Difference between revisions of "Converting microarray images"

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(→‎Imagemagick: rm prune, test ex: find . -name "*.jpg" -print -exec echo '{}' \;)
(Change source-code blocks to standard format)
 
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= Imagemagick =
 
= Imagemagick =
 
Once installed, all image magick tools are accessed through the command line. The ''[http://www.imagemagick.org/script/identify.php identify]'' binary describes the format and characteristics of one or more image files. e.g.
 
Once installed, all image magick tools are accessed through the command line. The ''[http://www.imagemagick.org/script/identify.php identify]'' binary describes the format and characteristics of one or more image files. e.g.
−
{{code|
+
<source lang="bash">
−
<bash>
 
 
identify rose.jpg
 
identify rose.jpg
 
rose.jpg JPEG 640x480 DirectClass 87kb 0.050u 0:01
 
rose.jpg JPEG 640x480 DirectClass 87kb 0.050u 0:01
−
</bash>
+
</source>
−
}}
 
  
 
The ''[http://www.imagemagick.org/script/convert.php convert]'' binary is useful for resizing images, for example;
 
The ''[http://www.imagemagick.org/script/convert.php convert]'' binary is useful for resizing images, for example;
−
{{code|
+
<source lang="bash">
−
<bash>
 
 
convert -size 800x600 input.jpg'[80x60]' output.png
 
convert -size 800x600 input.jpg'[80x60]' output.png
 
convert input.jpg --resize 80x60 output.png
 
convert input.jpg --resize 80x60 output.png
 
convert input.jpg --resize 10% output.png
 
convert input.jpg --resize 10% output.png
 
convert input.jpg -resize 8% -quality 0 output.png
 
convert input.jpg -resize 8% -quality 0 output.png
−
</bash>
+
</source>
−
}}
 
 
will resize and convert a  [[wikipedia:JPEG|JPEG]] to a  [[wikipedia:PNG|PNG]]. The ''[http://www.imagemagick.org/script/mogrify.php mogrify]'' binary will convert an entire directory of images;
 
will resize and convert a  [[wikipedia:JPEG|JPEG]] to a  [[wikipedia:PNG|PNG]]. The ''[http://www.imagemagick.org/script/mogrify.php mogrify]'' binary will convert an entire directory of images;
−
{{code|
+
<source lang="bash">
−
<bash>
 
 
mogrify -format png -size 800x600 *.jpg  # reverse input/output order
 
mogrify -format png -size 800x600 *.jpg  # reverse input/output order
 
mogrify -format png -resize 8% -rotate -90 *.jpg
 
mogrify -format png -resize 8% -rotate -90 *.jpg
−
</bash>
+
</source>
−
}}
 
 
''Note- This appears to be memory hungry for a directory with images of large file size. In this case use the bash binary 'xargs' of a for loop, for example;
 
''Note- This appears to be memory hungry for a directory with images of large file size. In this case use the bash binary 'xargs' of a for loop, for example;
 
<table class=document-code><tr><td>  
 
<table class=document-code><tr><td>  
−
{{code|
+
<source lang="bash">
−
<bash>
+
# Use a shell loop
−
# Use a shell loop
 
 
   mkdir thumbnails
 
   mkdir thumbnails
 
   for $f in *.jpg
 
   for $f in *.jpg
Line 51: Line 44:
 
   # is the simpler (without needing a sub-shell) form...
 
   # is the simpler (without needing a sub-shell) form...
 
   ls *.jpg | xargs  -I FILE  convert FILE -thumbnail 200x90 th_FILE.gif
 
   ls *.jpg | xargs  -I FILE  convert FILE -thumbnail 200x90 th_FILE.gif
−
</bash>
+
</source>
−
}}
 
  
 
== Commands for microarray images ==
 
== Commands for microarray images ==
−
{{code|<bash>
+
<source lang="bash">
−
# Use a BASH shell loop
+
# Use a BASH shell loop
 
   dir=PNG
 
   dir=PNG
 
   if [ ! -d $dir ] ; then
 
   if [ ! -d $dir ] ; then
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     convert "$file" -resize 7% -rotate -90 -quality 0 $dir/"${file%%\.jpg}.png"
 
     convert "$file" -resize 7% -rotate -90 -quality 0 $dir/"${file%%\.jpg}.png"
 
   done
 
   done
−
</bash>
+
</source>
−
}}
 
 
The bash script need to be put somewhere so it can be called from inside the directory of all the JPEG files;
 
The bash script need to be put somewhere so it can be called from inside the directory of all the JPEG files;
−
{{code|<bash>
+
<source lang="bash">
 
../convert_images dir=PNG
 
../convert_images dir=PNG
−
</bash>
+
</source>
−
}}
 
  
 
''Note- The original source quality influences the cut down PNG's here. Ideally JPEG's of the highest possible quality should go into making cut down PNG's since the original TIFF's are proprietary 26-bit format''
 
''Note- The original source quality influences the cut down PNG's here. Ideally JPEG's of the highest possible quality should go into making cut down PNG's since the original TIFF's are proprietary 26-bit format''
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;Converting PNG's
 
;Converting PNG's
−
{{code|<bash>
+
<source lang="bash">
 
# Use a BASH shell loop
 
# Use a BASH shell loop
 
in=png
 
in=png
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   convert "$file" -resize 135x135 -quality 0 $dir/"${file%%\.$in}.$out"
 
   convert "$file" -resize 135x135 -quality 0 $dir/"${file%%\.$in}.$out"
 
done
 
done
−
</bash>
+
</source>
−
}}
 
  
 
== Usage example ==
 
== Usage example ==

Latest revision as of 16:54, 22 May 2015

Microarray images are generally stored as 16-bit TIFF images (usually around 100Mb in size. An alternative lossy image format is JPEG format, which is still bloated at around 40Mb filesize. Investigating the image size of a typical GenePix derived JPEG image, the pixel size is 4400 × 14300 pixels (72 pixels per inch) with an aspect ratio of 3.25 . A general visual summary of these lossy images is all that is required where they could be converted to a much smaller PNG image type using an appropriate program such as ImageMagick or Gimp which allows batch processing of multiple images a once.

Imagemagick

Once installed, all image magick tools are accessed through the command line. The identify binary describes the format and characteristics of one or more image files. e.g. 

identify rose.jpg
rose.jpg JPEG 640x480 DirectClass 87kb 0.050u 0:01

The convert binary is useful for resizing images, for example; 

convert -size 800x600 input.jpg'[80x60]' output.png
convert input.jpg --resize 80x60 output.png
convert input.jpg --resize 10% output.png
convert input.jpg -resize 8% -quality 0 output.png

will resize and convert a JPEG to a PNG. The mogrify binary will convert an entire directory of images; 

mogrify -format png -size 800x600 *.jpg  # reverse input/output order
mogrify -format png -resize 8% -rotate -90 *.jpg

Note- This appears to be memory hungry for a directory with images of large file size. In this case use the bash binary 'xargs' of a for loop, for example; 

# Use a shell loop
  mkdir thumbnails
  for $f in *.jpg
  do   convert $f -thumbnail 200x90 thumbnails/$f.gif
  done

  # Use find
  # this also provides the ability to recurse though directories by removing
  # the -prune option, as well as doing other file checks (like imgae type,
  # or the disk space used by an image).
  find *  -name '*.jpg' \
         -exec  convert '{}' -thumbnail 200x90 thumbnails/'{}'.gif \;

  # Use xargs -- with a shell wrapper to duplicate the argument.
  # This can be combined with find insted of "ls"
  ls *.jpg | xargs -n1 sh -c 'convert $0 -thumbnail 200x90 thumbnails/$0.gif'

  # an alturnive method on linux (rather than plain unix)
  # is the simpler (without needing a sub-shell) form...
  ls *.jpg | xargs  -I FILE   convert FILE -thumbnail 200x90 th_FILE.gif

Commands for microarray images

# Use a BASH shell loop
  dir=PNG
  if [ ! -d $dir ] ; then
  mkdir $dir
  fi
  for file in *.jpg 
  do  
    echo "[ Converting $file ]"
    convert "$file" -resize 7% -rotate -90 -quality 0 $dir/"${file%%\.jpg}.png"
  done

The bash script need to be put somewhere so it can be called from inside the directory of all the JPEG files; 

../convert_images dir=PNG

Note- The original source quality influences the cut down PNG's here. Ideally JPEG's of the highest possible quality should go into making cut down PNG's since the original TIFF's are proprietary 26-bit format

It may be necessary to remove metadata using tools such as OptiPNG or Pngcrush

Converting PNG's
# Use a BASH shell loop
in=png
out=png
dir=PNG

if [ ! -d $dir ] ; then
mkdir $dir
fi
for file in *.$in
do
  echo "[ Converting $file ]"
  convert "$file" -resize 135x135 -quality 0 $dir/"${file%%\.$in}.$out"
done

Usage example

Using wiki tables, targets files can include actual images for quick visual inspection.

Targets example.png

See also

Retrieved from "https://organicdesign.nz/wiki/index.php?title=Converting_microarray_images&oldid=119779"