[Rtk-users] The preprocessing for .bmp and .tif images

[Chao Wu]

Sorry, not "neworigin" but "newspacing"

2015-06-16 19:56 GMT+02:00 Chao Wu <wuchao04 at gmail.com>:

> Then it probably means the pixel size RECORDED IN TIF is 1 mm, or the
> pixel size is NOT SET and then by default of itk/rtk 1 mm...
> By the way with the latest version of rtk you can overwrite the projection
> image metadata (including pixel size) with command line argument. You can
> try to put --neworigin 0.127 and see what happens.
>
> Regards,
> Chao
>
>
> 2015-06-16 19:42 GMT+02:00 Guangming Zang <guangming.zang at kaust.edu.sa>:
>
>> Thanks Chao and Simon.
>> Yes, my .tif images are 16 bit depth( uint16 ) , i think it is the same
>> with unsigned short.
>> Another question related to  geometry is that, several months ago, i
>> asked the tif file geometey settings, and Chao replied and kindly
>> pointed that
>> <http://webcache.googleusercontent.com/search?q=cache:1KHuL-ayALwJ:public.kitware.com/pipermail/rtk-users/2014-November/000621.html+&cd=1&hl=en&ct=clnk&gl=sa>
>> i should be careful about image's dpi
>> But, i still can not understand why it is related to image's dpi.
>>  For example, my tif images' information and some geometry information
>> from scanner are like this:
>> * 1916*1536 dimensions *
>> *  pixelsize 0.127*
>> *  SDD  983*
>> *  SID    413*
>> The interesting part is that, when using  rtksimulatedgeometry  command
>> ,  i set all parameters identical to physical distance (mm). it does not
>> show anything, not matter care about dpi or not(suppose   rtkfdk command
>> after that  is correct). i.e.,
>> 1. rtksimulatedgeometry -n 360 -o geometry.xml   --sdd="983"
>> --sid="413"    --proj_iso_x="-121.666" --proj_iso_y="-97.536"
>>
>> or change the sid to 2/3 *sid because of  300 dpi instead of 200 dpi
>> 2. rtksimulatedgeometry -n 360 -o geometry.xml   --sdd="655.3333"
>> --sid="413"    --proj_iso_x="-121.666" --proj_iso_y="-97.536"
>>
>>
>> But when i set the *sdd *divide by pixelsize(0.127),  and other
>> parameters like this, it reconstructed a  volume seems correct(at least
>> show the whole object)
>>
>> 3. rtksimulatedgeometry -n 360 -o geometry.xml   --sdd="7740.15748"
>> --sid="413.423889"    --proj_iso_x="-958" -proj_iso_y="-768"
>>
>> so would you please help me to find what happened??
>>
>> Sorry , again for this long letter. :(
>>
>> Thanks very much.
>>
>> With my Regards
>> Guangming
>>
>>
>>
>>
>>
>> *Guangming Zang (Alex)*
>> *King Abdullah University of Science and Technology(KAUST)*
>> *University of Chinese Academy of Sciences(UCAS)*
>>
>>
>>
>>
>> 2015-06-16 17:43 GMT+03:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>>
>>> Hi,
>>> This is correct if your tif is of type "unsigned short".
>>> Simon
>>>
>>> On Tue, Jun 16, 2015 at 4:41 PM, Chao Wu <wuchao04 at gmail.com> wrote:
>>> > Look at http://www.openrtk.org/Doxygen/dot_inline_dotgraph_16.png
>>> > For tif and bmp I think they go through the left most path (except for
>>> the
>>> > Elekta branch).
>>> >
>>> >
>>> > 2015-06-16 15:47 GMT+02:00 Guangming Zang <guangming.zang at kaust.edu.sa
>>> >:
>>> >>
>>> >> Hi RTK community,
>>> >> Sorry to bother you again,  but i was wondering for the projections
>>> in the
>>> >> format of .bmp and .tif files. (e.g., say the bmp images  range from
>>> >> [0,255], tif images range from [1,521]) . what are the next steps and
>>> >> preprocessing pipelines in RTK for bmp and tif ?? I look into the
>>> >> rtkProjectionsReader.txx, however, for me, i think it does not explain
>>> >> clearly.
>>> >> So anyone can help me?
>>> >>
>>> >> with my Regards
>>> >> Guangming
>>> >>
>>> >> Guangming Zang (Alex)
>>> >> King Abdullah University of Science and Technology(KAUST)
>>> >> University of Chinese Academy of Sciences(UCAS)
>>> >>
>>> >>
>>> >>
>>> >>
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>>>
>>
>>
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