maintenance release: pshell import, elog, documentation
* bugfixes in pshell import * updates to elog interface: templates, login, separate persistent and volatile data * new header and revision information in documentation
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.gitattributes
vendored
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20
.gitattributes
vendored
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@ -0,0 +1,20 @@
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.git* export-ignore
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#*.ipf diff=igorpro
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# git diff --check should output something useful
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*.ipf whitespace=indent-with-non-tab,tabwidth=4
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# mark files as binary
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# you can also add -delta if you regularly
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# commit large files of these types
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*.ibw binary
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*.xop binary
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*.pxp binary
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*.pxt binary
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*.uxp binary
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*.uxt binary
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*.ihf binary
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*.ifn binary
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*.ift binary
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# automatic end of line normalization
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*.ipf eol=lf
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1
.gitignore
vendored
1
.gitignore
vendored
@ -4,3 +4,4 @@
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*.ipfT*
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doc/html/*
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doc/latex/*
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@ -38,7 +38,7 @@ PROJECT_NAME = "PEARL Procedures"
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# could be handy for archiving the generated documentation or if some version
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# control system is used.
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PROJECT_NUMBER =
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PROJECT_NUMBER = $(REVISION)
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# Using the PROJECT_BRIEF tag one can provide an optional one line description
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# for a project that appears at the top of each page and should give viewer a
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@ -1647,7 +1647,7 @@ EXTRA_PACKAGES =
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# to HTML_HEADER.
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# This tag requires that the tag GENERATE_LATEX is set to YES.
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LATEX_HEADER =
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LATEX_HEADER = src/header.tex
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# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
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# generated LaTeX document. The footer should contain everything after the last
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@ -11,7 +11,7 @@ DOX=doxygen
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DOXOPTS=
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LATEX_DIR=latex
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REVISION=$(shell git describe --always --tags --dirty --long)
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REVISION=$(shell git describe --always --tags --dirty --long || echo "unknown, "`date +"%F %T %z"`)
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export REVISION
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all: docs
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@ -19,7 +19,7 @@ all: docs
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docs: doxygen pdf
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doxygen:
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$(DOX) $(DOXOPTS) Doxyfile
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$(DOX) $(DOXOPTS) config.dox
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pdf: doxygen
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-$(MAKE) -C $(LATEX_DIR)
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@ -27,3 +27,4 @@ pdf: doxygen
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clean:
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-rm latex/*
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-rm html/*
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149
doc/src/header.tex
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149
doc/src/header.tex
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% Latex header for doxygen 1.8.9.1
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%
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% To generate this file, call:
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% doxygen -w latex header.tex footer.tex doxygen.sty
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% and substitute the placeholders:
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% $title, $datetime, $date, $doxygenversion, $projectname, $projectnumber, $projectbrief, $projectlogo
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% (or diff and merge with previous version)
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%
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\documentclass[twoside]{book}
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% Packages required by doxygen
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\usepackage{fixltx2e}
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\usepackage{calc}
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\usepackage{doxygen}
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\usepackage[export]{adjustbox} % also loads graphicx
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\usepackage{graphicx}
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\usepackage[utf8]{inputenc}
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\usepackage{makeidx}
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\usepackage{multicol}
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\usepackage{multirow}
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\PassOptionsToPackage{warn}{textcomp}
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\usepackage{textcomp}
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\usepackage[nointegrals]{wasysym}
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\usepackage[table]{xcolor}
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% Font selection
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\usepackage[T1]{fontenc}
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\usepackage[scaled=.90]{helvet}
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\usepackage{courier}
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\usepackage{amssymb}
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\usepackage{sectsty}
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\renewcommand{\familydefault}{\sfdefault}
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\allsectionsfont{%
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\fontseries{bc}\selectfont%
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\color{darkgray}%
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}
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\renewcommand{\DoxyLabelFont}{%
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\fontseries{bc}\selectfont%
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\color{darkgray}%
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}
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\newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}}
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% Page & text layout
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\usepackage{geometry}
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\geometry{%
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a4paper,%
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top=2.5cm,%
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bottom=2.5cm,%
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left=2.5cm,%
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right=2.5cm%
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}
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\tolerance=750
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\hfuzz=15pt
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\hbadness=750
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\setlength{\emergencystretch}{15pt}
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\setlength{\parindent}{0cm}
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\setlength{\parskip}{0.2cm}
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\makeatletter
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\renewcommand{\paragraph}{%
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\@startsection{paragraph}{4}{0ex}{-1.0ex}{1.0ex}{%
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\normalfont\normalsize\bfseries\SS@parafont%
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}%
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}
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\renewcommand{\subparagraph}{%
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\@startsection{subparagraph}{5}{0ex}{-1.0ex}{1.0ex}{%
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\normalfont\normalsize\bfseries\SS@subparafont%
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}%
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}
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\makeatother
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% Headers & footers
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\usepackage{fancyhdr}
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\pagestyle{fancyplain}
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\fancyhead[LE]{\fancyplain{}{\bfseries\thepage}}
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\fancyhead[CE]{\fancyplain{}{}}
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\fancyhead[RE]{\fancyplain{}{\bfseries\leftmark}}
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\fancyhead[LO]{\fancyplain{}{\bfseries\rightmark}}
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\fancyhead[CO]{\fancyplain{}{}}
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\fancyhead[RO]{\fancyplain{}{\bfseries\thepage}}
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\fancyfoot[LE]{\fancyplain{}{}}
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\fancyfoot[CE]{\fancyplain{}{}}
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\fancyfoot[RE]{\fancyplain{}{\bfseries\scriptsize $projectnumber}}
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\fancyfoot[LO]{\fancyplain{}{\bfseries\scriptsize $projectnumber}}
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\fancyfoot[CO]{\fancyplain{}{}}
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\fancyfoot[RO]{\fancyplain{}{}}
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\renewcommand{\footrulewidth}{0.4pt}
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\renewcommand{\chaptermark}[1]{%
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\markboth{#1}{}%
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}
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\renewcommand{\sectionmark}[1]{%
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\markright{\thesection\ #1}%
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}
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% Indices & bibliography
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\usepackage{natbib}
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\usepackage[titles]{tocloft}
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\setcounter{tocdepth}{3}
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\setcounter{secnumdepth}{5}
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\makeindex
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% Hyperlinks (required, but should be loaded last)
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\usepackage{ifpdf}
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\ifpdf
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\usepackage[pdftex,pagebackref=true]{hyperref}
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\else
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\usepackage[ps2pdf,pagebackref=true]{hyperref}
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\fi
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\hypersetup{%
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colorlinks=true,%
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linkcolor=blue,%
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citecolor=blue,%
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unicode%
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}
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% Custom commands
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\newcommand{\clearemptydoublepage}{%
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\newpage{\pagestyle{empty}\cleardoublepage}%
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}
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%===== C O N T E N T S =====
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\begin{document}
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% Titlepage & ToC
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\hypersetup{pageanchor=false,
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bookmarks=true,
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bookmarksnumbered=true,
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pdfencoding=unicode
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}
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\pagenumbering{roman}
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\begin{titlepage}
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\vspace*{7cm}
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\begin{center}%
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{\Large $projectname}\\
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\vspace*{1cm}
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{\large $projectbrief }\\
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\vspace*{0.5cm}
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{\small Version $projectnumber}\\
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\vspace*{0.5cm}
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{\small $datetime}\\
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\end{center}
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\end{titlepage}
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\clearemptydoublepage
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\tableofcontents
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\clearemptydoublepage
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\pagenumbering{arabic}
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\hypersetup{pageanchor=true}
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%--- Begin generated contents ---
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@ -21,7 +21,7 @@ Users of PEARL Procedures are requested to coordinate and share the development
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Please read and respect the respective license agreements.
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\author Matthias Muntwiler, <mailto:matthias.muntwiler@psi.ch>
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\version This documentation is compiled from revision $(REVISION).
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\version This documentation is compiled from version $(REVISION).
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\copyright 2009-2016 by [Paul Scherrer Institut](http://www.psi.ch)
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\copyright Licensed under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0)
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*/
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@ -1893,13 +1893,12 @@ end
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///
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/// @param x, y projected Cartesian coordinate
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///
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/// @param projection mapping function from polar to cartesian coordinates
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/// @param projection mapping function from polar to cartesian coordinates.
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/// projections 0-2 have no effect on the azimuthal coordinate.
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/// @arg 0 linear
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/// @arg 1 stereographic (default)
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/// @arg 2 azimuthal
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///
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/// projections 0-2 have no effect on the azimuthal coordinate
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///
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/// @param zeroAngle zeroAngleWhere parameter of polar graphs
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/// @arg 0 (default) zero is at the 3 o'clock position
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/// @arg 180 zero is at the 9 o'clock position
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File diff suppressed because it is too large
Load Diff
@ -55,10 +55,8 @@ menu "PEARL"
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end
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submenu "Services"
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PearlMenuEnableFunc("pearl_elog") + "ELOG Experiments", /Q, pearl_elog("Experiments")
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help = {"Create entries in ELOG experiments logbook"}
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PearlMenuEnableFunc("pearl_elog") + "ELOG Calculations", /Q, pearl_elog("Calculations")
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help = {"Create entries in ELOG calculations logbook"}
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PearlMenuEnableFunc("pearl_elog") + "Open ELOG Panel", /Q, pearl_elog("")
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help = {"Open an ELOG panel to send entries to an ELOG logbook"}
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end
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submenu "Sample Preparation"
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@ -637,6 +637,7 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
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string datasets = psh5_list_scan_datasets(fileID, scanpath)
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string datasetname = ""
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variable index
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// todo: this should be generalized
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if (strsearch(datasets, "ScientaImage", 0) >= 0)
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datasetname = "ScientaImage"
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@ -644,17 +645,24 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
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datasetname = "ScientaSpectrum"
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elseif (strsearch(datasets, "ScientaEnergyDistribution", 0) >= 0)
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datasetname = "ScientaEnergyDistribution"
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elseif (strsearch(datasets, "ImageEnergyDistribution", 0) >= 0)
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datasetname = "ImageEnergyDistribution"
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elseif (strsearch(datasets, "Counts", 0) >= 0)
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datasetname = "Counts"
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elseif (strsearch(datasets, "SampleCurrent", 0) >= 0)
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datasetname = "SampleCurrent"
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else
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datasetname = StringFromList(0, datasets)
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index = ItemsInList(datasetname, "/") - 1
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datasetname = StringFromList(index, datasetname, "/")
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endif
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if (strlen(datasetname) == 0)
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return ""
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endif
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string datasetpath
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datasetpath = scanpath + "/" + datasetname
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datasetpath = ReplaceString("//", datasetpath, "/")
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STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
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InitHDF5DataInfo(di)
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variable err = HDF5DatasetInfo(fileID, datasetpath, 0, di)
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@ -667,6 +675,10 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
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if (di.ndims < 3)
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HDF5LoadData /O /Q /Z fileID, datasetpath
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dataname = StringFromList(0, S_waveNames)
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wave /z data = $dataname
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if (waveexists(data))
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ps_set_dimlabels(data)
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endif
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else
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variable dim2start = 0
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variable dim2count = 1
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@ -1000,10 +1012,12 @@ function ps_set_dimlabels(data)
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setdimlabel 0, -1, $kEnergyDimLabel, data
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break
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case "ImageAngleDistribution":
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case "ScientaAngleDistribution":
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setdimlabel 0, -1, $kScanDimLabel, data
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setdimlabel 1, -1, $kAngleDimLabel, data
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break
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case "ImageEnergyDistribution":
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case "ScientaEnergyDistribution":
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setdimlabel 0, -1, $kScanDimLabel, data
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setdimlabel 1, -1, $kEnergyDimLabel, data
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break
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