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

Tue Jun 16 15:06:08 EDT 2015

Well, very interesting.
After taking Chao's advice and use the command --newspacing 0.127 in
rtkfdk, i can got the correct result when the parameters are set identical
to  physical unit (mm). i.e.,
the commands are:

rtksimulatedgeometry -n 360 -o geometry.xml   --sdd="983"     --sid="413"
 --proj_iso_x="-121.666" --proj_iso_y="-97.536"
rtkfdk -p D:\Compare\FinalRTK\bin\Release\TOY -r .*.tif   -o  Result\T1.mha
-g geometry.xml --newspacing 0.127 --spacing 1,1,1 --dimension 100,100,100

in which the geometry setting make more sense than before.
Thanks!

Best regards
Guangming

*Guangming Zang (Alex)*
*King Abdullah University of Science and Technology(KAUST)*
*University of Chinese Academy of Sciences(UCAS)*

2015-06-16 21:14 GMT+03:00 Guangming Zang <guangming.zang at kaust.edu.sa>:

> Hi Chao,
> Thanks so much for your kind and very prompt reply.
>
> Actually,  we do not have the pixel size information in image. what we
> know about TIF image is :
> *1916*1536 dimensions*
> *300 dpi*
> *16 bit depth*
>
> And also i  have the information in the geometry .xml file about the
> detector:
>
> DetectorPixelsX=1916
> DetectorPixelsY=1536
> DetectorPixelSizeX=0.127
> DetectorPixelSizeY=0.127
>
> and the tif images's X and Y are the same with Detector(i.e., 1916*1536)
>  so that's why i think the pixelsize IN  TIF is 0.127.
> Sure  i downloaded the latest version of RTK this afternoon and have not
> tried it yet. Thanks very much for this important information.
>
> Best regards
> Guangming
>
>
>
>
>
> *Guangming Zang (Alex)*
> *King Abdullah University of Science and Technology(KAUST)*
> *University of Chinese Academy of Sciences(UCAS)*
>
>
>
>
> 2015-06-16 20:58 GMT+03:00 Chao Wu <wuchao04 at gmail.com>:
>
>> 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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