Mike Mikailov
f4e3e76514
Update readme.md
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| heatmap_stitch | 5 gadi atpakaļ | |
| image_patch_extract | 5 gadi atpakaļ | |
| prediction | 5 gadi atpakaļ | |
| readme.md | 5 gadi atpakaļ | |
| set_env.sh | 5 gadi atpakaļ | |
| time_all_stats_pred.sh | 5 gadi atpakaļ |
readme.md
1 Image patch extraction
2 Prediction
3 Heatmap stitching
4 Retreiving run-time statistics
1 Image patch extraction
- Adjust configuration parameters in files, config_testing_cn_true.txt, config_normal_cn_true.txt, config_tumor_cn_true.txt, config_testing.txt, config_normal.txt and config_tumor.txt.
Run the following commands to launch Son of Grid Engine (SGE) jobs to extract, group patches in HDF5 files and create a lookup table for every HDF5 file.
1.1 With color normalization
qsub split_main.sh ./config_testing_cn_true.txt
qsub split_main.sh ./config_normal_cn_true.txt
qsub split_main.sh ./config_tumor_cn_true.txt
1.2 Without color normalization
- qsub split_main.sh ./config_testing.txt
- qsub split_main.sh ./config_normal.txt
- qsub split_main.sh ./config_tumor.txt
1.3 Creating lookup tables
- bash create_lookup_grp.sh ./config_testing.txt
- bash create_lookup_grp.sh ./config_normal.txt
- bash create_lookup_grp.sh ./config_tumor.txt
The lookup tables are created only once.
2 Prediction
The following commands launch SGE jobs to generate prediction matrices.
2.1 With color normalization
- qsub process_main.sh ./config_testing_cn_true.txt
- qsub process_main.sh ./config_normal_cn_true.txt
- qsub process_main.sh ./config_tumor_cn_true.txt
2.2 Without color normalization
- qsub process_main.sh ./config_testing.txt
- qsub process_main.sh ./config_normal.txt
- qsub process_main.sh ./config_tumor.txt
3 Heatmap stitching
After the predictions matrices have been generated an SGE job using heatmap_main.sh SGE scrip could be launched to genertae heatmaps. Two arguments for this launch are: a) type of the slides (test, normal or tumor); b) the root directory of the results, like in below example run:
- qsub heatmap_main.sh test /scratch/mikem/UserSupport/weizhe.li/runs_process_cn_True/testing_wnorm_448_400_7690953
4 Retreiving run-time statistics
In time_all_stats_pred.sh file adjust job results root directory, DIR and slides type, PREFIX (normal, test or tumor), like below:
- DIR=/scratch/mikem/UserSupport/weizhe.li/runs_process_cn_False/normal_wnorm_448_400_7691563
- PREFIX=normal
Then run:
- time bash ./time_all_stats_pred.sh