Thank you for your prompt reply.
Yes, sorry; I meant another HDR format.
I think that one can write a DICOM image using ITK. But, yes, without ITK, I
have no idea what the DICOM's specs are.
The MHA specs you found seem about right. It is not very popular outside ITK
community, since it is ITK's native file format. You can find a torus in an
mha format here: http://www.cs.wm.edu/~pfot/images/torus.mha. I can create
an nrrd image too, if you think that it will help.
Could you provide link for PicoScan STP format? Is the WSxM STP format as
described in http://www.nanotec.es/products/wsxm/file_structure.php ?
I really appreciate your help,
Regards,
Panagiotis
On Wed, May 11, 2011 at 4:54 PM, David Necas (Yeti) <[email protected]>wrote:
> On Wed, May 11, 2011 at 03:22:19PM -0400, Panagiotis Foteinos wrote:
> > I see that Gwyddion supports .hdr reading but no .hdr writing. Is it
> > difficult to write an .hdr exporter? hdr is supported by ITK.
>
> I don't think this is the same .hdr. AFAIK the only .hdr files Gwyddion
> reads are the headers of Unisoku multi-part data.
>
> > ITK also
> > supports the creation of such images. So you might not even have to study
> > the specs. DICCOM and NRRD formats are also very popular in medical
> > community for data representation, since the pixel values can be
> literally
> > anything (doubles, vectors, you name it). In fact, the output of CT and
> MRI
> > scanners is DICOM series. Of course, the best choice is ITK's native
> image
> > format MHA.
>
> I looked at DICOM before but I got lost. It is thousands of pages of
> convoluted specification legalese irrelevant to Gwyddion that does not
> assign any medical meaning to the data it works with. In fact, Gwyddion
> rarely cares about any meaning at all – it just offers the tools and the
> user decides what makes sense (this is quite different from the medical
> application where everyone needs to cover his ass). Is any example or
> tutorial available to how to write a simple DICOM-compatible 2D data
> file with no medical meaning implied?
>
> I did not know NRRD; but it looks much saner and I will probably
> implement it.
>
> If MHA is the same MHA as shown here
>
> http://code.google.com/p/brainseg/wiki/FileFormats
>
> then this is also reasonable although I cannot find any proper MHA
> specification. Apparently everyone assumes you use ITK to work with MHA
> files... (Well, we are guilty of the same with GWY that has never been
> meant to be an exchange format – but it is still specified at least on
> the self-describing level.)
>
> > Meanwhile, I might need to write my own "dummy" MHA exporter just to get
> the
> > job done, since I have a timetable to follow. Which brings me to the next
> > question: Is it better to start from the raw data (usually in excell
> format)
> > and export to an ITK format, or start from the STP image? Precision-wise.
>
> Raw data in Excel format can mean various things but, in principle, it
> can represent double-precision floating point data.
>
> I know at least two STP formats, the old Molecular Imaging PicoScan one
> and the WSxM one. The former contains 16bit integral data, the latter
> can contain different data, including double-precision floating point.
>
> Using the raw data of whatever kind means that you won't lose precision
> in the process by definition (except possibly in the final export step).
> Going through other representations may lose precision but it depends.
>
> > And my last (newbie-ish question) is as follows: I am searching for the
> > specs of the STP format, but completely unsuccessfully... Does anybody
> know
> > where to get it from?
>
> Which one? I can probably find something about the PicoScan format, the
> WSxM format description can be found on-line.
>
> Regards,
>
> Yeti
>
>
>
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