Hi all,
A little while back, Marc O'Brien (marcus@icr.ac.uk) posted his very
nifty TIFF_to_DICOM.c utility. Just on its own, this piece of code is
pretty legendary and I'd like to thank Marc for sharing it with all of
us.
However, I needed a solution that I could quickly port between
platforms, so I set out upon the task of writing a DICOM writer that
uses 100% IDL code, loosely based on Marc's program, and, now I have
dicom_writer v0.1, which should be attached to this newsgroup message :)
Please find attached two files - dicom_writer.pro and dicom_example.pro.
Using dicom_writer is a snap:
> rows = 20
> cols = 20
> bpp = 1
> image = BYTESCL(indgen(rows,cols))
> dicom_writer, 'test.dcm', rows, cols, bpp, image
This would create a boring DICOM image called test.dcm in the current
directory. To test if it works, use dicom_example to load the file. Look
at the source for better instructions and explanations.
At the moment dicom_writer is extremely basic - it'll only write a
single slice and I've filled in most of the important fields with dummy
data. However, the code itself is very simple and can be easily
customised. I'm still working on it, but if you make any improvments I'd
love to hear about it :)
Next on the list is a better and more comprehensive way to fill in the
fields in the DICOM header, and perhaps part 10 DICOM compiance (!!).
Remember, its pretty raw at the moment and has little in the way of
error checking; if it bites your pet or causes hallucinations then you
probably need to wait for the next release :P
Anyway, hope some of you find it useful, and I'd love to hear if you do
get it working successfully :)
Cheers,
Bhautik
--
/--------------------------------------------------(__)----- ----\
| nbj@imag.wsahs.nsw.gov.au | phone: 0404032617 |..|--\ -moo |
| ICQ #: 2464537 | http://cow.mooh.org | |--| |
|---------------------------+----------------------\OO/|| ------/
| international |
| roast. my sanity has gone |
| its lost forever |
\---------------------------/
;
; NAME:
; DICOM_WRITER
;
; VERSION:
; 0.1
;
; 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 rows, cols, bpp, image
;
; INPUT:
; filename - string containing name of dicom file to be written to
; rows - number of rows in image
; cols - number of columns in image
; 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!
;
; EXAMPLE:
; Create a horrendously boring byte image and store it in a
; dicom file, ~/test.dcm :
;
; > rows = 20
; > cols = 20
; > bpp = 1
; > image = BYTESCL(indgen(rows,cols))
; > dicom_writer, ~/test.dcm, rows, cols, bpp, image
;
; HISTORY:
; Based on Marc O'Briens (marcus@icr.ac.uk) TIFF_to_DICOM.c
; version 0.1 08-01-2002 - first working version produced
;
; 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.
;
pro dicom_writer, filename, rows, cols, bpp, image
;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'
OPENW, 1, filename
; DICOM tags - feel free to add more!
;0008 tags
;MR type
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0008'x,'ORIGINAL\\PRIMARY\\ OTHER'))
;Instance date
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0012'x,'20020108'))
;Instance time
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0013'x,'000000.00000'))
;SOP class
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0016'x,SOPClass))
;SOP instance
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0018'x,SOPInstance))
;Modality
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0060'x,'MR'))
;Manufacturer
WRITEU, 1, BYTE(generate_stringtag('0008'x,'0070'x,'GE'))
;Study Physicians Name
; WRITEU, 1, BYTE(generate_stringtag('0008'x,'0012'x,'chewbacca wookiee'))
;0010 tags
;Patient name
WRITEU, 1, BYTE(generate_stringtag('0010'x,'0010'x,'Jabba the Hutt'))
;Patient ID
WRITEU, 1, BYTE(generate_stringtag('0010'x,'0020'x,'TK247'))
;Patient birth date
WRITEU, 1, BYTE(generate_stringtag('0010'x,'0030'x,'20010820'))
;Patient sex
WRITEU, 1, BYTE(generate_stringtag('0010'x,'0040'x,'M'))
;0018 tags
;Acquisition type
WRITEU, 1, BYTE(generate_stringtag('0018'x,'0023'x,'2D'))
;Slice thickness
WRITEU, 1, BYTE(generate_stringtag('0018'x,'0050'x,STRING(thickness)))
;0020 tags
;Study instance
WRITEU, 1, BYTE(generate_stringtag('0020'x,'000D'x,StudyInstanceUID))
;Series instance UID
WRITEU, 1, BYTE(generate_stringtag('0020'x,'000E'x,SeriesInstanceUID))
;StudyID
WRITEU, 1, BYTE(generate_stringtag('0020'x,'0010'x,StudyID))
;Series number
WRITEU, 1, BYTE(generate_stringtag('0020'x,'0011'x,STRING(seriesnum)))
;Image number
WRITEU, 1, BYTE(generate_stringtag('0020'x,'0013'x,STRING(imagenum)))
;0028 tags
;samples per pixel
WRITEU, 1, BYTE(generate_UStag('0028'x,'0002'x,1))
;Photometric interpretation
WRITEU, 1, BYTE(generate_stringtag('0028'x,'0004'x,'MONOCHROME2'))
;Rows in image
WRITEU, 1, BYTE(generate_UStag('0028'x,'0010'x,rows))
;Columns in image
WRITEU, 1, BYTE(generate_UStag('0028'x,'0011'x,rows))
;pixel spacing
WRITEU, 1, BYTE(generate_stringtag('0028'x,'0030'x,spacing))
;bits allocated per sample
WRITEU, 1, BYTE(generate_UStag('0028'x,'0100'x,bpp*8))
;bits stored per sample
WRITEU, 1, BYTE(generate_UStag('0028'x,'0101'x,bpp*8))
;high bit
WRITEU, 1, BYTE(generate_UStag('0028'x,'0102'x,(bpp*8)-1))
;pixel representation
WRITEU, 1, BYTE(generate_UStag('0028'x,'0103'x,'0000'x))
;write image data
imsize=rows*cols*bpp
WRITEU, 1, BYTE(generate_pixeltag('7FE0'x,'0010'x,imsize))
WRITEU, 1, BYTE(image)
CLOSE, 1
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
;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)
byteorder,val,/SWAP_IF_LITTLE_ENDIAN
for i=0,(num-1) do begin
tmpres=BYTE(ISHFT(val, offset) AND 255)
ret[i]=tmpres
offset=offset-8
endfor
return, ret
end
PRO Dicom_Example
filename=dialog_pickfile()
object = Obj_New('IDLffDicom')
ok = object->Read(filename)
IF NOT ok THEN BEGIN
Print, 'File: "' + filename + '" cannot be read. Returning...'
RETURN
ENDIF
name = object->GetValue('0010'x, '0010'x)
IF Ptr_Valid(name[0]) THEN Print, 'name: ', *name[0]
image = object->GetValue('7Fe0'x, '0010'x)
;IF Ptr_Valid(image[0]) THEN tvscl, BytScl(*image[0])
im_type = object->GetValue('0008'x,'0008'x)
IF Ptr_Valid(im_type[0]) THEN PRINT,'im_type: ',*im_type[0]
modality = object->GetValue('0008'x,'0060'x)
IF Ptr_Valid(modality[0]) THEN PRINT,'modality: ',*modality[0]
slice_spacing = object->GetValue('0018'x,'0088'x)
IF Ptr_Valid(slice_spacing[0]) THEN PRINT,'slice_spacing: ',*slice_spacing[0]
image_number = object->GetValue('0020'x,'0013'x)
IF Ptr_Valid(image_number[0]) THEN PRINT, 'image_number: ',*image_number[0]
rows = object->GetValue('0028'x,'0010'x)
IF Ptr_Valid(rows[0]) THEN PRINT, 'rows: ',*rows[0]
cols = object->GetValue('0028'x,'0011'x)
IF Ptr_Valid(cols[0]) THEN PRINT, 'cols: ',*cols[0]
spatial_res = object->GetValue('0018'x,'1050'x)
IF Ptr_Valid(spatial_res[0]) THEN PRINT, 'spatial_res: ',*spatial_res[0]
aspect_ratio = object ->GetValue('0028'x,'0034'x)
IF Ptr_Valid(aspect_ratio[0]) THEN PRINT, 'aspect_ratio: ',*aspect_ratio[0]
rows = object->GetValue('0028'x,'0010'x)
IF Ptr_Valid(rows[0]) THEN PRINT, 'rows: ',*rows[0]
cols = object->GetValue('0028'x,'0011'x)
IF Ptr_Valid(cols[0]) THEN PRINT, 'cols: ',*cols[0]
xys=object->GetValue('0028'x,'0030'x)
IF Ptr_Valid(xys[0]) THEN PRINT, 'xys: ',*xys[0]
zs = object->GetValue('0018'x,'0050'x)
IF Ptr_Valid(zs[0]) THEN PRINT,'zs: ',*zs[0]
xys=*xys[0]
zs=*zs[0]
sp=strpos(xys,'\')
voxelsizes=[FLOAT(strmid(xys,0,sp)), FLOAT(strmid(xys,sp+1)),FLOAT(zs)]
xy=[FLOAT(*rows[0]),FLOAT(*cols[0])]
print, voxelsizes
print, xy
zzzz=*image[0]
Obj_Destroy, object
Ptr_Free, name
Ptr_Free, image
END
|
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