|
@@ -7,17 +7,12 @@
|
|
|
# 1 Image patch extraction
|
|
# 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*.
|
|
- 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 commands listed in the following subsections to launch Son of Grid Engine (SGE) jobs to extract, group patches in HDF5 files and create a lookup table for every HDF5 file.
|
|
- Run the commands listed in the following subsections 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
|
|
|
|
|
|
|
+## 1.2 Extract and group
|
|
|
- qsub split_main.sh ./config_testing.txt
|
|
- qsub split_main.sh ./config_testing.txt
|
|
|
- qsub split_main.sh ./config_normal.txt
|
|
- qsub split_main.sh ./config_normal.txt
|
|
|
- qsub split_main.sh ./config_tumor.txt
|
|
- qsub split_main.sh ./config_tumor.txt
|
|
|
|
|
|
|
|
-## 1.3 Creating lookup tables
|
|
|
|
|
|
|
+## 1.3 Creat lookup tables
|
|
|
- bash create_lookup_grp.sh ./config_testing.txt
|
|
- bash create_lookup_grp.sh ./config_testing.txt
|
|
|
- bash create_lookup_grp.sh ./config_normal.txt
|
|
- bash create_lookup_grp.sh ./config_normal.txt
|
|
|
- bash create_lookup_grp.sh ./config_tumor.txt
|
|
- bash create_lookup_grp.sh ./config_tumor.txt
|
Mike Mikailov