--- a
+++ b/pipeline
@@ -0,0 +1,41 @@
+#!/bin/sh
+
+# directory of project folder
+DIR="/Users/yijun/panc"
+DATADIR="${DIR}/data"
+CODEDIR="${DIR}/repo"
+
+
+# which fold to experiment, set it to 0 / 1/ 2/ 3
+cur_fold=0
+
+# settings same as in fixed-point
+FOLDS=4
+LOW_RANGE=-100
+HIGH_RANGE=240
+ORGAN_NUMBER=1
+MARGIN=20
+# to build a uniform dimension for input of NN
+ZMAX=160
+YMAX=256
+XMAX=192
+# parameters of training
+epoch=10
+init_lr=1e-5
+# model to test
+model_test=unet_fd${cur_fold}_Z_ep${epoch}_lr${init_lr}
+# if want to view visualization of model's prediction slice by slice, set vis to true
+vis=false
+
+# ---------------- programs -------------------
+# slice the 3d volumn to 2d slices
+python slice.py ${DATADIR} ${ORGAN_NUMBER} ${FOLDS} ${LOW_RANGE} ${HIGH_RANGE}
+
+# create data for training
+python data.py ${DATADIR} ${cur_fold} Z ${ZMAX} ${YMAX} ${XMAX} ${MARGIN} ${ORGAN_NUMBER} ${LOW_RANGE} ${HIGH_RANGE}
+
+# train the model
+python unet.py ${DATADIR} ${cur_fold} Z ${epoch} ${init_lr}
+
+# test the model
+python testvis.py ${DATADIR} ${model_test} ${cur_fold} Z ${ZMAX} ${YMAX} ${XMAX} ${HIGH_RANGE} ${LOW_RANGE} ${MARGIN} ${vis}