Re: [Gdcm-hackers] want to use gdcm to find pixel data offsets in file

[Aaron B. <bo...@gm...>]

Thanks, Mark. I would be happy to send you some sample images.
We are using Pegasus Pict tools to do the compression.

The reason why I don't want to read the files is because I am writing
a streaming
server.  I want to simply send the raw pixel data over a socket, using sendfile
to avoid any copying into user space.

Thanks again for your help.

Aaron



On Wed, May 25, 2011 at 5:25 PM, Mark Roden <mm...@gm...> wrote:
> Ah, well, it doesn't work with j2k compression because we couldn't get
> any files that were j2k compressed and also were compressed via
> subregions.  All the examples we got compressed the entire image in
> one go, which meant that getting just one region would require
> decompressing the entire image anyway, so it wouldn't have been
> useful.
>
> Would it be possible to submit your image so we could extend the
> functionality of the reader to include this type in the future?
>
> And out of curiousity, why wouldn't you want the reader to do the
> reading?  It's what readers do...
>
> On Wed, May 25, 2011 at 12:01 PM, Aaron Boxer <bo...@gm...> wrote:
>> Thanks very much, Mark! This is perfect.
>> So, it looks like I could just modify the read method to return the
>> offset and size rather than actually
>> do the reading.
>>
>> One complication:  the file is going to be streamed in from a NAS, in
>> 1 K chunks (chunk size is configurable).
>> Also, the files are all JPEG2K compressed.
>>
>>
>>
>> On Wed, May 25, 2011 at 2:29 PM, Mark Roden <mm...@gm...> wrote:
>>> Hi Aaron,
>>>
>>> Actually, you can use the gdcmStreamImageReader to read portions of
>>> the image at a time.  I'm not sure how the frames are stored in your
>>> particular image (are they different planes in Z, for instance?).
>>>
>>> Once you have the header information, you can then use the
>>> DefinePixelExtent method to indicate which portion of the image you
>>> want.  You can take any xyz extent, so x from 0-37, y from 10-23, and
>>> z from 4 - 7, for instance.
>>>
>>> Once that's done, call DetermineProperBufferLength to get the size of
>>> the buffer that you will need to create to store the data.  This
>>> function will take into account number of bytes per pixel and so
>>> forth, so if you have an rgb image, with each pixel having 16 bits,
>>> then this buffer length will return (x extent*y extent * z extent *
>>> 6).
>>>
>>> Then just call read with the buffer you've made in the previous step,
>>> and that subregion will be read in.
>>>
>>> HTH,
>>> Mark
>>>
>>> On Wed, May 25, 2011 at 11:15 AM, Aaron Boxer <bo...@gm...> wrote:
>>>> Hello!
>>>>
>>>> I want to create a method that will parse a dicom file up until the
>>>> pixel data, and then
>>>> return the pixel data size and offset in the file. ( I don't want to
>>>> read in the pixel data).
>>>> If the data is compressed, I just want the offset to the compressed
>>>> data. Also, if it is a multi-frame image, I would like a list of all
>>>> of the frames, with offset and size.
>>>>
>>>> Mathieu has kindly pointed me to the gdcmStreamImageReader class. From
>>>> a quick look,
>>>> it seems that this class will do part of the job. It parses up until
>>>> the pixel data, and then
>>>> reads the rest of the file in all at once. Can anyone suggest any
>>>> existing classes that can
>>>> help me to parse a multi-frame object, and get the frame offsets?
>>>>
>>>> Thanks!!
>>>> Aaron
>>>>
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>>
>