[Rtk-users] get simpleRTK image from array

[sare Borhani]

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
>>
>> _______________________________________________
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>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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