From 64d99c1f3cddec9f1a75da2df2ece6209bf2b09e Mon Sep 17 00:00:00 2001
From: PaulBautin <49245398+PaulBautin@users.noreply.github.com>
Date: Tue, 8 Sep 2020 11:13:38 -0400
Subject: [PATCH] Freeze config files for processing on compute canada: graham
 (#73)

* - parameter config files for processing on graham

* - change username in sbatch account

* - change dataset name in config_sct_run_batch

* - change account and mail in job template

* - add emailing to job template

* remove mail-type END
---
 config_script.yml => config_script_t2.yml | 18 ++++++++----------
 config_sct_run_batch.yml                  |  8 ++++----
 job_template.sh                           |  9 +++++++++
 run_all.py                                |  2 +-
 4 files changed, 22 insertions(+), 15 deletions(-)
 rename config_script.yml => config_script_t2.yml (63%)
 create mode 100644 job_template.sh

diff --git a/config_script.yml b/config_script_t2.yml
similarity index 63%
rename from config_script.yml
rename to config_script_t2.yml
index 7252b47..983fb59 100644
--- a/config_script.yml
+++ b/config_script_t2.yml
@@ -3,21 +3,19 @@
 # process_data.sh
 # ---------------
 # Number of transformations to apply to each subject
-n_transfo: 2
+n_transfo: 30
 # Rescaling factor to apply to each subject. Note: value '1' should always be present.
 rescaling:
   - 1
+  - 0.99
+  - 0.98
+  - 0.97
+  - 0.96
   - 0.95
+  - 0.94
+  - 0.93
 # Contrasts on which to perform the analysis. Available values are: 't1', 't2'
-contrast: "t1"
-transfo_file: transfo_values.csv
-
-# manual_labeling_correction.sh
-# -----------------------------
-# TODO: fetch path_output from yml config input to sct_run_batch
-PATH_ORIGINAL_RESULTS: "csa_atrophy_results/results"
-PATH_ORIGINAL_CSV: "csa_atrophy_results/data_processed"
-PATH_DESTINATION_RESULTS: "csa_atrophy_results_corrected/results"
+contrast: "t2"
 
 # csa_atrophy_stat.py
 # -------------------
diff --git a/config_sct_run_batch.yml b/config_sct_run_batch.yml
index 355b295..94699c5 100644
--- a/config_sct_run_batch.yml
+++ b/config_sct_run_batch.yml
@@ -1,8 +1,8 @@
 # config file for sct_run_batch
-path_data: spinegeneric_r20200801
-path_output: csa_atrophy_results
-script: process_data.sh
-script_args: config_script.yml
+path_data: /scratch/pabaua/data-multi-subject-p
+path_output: /scratch/pabaua/results_csa_t2
+script: /home/pabaua/csa-atrophy/process_data.sh
+script_args: /home/pabaua/csa-atrophy/config_script_t2.yml
 jobs: -1
 batch_log: sct_run_batch_log.txt
 continue_on_error: 1
diff --git a/job_template.sh b/job_template.sh
new file mode 100644
index 0000000..222eda8
--- /dev/null
+++ b/job_template.sh
@@ -0,0 +1,9 @@
+#SBATCH --account=def-jcohen
+#SBATCH --time=0-08:00        # time (DD-HH:MM)
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=32    # number of OpenMP processes
+#SBATCH --mem=128G
+#SBATCH --mail-user=paul.bautin@polymtl.ca
+#SBATCH --mail-type=ALL
+
+cd $SCRATCH
diff --git a/run_all.py b/run_all.py
index 7c0c4b9..625f751 100644
--- a/run_all.py
+++ b/run_all.py
@@ -71,7 +71,7 @@ def main():
         path_job_template = os.path.abspath(os.path.expanduser(arguments.job_template))
         job_template = open(path_job_template, 'r').read()
     else:
-        job_template = """#SBATCH --account=def-jcohen
+        job_template = """#SBATCH --account=def-pabaua
 #SBATCH --time=0-08:00        # time (DD-HH:MM)
 #SBATCH --nodes=1
 #SBATCH --cpus-per-task=32    # number of OpenMP processes