From e5306ed9a8b43dab5437f55efd54c1c1cc61d7fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marc=20W=C3=A4ckerlin?= <marc@mrw.sh>
Date: Fri, 26 Aug 2016 14:24:29 +0000
Subject: [PATCH] documentation updated

---
 ax_init_standard_project.m4 |  5 ++-
 bootstrap.sh                |  6 ++-
 doc/style.css               | 13 +++++-
 src/neuron.hxx              | 86 ++++++++++++++++++++++++++++---------
 4 files changed, 86 insertions(+), 24 deletions(-)

diff --git a/ax_init_standard_project.m4 b/ax_init_standard_project.m4
index 7c6a416..77fbac8 100644
--- a/ax_init_standard_project.m4
+++ b/ax_init_standard_project.m4
@@ -171,12 +171,13 @@ AC_DEFUN([AX_INIT_STANDARD_PROJECT], [
   AX_SUBST(NUMBERS)
   AX_SUBST(HOME)
   if test -f README.md; then
-    README=$()
+    README=$(tail -n +3 README.md)
     DESCRIPTION=$(head -1 README.md)
   else
     README=$(tail -n +3 README)
     DESCRIPTION=$(head -1 README)
   fi
+  README_ESCAPED=$(echo "$README" | sed ':a;N;$!ba;s/\n/\\n/g;s,",\\",g')
   if which pandoc 2>&1 > /dev/null; then   
     README_HTML=$(echo "$README" | pandoc -f markdown_github -t html | sed ':a;N;$!ba;s,\\\(.\),\\\\<span>\1</span>,g;s/\n/\\n/g;s,",\\",g;s,  ,\&nbsp;\&nbsp;,g')
   else
@@ -184,6 +185,8 @@ AC_DEFUN([AX_INIT_STANDARD_PROJECT], [
   fi
   AX_SUBST(README)
   _AM_SUBST_NOTMAKE([README])
+  AX_SUBST(README_ESCAPED)
+  _AM_SUBST_NOTMAKE([README_ESCAPED])
   AX_SUBST(README_HTML)
   _AM_SUBST_NOTMAKE([README_HTML])
   AX_SUBST(DESCRIPTION)
diff --git a/bootstrap.sh b/bootstrap.sh
index 8a7c967..466ec5a 100755
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -529,7 +529,11 @@ ${DEFAULT_PROJECT_NAME}
 add description for ${DEFAULT_PROJECT_NAME}
 EOF
 to configure.ac <<EOF && notice "please edit configure.ac, then rerun $0" && exit 0
-${HEADER}m4_define(x_package_name, ${DEFAULT_PROJECT_NAME}) # project's name
+${HEADER}# default is generated from AUTHORS and project name
+PROJECT_URL=
+SOURCE_DOWNLOAD=
+
+m4_define(x_package_name, ${DEFAULT_PROJECT_NAME}) # project's name
 m4_define(x_major, 0) # project's major version
 m4_define(x_minor, 0) # project's minor version
 m4_include(ax_init_standard_project.m4)
diff --git a/doc/style.css b/doc/style.css
index 7aa5ff7..8765b9a 100644
--- a/doc/style.css
+++ b/doc/style.css
@@ -1,5 +1,16 @@
 #titlearea {
   display: flex;
   justify-content: space-between;
-  align-items: flex-end;
+  align-items: flex-begin;
+}
+#titlearea nav {
+  padding: 0;
+  margin: 0;
+}
+#titlearea nav a {
+  background-color: lightgray;
+  border: 1px solid gray;
+  color: black;
+  padding: 1ex;
+  margin: 0;
 }
diff --git a/src/neuron.hxx b/src/neuron.hxx
index c852ee7..e9629b1 100644
--- a/src/neuron.hxx
+++ b/src/neuron.hxx
@@ -11,6 +11,56 @@
 
     @section neuro-intro Overview
 
+    @subsection nature Natural Neural Network
+
+    From <a href="https://en.wikipedia.org/wiki/Neuron">Wikipedia</a>:
+    «A neuron is an electrically excitable cell that processes and
+    transmits information through electrical and chemical
+    signals. These signals between neurons occur via synapses,
+    specialized connections with other cells. Neurons can connect to
+    each other to form neural networks. Neurons are the core
+    components of the brain and spinal cord of the central nervous
+    system, and of the ganglia of the peripheral nervous system.» The
+    neuron connects with dendrites to the world or to the axon of
+    other neuirons. The neurites (dendrite or axon) transport
+    electrical stimulation to the cell, which emits the signal to the
+    dendrites if the activation reaches a certain level.
+
+    @dot
+    digraph g {
+      rankdir=LR;
+      ranksep=0.8;
+      node [shape=hexagon];
+      edge [arrowhead=none];
+      subgraph clusterInput {
+        label="sensors";
+        color="white";
+        node [shape=point];
+        I0; I1; I2; I3; I4; I5; I6; I7; I8 I9;
+      }
+      subgraph clusterOutput {
+        label="actors";
+        color="white";
+        node [shape=point];
+        O0; O1; O2; O3; O4; O5; O6;
+      }
+      I1 -> Cell1 [label="axon";taillabel="synapse"];
+      { I2; I3; I4; } -> Cell1;
+      { I5; I6; I7; I8; } -> Cell2;
+      { I4; I6; I9; I0; } -> Cell3;
+      Cell1 -> Cell8 [label="axon / dendrite"];
+      Cell1 -> { Cell2; Cell4; Cell5; }
+      Cell2 -> { Cell4; Cell5; Cell6; Cell8; }
+      Cell3 -> { Cell4; Cell6; Cell7; Cell8; }
+      { Cell4; Cell5; Cell6 } -> { Cell7; Cell8; }
+      Cell7 -> { O0; O1; O2 };
+      Cell8 -> { O3; O4; O5; };
+      Cell8 -> O6 [label="dendrite"];
+    }
+    @enddot
+    
+    @subsection art Artificial Neural Network
+
     A complex neural network can be imitiated as a vector @c I of @c i
     input values, a vector @c O of @c o output values and any number
     @c l of hidden layers, where each of them contains @c h
@@ -67,26 +117,12 @@
         Ox [label=<O<SUB>…</SUB>>];
         Oo [label=<O<SUB>o</SUB>>];
       }
-      I1 -> { H11; H12; H1x; H1h; }
-      I2 -> { H11; H12; H1x; H1h; }
-      Ix -> { H11; H12; H1x; H1h; }
-      Ii -> { H11; H12; H1x; H1h; }
-      H11 -> { H21; H22; H2x; H2h; }
-      H12 -> { H21; H22; H2x; H2h; }
-      H1x -> { H21; H22; H2x; H2h; }
-      H1h -> { H21; H22; H2x; H2h; }
-      H21 -> { Hx1; Hx2; Hxx; Hxh; }
-      H22 -> { Hx1; Hx2; Hxx; Hxh; }
-      H2x -> { Hx1; Hx2; Hxx; Hxh; }
-      H2h -> { Hx1; Hx2; Hxx; Hxh; }
-      Hx1 -> { Hl1; Hl2; Hlx; Hlh; }
-      Hx2 -> { Hl1; Hl2; Hlx; Hlh; }
-      Hxx -> { Hl1; Hl2; Hlx; Hlh; }
-      Hxh -> { Hl1; Hl2; Hlx; Hlh; }
-      Hl1 -> { O1; O2; Ox; Oo; }
-      Hl2 -> { O1; O2; Ox; Oo; }
-      Hlx -> { O1; O2; Ox; Oo; }
-      Hlh -> { O1; O2; Ox; Oo; }
+      { I1; I2; Ix; Ii; }
+      -> { H11; H12; H1x; H1h; }
+      -> { H21; H22; H2x; H2h; }
+      -> { Hx1; Hx2; Hxx; Hxh; }
+      -> { Hl1; Hl2; Hlx; Hlh; }
+      -> { O1; O2; Ox; Oo; }
     }
     @enddot
 
@@ -110,7 +146,15 @@
     @endcode
     
     @section neuro-backward Back Propagation
-    
+
+    @page biblio Bibliography
+
+     - <a href="http://www.tornau.name/wp-content/uploads/2009/04/studiumsmaterialien/neuronale_netze_zusammefassung.pdf">Vorlesung Neuronale Netze - Zusammenfassung - Christoph Tornau</a>
+     - <a href="http://www.neuronalesnetz.de/">Neuronale Netze — Eine Einführung</a>
+     - <a href="http://alphard.ethz.ch/hafner/Vorles/Optim/ANN/Artificial%20Neural%20Network%20based%20Curve%20Prediction%20Documentation.pdf">Artificial Neural Network based Curve Prediction</a>
+     - <a href="http://cs231n.github.io/convolutional-networks/">Convolutional Neural Networks (CNNs / ConvNets)</a>
+     - <a href="https://www.tensorflow.org/versions/r0.9/tutorials/index.html">TensorFlow utorials</a>
+     - <a href="http://alphard.ethz.ch/hafner/Vorles/Optim/ANN/Artificial%20Neural%20Network%20based%20Curve%20Prediction%20Documentation.pdf">Artificial Neural Network based Curve Prediction</a>
 
     */
 template