{"id":353,"date":"2017-11-14T09:17:13","date_gmt":"2017-11-14T14:17:13","guid":{"rendered":"https:\/\/health.uconn.edu\/connjur\/?page_id=353"},"modified":"2018-01-29T09:51:35","modified_gmt":"2018-01-29T14:51:35","slug":"spectrum-translator-configuration","status":"publish","type":"page","link":"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/","title":{"rendered":"Spectrum Translator Configuration"},"content":{"rendered":"<div id=\"pl-353\"  class=\"panel-layout\" ><div id=\"pg-353-0\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-353-0-0\"  class=\"panel-grid-cell\" ><div id=\"panel-353-0-0-0\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-first-child panel-last-child\" data-index=\"0\" ><div class=\"textwidget\"><p><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/\">Back<\/a><\/p>\n<h3>Table of Contents<\/h3>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#overview\">Overview<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#XMLdocumentheader\">XML Document Header<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#convertelement\">Convert Element<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#controlelement\">Control Element<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#ignoreextradata\">Ignoreextradata<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#loglevel\">Loglevel<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#overwrite\">Overwrite<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#metadataelement\">Metadata Element<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#commentelement\">Comment Element<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#dimnameelement\">Dimname Element<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#sourceanddestination\">Source and Destination Elements<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#format\">Format<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#name\">Name<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#pattern\">Pattern<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#option\">Option<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#destinationelement\">Destination Element<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#dimseq\">Dimseq<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#endian\">Endian<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#datatype\">Datatype<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#semanticelement\">Semantic Element<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#op\">OP<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#completesampleXML\">Complete Sample XML File<\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#commandelineonly\">Command Line Only Options<\/a>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#nonuniform\">Nonuniform Processing Options<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#summary\">Summary Table<\/a><\/li>\n<\/ul>\n<h3><a id=\"overview\"><\/a>Overview<\/h3>\n<p>The Connjur file converter may be configured via command line arguments, or an XML (eXtensible Markup Language) file. If an option is specified in both the XML file and the command line the command line setting is effective.<br \/> Command line arguments typically may be specified with a short option, e.g.\u00a0<i>-h<\/i>\u00a0or a long option e.g.\u00a0<i>--help<\/i>. Either may be used; they are functionality equivalent.<\/p>\n<p>Two types of control constructs are supported: flags, which are present or not, and options, which take a value as an argument. Flags and options are contained within section XML elements. Depending on the particular element, options are specified as XML<i>attributes<\/i>, e.g. &lt;option name=\"Magnetic\" \/&gt;, or as XML\u00a0<i>values<\/i>, e.g. &lt;format&gt;varian&lt;\/format&gt;.<\/p>\n<p>To prevent file converter misbehavior due to ambiguous directives, the XML file must be both well-formed and valid with respect to the file converter XML Schema packaged within the application. A validating editor, such as the free\u00a0<a href=\"http:\/\/www.syntext.com\/products\/serna-free\/\" class=\"broken_link\">Serna Free<\/a>\u00a0or a commercial product such as XMLSpy is maybe be help for writing the configuration file properly, but it is not required. The file may be validated by the file converter using the\u00a0<a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#commandelineonly\">check XML file<\/a>\u00a0option.<\/p>\n<h3><a id=\"XMLdocumentheader\"><\/a>XML Document Header<\/h3>\n<p>Each XML document should begin with the following lines:<\/p>\n<pre>&lt;?xml version=\"1.0\" encoding=\"UTF-8\"?&gt;\n&lt;convert\nxmlns=\"http:\/\/connjur.uchc.edu\"\nxmlns:xsi=\"http:\/\/www.w3.org\/2001\/XMLSchema-instance\" \nxsi:schemaLocation=\"http:\/\/connjur.uchc.edu jar:converterOptions.xsd\"&gt; \n<\/pre>\n<h3><a id=\"convertelement\"><\/a>Convert Element<\/h3>\n<p>The top level XML element is the\u00a0<i>convert<\/i>. Within convert are five possible sub-elements (\u00a0<a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#controlelement\">control<\/a>,\u00a0<a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#metadataelement\">metadata<\/a>,\u00a0<a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#sourceanddestination\">source<\/a>,\u00a0<a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#destinationelement\">destination<\/a>, and\u00a0<a href=\"https:\/\/health.uconn.edu\/connjur\/documentation\/spectrum-translator\/spectrum-translator-configuration\/#semanticelement\">semantic<\/a>). Each element is optional.<\/p>\n<h4><a id=\"controlelement\"><\/a>Control Element<\/h4>\n<p>The\u00a0<i>control<\/i>\u00a0section contains two possible options as outlined below.<\/p>\n<h4><a id=\"ignoreextradata\"><\/a>Ignoreextradata<\/h4>\n<p><i>&lt;ignoredextradata \/&gt;.<\/i>\u00a0Flag. By default the file converter considers extra data in the vendor specific binary file as an error. Extra data may represent a misreading of metadata, indicating an increased risk of incorrect file conversion. This option suppresses the extra data error.<br \/> Command line equivalent: -ie, --ignoreextradata<\/p>\n<h4><a id=\"loglevel\"><\/a>Loglevel<\/h4>\n<p><i>&lt;loglevel&gt;INFO&lt;\/loglevel&gt;<\/i>\u00a0Option. The file converter has the ability to display processing information. By default only fatal errors are logged but may be useful in diagnosing errors. The allowed levels are OFF, ALL, DEBUG, INFO, WARN, ERROR, FATAL.<br \/> Command line equivalent: -ll, --loglevel. Finer grained control over logging is provided by using a log4j.properties file. Note use of debug or info will produce signficant output and substantially slow down file conversion.<\/p>\n<h4><a id=\"overwrite\"><\/a>Overwrite<\/h4>\n<p><i>&lt;overwrite \/&gt;.<\/i>\u00a0Flag. By default the file converter will not overwrite existing binary or metadata files. This option instructs the file converter to overwrite existing files.<br \/> Command line equivalent: -f, --force<\/p>\n<h3><a id=\"metadataelement\"><\/a>Metadata Element<\/h3>\n<p>The\u00a0<i>metadata<\/i>\u00a0section allows specification of additional data not determinable from the specified input files. Not all metadata is used by all vendor formats; metadata not supported by the particular output format will not be utilized.<\/p>\n<h4><a id=\"commentelement\"><\/a>Comment Element<\/h4>\n<p>&lt;comment value=\"Comment about file\" \/&gt; Option. Specifies a note about the converted file.<\/p>\n<h4><a id=\"dimnameelement\"><\/a>Dimname Element<\/h4>\n<p>&lt;dimname dim=\"1\" name=\"H1\" \/&gt; Option. Specifies the name (label) for a dimension.<\/p>\n<h3><a id=\"sourceanddestination\"><\/a>Source and Destination Elements<\/h3>\n<p>The\u00a0<i>source<\/i>\u00a0and\u00a0<i>destination<\/i>\u00a0elements specifies the file converter input and output. They share common subelements.<\/p>\n<h4><a id=\"format\"><\/a>Format<\/h4>\n<p><i>&lt;format&gt;nmrpipe&lt;format&gt;<\/i>\u00a0Option. The vendor specific file format.<br \/> Command line equivalents: -st, --srctype (input), -dt, --desttype (output).<\/p>\n<h4><a id=\"name\"><\/a>Name<\/h4>\n<p><i>&lt;name type=\"file\"&gt;input.dat&lt;\/name&gt;<\/i>\u00a0Option. Specify name and type of input or output file.\u00a0<i>type<\/i>\u00a0must be \"file\" or \"directory\" and depends on the vendor format selected. Some formats require use of\u00a0<i>pattern<\/i>\u00a0instead.\u00a0<i>name<\/i>\u00a0and\u00a0<i>pattern<\/i>\u00a0should not be both be specified.<br \/> Command line equivalents for files: -sf, --srcfile (input) or -df, --destfile (output).<br \/> Command line equivalents for directories: -sd, --srcdir (input) or -dd, --destdir (output).<\/p>\n<h4><a id=\"pattern\"><\/a>Pattern<\/h4>\n<p><i>&lt;pattern&gt;input%02d.dat&lt;\/name&gt;<\/i>\u00a0Option. Specify pattern for multiple input or output file names. A pattern requires one or more specifications of the form\u00a0<i>%02d<\/i>; these are replaced with a sequence of integers upon processing. The number, in this example \"2,\" indicates the width of integer field. The example would expand to input01.dat, input02.dat, etc.<br \/> <span class=\"expl\">Currently pattern is used only for NMRPipe 3D and 4D data sets.<\/span><br \/> Command line equivalents: -sp, --srcpattern (input) or -dp, --destpattern (output).<\/p>\n<h4><a id=\"option\"><\/a>Option<\/h4>\n<p><i>&lt;option name=\"some_option\" value=\"10\" \/&gt;<\/i>\u00a0Option.<br \/> <i>&lt;option name=\"some_flag\" \/&gt;<\/i>\u00a0Flag.<br \/> (Note: the above are examples of syntax, not actual options.) Vendor format specific option. The\u00a0<a href=\"http:\/\/connjur.uchc.edu\/docs\/st\/configuration\/#help\" class=\"broken_link\">help<\/a>\u00a0command line option provides a list of these.<br \/> Command line equivalent: -some_option 10 or -some_flag.<\/p>\n<h3><a id=\"destinationelement\"><\/a>Destination Element<\/h3>\n<p>In addition to the common elements listed above, the following elements may be present only in the\u00a0<i>destination<\/i>\u00a0section.<\/p>\n<h4><a id=\"dimseq\"><\/a>Dimseq<\/h4>\n<p><i>&lt;dimseq&gt;312&lt;dimseq&gt;<\/i>\u00a0Option. Specify output sequence of NMR dimensions. In the example given, input dimension 3 would be output as the first dimension, 1 as the second, and 2 as the third.<br \/> Command line equivalent: -ds, --dimseq.<a id=\"endian\" name=\"endian\"><\/a><\/p>\n<h4><a id=\"endian\"><\/a>Endian<\/h4>\n<p><i>&lt;endian&gt;big&lt;\/endian&gt;<\/i>\u00a0Option. Specify the\u00a0<a href=\"http:\/\/en.wikipedia.org\/wiki\/Endianness\">endianness<\/a>\u00a0of the binary output data file(s). Valid values are\u00a0<i>big<\/i>,<i>little<\/i>.<br \/> Command line equivalent: -e, --endian<\/p>\n<h4><a id=\"datatype\"><\/a>Datatype<\/h4>\n<p><i>&lt;datatype&gt;ieee_float32&lt;\/datatype&gt;<\/i>\u00a0Option. Specify the numeric output type. Not all formats are valid for all vendor formats, and the Spectrum Translator will not perform conversions which truncate data (e.g. converting floating point numbers to integers). Valid values are\u00a0<i>ieee_float32<\/i>,<i>int32<\/i>,<i>short_int<\/i>.<br \/> Command line equivalent: none<\/p>\n<h3><a id=\"semanticelement\"><\/a>Semantic Element<\/h3>\n<p>Semantic operations may be specified, in order, by one or more\u00a0<i>op<\/i>\u00a0elements.<\/p>\n<h4><a id=\"op\"><\/a>OP<\/h4>\n<p><i>&lt;op name=\"negateimaginaries\"\/&gt;<\/i>Flag. Semantic operation which requires no parameters.<\/p>\n<p><i>&lt;op name=\"rancekay\"&gt;1&lt;\/op&gt;<\/i>Flag. Semantic operation which requires a parameter.<\/p>\n<h3><a id=\"completesampleXML\"><\/a>Complete Sample XML File<\/h3>\n<p>Below is a complete sample of an XML file. Individual elements and sections are optional and may be omitted in actual configuration files:<\/p>\n<pre>&lt;?xml version=\"1.0\" encoding=\"utf-8\"?&gt;\n&lt;convert xmlns=\"http:\/\/connjur.uchc.edu\"\nxmlns:xsi=\"http:\/\/www.w3.org\/2001\/XMLSchema-instance\"\nxsi:schemaLocation=\"http:\/\/connjur.uchc.edu jar:converterOptions.xsd\"&gt;\n\n  &lt;control&gt;\n    &lt;loglevel&gt;info&lt;\/loglevel&gt; <span class=\"expl\">Display logging messages info level and above.<\/span>\n    &lt;ignoreextradata \/&gt; <span class=\"expl\">Ignore leftover data in binary file.<\/span>\n    &lt;overwrite \/&gt; <span class=\"expl\">Overwrite existing \"nhsqc.sec\" and \"nhsqc.par\" files.<\/span>\n  &lt;\/control&gt;\n  &lt;metadata&gt;\n    &lt;comment value=\"nmrpipe to rowland conversion\" \/&gt; <span class=\"expl\">Add this comment to output if supported by writer.<\/span>\n    &lt;dimname dim=\"1\" name=\"15N\" \/&gt; <span class=\"expl\">Label the first converted dimension as \"15N\", if supported by writer.<\/span>\n    &lt;dimname dim=\"2\" name=\"1H\" \/&gt; <span class=\"expl\">Label the second converted dimension as \"1H\", if supported by writer.<\/span>\n  &lt;\/metadata&gt;\n  &lt;source&gt;\n    &lt;format&gt;nmrpipe&lt;\/format&gt; <span class=\"expl\">Input format is <a href=\"http:\/\/spin.niddk.nih.gov\/NMRPipe\/\">NMRPipe<\/a>.<\/span>\n    &lt;name type=\"file\"&gt;nhsqc.dat&lt;\/name&gt; <span class=\"expl\">Input is file named \"nhsqc.dat\".<\/span>\n    &lt;option name=\"city\" value=\"farmington\" \/&gt; &lt;!-- not a real option --&gt; <span class=\"expl\">Demonstration of setting option with value.<\/span>\n    &lt;option name=\"uchc\" \/&gt; &lt;!-- not a real option --&gt; <span class=\"expl\">Demonstration of setting flag.<\/span>\n  &lt;\/source&gt;\n  &lt;destination&gt;\n    &lt;format&gt;rowland&lt;\/format&gt; <span class=\"expl\"> Output format is <a href=\"http:\/\/rnmrtk.uchc.edu\/rnmrtk\/RNMRTK.html\">Rowland Toolkit<\/a>.<\/span>\n    &lt;name type=\"directory\"&gt;mydata&lt;\/name&gt; <span class=\"expl\">Output is directory named \"mydata\".<\/span>\n    &lt;dimseq&gt;21&lt;\/dimseq&gt; <span class=\"expl\">Output input dimension 1 as output dimension 2, and input dimension 2 as output #1.<\/span>\n    &lt;endian&gt;big&lt;\/endian&gt; <span class=\"expl\">Output binary data in <a href=\"http:\/\/en.wikipedia.org\/wiki\/Endianness\">big endian<\/a>.<\/span>\n    &lt;datatype&gt;ieee_float32&lt;\/datatype&gt; <span class=\"expl\">Output data in IEEE floating point format.<\/span>\n  &lt;\/destination&gt;\n  &lt;semantic&gt;\n    &lt;op name=\"negateimaginaries\/&gt; <span class=\"expl\">After reading data, first negate imaginary values.<\/span>\n    &lt;op name=\"rancekay&gt;1&lt;\/$gt; <span class=\"expl\">After negating imaginary values, preform Rance Kay correction on the first dimension.<\/span> \n  &lt;\/semantic&gt;\n&lt;\/convert&gt;\n     \n<\/pre>\n<h3><a id=\"commandelineonly\"><\/a>Command Line Only Options<\/h3>\n<p>The following options are only available via the command line:<\/p>\n<ul>\n<li><a id=\"help\" name=\"help\"><\/a><i>help<\/i>\u00a0-h, --help. show command line help.<\/li>\n<li><i>xmlfile<\/i>\u00a0-x, --xmlfile. Specify xml file name.<\/li>\n<li><i>xml help<\/i>\u00a0-xh, --xmlhelp. Show xml specific options.<\/li>\n<li><a id=\"check_xml\" name=\"check_xml\"><\/a><i>validate xml<\/i>\u00a0-cx,--checkxmlfile. Validate xml file for correct formatting without executing file conversion.<\/li>\n<li><i>extract schema<\/i>\u00a0-dx,--dumpschema. Extract copy of\u00a0<a href=\"http:\/\/www.w3.org\/XML\/Schema\" class=\"broken_link\">W3C Schema<\/a>\u00a0from Java jar file.<\/li>\n<\/ul>\n<h3><a id=\"nonuniform\"><\/a>Non Uniform Sample Options<\/h3>\n<p>The following nonuniform processing options have been added to the command line. Bruker non-uniform conversion is not currently supported.<\/p>\n<h4>Non-uniform Input<\/h4>\n<ul>\n<li><i>-scd,--schedulein<\/i>\u00a0<b>required for non-uniform samples<\/b>\u00a0nonuniform data schedule file<\/li>\n<li><i>-avg,--averaged<\/i>\u00a0output data has transient values averaged<\/li>\n<li><i>-ctdin,--counted<\/i>\u00a0input counted schedule file<\/li>\n<li><i>-sparse<\/i>\u00a0output nonuniform data in uniform format with missing values zero filled<\/li>\n<li><i>-tran,--transients<\/i>\u00a0nonuniform input data has transients (duplicate lines in schedule file<\/li>\n<\/ul>\n<h4>Uniform Input<\/h4>\n<ul>\n<li><i>-compress<\/i>\u00a0compress sparse (contains fids with all zeros) uniform data to nonuniform<\/li>\n<\/ul>\n<h3>Command Line Examples<\/h3>\n<p>java -jar ConnjurST.jar -st varian -sd vdata -dt nmrpipe -df mydata.pip<br \/> <span class=\"expl\">Convert Varian data in directory named \"vdata\" into a NMRPipe file named \"mydata.pip\"<\/span><\/p>\n<p>java -jar ConnjurST.jar -st rowland -sf data.dat -dt nmrpipe -dp mydata%02d.pip<br \/> <span class=\"expl\">Convert Rowland toolkit file named \"fid\" into a set of NMRPipe file named \"mydata01.pip, mydata02.pip ...\"<\/span><\/p>\n<p>connjurst -nonuniform -st varian -sd 2dnus -schedulein varian.scd -dt rowland -df r2d.sec<br \/> <span class=\"expl\">Convert nonuniform varian sample in directory \"2dnus\" with schedule file \"varian.scd\" to nonuniform rowland file \"r2d.sec\" (using default output schedule file name).<\/span><\/p>\n<h3><a id=\"summary\"><\/a>Summary Table<\/h3>\n<p>The following table summarizes the avaiable options:<\/p>\n<table summary=\"available options\">\n<tbody>\n<tr valign=\"top\">\n<th>Item<\/th>\n<th>Type<\/th>\n<th>Command<br \/> line<br \/> short<\/th>\n<th>Command<br \/> line<br \/> long<\/th>\n<th>XML section<\/th>\n<th>XML element<\/th>\n<th>XML attribute(s)<\/th>\n<th>Example value<\/th>\n<\/tr>\n<tr>\n<td>Source type<\/td>\n<td>Option<\/td>\n<td>-st<\/td>\n<td>--srctype<\/td>\n<td>source<\/td>\n<td>format<\/td>\n<td>none<\/td>\n<td>nmrpipe<\/td>\n<\/tr>\n<tr>\n<td>Source file name<\/td>\n<td>Option<\/td>\n<td>-sf<\/td>\n<td>--srcfile<\/td>\n<td>source<\/td>\n<td>name<\/td>\n<td>type=\"<i>file<\/i>\"<\/td>\n<td>2Dspectrum.dat<\/td>\n<\/tr>\n<tr>\n<td>Source directory name<\/td>\n<td>Option<\/td>\n<td>-sd<\/td>\n<td>--srcdir<\/td>\n<td>source<\/td>\n<td>name<\/td>\n<td>type=\"<i>directory<\/i>\"<\/td>\n<td>nhsqc<\/td>\n<\/tr>\n<tr>\n<td>Source name pattern<\/td>\n<td>Option<\/td>\n<td>-sp<\/td>\n<td>--srcpattern<\/td>\n<td>source<\/td>\n<td>pattern<\/td>\n<td>none<\/td>\n<td>3D%02d.dat<\/td>\n<\/tr>\n<tr>\n<td>Generic source option<\/td>\n<td>Option<\/td>\n<td>None<\/td>\n<td>--<i>option_name<\/i><\/td>\n<td>source<\/td>\n<td>option<\/td>\n<td>name=\"<i>option_name<\/i>\", value=\"<i>value<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Generic source flag<\/td>\n<td>Flag<\/td>\n<td>None<\/td>\n<td>--<i>flag_name<\/i><\/td>\n<td>source<\/td>\n<td>option<\/td>\n<td>name=\"<i>flag_name<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Destination type<\/td>\n<td>Option<\/td>\n<td>-dt<\/td>\n<td>--desttype<\/td>\n<td>destination<\/td>\n<td>format<\/td>\n<td>none<\/td>\n<td>varian<\/td>\n<\/tr>\n<tr>\n<td>Destination file name<\/td>\n<td>Option<\/td>\n<td>-df<\/td>\n<td>--destfile<\/td>\n<td>destination<\/td>\n<td>name<\/td>\n<td>type=\"<i>file<\/i>\"<\/td>\n<td>spectrum.dat<\/td>\n<\/tr>\n<tr>\n<td>Destination directory name<\/td>\n<td>Option<\/td>\n<td>-dd<\/td>\n<td>--destdir<\/td>\n<td>destination<\/td>\n<td>name<\/td>\n<td>type=\"<i>directory<\/i>\"<\/td>\n<td>converted<\/td>\n<\/tr>\n<tr>\n<td>Destination name pattern<\/td>\n<td>Option<\/td>\n<td>-dp<\/td>\n<td>--destpattern<\/td>\n<td>destination<\/td>\n<td>pattern<\/td>\n<td>none<\/td>\n<td>out%02d-%03d.dat<\/td>\n<\/tr>\n<tr>\n<td>Output dimension order<\/td>\n<td>Option<\/td>\n<td>-ds<\/td>\n<td>--dimseq<\/td>\n<td>destination<\/td>\n<td>dimseq<\/td>\n<td>none<\/td>\n<td>132<\/td>\n<\/tr>\n<tr>\n<td>Output endianness<\/td>\n<td>Option<\/td>\n<td>-e<\/td>\n<td>--endian<\/td>\n<td>destination<\/td>\n<td>endian<\/td>\n<td>none<\/td>\n<td>little<\/td>\n<\/tr>\n<tr>\n<td>Output datatype<\/td>\n<td>Option<\/td>\n<td>none<\/td>\n<td>none<\/td>\n<td>destination<\/td>\n<td>datatype<\/td>\n<td>none<\/td>\n<td>ieee_float32<\/td>\n<\/tr>\n<tr>\n<td>Generic destination option<\/td>\n<td>Option<\/td>\n<td>None<\/td>\n<td>--<i>option_name<\/i><\/td>\n<td>destination<\/td>\n<td>option<\/td>\n<td>name=\"<i>option_name<\/i>\", value=\"<i>value<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Generic destination flag<\/td>\n<td>Flag<\/td>\n<td>None<\/td>\n<td>--<i>flag_name<\/i><\/td>\n<td>destination<\/td>\n<td>option<\/td>\n<td>name=\"<i>flag_name<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Data set comment<\/td>\n<td>Option<\/td>\n<td>None<\/td>\n<td>None<\/td>\n<td>metadata<\/td>\n<td>comment<\/td>\n<td>value=\"<i>comment<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Dimension name<\/td>\n<td>Option<\/td>\n<td>None<\/td>\n<td>None<\/td>\n<td>metadata<\/td>\n<td>dimname<\/td>\n<td>dim=\"<i>1<\/i>\" name=\"<i>H1<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Log level<\/td>\n<td>Option<\/td>\n<td>-ll<\/td>\n<td>--loglevel<\/td>\n<td>control<\/td>\n<td>loglevel<\/td>\n<td>none<\/td>\n<td>INFO<\/td>\n<\/tr>\n<tr>\n<td>Extra data<\/td>\n<td>Flag<\/td>\n<td>-ie<\/td>\n<td>--ignoreextradata<\/td>\n<td>control<\/td>\n<td>ignoreextradata<\/td>\n<td>none<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Overwrite existing files<\/td>\n<td>Flag<\/td>\n<td>-f<\/td>\n<td>--force<\/td>\n<td>control<\/td>\n<td>overwrite<\/td>\n<td>none<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Semantic Operation<\/td>\n<td>Flag<\/td>\n<td>-op<\/td>\n<td>--operation<\/td>\n<td>semantic<\/td>\n<td>op<\/td>\n<td>name=\"<i>operation_name<\/i>\"<\/td>\n<td>none<\/td>\n<\/tr>\n<tr>\n<td>Semantic Operation<\/td>\n<td>Option<\/td>\n<td>-op<\/td>\n<td>--operation<\/td>\n<td>semantic<\/td>\n<td>op<\/td>\n<td>name=\"<i>operation_name<\/i>\"<\/td>\n<td>1<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>BackTable of ContentsOverviewXML Document HeaderConvert ElementControl ElementIgnoreextradataLoglevelOverwriteMetadata ElementComment ElementDimname ElementSource and Destination ElementsFormatNamePatternOptionDestination ElementDimseqEndianDatatypeSemantic ElementOPComplete Sample XML FileCommand Line Only OptionsNonuniform Processing OptionsSummary TableOverviewThe Connjur file converter may be configured via command line arguments, or an XML (eXtensible Markup Language) file. If an option is specified in both the XML file and the command line [&hellip;]<\/p>\n","protected":false},"author":38,"featured_media":0,"parent":307,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"publishpress_future_action":{"enabled":false,"date":"2026-04-11 20:22:09","action":"change-status","newStatus":"draft","terms":[],"taxonomy":""},"_links":{"self":[{"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/pages\/353"}],"collection":[{"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/users\/38"}],"replies":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/comments?post=353"}],"version-history":[{"count":44,"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/pages\/353\/revisions"}],"predecessor-version":[{"id":617,"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/pages\/353\/revisions\/617"}],"up":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/pages\/307"}],"wp:attachment":[{"href":"https:\/\/health.uconn.edu\/connjur\/wp-json\/wp\/v2\/media?parent=353"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}