Added table of contents. Fixes #2053 Fixes #1738 (3e081e31) · Commits · aflab / astrogeology / ISIS3

isis/src/docsys/documents/CommandLine/CommandLine.xml

+97 −42

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		@@ -3,8 +3,48 @@
		<files>
		<file>
		<body>

		<h2>Introduction</h2>
		<h3>Table of Contents</h3>
		<ol type="I">
		<li><a href="#Introduction">Introduction</a></li>
		<li><a href="#Invoking a Program">Invoking a Program</a></li>
		<li><a href="#Application Specific Parameters">Application Specific Parameters</a></li>
		<li><a href="#Integer and Double Parameters">Integer and Double Parameters</a></li>
		<li><a href="#String Parameters">String Parameters</a></li>
		<li><a href="#Special Characters">Special Characters</a></li>
		<li><a href="#Lists of String Parameters">Lists of String Parameters</a></li>
		<li><a href="#Boolean Parameters">Boolean Parameters</a></li>
		<li><a href="#Inclusive and Exclusive Parameters">Inclusive and Exclusive Parameters</a></li>
		<li><a href="#Cube Attributes">Cube Attributes</a></li>
		<ol type="i">
		<li><a href="#Output Cube Attributes">Output Cube Attributes</a></li>
		<li><a href="#Pixel Type">Pixel Type</a></li>
		<li><a href="#Output Pixel Range">Output Pixel Range</a></li>
		<li><a href="#Label Format">Label Format</a></li>
		<li><a href="#Pixel Storage Order">Pixel Storage Order</a></li>
		<li><a href="#Storage Format">Storage Format</a></li>
		<li><a href="#Input Cube Attributes">Input Cube Attributes</a></li>
		</ol>
		<li><a href="#Reserved Parameters">Reserved Parameters</a></li>
		<ol type="i">
		<li><a href="#-webhelp and -help Parameters">-Webhelp and -Help Parameters</a></li>
		<li><a href="#-last Parameter">-Last Parameter</a></li>
		<li><a href="#-restore Parameter">-Restore Parameter</a></li>
		<li><a href="#-gui Parameter">-Gui Parameter</a></li>
		<li><a href="#-nogui Parameter">-Nogui Parameter</a></li>
		<li><a href="#-batchlist Parameter">-Batchlist Parameter</a></li>
		<li><a href="#-errlist Parameter">-Errlist Parameter</a></li>
		<li><a href="#-onerror Parameter">-Onerror Parameter</a></li>
		<li><a href="#-preference Parameter">-Preference Parameter</a></li>
		<li><a href="#-log Parameter">-Log Parameter</a></li>
		<li><a href="#-info Parameter">-Info Parameter</a></li>
		<li><a href="#-save Parameter">-Save Parameter</a></li>
		<li><a href="#-verbose Parameter">-Verbose Parameter</a></li>
		</ol>
		<li><a href="#Error Status">Error Status</a></li>
		</ol>

		<!-- Introduction -->
		<h2><a name="Introduction">Introduction</a></h2>
		<p>
		This section describes how to run ISIS programs on the command line
		instead of the GUI. This is particularly useful 1) to setup shell
		@@ -12,7 +52,8 @@
		on cubes or if 2) you prefer keyboarding over mousing.
		</p>

		<h2>Invoking a Program</h2>
		<!-- Invoking a Program -->
		<h2><a name="Invoking a Program">Invoking a Program</a></h2> Pixel Range
		<p>
		To start an ISIS program, simply type its name, for example, <i>lowpass</i>.
		This starts the program under the GUI; however, if you provide anything
		@@ -54,7 +95,8 @@ lowpass from=moon.cub to=moon.lpf.cub lines=4 samples=5 minimum=1
		End_Group
		</pre>

		<h2>Application Specific Parameters</h2>
		<!-- Application Specific Parameters -->
		<h2><a name="Application Specific Parameters">Application Specific Parameters</a></h2>
		<p>
		All ISIS command lines take the following form:
		</p>
		@@ -162,7 +204,9 @@ lowpass S=5 LIN=5 F=moon.cub T=moon.lpf.cub
		Working
		100% Processed
		</pre>
		<h2>Integer and Double Parameters</h2>

		<!-- Integer and Double Parameters -->
		<h2><a name="Integer and Double Parameters">Integer and Double Parameters</a></h2>
		<p>
		The documentation for each application indicates the valid data type
		of each parameter. The examples below show the values entered as
		@@ -216,8 +260,8 @@ lowpass f=moon.cub t=moon.lpf.cub s=5 lin=5 low=5 high=3
		End_Group
		</pre>


		<h2>String Parameters</h2>
		<!-- String Parameters -->
		<h2><a name="String Parameters">String Parameters</a></h2>
		<p>
		String parameters can be slightly more complicated because of operating
		system intricacies. The difference is in one word strings versus multiple
		@@ -340,8 +384,8 @@ tabledump from=input.cub name="some table"
		and the second example shows two spaces between "some" and "table."
		</p>


		<h2>Special Characters</h2>
		<!-- Special Characters -->
		<h2><a name="Special Characters">Special Characters</a></h2>

		<p>
		When running an ISIS application from the command line, there may be conflicts
		@@ -596,8 +640,8 @@ would result in
		ls tests*
		</pre>


		<h2>Lists of String Parameters</h2>
		<!-- Lists of String Parameters -->
		<h2><a name="Lists of String Parameters">Lists of String Parameters</a></h2>
		<p>
		Some applications will restrict the values of string parameters to a
		pre-defined list. We will use the <i>raw2isis</i> GUI below as a guide for
		@@ -643,7 +687,8 @@ raw2isis bittype=unsigned from=file.raw to=file.cub line=500 samp=500
		File size 371 x 600, 40.9 KB
		</p>

		<h2>Boolean Parameters</h2>
		<!-- Boolean Parameters -->
		<h2><a name="Boolean Parameters">Boolean Parameters</a></h2>
		<p>
		These parameters are represented by check boxes in the GUI. Command
		line examples of the use of a boolean parameter are
		@@ -661,7 +706,8 @@ foobar option=f
		The values are case insensitive. That is, Yes, YES, True, T, etc. work as well.
		</p>

		<h2>Inclusive and Exclusive Parameters</h2>
		<!-- Inclusive and Exclusive Parameters -->
		<h2><a name="Inclusive and Exclusive Parameters">Inclusive and Exclusive Parameters</a></h2>
		<p>
		The GUI has the ability to include or exclude parameters via stipling
		(graying out parameters). The application programs will throw an error
		@@ -694,7 +740,8 @@ The example below shows the correct usage:
		grid from=0145r_cal.cub to=gridtest.cub baseline=10 basesamp=20 mode=image
		</pre>

		<h2>Cube Attributes</h2>
		<!-- Cube Attributes -->
		<h2><a name="Cube Attributes">Cube Attributes</a></h2>
		<p>
		When a parameter is an input or output <def link="Cube">cube</def>, the
		GUI presents two extra buttons (1) file selection [dir] and (2) additional options [att].
		@@ -704,7 +751,7 @@ grid from=0145r_cal.cub to=gridtest.cub baseline=10 basesamp=20 mode=image
		be appended to the filename on the command line.
		</p>

		<h3>Output Cube Attributes</h3>
		<h3><a name="Output Cube Attributes">Output Cube Attributes</a></h3>
		<p>
		Below are examples of properties of an output <def link="Cube">cube</def> that
		users may specify:
		@@ -729,7 +776,7 @@ highpass from=temp.cub to=temp.hpf.cub+16bit line=51 samp=51
		highpass from=temp.cub to=temp.hpf.cub+8bit+-5.0:5.0 line=51 samp=51
		</pre>

		<h4>Pixel Type</h4>
		<h3><a name="Pixel Type">Pixel Type</a></h3>
		<p>
		This defines the output pixel type. There are three types of output pixels:
		UnsignedByte, SignedWord, and Real. Valid values and synonyms are given below:
		@@ -760,7 +807,7 @@ highpass from=temp.cub to=temp.hpf.cub+8bit+-5.0:5.0 line=51 samp=51
		output real pixels.
		</p>

		<h4>Output Pixel Range</h4>
		<h3><a name="Output Pixel Range">Output Pixel Range</a></h3>
		<p>
		When choosing an output pixel type other than Real/32-bit, the user must
		define the expected range of output pixels. The form is +minimum:maximum.
		@@ -782,7 +829,7 @@ moccal to=cal.cub+0.0:0.3
		the sacrifice is utilizing more disk space.
		</p>

		<h4>Label Format</h4>
		<h3><a name="Label Format">Label Format</a></h3>
		<p>
		The option exists to create attached or detached labels. The complete
		word must be used. The default option is read from the system-wide/user
		@@ -798,7 +845,7 @@ crop from=input.cub to=output.cub+attached
		Detached labels will be put in a separate file with an .lbl extension.
		</p>

		<h4>Pixel Storage Order</h4>
		<h3><a name="Pixel Storage Order">Pixel Storage Order</a></h3>
		<p>
		The two formats, lsb and msb are for least and most significant
		<def link="Byte">byte</def> orders respectively. The default is to use
		@@ -815,7 +862,7 @@ crop from=input.cub to=output.cub+msb
		</pre>


		<h4>Storage Format</h4>
		<h3><a name="Storage Format">Storage Format</a></h3>
		<p>
		The storage format of the file can be tile or band sequential. The
		default format is tile, which is preferable for most geometric
		@@ -842,7 +889,7 @@ lowpass from=input.cub to=output.cub+bandSequential+detached
		format that non-ISIS applications can read.
		</p>

		<h3>Input Cube Attributes</h3>
		<h3><a name="Input Cube Attributes">Input Cube Attributes</a></h3>
		<p>
		Input <def link="Cube">cube</def> attributes are significantly less complicated
		than those of output. They allow the user to select the <def link="Band">bands</def>
		@@ -875,7 +922,8 @@ ratio num=input.cub den=input.cub+5 to=dividebyband5.cub
		+8,4,2
		</pre>

		<h2>Reserved Parameters</h2>
		<!-- Reserved Parameters -->
		<h2><a name="Reserved Parameters">Reserved Parameters</a></h2>
		<p>
		All ISIS applications have a suite of reserved parameters that can be specified.
		The options are listed below:
		@@ -913,7 +961,7 @@ equalizer -l
		conflicts of this sort.
		</p>

		<h3>-webhelp and -help Parameters</h3>
		<h3><a name="-webhelp and -help Parameters">-webhelp and -help Parameters</a></h3>
		<p>
		This parameter is used to obtain help on the program. Typing the
		<b>-webhelp</b> parameter will launch a browser containing the
		@@ -987,7 +1035,7 @@ Group = GAIN
		End_Group
		</pre>

		<h3>-last Parameter</h3>
		<h3><a name="-last Parameter">-last Parameter</a></h3>
		<p>
		This parameter will run the program using the parameter settings from
		the previous program run, if a parameter file exists
		@@ -1006,11 +1054,12 @@ highpass -last
		highpass -last from=next.cub to=next.hpf.cub
		</pre>

		<h3>-restore Parameter</h3>
		<h3><a name="-restore Parameter">-restore Parameter</a></h3>
		<p>
		This parameter allows the user to run the programs with the parameters from
		a file. In particular, a file saved using the GUI save mode or a session
		log. Example:
		This parameter must be used in conjunction with a PVL file similar to the
		one created using the -save parameter (see Reserved Parameter -save).
		It allows the user to run the programs with the parameters from that file.
		Example:
		</p>

		<pre style="padding-left:2em;">
		@@ -1018,12 +1067,17 @@ highpass -restore=guiSave.par
		</pre>

		<p>
		Either will look for the last occurrence of Group=UserParameters in
		Object=highpass in the specified file. Parameter values will be loaded
		from that group.
		In this example, the program will look for the last occurrence of
		Group=UserParameters in the guiSave.par file and load the parameter
		values into Group=UserParameters of Object=highpass.
		</p>
		Parameter values can be modified on the fly in the same way as the -last
		Reserved Parameter example.
		<p>

		</p>

		<h3>-gui Parameter</h3>
		<h3><a name="-gui Parameter">-gui Parameter</a></h3>

		<p>
		This parameter invokes the GUI. Other parameter names and values
		@@ -1042,7 +1096,7 @@ highpass -last -gui
		appropriate fields, but does not execute the program.
		</p>

		<h3>-nogui Parameter</h3>
		<h3><a name="-nogui Parameter">-nogui Parameter</a></h3>

		<p>
		This parameter forces the GUI not to run. Its main intention is to be
		@@ -1053,7 +1107,7 @@ highpass -last -gui
		csspck2spk -nogui
		</pre>

		<h3>-batchlist Parameter</h3>
		<h3><a name="-batchlist Parameter">-batchlist Parameter</a></h3>

		<p>
		This parameter allows the user to run a program multiple times on a list
		@@ -1090,7 +1144,7 @@ highpass from=/work2/eribelin/viking/f348b26.cub to=/work2/eribelin/viking/hpf/f
		highpass from=/work2/eribelin/viking/f319b19.cub to=/work2/eribelin/viking/hpf/f319b19.cub lines=5 samples=5
		</pre>

		<h3>-errlist Parameter</h3>
		<h3><a name="-errlist Parameter">-errlist Parameter</a></h3>

		<p>
		This parameter will save the lines from the batch list file that failed
		@@ -1112,7 +1166,7 @@ highpass -batchlist=batchList.txt from=\$1\$2 to=\$1/hpf/\$2 lines=5 samples=5 -
		highpass -batchlist=errList.txt from=\$1\$2 to=\$1/hpf/\$2 lines=5 samples=5 -errlist=errList2.txt
		</pre>

		<h3>-onerror Parameter</h3>
		<h3><a name="-onerror Parameter">-onerror Parameter</a></h3>

		<p>
		This parameter can be used with all parameters, and the -batchlist and
		@@ -1134,7 +1188,7 @@ highpass -batchlist=batchList.txt from=\$1\$2 to=\$1/hpf/\$2 lines=5 samples=5 -
		of the failures will be in the <b>print.prt</b> file.
		</p>

		<h3>-preference Parameter</h3>
		<h3><a name="-preference Parameter">-preference Parameter</a></h3>

		<p>
		This parameter can be used with all parameters, and reserved parameters.
		@@ -1150,7 +1204,7 @@ highpass from=input.cub to=output.cub lines=5 samples=5 -preference=myHighpassPr
		with the preferences in the file <b>myHighpassPrefs</b>.
		</p>

		<h3>-log Parameter</h3>
		<h3><a name="-log Parameter">-log Parameter</a></h3>

		<p>
		This parameter can be used with all parameters including the reserved
		@@ -1175,7 +1229,7 @@ highpass from=input.cub to=output.cub lines=5 samples=5 -log=temp.prt
		the session log information will be saved there.
		</p>

		<h3>-info Parameter</h3>
		<h3><a name="-info Parameter">-info Parameter</a></h3>

		<p>
		This parameter can be used with all parameters including the reserved
		@@ -1199,7 +1253,7 @@ highpass from=input.cub to=output.cub lines=5 samples=5 -info=debug.log
		to <b>debug.log</b>.
		</p>

		<h3>-save Parameter</h3>
		<h3>-<a name="-save Parameter">-save Parameter</a></h3>

		<p>
		This parameter can be used with all parameters, and reserved parameters
		@@ -1224,7 +1278,7 @@ highpass from=input.cub to=output.cub lines=5 samples=5 -save
		in the current directory.
		</p>

		<h3>-verbose Parameter</h3>
		<h3><a name="-verbose Parameter">-verbose Parameter</a></h3>

		<p>
		This parameter can be used with all parameters including the reserved
		@@ -1242,7 +1296,8 @@ highpass from=input.cub to=output.cub lines=5 samples=5 -verbose
		was executed.
		</p>

		<h2>Error Status</h2>
		<!-- Error Status -->
		<h2><a name="Error Status">Error Status</a></h2>

		<p>
		In the command line mode, programs exit with a status indicating