Hi Bhautik,
Thanks for all the nice comments about TIFF_TO_DICOM.c, if I'd realized
anyone would appreciate it I'd have made certain the file comments
actually reflected its current usage, DUH! Oh and that I had my current
e-mail address on it (m.obrien@sghms.ac.uk).
Love the DICOM_WRITER for IDL, took a little bit of playing for ctn
dicom software to open the created files. I believe that the minimum
bits per pixel supported by the standard is 16. I've attached a
slightly hacked version that sets bpp internally irrespective of the
image type coming in. Had played with the idea of allowing floats and
setting pixel representation according to image array type, but settled
on bytscl and a conversion to uint for now. See what you think.
Trivial bit, physicians name tag is 0008,0090 (some readers will drop
the file if the tags are out of order).
I'm sure all the med image people out there that use IDL love you :)
Thanks for an excellent bit of porting, I'd been putting it off for
ages.
Marc
--
Tel: 0208 725 2857
Fax: 0208 725 2992
St George's Hospital Medical School
Department of Biochemistry and Immunology
Cranmer Terrace
Tooting
London SW17 0RE
;
; NAME:
; DICOM_WRITER
;
; VERSION:
; 0.11
;
; PURPOSE:
; Generate a dicom file from within RSI IDL
;
; AUTHOR:
; Bhautik Joshi
;
; EMAIL:
; bjoshi@geocities.com
;
; HOMEPAGE:
; http://cow.mooh.org
;
; USE:
; DICOM_WRITER, filename, image
;
; INPUT:
; filename - string containing name of dicom file to be written to
; bpp - number of _bytes_ per pixel in the image
; image - byte formatted version of image
;
; NOTES ON USAGE:
; * At the moment the program only writes to a single slice
; * The input image must be squashed into a 1D array of bytes before
; it can be used in dicom_writer
; * bpp specifies the number of bytes (not bits!!) per pixel
; * Extra dicom tags can be easily added (see body of program)
; * There is little to no error-checking at the moment, so be
; careful!
; * Analyse seems to need a minimum image size of somewhere around
; 100x100
;
; EXAMPLE:
; Create a horrendously boring byte image and store it in a
; dicom file, test.dcm :
;
; > rows = 200
; > cols = 200
; > bpp = 1
; > image = BYTESCL(indgen(rows,cols))
; > dicom_writer, 'test.dcm', bpp, image
;
; HISTORY:
; Based on Marc O'Briens (marcus@sghms.ac.uk) TIFF_to_DICOM.c
; version 0.1 08-01-2002 - first working version produced
; version 0.11 09-01-2002 - fixed endian-ness issue & added get_lun
; functionality
;
; TODO:
; * Allow for more robust dicom writing
; * Expand the number of tags written (using DICOM data
; dictionary)
; * Part 10 compliance (!!!!!!!!!!!)
;
; DISCLAIMER:
;
; Permission to use, copy, modify, and distribute this software and its
; documentation for any purpose and without fee is hereby granted,
; provided that the above copyright notice appear in all copies and that
; both that copyright notice and this permission notice appear in
; supporting documentation.
;
; This file is provided AS IS with no warranties of any kind. The author
; shall have no liability with respect to the infringement of copyrights,
; trade secrets or any patents by this file or any part thereof. In no
; event will the author be liable for any lost revenue or profits or
; other special, indirect and consequential damages.
;
; The author accepts no responsibility for any action arising from use of
; this package. The software is not guaranteed to write compliant DICOM
; files. If it causes damage to you or your system, you have been warned -
; this is a work in progress. If it bites your dog, its not my fault. If
; it causes you to curl up on the floor in the foetal position muttering
; about pixies and mushrooms, its not my fault. If it causes you or someone
; else to spontaneously burst into song and dance, its not my fault but
; I'd like to hear about it. You have been warned.
;
;convert a value, val, that is num bytes long, into
;a series of ordered bytes
function getbytes, val, num
ret=BYTARR(num)
offset=0
;work in big endian ONLY
;val=swap_endian(val)
if (!version.arch eq 'x86') then begin
byteorder,val,/SWAP_IF_BIG_ENDIAN
endif else begin
byteorder,val,/SWAP_IF_LITTLE_ENDIAN
endelse
for i=0,(num-1) do begin
tmpres=BYTE(ISHFT(val, offset) AND 255)
ret[i]=tmpres
offset=offset-8
endfor
return, ret
end
;write any tag
function generate_anytag, group, element, data
rs=[getbytes(group,2),getbytes(element,2)]
;correct to even length if necessary
bs=BYTE(data)
nl=n_elements(bs)
if ((nl mod 2) ne 0) then begin
bs=[bs,BYTE(0)]
nl=nl+1
end
;size of field
rs=[rs,getbytes(nl,2)]
;padding
rs=[rs,[0,0]]
;string itself
rs=[rs,bs]
return, rs
end
;generate string tag
function generate_stringtag, group, element, string
return, generate_anytag(group, element, BYTE(string))
end
;generate binary element (unsigned short) tag
function generate_UStag, group, element, val
param=getbytes(val,2)
return, generate_anytag(group,element,param)
end
;generate pixel tag
function generate_pixeltag, group, element, val
return, [getbytes(group,2),getbytes(element,2), getbytes(val,4)]
end
;generate unsigned long tag
function generate_ULtag, group, element, val
param=getbytes(val,4)
return, generate_anytag(group,element,param)
end
pro dicom_writer, filename, image
; bytescl and convert input image to 16bit unsigned integer
sz=size(image)
image = reform(UINT(BYTSCL(image)),sz[1],sz[2])
;dummy fill-in variables.
random= '123456'
SOPClass = '1.2.840.10008.5.1.4.1.1.20'
SOPInstance = '1.2.840.10008.5.1.4.1.1.20.1'
StudyID = '1.2.3.4'
StudyInstanceUID = SOPInstance + random
SeriesInstanceUID = StudyInstanceUID
RelFrameOfReferenceUID = StudyInstanceUID
SeriesInstanceUID = SeriesInstanceUID + '.1'
RelFrameOfReferenceUID = RelFrameOfReferenceUID + '.2'
StudyID = StudyID + 'SIGNA '
;image variables
Seriesnum=0
Imagenum=0
thickness=1.0
spacing='1.0\\1.0'
rows=sz[1]
cols=sz[2]
bpp=2
GET_LUN, U
OPENW, U, filename
; DICOM tags - feel free to add more!
;0008 tags
;MR type
WRITEU, U, BYTE(generate_stringtag('0008'x,'0008'x,'ORIGINAL\\PRIMARY\\ OTHER'))
;Instance date
WRITEU, U, BYTE(generate_stringtag('0008'x,'0012'x,'20020108'))
;Instance time
WRITEU, U, BYTE(generate_stringtag('0008'x,'0013'x,'000000.00000'))
;SOP class
WRITEU, U, BYTE(generate_stringtag('0008'x,'0016'x,SOPClass))
;SOP instance
WRITEU, U, BYTE(generate_stringtag('0008'x,'0018'x,SOPInstance))
;Modality
WRITEU, U, BYTE(generate_stringtag('0008'x,'0060'x,'MR'))
;Manufacturer
WRITEU, U, BYTE(generate_stringtag('0008'x,'0070'x,'GE'))
;Study Physicians Name
WRITEU, U, BYTE(generate_stringtag('0008'x,'0090'x,'fizzy'))
;0010 tags
;Patient name
WRITEU, U, BYTE(generate_stringtag('0010'x,'0010'x,'A Patient'))
;Patient ID
WRITEU, U, BYTE(generate_stringtag('0010'x,'0020'x,'TK247'))
;Patient birth date
WRITEU, U, BYTE(generate_stringtag('0010'x,'0030'x,'20020111'))
;Patient sex
WRITEU, U, BYTE(generate_stringtag('0010'x,'0040'x,'F'))
;0018 tags
;Acquisition type
WRITEU, U, BYTE(generate_stringtag('0018'x,'0023'x,'2D'))
;Slice thickness
WRITEU, U, BYTE(generate_stringtag('0018'x,'0050'x,STRING(thickness)))
;0020 tags
;Study instance
WRITEU, U, BYTE(generate_stringtag('0020'x,'000D'x,StudyInstanceUID))
;Series instance UID
WRITEU, U, BYTE(generate_stringtag('0020'x,'000E'x,SeriesInstanceUID))
;StudyID
WRITEU, U, BYTE(generate_stringtag('0020'x,'0010'x,StudyID))
;Series number
WRITEU, U, BYTE(generate_stringtag('0020'x,'0011'x,STRING(seriesnum)))
;Image number
WRITEU, U, BYTE(generate_stringtag('0020'x,'0013'x,STRING(imagenum)))
;0028 tags
;samples per pixel
WRITEU, U, BYTE(generate_UStag('0028'x,'0002'x,1))
;Photometric interpretation
WRITEU, U, BYTE(generate_stringtag('0028'x,'0004'x,'MONOCHROME2'))
;Rows in image
WRITEU, U, BYTE(generate_UStag('0028'x,'0010'x,rows))
;Columns in image
WRITEU, U, BYTE(generate_UStag('0028'x,'0011'x,cols))
;pixel spacing
WRITEU, U, BYTE(generate_stringtag('0028'x,'0030'x,spacing))
;bits allocated per sample
WRITEU, U, BYTE(generate_UStag('0028'x,'0100'x,bpp*8))
;bits stored per sample
WRITEU, U, BYTE(generate_UStag('0028'x,'0101'x,bpp*8))
;high bit
WRITEU, U, BYTE(generate_UStag('0028'x,'0102'x,(bpp*8)-1))
;pixel representation
WRITEU, U, BYTE(generate_UStag('0028'x,'0103'x,'0000'x))
;write image data
imsize=rows*cols*bpp
WRITEU, U, BYTE(generate_pixeltag('7FE0'x,'0010'x,imsize))
WRITEU, U, image
CLOSE, U
FREE_LUN, U
end
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