From 8d7b6b99904d722510b6cfe9eed8f072d11d8907 Mon Sep 17 00:00:00 2001
From: "W. Trevor King" <wking@tremily.us>
Date: Wed, 15 May 2013 16:27:38 -0400
Subject: [PATCH] local_cmmds.tex: Factor out TikZ stack figure into \tikzstack

Keeping changes syncronized by hand is madness :p.

I also added arrows (after suggestions from both Mom and Prof. Cruz)
showing data flow to/from the physical nodes to their associated
software package.  There's also a new dashed separator between the
software packages and the physical nodes.
---
 src/calibcant/procedure.tex | 59 +-------------------------
 src/local_cmmds.tex         | 83 +++++++++++++++++++++++++++++++++++++
 src/packages.tex            |  1 +
 src/pyafm/stack.tex         | 59 +-------------------------
 4 files changed, 86 insertions(+), 116 deletions(-)

diff --git a/src/calibcant/procedure.tex b/src/calibcant/procedure.tex
index 79fa069..cfbc6af 100644
--- a/src/calibcant/procedure.tex
+++ b/src/calibcant/procedure.tex
@@ -10,64 +10,7 @@ parameters $G_{1f}$, $f_0$, and $\beta_f$.  I've written the
 on packages in the \pyafm\ stack (\cref{fig:calibcant:stack}).
 
 \begin{figure}
-  \begin{tikzpicture}[decoration={
-      markings,%  switch on markings
-      mark=%  add a mark for screw threading
-        between positions 0 and 1 step 1pt
-        with
-        {
-          \draw (0, 2pt) -- (1pt, -2pt);
-        }
-      }
-      ]
-    \tikzstyle{every node}=[text depth=0pt, rounded rectangle,
-      draw=blue!50, very thick, minimum height=1.7em]
-    \node[shape=rectangle,draw=none,inner sep=0]
-      (image) at (0,0) {
-      \asyinclude{figures/schematic/afm}};
-    \node[shape=rectangle,draw=black, semithick]
-      (daq) at ($(image.south west) + (-0.5, -1)$) {DAQ card};
-    \node[shape=rectangle,draw=black, semithick]
-      (motor) at ($(image.south) + (0, -1)$) {motor};
-    %\draw[
-    \coordinate (thermocouple) at ($(image.west) + (1, -4pt)$);
-    \node (pycomedi) at ($(daq) + (-5,0)$) {pycomedi};
-    \node (pypiezo) at ($(pycomedi) + (0,1)$) {pypiezo};
-    \node (pyafm) at ($(pypiezo) + (0,1)$) {pyafm};
-    \node[black!20] (unfold-protein) at ($(pyafm) + (0,1)$) {unfold-protein};
-    \node (stepper) at ($(pycomedi) + (2,1)$) {stepper};
-    \node (pypid) at ($(stepper) + (2,0)$) {pypid};
-    \node (h5config) at ($(pycomedi) + (-3,0)$) {h5config};
-    \node (calibcant) at ($(unfold-protein) + (-3,0)$) {calibcant};
-    \draw (pypiezo) -- (pyafm);
-    \draw (stepper) -- (pyafm);
-    \draw (pypid) -- (pyafm);
-    \draw[black!20] (pyafm) -- (unfold-protein);
-    \draw (h5config) -- (pypiezo);
-    \draw (h5config) -- (pyafm);
-    \draw[black!20] (h5config) -- (unfold-protein);
-    \draw (pyafm) -- (calibcant);
-    \draw (h5config) -- (calibcant);
-    \draw[purple] (pypid) -- (thermocouple);
-    % begin thermometer symbol
-    \draw[blue!20, line width=4pt, cap=round]
-      (thermocouple) -- ($(thermocouple) + (0,12pt)$);
-    \fill[blue!20] (thermocouple) circle (5pt);
-    \draw[red, line width=2pt, cap=butt]
-      (thermocouple) -- ($(thermocouple) + (0,8pt)$);
-    \fill[red] (thermocouple) circle (4pt);
-    % end thermometer symbol
-    % begin motor screw
-    \draw[black!20, line width=4pt]
-      (motor) -- (image.south);   % shaft with decoration threads
-    \draw[black, decorate, ultra thin]
-      (motor) -- (image.south);   % shaft with decoration threads
-    % end motor screw
-    \draw[red]
-      (pypiezo) -- (pycomedi) -- (daq) -- ($(image.south) + (-6pt, 0)$);
-    \draw[red, line width=2pt] (pycomedi) -- (daq);
-    \draw[blue] (stepper) -- (pycomedi) -- (daq) -- (motor);
-  \end{tikzpicture}
+  \tikzstack{black!20}{}
   \caption{Dependency graph for \calibcant, which shares the
     \pyafm\ stack with \unfoldprotein.  Only the ``brain'' module
     changed with respect to
diff --git a/src/local_cmmds.tex b/src/local_cmmds.tex
index 30a85b0..d7c9fc4 100644
--- a/src/local_cmmds.tex
+++ b/src/local_cmmds.tex
@@ -194,3 +194,86 @@
 \newcommand{\sawsim}{\citetalias{king10}}
 \newcommand{\stepper}{\citetalias{stepper}}
 \newcommand{\unfoldprotein}{\citetalias{unfold-protein}}
+
+% draw a thermometer in TikZ
+% usage: \thermometer{bulb-location}
+\newcommand{\thermometer}[1]{
+  \draw[blue!20, line width=4pt, cap=round] #1 -- +(0, 12pt);
+  \fill[blue!20] #1 circle (5pt);
+  \draw[red, line width=2pt, cap=butt] #1 -- +(0, 8pt);
+  \fill[red] #1 circle (4pt);
+}
+
+% shared figure between pyafm and calibcant
+% usage: \tikzstack{unfold-protein-color}{calibcant-color}
+\newcommand{\tikzstack}[2]{%
+  \begin{tikzpicture}[decoration={
+      markings,%  switch on markings
+      mark=%  add a mark for screw threading
+        between positions 0 and 1 step 1pt
+        with
+        {
+          \draw (0, 2pt) -- (1pt, -2pt);
+        }
+      }
+      ]
+    \tikzstyle{every node}=[text depth=0pt, rounded rectangle,
+      draw=blue!50, very thick, minimum height=1.7em]
+    % hardware nodes and coordinates
+    \node[shape=rectangle,draw=none,inner sep=0]
+      (image) at (0,0) {
+      \asyinclude{figures/schematic/afm}};
+    \node[shape=rectangle,draw=black, semithick]
+      (daq) at ($(image.south west) + (-0.25, -1)$) {DAQ card};
+    \node[shape=rectangle,draw=black, semithick]
+      (motor) at ($(image.south) + (0, -1)$) {motor};
+    \coordinate (thermocouple) at ($(image.west) + (1.4, -4pt)$);
+    \thermometer{(thermocouple)}
+    \coordinate (photodiode) at ($(image.west) + (1, 26pt)$);
+    \coordinate (piezo) at ($(image.south) + (-6pt, 0)$);
+    \draw[black!20,dashed] ($(daq.south west) + (-10pt, 0)$) -- +(0, 4);
+    % software nodes
+    \node (pycomedi) at ($(daq) + (-6,0)$) {pycomedi};
+    \node (pypiezo) at ($(pycomedi) + (0,1)$) {pypiezo};
+    \node (pyafm) at ($(pypiezo) + (0,1)$) {pyafm};
+    \node[#1] (unfold-protein) at ($(pyafm) + (0,1)$) {unfold-protein};
+    \node (stepper) at ($(pycomedi) + (2,1)$) {stepper};
+    \node (pypid) at ($(stepper) + (2,0)$) {pypid};
+    \node (h5config) at ($(pycomedi) + (-3,0)$) {h5config};
+    \node[#2] (calibcant) at ($(unfold-protein) + (-3,0)$) {calibcant};
+    % software connections
+    \draw (pypiezo) -- (pyafm);
+    \draw (stepper) -- (pyafm);
+    \draw (pypid) -- (pyafm);
+    \draw[#1] (pyafm) -- (unfold-protein);
+    \draw (h5config) -- (pypiezo);
+    \draw (h5config) -- (pyafm);
+    \ifthenelse{\equal{#1}{}}{%  draw unfold-protein in black (the default)
+      \draw[#2] (pyafm) -- (calibcant);
+      \draw[#1] (h5config) -- (unfold-protein);%  default path on top
+      }{%
+      \draw[#1] (h5config) -- (unfold-protein);
+      \draw[#2] (pyafm) -- (calibcant);%  default path on top
+      }
+    \draw[#2] (h5config) -- (calibcant);
+    % hardware connections
+    \begin{pgfonlayer}{background}
+      \draw[purple, ->] (thermocouple) -- (pypid);
+    \end{pgfonlayer}
+    % begin motor screw
+    \draw[black!20, line width=4pt]
+      (motor) -- (image.south);   % shaft with decoration threads
+    \draw[black, decorate, ultra thin]
+      (motor) -- (image.south);   % shaft with decoration threads
+    % end motor screw
+    \draw[red, <->] (pypiezo) -- (pycomedi);
+    \draw[red, <->, line width=2pt] (pycomedi) -- (daq);
+    \draw[red, ->] (daq) -- (piezo);
+    \begin{pgfonlayer}{background}
+      \draw[red, ->, out=180, in=90] (photodiode) to (daq.north);
+    \end{pgfonlayer}
+    \draw[blue, ->] (stepper) -- (pycomedi);
+    \draw[blue, ->] (pycomedi) -- (daq);
+    \draw[blue, ->] (daq) -- (motor);
+  \end{tikzpicture}
+}
diff --git a/src/packages.tex b/src/packages.tex
index 7b31473..596e996 100644
--- a/src/packages.tex
+++ b/src/packages.tex
@@ -83,6 +83,7 @@
 \usepackage{pgf}          % fancy graphics
 \usepackage{tikz}         % a nice, inline PGF frontend
 \usetikzlibrary{automata} % graph-theory library
+\usetikzlibrary{backgrounds} % background layers
 \usetikzlibrary{calc}     % coordinate-calculation library
 \usetikzlibrary{decorations.markings}       % custom marks
 \usetikzlibrary{decorations.pathreplacing}  % braces and other fancy paths
diff --git a/src/pyafm/stack.tex b/src/pyafm/stack.tex
index 2b2c454..69d2f75 100644
--- a/src/pyafm/stack.tex
+++ b/src/pyafm/stack.tex
@@ -13,64 +13,7 @@ experiment logic to \pyafm\ to carry out velocity-clamp force
 spectroscopy (\cref{fig:pyafm:stack}).
 
 \begin{figure}
-  \begin{tikzpicture}[decoration={
-      markings,%  switch on markings
-      mark=%  add a mark for screw threading
-        between positions 0 and 1 step 1pt
-        with
-        {
-          \draw (0, 2pt) -- (1pt, -2pt);
-        }
-      }
-      ]
-    \tikzstyle{every node}=[text depth=0pt, rounded rectangle,
-      draw=blue!50, very thick, minimum height=1.7em]
-    \node[shape=rectangle,draw=none,inner sep=0]
-      (image) at (0,0) {
-      \asyinclude{figures/schematic/afm}};
-    \node[shape=rectangle,draw=black, semithick]
-      (daq) at ($(image.south west) + (-0.5, -1)$) {DAQ card};
-    \node[shape=rectangle,draw=black, semithick]
-      (motor) at ($(image.south) + (0, -1)$) {motor};
-    %\draw[
-    \coordinate (thermocouple) at ($(image.west) + (1, -4pt)$);
-    \node (pycomedi) at ($(daq) + (-5,0)$) {pycomedi};
-    \node (pypiezo) at ($(pycomedi) + (0,1)$) {pypiezo};
-    \node (pyafm) at ($(pypiezo) + (0,1)$) {pyafm};
-    \node (unfold-protein) at ($(pyafm) + (0,1)$) {unfold-protein};
-    \node (stepper) at ($(pycomedi) + (2,1)$) {stepper};
-    \node (pypid) at ($(stepper) + (2,0)$) {pypid};
-    \node (h5config) at ($(pycomedi) + (-3,0)$) {h5config};
-    \node[black!20] (calibcant) at ($(unfold-protein) + (-3,0)$) {calibcant};
-    \draw (pypiezo) -- (pyafm);
-    \draw (stepper) -- (pyafm);
-    \draw (pypid) -- (pyafm);
-    \draw (pyafm) -- (unfold-protein);
-    \draw[black!20] (pyafm) -- (calibcant);
-    \draw (h5config) -- (pypiezo);
-    \draw (h5config) -- (pyafm);
-    \draw (h5config) -- (unfold-protein);
-    \draw[black!20] (h5config) -- (calibcant);
-    \draw[purple] (pypid) -- (thermocouple);
-    % begin thermometer symbol
-    \draw[blue!20, line width=4pt, cap=round]
-      (thermocouple) -- ($(thermocouple) + (0,12pt)$);
-    \fill[blue!20] (thermocouple) circle (5pt);
-    \draw[red, line width=2pt, cap=butt]
-      (thermocouple) -- ($(thermocouple) + (0,8pt)$);
-    \fill[red] (thermocouple) circle (4pt);
-    % end thermometer symbol
-    % begin motor screw
-    \draw[black!20, line width=4pt]
-      (motor) -- (image.south);   % shaft with decoration threads
-    \draw[black, decorate, ultra thin]
-      (motor) -- (image.south);   % shaft with decoration threads
-    % end motor screw
-    \draw[red]
-      (pypiezo) -- (pycomedi) -- (daq) -- ($(image.south) + (-6pt, 0)$);
-    \draw[red, line width=2pt] (pycomedi) -- (daq);
-    \draw[blue] (stepper) -- (pycomedi) -- (daq) -- (motor);
-  \end{tikzpicture}
+  \tikzstack{}{black!20}
   \caption{Dependency graph for my modular experiment control
     stack.\label{fig:pyafm:stack}}
 \end{figure}
-- 
2.26.2