
| $QUPATH script -p "$project_file" -i "$img_name" "$scipt_path" |
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| def outputPath = buildFilePath(PROJECT_BASE_DIR,"img_list.txt") | |
| def imgList = getProject().getImageList() | |
| def file = new File(outputPath) | |
| file.withWriter { writer -> | |
| imgList.each { value -> | |
| writer.writeLine(value.toString()) | |
| } | |
| } |
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