| Reading Multiple DICOM Files [message #65566] |
Sun, 08 March 2009 16:02  |
Jye
Messages: 17
Registered: May 2008
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Junior Member |
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Hi Everyone,
Im currently putting together an application that needs to read the
image data from numerous DICOM files, currently 900 but this will
possible go up to about 2000.
ATM I have a simple FOR loop :( which steps through each file, makes
an object using Robbies GDLffDICOM and then reads the images data into
a matrix. The object is then destroyed and the loop repeated. This is
horribly slow as you would all imagine and takes about 90sec to read
all of the images.
Has anyone come across a fast way of reading numerous DICOM files? The
problem would have easily been solved if only OBJARR could be used as
a normal array :(
Cheers
Jye
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| Re: Reading Multiple DICOM Files [message #65825 is a reply to message #65566] |
Thu, 26 March 2009 06:32  |
Mike[2]
Messages: 99
Registered: December 2005
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Member |
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On Mar 8, 7:02 pm, Jye <jye.sm...@gmail.com> wrote:
> ATM I have a simple FOR loop :( which steps through each file, makes
> an object using Robbies GDLffDICOM and then reads the images data into
> a matrix. The object is then destroyed and the loop repeated. This is
> horribly slow as you would all imagine and takes about 90sec to read
> all of the images.
Jye,
Another thing that may speed this up is to use the same GDLffDICOM
without destroying it between files. I do this using IDLffDICOM by
calling obj->reset when I'm done with each file and obj->read
(filename) to read a new file. On my machines this is very fast,
including checking numerous other tags, rotating the image and
inserting the slice into a predefined array. All of this is highly
dependent on cpu and disk performance, so YMMV.
Mike
dcm = obj_new('IDLffDICOM')
xdim = *(dcm->GetValue('0028'x,'0010'x))[0]
ydim = *(dcm->GetValue('0028'x,'0011'x))[0]
tdim = 1
;; Read slice locations:
for i = 0, Nfiles-1 do begin
dcm->reset
var = dcm->Read(filelist[i])
slice_locations[i] = *(dcm->GetValue('0020'x,'1041'x))[0]
endfor
;; Sort by slice location:
sorted_indeces = sort(slice_locations)
sorted_slice_locations = slice_locations[sort(slice_locations)]
slice_locations = sorted_slice_locations[uniq(sorted_slice_locations)]
zdim = n_elements(slice_locations)
;; Read image data
data = intarr(xdim, ydim, zdim, tdim)
for i = 0, Nfiles-1 do begin
dcm->Reset
var = dcm->Read(filelist[i])
location = float(*(dcm->GetValue('0020'x,'1041'x))[0])
z = where(reverse(slice_locations) eq location)
;; There may be a preview icon with the data, so check each slice
;; until I find the one that has the correct size. I'm assuming
that
;; there is only one of these per file!
dcm_ptr = dcm->GetValue('7fe0'x,'0010'x,/no_copy)
done = 0
j = 0
while (not done) do begin
slice = rotate(*(dcm->GetValue('7fe0'x,'0010'x))[j], 7)
s = size(slice, /structure)
if (s.dimensions[0] eq xdim) and (s.dimensions[1] eq ydim) then
done = 1
j = j + 1
endwhile
data[*,*,z] = slice
endfor
obj_destroy, dcm
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