[ITK-users] [ITK] Using Python SimpleITK to Read/Write to BytesIO instance rather than file

[Richard Beare]

If you are trying to avoid IO, and the other packages already deal with
streams, an option may be to stream into a numpy array + a python metadata
structure, and convert that to a SimpleITK image. Obviously will be a
little messy and incur a memory overhead, but could avoid disk IO.

On Thu, Oct 27, 2016 at 2:37 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hi,
>
> Have you done a performance comparison? These other libraries may just
> download and cache the files, before doing file IO.
>
> I recall there was a URL/HTTP based ITK ImageIO, but that just downloaded
> the files and then use the actual file ImageIO. It was wrapped in a nice
> package to enable seamless passing of “http” URLS as filename strings to
> ITK.
>
> HTH,
> Brad
>
> > On Oct 26, 2016, at 11:26 AM, Brian E Chapman <Brian.Chapman at utah.edu>
> wrote:
> >
> > Ziv,
> >
> > Thanks for your reply and the pointer to opneigtlink. Our main
> motivation is speed: just trying to save the write-to-disk/read-from-disk
> costs. Using PyDICOM we can read directly from Girder via streams and I
> believe we also can with nibabel. But ultimately our processing will be
> done with ITK and I was hoping to have SimpleITK so I was hoping to avoid
> all the challenges of reading in one format, passing to simpleitk and
> trying to keep track of all the meta data appropriately in the process.
> >
> > Brian
> >
> > ------
> > Brian E. Chapman, Ph.D.
> > Associate Professor
> > Department of Radiology and Imaging Sciences
> > University of Utah
> >
> >> On Oct 26, 2016, at 8:22 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <
> zivrafael.yaniv at nih.gov> wrote:
> >>
> >> Hi Brian,
> >>
> >> Currently ITK/SimpleITK do not have components for reading an image
> >> directly from a stream. We usually download, save to disk, and read from
> >> disk using the appropriate IO. We used this approach with our Jupyter
> >> notebooks where the read function either finds the data in a cache or
> >> fetches it from MIDAS into the cache and then reads it
> >> (https://github.com/InsightSoftwareConsortium/
> SimpleITK-Notebooks/blob/mast
> >> er/downloaddata.py).
> >>
> >> The challenge with streaming is that we currently don't have a protocol
> >> for interpreting the streamed data (meta-data-dictionary +
> intensity/color
> >> values). A possible solution is to use a client-server architecture with
> >> the OpenIGTLink protocol (http://openigtlink.org). You can transfer
> >> meta-data (patient name etc.) and complete images. See the specification
> >> on their website.
> >>
> >> Out of curiosity, what is the motivation for the streaming only approach
> >> (girder -> SimpleITK -> girder)?
> >>
> >>  hope this helps
> >>    Ziv
> >>
> >>
> >>
> >>
> >>
> >> On 10/25/16, 5:15 PM, "Brian E Chapman" <Brian.Chapman at utah.edu> wrote:
> >>
> >>> Hi,
> >>>
> >>> We are looking at using SimpleITK in conjunction with Girder to read
> >>> images from girder manipulate the images with a Python script and then
> >>> write the contents back up to Girder. We would prefer to do this using
> >>> Byte streams rather than saving to a local file, reading/writing to the
> >>> local file and then uploading the file to Girder, but we have not been
> >>> able to find a way within SimpleITK (within Python) to read and write
> >>> from/to streams rather than files.
> >>>
> >>> Any guidance would be appreciated.
> >>>
> >>> Brian
> >>>
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