1
\contentsline {section}{\numberline {1}Foreword}{1}{section.1}
2
\contentsline {subsection}{\numberline {1.1}Introduction}{1}{subsection.1.1}
3
\contentsline {subsubsection}{\numberline {1.1.1}Background}{1}{subsubsection.1.1.1}
4
\contentsline {subsubsection}{\numberline {1.1.2}What is Open Source?}{1}{subsubsection.1.1.2}
5
\contentsline {subsection}{\numberline {1.2}Requirements}{2}{subsection.1.2}
6
\contentsline {subsection}{\numberline {1.3}Platform specific notes}{2}{subsection.1.3}
7
\contentsline {subsection}{\numberline {1.4}Getting help}{3}{subsection.1.4}
8
\contentsline {subsection}{\numberline {1.5}Who wrote this program?}{3}{subsection.1.5}
9
\contentsline {subsection}{\numberline {1.6}Alternate documentation}{3}{subsection.1.6}
10
\contentsline {subsection}{\numberline {1.7}Helping out}{3}{subsection.1.7}
11
\contentsline {section}{\numberline {2}Basics}{3}{section.2}
12
\contentsline {subsection}{\numberline {2.1}Getting started}{3}{subsection.2.1}
13
\contentsline {subsubsection}{\numberline {2.1.1}Licence}{3}{subsubsection.2.1.1}
14
\contentsline {subsubsection}{\numberline {2.1.2}Installing the program}{4}{subsubsection.2.1.2}
15
\contentsline {subsection}{\numberline {2.2}Understanding the interface}{4}{subsection.2.2}
16
\contentsline {subsubsection}{\numberline {2.2.1}The 3D View}{5}{subsubsection.2.2.1}
17
\contentsline {paragraph}{Basic movement}{5}{figure.3}
18
\contentsline {subsubsection}{\numberline {2.2.2}Plot area}{6}{subsubsection.2.2.2}
19
\contentsline {subsubsection}{\numberline {2.2.3}Console}{6}{subsubsection.2.2.3}
20
\contentsline {subsubsection}{\numberline {2.2.4}Tools panel}{7}{subsubsection.2.2.4}
21
\contentsline {subsection}{\numberline {2.3}Usage fundamentals}{8}{subsection.2.3}
22
\contentsline {section}{\numberline {3}Quick start}{9}{section.3}
23
\contentsline {subsection}{\numberline {3.1}Loading data}{9}{subsection.3.1}
24
\contentsline {subsection}{\numberline {3.2}Loading an analysis}{9}{subsection.3.2}
25
\contentsline {subsection}{\numberline {3.3}Ranging}{9}{subsection.3.3}
26
\contentsline {subsection}{\numberline {3.4}Spectrum}{10}{subsection.3.4}
27
\contentsline {subsection}{\numberline {3.5}Composition profiles}{10}{subsection.3.5}
28
\contentsline {subsection}{\numberline {3.6}Counting Points and measuring volume}{11}{subsection.3.6}
29
\contentsline {subsection}{\numberline {3.7}Concentration surface and slices}{11}{subsection.3.7}
30
\contentsline {section}{\numberline {4}Understanding the program}{14}{section.4}
31
\contentsline {subsection}{\numberline {4.1}Filters}{14}{subsection.4.1}
32
\contentsline {subsection}{\numberline {4.2}Trees}{14}{subsection.4.2}
33
\contentsline {subsection}{\numberline {4.3}Stashes}{15}{subsection.4.3}
34
\contentsline {subsection}{\numberline {4.4}Plots}{16}{subsection.4.4}
35
\contentsline {subsection}{\numberline {4.5}Cameras}{16}{subsection.4.5}
36
\contentsline {subsection}{\numberline {4.6}Effects}{17}{subsection.4.6}
37
\contentsline {subsection}{\numberline {4.7}Program actions}{17}{subsection.4.7}
38
\contentsline {subsubsection}{\numberline {4.7.1}Save}{17}{subsubsection.4.7.1}
39
\contentsline {subsubsection}{\numberline {4.7.2}Undo}{17}{subsubsection.4.7.2}
40
\contentsline {subsubsection}{\numberline {4.7.3}Raw Data}{17}{subsubsection.4.7.3}
41
\contentsline {subsubsection}{\numberline {4.7.4}Export Menu}{17}{subsubsection.4.7.4}
42
\contentsline {subsubsection}{\numberline {4.7.5}Autosave}{18}{subsubsection.4.7.5}
43
\contentsline {subsubsection}{\numberline {4.7.6}Export Animation}{18}{subsubsection.4.7.6}
44
\contentsline {section}{\numberline {5}Detailed Reference}{22}{section.5}
45
\contentsline {subsection}{\numberline {5.1}Data types}{22}{subsection.5.1}
46
\contentsline {subsubsection}{\numberline {5.1.1}Ions}{22}{subsubsection.5.1.1}
47
\contentsline {subsubsection}{\numberline {5.1.2}Plots}{22}{subsubsection.5.1.2}
48
\contentsline {subsubsection}{\numberline {5.1.3}Range}{22}{subsubsection.5.1.3}
49
\contentsline {subsubsection}{\numberline {5.1.4}Voxels}{22}{subsubsection.5.1.4}
50
\contentsline {subsubsection}{\numberline {5.1.5}Drawables}{22}{subsubsection.5.1.5}
51
\contentsline {subsection}{\numberline {5.2}Filters}{22}{subsection.5.2}
52
\contentsline {subsubsection}{\numberline {5.2.1}Data load}{23}{subsubsection.5.2.1}
53
\contentsline {subsubsection}{\numberline {5.2.2}Downsampling}{24}{subsubsection.5.2.2}
54
\contentsline {subsubsection}{\numberline {5.2.3}Ion Information}{24}{subsubsection.5.2.3}
55
\contentsline {subsubsection}{\numberline {5.2.4}Ranging}{25}{subsubsection.5.2.4}
56
\contentsline {subsubsection}{\numberline {5.2.5}Bounding Box}{26}{subsubsection.5.2.5}
57
\contentsline {subsubsection}{\numberline {5.2.6}Clipping}{26}{subsubsection.5.2.6}
58
\contentsline {subsubsection}{\numberline {5.2.7}Spectrum}{26}{subsubsection.5.2.7}
59
\contentsline {subsubsection}{\numberline {5.2.8}Profile}{27}{subsubsection.5.2.8}
60
\contentsline {subsubsection}{\numberline {5.2.9}Spatial Analysis}{27}{subsubsection.5.2.9}
61
\contentsline {paragraph}{Algorithms}{27}{section*.3}
62
\contentsline {subsubsection}{\numberline {5.2.10}Clustering analysis}{28}{subsubsection.5.2.10}
63
\contentsline {subsubsection}{\numberline {5.2.11}External Program}{29}{subsubsection.5.2.11}
64
\contentsline {paragraph}{Command syntax: }{29}{section*.4}
65
\contentsline {paragraph}{Prior to program execution:}{30}{section*.5}
66
\contentsline {paragraph}{After program execution:}{30}{section*.6}
67
\contentsline {subsubsection}{\numberline {5.2.12}Annotation}{30}{subsubsection.5.2.12}
68
\contentsline {paragraph}{Text}{30}{section*.7}
69
\contentsline {paragraph}{Arrow, Arrow with Text}{31}{section*.8}
70
\contentsline {paragraph}{Angle Measurement}{31}{section*.9}
71
\contentsline {subsubsection}{\numberline {5.2.13}Voxels}{31}{subsubsection.5.2.13}
72
\contentsline {subsection}{\numberline {5.3}Ion Colour}{32}{subsection.5.3}
73
\contentsline {subsection}{\numberline {5.4}Ion Transform}{33}{subsection.5.4}
74
\contentsline {section}{\numberline {6}Attributions}{33}{section.6}
75
\contentsline {section}{\numberline {7}Licence}{34}{section.7}
76
\contentsline {section}{\numberline {8}Appendices}{34}{section.8}
77
\contentsline {subsection}{\numberline {8.1}Paths}{34}{subsection.8.1}
78
\contentsline {subsection}{\numberline {8.2}File formats}{34}{subsection.8.2}
79
\contentsline {subsubsection}{\numberline {8.2.1}State file}{34}{subsubsection.8.2.1}
80
\contentsline {subsubsection}{\numberline {8.2.2}Range files}{35}{subsubsection.8.2.2}
81
\contentsline {subsubsection}{\numberline {8.2.3}POS files}{36}{subsubsection.8.2.3}
82
\contentsline {subsubsection}{\numberline {8.2.4}Text files}{36}{subsubsection.8.2.4}
83
\contentsline {subsection}{\numberline {8.3}External Program Examples}{37}{subsection.8.3}
84
\contentsline {subsubsection}{\numberline {8.3.1}Scilab}{37}{subsubsection.8.3.1}
85
\contentsline {subsubsection}{\numberline {8.3.2}Python}{41}{subsubsection.8.3.2}
86
\contentsline {subsubsection}{\numberline {8.3.3}Bash}{43}{subsubsection.8.3.3}
87
\contentsline {subsubsection}{\numberline {8.3.4}C/C++}{45}{subsubsection.8.3.4}
88
\contentsline {subsection}{\numberline {8.4}Modifying the program}{49}{subsection.8.4}
89
\contentsline {subsubsection}{\numberline {8.4.1}Development tools}{49}{subsubsection.8.4.1}
90
\contentsline {subsubsection}{\numberline {8.4.2}Getting yourself set up}{50}{subsubsection.8.4.2}
91
\contentsline {subsubsection}{\numberline {8.4.3}Changing stuff}{50}{subsubsection.8.4.3}
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docs/manual-latex/manual.toc
