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

.gitattributes

@@ -0,0 +1,20 @@
+.git* export-ignore
+#*.ipf diff=igorpro
+# git diff --check should output something useful
+*.ipf whitespace=indent-with-non-tab,tabwidth=4
+# mark files as binary
+# you can also add -delta if you regularly
+# commit large files of these types
+*.ibw binary
+*.xop binary
+*.pxp binary
+*.pxt binary
+*.uxp binary
+*.uxt binary
+*.ihf binary
+*.ifn binary
+*.ift binary
+
+# automatic end of line normalization
+*.ipf eol=lf
+

.gitignore

@@ -4,3 +4,4 @@
 *.ipfT*
 doc/html/*
 doc/latex/*
+

doc/config.dox

@@ -38,7 +38,7 @@ PROJECT_NAME           = "PEARL Procedures"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         = $(REVISION)
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -1647,7 +1647,7 @@ EXTRA_PACKAGES         =
 # to HTML_HEADER.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-LATEX_HEADER           = 
+LATEX_HEADER           = src/header.tex
 
 # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
 # generated LaTeX document. The footer should contain everything after the last

doc/makefile

@@ -11,7 +11,7 @@ DOX=doxygen
 DOXOPTS=
 LATEX_DIR=latex
 
-REVISION=$(shell git describe --always --tags --dirty --long)
+REVISION=$(shell git describe --always --tags --dirty --long || echo "unknown, "`date +"%F %T %z"`)
 export REVISION
 
 all: docs
@@ -19,7 +19,7 @@ all: docs
 docs: doxygen pdf
 
 doxygen:
-	$(DOX) $(DOXOPTS) Doxyfile
+	$(DOX) $(DOXOPTS) config.dox
 
 pdf: doxygen
 	-$(MAKE) -C $(LATEX_DIR)
@@ -27,3 +27,4 @@ pdf: doxygen
 clean:
 	-rm latex/*
 	-rm html/*
+

doc/src/header.tex

@@ -0,0 +1,149 @@
+% Latex header for doxygen 1.8.9.1
+%
+% To generate this file, call:
+% doxygen -w latex header.tex footer.tex doxygen.sty
+% and substitute the placeholders:
+% $title, $datetime, $date, $doxygenversion, $projectname, $projectnumber, $projectbrief, $projectlogo
+% (or diff and merge with previous version)
+%
+\documentclass[twoside]{book}
+
+% Packages required by doxygen
+\usepackage{fixltx2e}
+\usepackage{calc}
+\usepackage{doxygen}
+\usepackage[export]{adjustbox} % also loads graphicx
+\usepackage{graphicx}
+\usepackage[utf8]{inputenc}
+\usepackage{makeidx}
+\usepackage{multicol}
+\usepackage{multirow}
+\PassOptionsToPackage{warn}{textcomp}
+\usepackage{textcomp}
+\usepackage[nointegrals]{wasysym}
+\usepackage[table]{xcolor}
+
+% Font selection
+\usepackage[T1]{fontenc}
+\usepackage[scaled=.90]{helvet}
+\usepackage{courier}
+\usepackage{amssymb}
+\usepackage{sectsty}
+\renewcommand{\familydefault}{\sfdefault}
+\allsectionsfont{%
+  \fontseries{bc}\selectfont%
+  \color{darkgray}%
+}
+\renewcommand{\DoxyLabelFont}{%
+  \fontseries{bc}\selectfont%
+  \color{darkgray}%
+}
+\newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}}
+
+% Page & text layout
+\usepackage{geometry}
+\geometry{%
+  a4paper,%
+  top=2.5cm,%
+  bottom=2.5cm,%
+  left=2.5cm,%
+  right=2.5cm%
+}
+\tolerance=750
+\hfuzz=15pt
+\hbadness=750
+\setlength{\emergencystretch}{15pt}
+\setlength{\parindent}{0cm}
+\setlength{\parskip}{0.2cm}
+\makeatletter
+\renewcommand{\paragraph}{%
+  \@startsection{paragraph}{4}{0ex}{-1.0ex}{1.0ex}{%
+    \normalfont\normalsize\bfseries\SS@parafont%
+  }%
+}
+\renewcommand{\subparagraph}{%
+  \@startsection{subparagraph}{5}{0ex}{-1.0ex}{1.0ex}{%
+    \normalfont\normalsize\bfseries\SS@subparafont%
+  }%
+}
+\makeatother
+
+% Headers & footers
+\usepackage{fancyhdr}
+\pagestyle{fancyplain}
+\fancyhead[LE]{\fancyplain{}{\bfseries\thepage}}
+\fancyhead[CE]{\fancyplain{}{}}
+\fancyhead[RE]{\fancyplain{}{\bfseries\leftmark}}
+\fancyhead[LO]{\fancyplain{}{\bfseries\rightmark}}
+\fancyhead[CO]{\fancyplain{}{}}
+\fancyhead[RO]{\fancyplain{}{\bfseries\thepage}}
+\fancyfoot[LE]{\fancyplain{}{}}
+\fancyfoot[CE]{\fancyplain{}{}}
+\fancyfoot[RE]{\fancyplain{}{\bfseries\scriptsize $projectnumber}}
+\fancyfoot[LO]{\fancyplain{}{\bfseries\scriptsize $projectnumber}}
+\fancyfoot[CO]{\fancyplain{}{}}
+\fancyfoot[RO]{\fancyplain{}{}}
+\renewcommand{\footrulewidth}{0.4pt}
+\renewcommand{\chaptermark}[1]{%
+  \markboth{#1}{}%
+}
+\renewcommand{\sectionmark}[1]{%
+  \markright{\thesection\ #1}%
+}
+
+% Indices & bibliography
+\usepackage{natbib}
+\usepackage[titles]{tocloft}
+\setcounter{tocdepth}{3}
+\setcounter{secnumdepth}{5}
+\makeindex
+
+% Hyperlinks (required, but should be loaded last)
+\usepackage{ifpdf}
+\ifpdf
+  \usepackage[pdftex,pagebackref=true]{hyperref}
+\else
+  \usepackage[ps2pdf,pagebackref=true]{hyperref}
+\fi
+\hypersetup{%
+  colorlinks=true,%
+  linkcolor=blue,%
+  citecolor=blue,%
+  unicode%
+}
+
+% Custom commands
+\newcommand{\clearemptydoublepage}{%
+  \newpage{\pagestyle{empty}\cleardoublepage}%
+}
+
+%===== C O N T E N T S =====
+
+\begin{document}
+
+% Titlepage & ToC
+\hypersetup{pageanchor=false,
+             bookmarks=true,
+             bookmarksnumbered=true,
+             pdfencoding=unicode
+            }
+\pagenumbering{roman}
+\begin{titlepage}
+\vspace*{7cm}
+\begin{center}%
+{\Large $projectname}\\
+\vspace*{1cm}
+{\large $projectbrief }\\
+\vspace*{0.5cm}
+{\small Version $projectnumber}\\
+\vspace*{0.5cm}
+{\small $datetime}\\
+\end{center}
+\end{titlepage}
+\clearemptydoublepage
+\tableofcontents
+\clearemptydoublepage
+\pagenumbering{arabic}
+\hypersetup{pageanchor=true}
+
+%--- Begin generated contents ---

doc/src/mainpage.dox

@@ -21,7 +21,7 @@ Users of PEARL Procedures are requested to coordinate and share the development
 Please read and respect the respective license agreements.
 
 \author    Matthias Muntwiler, <mailto:matthias.muntwiler@psi.ch>
-\version   This documentation is compiled from revision $(REVISION).
+\version   This documentation is compiled from version $(REVISION).
 \copyright 2009-2016 by [Paul Scherrer Institut](http://www.psi.ch)
 \copyright Licensed under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0)
 */

pearl/pearl-anglescan-process.ipf

@@ -1893,13 +1893,12 @@ end
 ///
 /// @param	x, y				projected Cartesian coordinate
 ///
-/// @param	projection		mapping function from polar to cartesian coordinates
+/// @param	projection		mapping function from polar to cartesian coordinates.
+/// 							projections 0-2 have no effect  on the azimuthal coordinate.
 ///	@arg	0				linear
 ///	@arg	1				stereographic (default)
 ///	@arg	2				azimuthal
 ///
-/// 							projections 0-2 have no effect on the azimuthal coordinate
-///
 /// @param	zeroAngle		zeroAngleWhere parameter of polar graphs
 ///	@arg	0 (default)		zero is at the 3 o'clock position
 ///	@arg	180				zero is at the 9 o'clock position

pearl/pearl-menu.ipf

@@ -55,10 +55,8 @@ menu "PEARL"
 	end
 	
 	submenu "Services"
-		PearlMenuEnableFunc("pearl_elog") + "ELOG Experiments", /Q, pearl_elog("Experiments")
+		PearlMenuEnableFunc("pearl_elog") + "Open ELOG Panel", /Q, pearl_elog("")
-		help = {"Create entries in ELOG experiments logbook"}
+		help = {"Open an ELOG panel to send entries to an ELOG logbook"}
-		PearlMenuEnableFunc("pearl_elog") + "ELOG Calculations", /Q, pearl_elog("Calculations")
-		help = {"Create entries in ELOG calculations logbook"}
 	end
 	
 	submenu "Sample Preparation"

pearl/pearl-pshell-import.ipf

@@ -637,6 +637,7 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
 	
 	string datasets = psh5_list_scan_datasets(fileID, scanpath)
 	string datasetname = ""
+	variable index
 	// todo: this should be generalized
 	if (strsearch(datasets, "ScientaImage", 0) >= 0)
 		datasetname = "ScientaImage"
@@ -644,17 +645,24 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
 		datasetname = "ScientaSpectrum"
 	elseif (strsearch(datasets, "ScientaEnergyDistribution", 0) >= 0)
 		datasetname = "ScientaEnergyDistribution"
+	elseif (strsearch(datasets, "ImageEnergyDistribution", 0) >= 0)
+		datasetname = "ImageEnergyDistribution"
 	elseif (strsearch(datasets, "Counts", 0) >= 0)
 		datasetname = "Counts"
 	elseif (strsearch(datasets, "SampleCurrent", 0) >= 0)
 		datasetname = "SampleCurrent"
 	else
 		datasetname = StringFromList(0, datasets)
+		index = ItemsInList(datasetname, "/") - 1
+		datasetname = StringFromList(index, datasetname, "/")
 	endif
+	if (strlen(datasetname) == 0)
+		return ""
+	endif
+	
 	string datasetpath
 	datasetpath = scanpath + "/" + datasetname
 	datasetpath = ReplaceString("//", datasetpath, "/")
-	
 	STRUCT HDF5DataInfo di	// Defined in HDF5 Browser.ipf.
 	InitHDF5DataInfo(di)
 	variable err = HDF5DatasetInfo(fileID, datasetpath, 0, di)
@@ -667,6 +675,10 @@ function /s psh5_load_scan_preview(fileID, scanpath, [set_scale])
 	if (di.ndims < 3)
 		HDF5LoadData /O /Q /Z fileID, datasetpath
 		dataname = StringFromList(0, S_waveNames)
+		wave /z data = $dataname
+		if (waveexists(data))
+			ps_set_dimlabels(data)
+		endif
 	else
 		variable dim2start = 0
 		variable dim2count = 1
@@ -1000,10 +1012,12 @@ function ps_set_dimlabels(data)
 			setdimlabel 0, -1, $kEnergyDimLabel, data
 			break
 		case "ImageAngleDistribution":
+		case "ScientaAngleDistribution":
 			setdimlabel 0, -1, $kScanDimLabel, data
 			setdimlabel 1, -1, $kAngleDimLabel, data
 			break
 		case "ImageEnergyDistribution":
+		case "ScientaEnergyDistribution":
 			setdimlabel 0, -1, $kScanDimLabel, data
 			setdimlabel 1, -1, $kEnergyDimLabel, data
 			break