[Rtk-users] get simpleRTK image from array

[Simon Rit]

Hi,
I'm not sure what the problem is. Did you reset the image information
before reconstruction, after the GetImageFromArray?
reiImage.CopyInformation( source )
This is essential for the reconstruction to have the correct image
information, this is used by all geometric operations (projection,
backprojection, etc.).
Simon

On Mon, Apr 24, 2017 at 7:59 AM, sare Borhani <sareh.borhani at gmail.com>
wrote:

> Dear Simon,
>
> Thanks
> Now the problem is that , the new reconstructed image is shown black,
> although it has mean and max values. What can that problem come from?
>
> Best regards,
> Sareh
>
> On Tue, Apr 18, 2017 at 1:31 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr
> > wrote:
>
>> Hi,
>> You need to work with numpy, as explained in the help:
>>
>> >>> import SimpleRTK as srtk
>> >>> help(srtk.GetImageFromArray)
>> Help on function GetImageFromArray in module SimpleRTK.SimpleRTK:
>>
>> GetImageFromArray(arr, isVector=False)
>>     Get a SimpleRTK Image from a numpy array. If isVector is True, then a
>> 3D array will be treaded as a 2D vector image, otherwise it will be treaded
>> as a 3D image
>>
>> So in this example, you can obtain what you want by adding
>> import SimpleRTK as srtk
>>
>> at the beginning and then doing
>> a = srtk.GetArrayFromImage(reiImage)
>> b = (0.00000000018308 * np.power(a, 4)) - (0.000000117480729 *
>> np.power(a, 3)) + (0.00001747041637 * np.power(a, 2)) + 1.000021291118193 *
>> a
>> reiImage = srtk.GetImageFromArray(a)
>>
>> This should work.
>> Simon
>>
>> On Tue, Apr 18, 2017 at 9:23 AM, sare Borhani <sareh.borhani at gmail.com>
>> wrote:
>>
>>> Dear RTK.User,
>>>
>>> I'm using python wrapped version of RTK.
>>>
>>> I used the only example of that for reconstruction.It works perfectly.
>>> The problem is that I need to simulate an artifact on projection 2D
>>> images, so first I got each 2D images of stack reiImage by
>>> *srtk.GetArrayFromImage(reiImage) *and then I applied a polynomial on
>>> that to simulate an artifact.NOW need to extract these artifacted-images
>>> again to the simpleRTK image to be able to reconstruct it at the end. I
>>> thought maybe *srtk.GetImageFromArray* works, but it doesn't.
>>>
>>> rei.SetAxis(semiprincipalaxis)
>>> rei.SetGeometry( geometry )
>>> reiImage = rei.Execute(source)
>>>
>>> sampleList = []
>>> for rcount in range(0,127):
>>>     outputName = '/home/PycharmProjects/test/Sample'+ str(rcount)
>>>     #plt.imsave(outputName, srtk.GetArrayFromImage(reiImage [:,rcount,:]),  cmap='gray')
>>>     sampleList.append(srtk.GetArrayFromImage(reiImage [:,rcount,:]))
>>>
>>> test = np.zeros(np.shape(sampleList[0]),dtype=np.float32)
>>>
>>> bhImages = []
>>> for reiImage1 in sampleList:
>>>     #img = plt.imread('/home/PycharmProjects/reiOutput/Sample%d'%k)
>>>     #modifiedImg = sampleList[k]
>>>     artifactedreiImg= np.zeros(np.shape(reiImage1),dtype=np.float32)
>>>     for i in range (reiImage1.shape[0]):
>>>         for j in range (reiImage1.shape[1]):
>>>             a = reiImage1[i, j]
>>>             b = (0.00000000018308 * pow(a, 4)) - (0.000000117480729 * pow(a, 3)) + (0.00001747041637 * pow(a, 2)) + 1.000021291118193 * a
>>>
>>>             artifactedreiImg[i, j] = b
>>>
>>>     artifactedreiImg = artifactedreiImg.astype(np.float32)
>>>
>>>     bhImages.append(artifactedreiImg.astype(np.float32))
>>>     #plt.imsave(outputName, artifactedreiImg, cmap='gray')
>>>
>>>
>>> *for i,artifactedImage in enumerate(bhImages): bhImage[:,i,:]= srtk.GetImageFromArray(artifactedImage[:,:])*
>>>
>>> in last lines I tried to get the stack of artifacted images like reiImage and then paste bhImage instead of reiImage for the reconstruction part. But I got this eror message:TypeError: 'tuple' object does not support item assignment
>>>
>>> First I tried to change the reiImage but it seems its unwritable.
>>>
>>> Best regards,
>>> Sareh Borhani
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
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