Difference between revisions of "Using Shell scripting to lessen typing"
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The following example uses a Windows command shell to illustrate how you can shorten the number of keystrokes required. In this case, you would write a batch file to load a levelset VOI into an image. | The following example uses a Windows command shell to illustrate how you can shorten the number of keystrokes required. In this case, you would write a batch file to load a levelset VOI into an image. | ||
| − | <div style="font-style: normal; margin-bottom: 2pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> {| border="1" cellpadding="5" |+ |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">@echo off</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- %1 is the full path to the image file, though not </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- the file itself; we assume there to be a *01.dcm</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- file to exist in this directory.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | + | <div style="font-style: normal; margin-bottom: 2pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> {| border="1" cellpadding="5" |+ |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">@echo off</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- %1 is the full path to the image file, though not </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- the file itself; we assume there to be a *01.dcm</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- file to exist in this directory.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- VOI is assumed to be in the same directory with name </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">rem -- levelset1.xml</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">./mipav -i %1\*01.dcm -v %1\levelset1.xml</font></span><br /></font></div> |} <br /></font>'''</div> |
More efficient and more useful, starting MIPAV with multiple images is easily done in a simple script. Here is how it is done in BASH: | More efficient and more useful, starting MIPAV with multiple images is easily done in a simple script. Here is how it is done in BASH: | ||
| − | <div style="font-style: normal; margin-bottom: 2pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> {| border="1" cellpadding="5" |+ |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki>#! /bin/bash</nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># argument 1 is the file (with wild-cards) we want to open</nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># arg 1 must be escaped (with quotes) to allow the shell to send </nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># the wildcards unmolested to the script. Otherwise, the shell </nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># will try to expand the shorthand. This has a different effect.</nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | + | <div style="font-style: normal; margin-bottom: 2pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> {| border="1" cellpadding="5" |+ |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki>#! /bin/bash</nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># argument 1 is the file (with wild-cards) we want to open</nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># arg 1 must be escaped (with quotes) to allow the shell to send </nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># the wildcards unmolested to the script. Otherwise, the shell </nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><nowiki># will try to expand the shorthand. This has a different effect.</nowiki></font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">LISTING=`ls $1` # Generate the file listing</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">MIPARGS=</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> # For each file in the listing, prepend it with '-i' and </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> # the filename, then follow it with all the previous </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> # files.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> for FS in $LISTING;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">do</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> MIPARGS=" -i $FS $MIPARGS";</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">done</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> # start MIPAV:</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">./mipav $MIPARGS </font></span><br /></font></div> |} </font>'''</span><br /></font>'''</div> |
Although this script doesn't include the line <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">./mipav $MIPARGS</font></span> with a "<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">&</font></span>" to run MIPAV in the background, it could have. This would have the effect of exiting the script with MIPAV in the background; as it is, the script does not exit-and return control to you at the command line-until MIPAV exits. | Although this script doesn't include the line <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">./mipav $MIPARGS</font></span> with a "<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">&</font></span>" to run MIPAV in the background, it could have. This would have the effect of exiting the script with MIPAV in the background; as it is, the script does not exit-and return control to you at the command line-until MIPAV exits. | ||
<div style="font-style: normal; margin-bottom: 2pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Scripting toolbar<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1267744 <sup>1</sup>]Not all MIPAV algorithms are scriptable.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1265929 <sup>2</sup>]<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">Exit( )</font></span> end is auto added when the script is running from the command line with <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">-hide</font></span> key.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1332246 <sup>3</sup>]http://www.bic.mni.mcgill.ca/software/minc/<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1321156 <sup>4</sup>]<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">"do_output_new_image boolean true" </font></span>will indicate that the result image appears in a new image frame<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1321924 <sup>5</sup>]This saves only the image with margins, not the post-blurred image.<br /></font></div> | <div style="font-style: normal; margin-bottom: 2pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Scripting toolbar<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1267744 <sup>1</sup>]Not all MIPAV algorithms are scriptable.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1265929 <sup>2</sup>]<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">Exit( )</font></span> end is auto added when the script is running from the command line with <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">-hide</font></span> key.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1332246 <sup>3</sup>]http://www.bic.mni.mcgill.ca/software/minc/<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1321156 <sup>4</sup>]<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">"do_output_new_image boolean true" </font></span>will indicate that the result image appears in a new image frame<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 12pt; margin-right: 0pt; margin-top: 2pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [#1321924 <sup>5</sup>]This saves only the image with margins, not the post-blurred image.<br /></font></div> | ||
Revision as of 21:15, 15 February 2012
Using Shell scripting to lessen typing
Using shell scripts to reduce the amount of repetitive work is a common reason for writing a script. When best used, several small scripts that work in concert can reduce the amount of typing required and the amount of time needed and can automate tasks.
The following example uses a Windows command shell to illustrate how you can shorten the number of keystrokes required. In this case, you would write a batch file to load a levelset VOI into an image.
{| border="1" cellpadding="5" |+ |- |
@echo off
rem -- %1 is the full path to the image file, though not
rem -- the file itself; we assume there to be a *01.dcm
rem -- file to exist in this directory.
rem -- VOI is assumed to be in the same directory with name
rem -- levelset1.xml
./mipav -i %1\*01.dcm -v %1\levelset1.xml
|} More efficient and more useful, starting MIPAV with multiple images is easily done in a simple script. Here is how it is done in BASH:
{| border="1" cellpadding="5" |+ |- |
#! /bin/bash
# argument 1 is the file (with wild-cards) we want to open
# arg 1 must be escaped (with quotes) to allow the shell to send
# the wildcards unmolested to the script. Otherwise, the shell
# will try to expand the shorthand. This has a different effect.
LISTING=`ls $1` # Generate the file listing
MIPARGS=
# For each file in the listing, prepend it with '-i' and
# the filename, then follow it with all the previous
# files.
for FS in $LISTING;
do
MIPARGS=" -i $FS $MIPARGS";
done
# start MIPAV:
./mipav $MIPARGS
|} Although this script doesn't include the line ./mipav $MIPARGS with a "&" to run MIPAV in the background, it could have. This would have the effect of exiting the script with MIPAV in the background; as it is, the script does not exit-and return control to you at the command line-until MIPAV exits.
Scripting toolbar
[#1267744 1]Not all MIPAV algorithms are scriptable.
[#1265929 2]Exit( ) end is auto added when the script is running from the command line with -hide key.
[#1332246 3]http://www.bic.mni.mcgill.ca/software/minc/
[#1321156 4]"do_output_new_image boolean true" will indicate that the result image appears in a new image frame
[#1321924 5]This saves only the image with margins, not the post-blurred image.
