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Makefile diagram-generator: error out if image generation fails May 12, 2019
README.md
diagram-generator.lua
sample.md

README.md

Diagram Generator Lua Filter

Introduction

This Lua filter is used to create images with or without captions from code blocks. Currently PlantUML, Graphviz, TikZ and Python can be processed. This document also serves as a test document, which is why the subsequent test diagrams are integrated in every supported language.

Prerequisites

To be able to use this Lua filter, the respective external tools must be installed. However, it is sufficient if the tools to be used are installed. If you only want to use PlantUML, you don't need LaTeX or Python, etc.

PlantUML

To use PlantUML, you must install PlantUML itself. See the PlantUML website for more details. It should be noted that PlantUML is a Java program and therefore Java must also be installed.

By default, this filter expects the plantuml.jar file to be in the working directory. Alternatively, the environment variable PLANTUML can be set with a path. If, for example, a specific PlantUML version is to be used per pandoc document, the plantumlPath meta variable can be set.

Furthermore, this filter assumes that Java is located in the system or user path. This means that from any place of the system the java command is understood. Alternatively, the JAVA_HOME environment variable gets used. To use a specific Java version per pandoc document, use the javaPath meta variable. Please notice that JAVA_HOME must be set to the java's home directory e.g. c:\Program Files\Java\jre1.8.0_201\ whereas javaPath must be set to the absolute path of java.exe e.g. c:\Program Files\Java\jre1.8.0_201\bin\java.exe.

Example usage:

```{.plantuml caption="This is an image, created by **PlantUML**."}
@startuml
Alice -> Bob: Authentication Request Bob --> Alice: Authentication Response
Alice -> Bob: Another authentication Request Alice <-- Bob: another Response
@enduml
```

Graphviz

To use Graphviz you only need to install Graphviz, as you can read on its website. There are no other dependencies.

This filter assumes that the dot command is located in the path and therefore can be used from any location. Alternatively, you can set the environment variable DOT or use the pandoc's meta variable dotPath.

Example usage from the Graphviz gallery:

```{.graphviz caption="This is an image, created by **Graphviz**'s dot."}
digraph finite_state_machine {
	rankdir=LR;
	size="8,5"
	node [shape = doublecircle]; LR_0 LR_3 LR_4 LR_8;
	node [shape = circle];
	LR_0 -> LR_2 [ label = "SS(B)" ];
	LR_0 -> LR_1 [ label = "SS(S)" ];
	LR_1 -> LR_3 [ label = "S($end)" ];
	LR_2 -> LR_6 [ label = "SS(b)" ];
	LR_2 -> LR_5 [ label = "SS(a)" ];
	LR_2 -> LR_4 [ label = "S(A)" ];
	LR_5 -> LR_7 [ label = "S(b)" ];
	LR_5 -> LR_5 [ label = "S(a)" ];
	LR_6 -> LR_6 [ label = "S(b)" ];
	LR_6 -> LR_5 [ label = "S(a)" ];
	LR_7 -> LR_8 [ label = "S(b)" ];
	LR_7 -> LR_5 [ label = "S(a)" ];
	LR_8 -> LR_6 [ label = "S(b)" ];
	LR_8 -> LR_5 [ label = "S(a)" ];
}
```

TikZ

TikZ (cf. Wikipedia) is a description language for graphics of any kind that can be used within LaTeX (cf. Wikipedia).

Therefore a LaTeX system must be installed on the system. The TikZ code is embedded into a dynamic LaTeX document. This temporary document gets translated into a PDF document using LaTeX (pdflatex). Finally, Inkscape is used to convert the PDF file to the desired format.

Note: We are using Inkscape here to use a stable solution for the convertion. Formerly ImageMagick was used instead. ImageMagick is not able to convert PDF files. Hence, it uses Ghostscript to do so, cf. 1. Unfortunately, Ghostscript behaves unpredictable during Windows and Linux tests cases, cf. 2, 3, 4, 5, 6, etc. By using Inkscape, we need one dependency less and get rid of unexpected Ghostscript issues.

Due to this more complicated process, the use of TikZ is also more complicated overall. The process is error-prone: An insufficiently configured LaTeX installation or an insufficiently configured Inkscape installation can lead to errors. Overall, this results in the following dependencies:

  • Any LaTeX installation. This should be configured so that missing packages are installed automatically. This filter uses the pdflatex command which is available by the system's path. Alternatively, you can set the PDFLATEX environment variable. In case you have to use a specific LaTeX version on a pandoc document basis, you might set the pdflatexPath meta variable.

  • An installation of Inkscape. It is assumed that the inkscape command is in the path and can be executed from any location. Alternatively, the environment variable INKSCAPE can be set with a path. If a specific version per pandoc document is to be used, the inkscapePath meta-variable can be set.

In order to use additional LaTeX packages, use the optional additionalPackages attribute in your document, as in the example below.

Example usage from TikZ examples by Kjell Magne Fauske:

```{.tikz caption="This is an image, created by **TikZ i.e. LaTeX**."
     additionalPackages="\usepackage{adjustbox}"}
\usetikzlibrary{arrows}
\tikzstyle{int}=[draw, fill=blue!20, minimum size=2em]
\tikzstyle{init} = [pin edge={to-,thin,black}]

\resizebox{16cm}{!}{%
  \trimbox{3.5cm 0cm 0cm 0cm}{
    \begin{tikzpicture}[node distance=2.5cm,auto,>=latex']
      \node [int, pin={[init]above:$v_0$}] (a) {$\frac{1}{s}$};
      \node (b) [left of=a,node distance=2cm, coordinate] {a};
      \node [int, pin={[init]above:$p_0$}] at (0,0) (c)
        [right of=a] {$\frac{1}{s}$};
      \node [coordinate] (end) [right of=c, node distance=2cm]{};
      \path[->] (b) edge node {$a$} (a);
      \path[->] (a) edge node {$v$} (c);
      \draw[->] (c) edge node {$p$} (end) ;
    \end{tikzpicture}
  }
}
```

Python

In order to use Python to generate a diagram, your Python code must store the final image data in a temporary file with the correct format. In case you use matplotlib for a diagram, add the following line to do so:

plt.savefig("$DESTINATION$", dpi=300, fomat="$FORMAT$")

The placeholder $FORMAT$ gets replace by the necessary format. Most of the time, this will be png or svg. The second placeholder, $DESTINATION$ gets replaced by the path and file name of the destination. Both placeholders can be used as many times as you want. Example usage from the Matplotlib examples:

```{.py2image caption="This is an image, created by **Python**."}
import matplotlib
matplotlib.use('Agg')

import sys
import numpy as np
import matplotlib.pyplot as plt

# Fixing random state for reproducibility
np.random.seed(19680801)

dt = 0.01
t = np.arange(0, 30, dt)
nse1 = np.random.randn(len(t))                 # white noise 1
nse2 = np.random.randn(len(t))                 # white noise 2

# Two signals with a coherent part at 10Hz and a random part
s1 = np.sin(2 * np.pi * 10 * t) + nse1
s2 = np.sin(2 * np.pi * 10 * t) + nse2

fig, axs = plt.subplots(2, 1)
axs[0].plot(t, s1, t, s2)
axs[0].set_xlim(0, 2)
axs[0].set_xlabel('time')
axs[0].set_ylabel('s1 and s2')
axs[0].grid(True)

cxy, f = axs[1].cohere(s1, s2, 256, 1. / dt)
axs[1].set_ylabel('coherence')

fig.tight_layout()
plt.savefig("$DESTINATION$", dpi=300, fomat="$FORMAT$")
```

Precondition to use Python is a Python environment which contains all necessary libraries you want to use. To use, for example, the standard Anaconda Python environment on a Microsoft Windows system ...

  • set the environment variable PYTHON or the meta key pythonPath to c:\ProgramData\Anaconda3\python.exe

  • set the environment variable PYTHON_ACTIVATE or the meta key activatePythonPath to c:\ProgramData\Anaconda3\Scripts\activate.bat.

Pandoc will activate this Python environment and starts Python with your code.

How to run pandoc

This section will show, how to call Pandoc in order to use this filter with meta keys. The following command assume, that the filters are stored in the subdirectory filters. Further, this is a example for a Microsoft Windows system.

Command to use PlantUML (a single line):

pandoc.exe README.md -f markdown -t docx --self-contained --standalone --lua-filter=filters\diagram-generator.lua --metadata=plantumlPath:"c:\ProgramData\chocolatey\lib\plantuml\tools\plantuml.jar" --metadata=javaPath:"c:\Program Files\Java\jre1.8.0_201\bin\java.exe" -o README.docx

All available environment variables:

  • PLANTUML e.g. c:\ProgramData\chocolatey\lib\plantuml\tools\plantuml.jar; Default: plantuml.jar
  • INKSCAPE e.g. c:\Program Files\Inkscape\inkscape.exe; Default: inkscape
  • PYTHON e.g. c:\ProgramData\Anaconda3\python.exe; Default: n/a
  • PYTHON_ACTIVATE e.g. c:\ProgramData\Anaconda3\Scripts\activate.bat; Default: n/a
  • JAVA_HOME e.g. c:\Program Files\Java\jre1.8.0_201; Default: n/a
  • DOT e.g. c:\ProgramData\chocolatey\bin\dot.exe; Default: dot
  • PDFLATEX e.g. c:\Program Files\MiKTeX 2.9\miktex\bin\x64\pdflatex.exe; Default: pdflatex

All available meta keys:

  • plantumlPath
  • inkscapePath
  • pythonPath
  • activatePythonPath
  • javaPath
  • dotPath
  • pdflatexPath
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