Difference: DigitalMicrograph2TIF (1 vs. 6)

Revision 617 Sep 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
    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

  • Set ALLOWTOPICVIEW =

-- BillRice - 02 Jun 2006

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

  • Set ALLOWTOPICVIEW =

-- BillRice - 02 Jun 2006

Revision 402 Jun 2006 - Main.BillRice

 
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
    Stepup Procedure Command
    Step 3 convert all dm3 files to mrc format using dm2mrc find disk -name "*.dm3" -exec ~/convert.com {} \;
    Step 2 Need to be in imod environment imod_env
    Step 1 copy onto local directory, named disk cp -r /media/cdrecorder disk
Changed:
<
<
Step 4 convert all mrc files to tif find disk -name "*.mrc" -exec ~/replace.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 {} \;

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

  • Set ALLOWTOPICVIEW =

-- BillRice - 02 Jun 2006

Revision 302 Jun 2006 - Main.BillRice

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

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

  • Set ALLOWTOPICVIEW =

-- BillRice - 02 Jun 2006

Revision 202 Jun 2006 - Main.BillRice

 
META TOPICPARENT name="CemIT"
Changed:
<
<

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

>
>

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
Changed:
<
<
  • Step 1: copy onto local directory, named disk: cp -r /media/cdrecorder disk
  • Step 2: Need to be in imod environment: imod_env
  • 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 "*.dm3" -exec ~/replace.com {} \;
  • Step 5: remove all intermediate mrc files: find disk -name "*.mrc" -exec rm {} \;
>
>
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
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 "*.dm3" -exec ~/replace.com {} \;
Added:
>
>
Step 5 remove all intermediate mrc files find 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
Changed:
<
<		em2em < temp.txt
>
>		em2em < temp.txt > /dev/null
 rm temp.txt
Deleted:
<
<

convert.com

 
  • Set ALLOWTOPICVIEW =

-- BillRice - 02 Jun 2006

Revision 102 Jun 2006 - Main.BillRice

 
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 1: copy onto local directory, named disk: cp -r /media/cdrecorder disk
  • Step 2: Need to be in imod environment: imod_env
  • 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 "*.dm3" -exec ~/replace.com {} \;
  • Step 5: remove all intermediate mrc files: find 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
rm temp.txt

convert.com

  • Set ALLOWTOPICVIEW =

-- BillRice - 02 Jun 2006

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