From 59054b942b842b7fc15224e1100eda6026685302 Mon Sep 17 00:00:00 2001
From: Orso Meneghini <meneghini@fusion.gat.com>
Date: Tue, 6 Jun 2017 22:19:53 -0700
Subject: [PATCH] Fixed initialization issue for multiple runs in
 brainfuse_lib.c

---
 brainfuse_lib.c | 19 ++++++-------
 readme.md       | 74 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 82 insertions(+), 11 deletions(-)
 create mode 100644 readme.md

diff --git a/brainfuse_lib.c b/brainfuse_lib.c
index 2b22050..a414ff0 100644
--- a/brainfuse_lib.c
+++ b/brainfuse_lib.c
@@ -7,7 +7,7 @@
 #include <dirent.h>
 
 static unsigned int n_models=2; //number of nn physics models
-static unsigned int verbose=0;
+static unsigned int verbose=0;  //verbose output
 
 // arrays of pointers storing multiple ANNS instances,
 // of multiple ANNS ensembles, for different physics models
@@ -129,16 +129,6 @@ int load_anns(int global_nn_model, char *directory, char *basename){
     loaded_anns[model]=1;
   }
 
-  // Initialize memory
-  for(j = 0; j < anns[model][0]->num_input; j++){
-    data_avg[model]->input[0][j]=0.;
-    data_std[model]->input[0][j]=0.;
-  }
-  for(j = 0; j < anns[model][0]->num_output; j++){
-    data_avg[model]->output[0][j]=0.;
-    data_std[model]->output[0][j]=0.;
-  }
-
   return n;
 }
 
@@ -156,12 +146,19 @@ int load_anns__(int *global_nn_model, char *directory, char *basename){
 int load_anns_inputs(fann_type *data_in){
   unsigned int j;
   if (verbose)  printf("Reading ANNs input data %d inputs %d ouputs\n", anns[model][0]->num_input, anns[model][0]->num_output);
+  // load inputs
   for(j = 0; j < anns[model][0]->num_input; j++){
     if (verbose) printf("in  %02d: %3.3f\n",j+1,data_in[j]);
     data_avg[model]->input[0][j]=(fann_type)data_in[j];
     data_std[model]->input[0][j]=data_avg[model]->input[0][j];
     data_nrm[model]->input[0][j]=data_avg[model]->input[0][j];
   }
+  // Initialize outputs to zero
+  for(j = 0; j < anns[model][0]->num_output; j++){
+    data_avg[model]->output[0][j]=0.;
+    data_std[model]->output[0][j]=0.;
+    data_nrm[model]->output[0][j]=0.;
+  }
   if (verbose) printf("\n");
   return 0;
 }
diff --git a/readme.md b/readme.md
new file mode 100644
index 0000000..cf88689
--- /dev/null
+++ b/readme.md
@@ -0,0 +1,74 @@
+EPED1NN
+=======
+
+There are different scripts to run the EPED1-NN model
+
+Low level
+---------
+at the lowest level one can call the `brainfuse_run.exe` binary and pass the list
+of NN files (generally called brainfuse_XX.net) and an input file. For example:
+
+    cd eped1nn/samples
+    ../../brainfuse_run.exe ../models/EPED1_H_superH input_sample.dat
+
+here `EPED1_H_superH` is one of the models under the `models` directory
+
+The `input_sample.dat` has the format of:
+
+    N1
+    i1 i2 i3 i4 i5 i6 i7 i8 i9
+    i1 i2 i3 i4 i5 i6 i7 i8 i9
+    ...
+
+where:
+
+    N1 number of runs
+    i.. inputs (N1 lines)
+
+Upon run the `output.dat` and `output.std` files will be generated in the
+current working directory with the EPED1NN prediction and its standard deviation.
+Both files have format:
+
+    N1
+    o1 o2 o3 o4
+    o1 o2 o3 o4
+    ...
+
+where::
+
+    N1 number of runs
+    o.. outputs (N1 lines)
+
+Python wrapper
+--------------
+The `eped1nn` Python script wraps the `brainfuse_run.exe` executable.
+This Python script also generates a `epednn.profiles` file.
+
+    cd eped1nn/samples
+    ../eped1nn EPED1_H_superH input_sample.dat
+    
+
+Snyder EPED1 interface
+----------------------
+The `eped1nn_eped1` Python script mimics the I/O of Phil Snyder original IDL EPED1 worflow.
+The format of the input is for example in `eped1nn/samples/2015check.txt`.
+
+    cd eped1nn/samples
+    ../eped1nn_eped1 EPED1_H_superH 2015check.txt
+
+The output of the eped1nn_eped1 will append `out` to the input filename: `eped1nn/samples/2015check_out.txt`
+
+Installation
+------------
+Install the FANN library:
+
+    git clone git@github.com:libfann/fann.git
+    cd fann
+    cmake .
+    make
+
+Set in your .login file:
+
+    setenv FANN_ROOT loation_where_fann_was_cloned
+
+Run `./compile.sh` script