Difference: DigitalMicrograph2TIF (4 vs. 5)

Revision 516 Jul 2008 - Main.DavidCowburn

META TOPICPARENT	name="CemIT"

Conversion of a set of Digital Micrograph files to Tiff format:

Had a cd of dm3 files, with various filenames, spread across many directories
em2em did not recognize the files

Step Procedure Command

Step 1 copy onto local directory, named disk cp -r /media/cdrecorder disk

Step 2 Need to be in imod environment imod_env

Changed:

<
<

Step 3	convert all dm3 files to mrc format using dm2mrc	find disk -name "*.dm3" -exec ~/convert.com {} \;
Step 4	convert all mrc files to tif	find disk -name "*.mrc" -exec ~/replace.com {} \;
Step 5	remove all intermediate mrc files	find disk -name "*.mrc" -exec rm {} \;

>
>

Step 3	convert all dm3 files to mrc format using dm2mrc	Trash.findDFdf disk -name "*.dm3" -exec ~/convert.com {} \;
Step 4	convert all mrc files to tif	Trash.findDFdf disk -name "*.mrc" -exec ~/replace.com {} \;
Step 5	remove all intermediate mrc files	Trash.findDFdf disk -name "*.mrc" -exec rm {} \;

Files needed:

convert.com

#! /bin/csh -f
dm2mrc $1 $1:r.mrc

replace.com

#! /bin/csh -f
echo MRC > temp.txt
echo TIFF >> temp.txt
echo 2D >> temp.txt
echo NO >> temp.txt
echo $1 >> temp.txt
echo $1:r >> temp.txt
echo LINUX >> temp.txt
em2em < temp.txt > /dev/null
rm temp.txt

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-- BillRice - 02 Jun 2006

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