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annotate Database/Formats/Generate.sh @ 476:77f868063bb3

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cleanup
author Alain Mazy <am@osimis.io>
date Tue, 03 May 2022 17:10:29 +0200
parents 2a29bcff60a7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/bin/bash
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2
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3 set -e
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4
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5 # http://gdcm.sourceforge.net/html/gdcmconv.html
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7 gdcmconv -i ../Brainix/Epi/IM-0001-0001.dcm -o JpegLossless.dcm -L
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8 gdcmconv -i ../Brainix/Epi/IM-0001-0001.dcm -o Jpeg.dcm -J
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9 gdcmconv -i ../Brainix/Epi/IM-0001-0001.dcm -o Rle.dcm -R
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11 # Generate study/series/sop instance UID++++
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12 dcmodify -e '(0008,0005)' -m '(0010,0020)=FromGDCM' -gin -gst -gse JpegLossless.dcm
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13 dcmodify -e '(0008,0005)' -m '(0010,0020)=FromGDCM' -gin -gst -gse Jpeg.dcm
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14 dcmodify -e '(0008,0005)' -m '(0010,0020)=FromGDCM' -gin -gst -gse Rle.dcm
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16 rm -f JpegLossless.dcm.bak Jpeg.dcm.bak Rle.dcm.bak
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17
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18 gdcmraw -t PixelData ../Brainix/Epi/IM-0001-0001.dcm PixelData.raw
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19 convert -define png:include-chunks=none -define png:compression-level=9 -size 256x256 -depth 16 gray:PixelData.raw Brainix.png
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20
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21 gdcmraw -t PixelData ../KarstenHilbertRF.dcm PixelData.raw
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22 convert -define png:include-chunks=none -define png:compression-level=9 -size 512x464 -depth 8 gray:PixelData.raw KarstenHilbertRF.png
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24 # Decompress the multiframe image
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25 gdcmconv -w ../Multiframe.dcm tmp.dcm
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26 gdcmraw -t PixelData ./tmp.dcm PixelData.raw
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27 SIZE=$((512*512))
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28 dd if=PixelData.raw of=PixelData2.raw bs=$SIZE count=1 skip=0 &> /dev/null
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29 convert -define png:include-chunks=none -define png:compression-level=9 -size 512x512 -depth 8 gray:PixelData2.raw Multiframe0.png
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30 dd if=PixelData.raw of=PixelData2.raw bs=$SIZE count=1 skip=75 &> /dev/null
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31 convert -define png:include-chunks=none -define png:compression-level=9 -size 512x512 -depth 8 gray:PixelData2.raw Multiframe75.png
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33 # Decompress the signed CT image, ignoring the fact that the data is signed
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34 gdcmraw -t PixelData ../SignedCT.dcm PixelData.raw
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35 convert -define png:include-chunks=none -define png:compression-level=9 -size 512x512 -depth 16 gray:PixelData.raw SignedCT.png
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37 rm -f PixelData.raw PixelData2.raw tmp.dcm