[Insight-users] bash script to search example files for terms
Andrew Maclean
andrew.amaclean at gmail.com
Tue Oct 13 23:37:41 EDT 2009
Hi Darren
I am not sure whether replacing grep with find is worthwhile. For VTK
the search time went from 0.5s to 9.6s when using the grep option.
Would you mind if I put this in as a comment so that people can
uncomment it if they wish?
What do people think?
BTW the VTK version is Examples/SearchScript.sh.
Regards
Andrew
On Wed, Oct 14, 2009 at 5:28 AM, Darren Weber
<darren.weber.lists at gmail.com> wrote:
>
> Hi Luis,
>
> This version below uses 'grep' options to replace the 'find' utility; the
> grep options provide a case-insensitive search (-i) and recursion through
> directories (-r), with an include pattern to identify file types (.cxx,
> .tcl, .py). The script now has a 'continue' statement if the itkPath
> doesn't exist. (I don't have commit rights to the cvs.)
>
> #####BEGIN SCRIPT
> #!/bin/bash
>
> if [ $# -lt 1 ]; then
> echo "$0 'search term' ['search term' ...]"
> exit 1
> fi
>
> itkExamplePath="/opt/local/share/InsightToolkit/examples"
> itkTestingPath="/opt/local/share/InsightToolkit/testing"
>
> for term in $@; do
> echo
> echo "Search term: ${term}"
> for itkPath in "${itkExamplePath}" "${itkTestingPath}"; do
> if [ ! -d ${itkPath} ]; then
> echo "Path not found: ${itkPath}"
> echo "Modify script at $0"
> continue
> fi
> echo "Searching ITK files in: ${itkPath}"
> grep -l -E -i -r --include='*.cxx' --regexp=${term} ${itkPath}
> grep -l -E -i -r --include='*.tcl' --regexp=${term} ${itkPath}
> grep -l -E -i -r --include='*.py' --regexp=${term} ${itkPath}
> done
> done
> #####END SCRIPT
>
>
>
> This is an example run on my OSX-MacPorts system (with InsightToolkit @
> 3.16.0):
>
> $ itkSearchExamples.bash 'itkImageRegistrationMethod'
> Search term: itkImageRegistrationMethod
> Searching ITK files in: /opt/local/share/InsightToolkit/examples
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration12.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration13.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration14.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration15.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration4.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration6.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration7.cxx
> /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration8.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration1.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration10.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration11.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration12.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration13.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration14.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration15.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration16.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration17.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration18.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration1o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration2.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration2o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration3.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration3o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration4.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration4o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration5.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration5o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration6.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration6o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration7.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration7o.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration8.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration9.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistrationHistogramPlotter.cxx
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration3.tcl
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration4.tcl
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration5.tcl
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration3.py
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration4.py
> /opt/local/share/InsightToolkit/examples/Registration/ImageRegistration5.py
> Searching ITK files in: /opt/local/share/InsightToolkit/testing
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkAlgorithmsHeaderTest.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkAlgorithmsPrintTest4.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkAlgorithmsTests.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_1.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_10.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_11.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_12.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_13.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_14.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_15.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_16.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_2.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_3.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_4.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_5.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_6.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_7.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_8.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkImageRegistrationMethodTest_9.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkMultiResolutionImageRegistrationMethodTest_1.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkMultiResolutionImageRegistrationMethodTest_2.cxx
> /opt/local/share/InsightToolkit/testing/Code/Algorithms/itkPointSetToImageRegistrationTest_1.cxx
>
>
>
> Regards,
> Darren
>
>
>
>
>
>
>
> On Mon, Oct 12, 2009 at 6:40 PM, Luis Ibanez <luis.ibanez at kitware.com>
> wrote:
>>
>> Hi Darren,
>>
>> Thanks for the script.
>>
>> It has now been committed to the CVS repository as
>>
>> Insight/Examples/SearchScript.sh
>>
>> ---
>>
>> The second script,
>> are you suggesting it as a separate script ?
>> or as an improvement to the first one ?
>>
>>
>> Please let us know,
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ----------------------------
>> On Mon, Oct 12, 2009 at 4:15 PM, Darren Weber
>> <darren.weber.lists at gmail.com> wrote:
>> >
>> > Hi Luis,
>> >
>> > Please feel free to distribute it with the LGPL license (or a BSD
>> > license,
>> > or something that is compatible with the ITK license and general OSI
>> > principles).
>> >
>> > For a more portable solution, the itk*Path variables might be obtained
>> > automatically (how?). The search path could be an input parameter (but
>> > that
>> > almost defeats the convenience of this bash wrapper around a grep
>> > process).
>> >
>> > The grep command options list the files where the search term is found
>> > (not
>> > the lines of those files where the search term occurs). For a bit more
>> > value, it's possible to modify the script so that the entire grep loop
>> > returns an array of file paths, which could be piped into something
>> > like:
>> > less -p ${searchTerm} ${fileArray}[@]
>> > Then less would provide the means to page through the files.
>> >
>> > Here is another variation on the same thing - this one searches the
>> > testing
>> > path and it includes the .tcl and .py example files in the search. It
>> > might
>> > be called 'itkSearchFiles.bash' ?
>> >
>> > ###### BEGIN SCRIPT
>> > #!/bin/bash
>> >
>> > if [ $# -lt 1 ]; then
>> > echo "$0 'search term' ['search term' ...]"
>> > exit 1
>> > fi
>> >
>> > itkExamplePath="/opt/local/share/InsightToolkit/examples"
>> > itkTestingPath="/opt/local/share/InsightToolkit/testing/Code"
>> >
>> > for term in $@; do
>> > echo
>> > echo "Search term: ${term}"
>> > for itkPath in "${itkExamplePath}" "${itkTestingPath}" ; do
>> > if [ ! -d ${itkPath} ]; then
>> > echo "Path not found: ${itkPath}"
>> > fi
>> > echo "Searching ITK files in: ${itkPath}"
>> > grep -l -E -e ${term} ${itkPath}/*/*.cxx
>> > grep -l -E -e ${term} ${itkPath}/*/*.tcl
>> > grep -l -E -e ${term} ${itkPath}/*/*.py
>> > done
>> > done
>> > ###### END SCRIPT
>> >
>> >
>> > Take care,
>> > Darren
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Mon, Oct 12, 2009 at 12:26 PM, Luis Ibanez <luis.ibanez at kitware.com>
>> > wrote:
>> >>
>> >> Hi Darren,
>> >>
>> >> This is really useful !
>> >>
>> >> Thank you for sharing it.
>> >>
>> >> Do you see any reason for not adding this to the CVS
>> >> repository and distribute it along with ITK ?
>> >>
>> >> Please let us know,
>> >>
>> >>
>> >> Thanks
>> >>
>> >>
>> >> Luis
>> >>
>> >>
>> >> ---------------------------------------
>> >> On Mon, Oct 12, 2009 at 2:15 PM, Darren Weber
>> >> <darren.weber.lists at gmail.com> wrote:
>> >> >
>> >> > This is a short bash script (grep does the work) to search for terms
>> >> > in
>> >> > the
>> >> > InsightToolkit example files. It's a convenience wrapper that stores
>> >> > the
>> >> > path to the example files (.cxx in this case), the syntax of the grep
>> >> > call,
>> >> > and allows multiple terms to be given at once. Modify the example
>> >> > search
>> >> > path for your purposes (it could be modified to search for the tcl or
>> >> > python
>> >> > examples too). Modify the grep call as you like.
>> >> >
>> >> > #### BEGIN SCRIPT
>> >> > #!/bin/bash
>> >> >
>> >> > if [ $# -lt 1 ]; then
>> >> > echo "$0 'search term' ['search term' ...]"
>> >> > exit 1
>> >> > fi
>> >> >
>> >> > # Search the CXX files
>> >> > itkExamplePath="/opt/local/share/InsightToolkit/examples/*/*.cxx"
>> >> > echo "Searching ITK .cxx files in: ${itkExamplePath}"
>> >> >
>> >> > for term in $@; do
>> >> > echo
>> >> > echo "Search term: ${term}"
>> >> > grep -l -E -e ${term} ${itkExamplePath}
>> >> > done
>> >> > #### END SCRIPT
>> >> >
>> >> > This is an example call on my platform:
>> >> >
>> >> > $ itkSearchExamples.bash 'TransformWriter' 'TransformReader'
>> >> > Searching ITK .cxx files in:
>> >> > /opt/local/share/InsightToolkit/examples/*/*.cxx
>> >> >
>> >> > Search term: TransformWriter
>> >> > /opt/local/share/InsightToolkit/examples/IO/TransformReadWrite.cxx
>> >> >
>> >> > Search term: TransformReader
>> >> > /opt/local/share/InsightToolkit/examples/IO/TransformReadWrite.cxx
>> >> >
>> >> >
>> >> > /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration14.cxx
>> >> >
>> >> >
>> >> > /opt/local/share/InsightToolkit/examples/Registration/DeformableRegistration8.cxx
>> >> >
>> >> > Take care,
>> >> > Darren
>> >> >
>> >> >
>> >> > _____________________________________
>> >> > Powered by www.kitware.com
>> >> >
>> >> > Visit other Kitware open-source projects at
>> >> > http://www.kitware.com/opensource/opensource.html
>> >> >
>> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >> >
>> >> > Follow this link to subscribe/unsubscribe:
>> >> > http://www.itk.org/mailman/listinfo/insight-users
>> >> >
>> >> >
>> >
>> >
>
>
> _____________________________________
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>
> Visit other Kitware open-source projects at
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--
___________________________________________
Andrew J. P. Maclean
Centre for Autonomous Systems
The Rose Street Building J04
The University of Sydney 2006 NSW
AUSTRALIA
Ph: +61 2 9351 3283
Fax: +61 2 9351 7474
URL: http://www.acfr.usyd.edu.au/
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