Update readme.md

readme.md

@@ -7,19 +7,25 @@
 # 1 Image patch extraction
 - Adjust configuration parameters in files *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. 
-## 1.2 Extract and group
+## 1.1 Extract and group
 - qsub split_main.sh ./config_testing.txt  
 -- *split_main.sh* in turn submits *split_grp.sh* which in turns runs *split_grp.py* in array job fashion. Every task in the array job processes one slide.
 - qsub split_main.sh ./config_normal.txt  
 - qsub split_main.sh ./config_tumor.txt  
 
-## 1.3 Create lookup tables
+## 1.2 Create 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 and used at [Prediction](#2-prediction) stage for launching array job tasks. These tasks are run in parallel and scalable manner - if there are not enough resourcs for running all tasks then they are queued up automatically and started as resources become available. Each task processes only one group. 
 
+## 1.3 Retreiving wall-clock time statistics for extraction and grouping
+Run *time_stats_sg_V2.sh* Linux scrip with two arguments, type of slides (test, normal or tumor) and the root directory of the results:
+- time bash time_stats_sg_V2.sh [test | normal | tumor] ROOT_DIR  
+As an example run:  
+- time bash wall_clock_time_split_group_V2.sh test /scratch/mikem/UserSupport/weizhe.li/runs_split_group/448_400_7691440  
+
 # 2 Prediction
 - Additionally adjust configuration parameters in files, *config_testing_cn_true.txt*, *config_normal_cn_true.txt*, *config_tumor_cn_true.txt*.
 - Run commands listed in the below subsections to launch SGE jobs to generate prediction matrices.
@@ -38,7 +44,7 @@ The lookup tables are created only once and used at [Prediction](#2-prediction)
 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
+# 4 Retreiving run-time statistics for prediction
 ## 4.1 CPU time
 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