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<div class="moz-cite-prefix">Hi Fausto,<br>
if you want to accomplish all the stuff entirely from the
scipy/scikit side, I think you could use [1] and [2] (check the
matching between documentation version and library version).<br>
<br>
HTH.<br>
Best.<br>
<br>
Paolo<br>
<br>
[1]
<a class="moz-txt-link-freetext" href="http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.ndimage.interpolation.rotate.html">http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.ndimage.interpolation.rotate.html</a><br>
[2]
<a class="moz-txt-link-freetext" href="http://scikit-image.org/docs/dev/api/skimage.transform.html#skimage.transform.rotate">http://scikit-image.org/docs/dev/api/skimage.transform.html#skimage.transform.rotate</a><br>
<br>
<br>
<br>
On 04/05/2016 20:40, fausto milletarì wrote:<br>
</div>
<blockquote
cite="mid:6DA80880-E1D3-42EF-B32F-81020FF76C1B@gmail.com"
type="cite">
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charset=windows-1252">
Hello,
<div class=""><br class="">
<div class="">I thank you for you fast and accurate answer. This
was exactly what I was looking for. Actually I don’t need to
visualise the data but further process it in a common
reference frame. I think that your answer solves the problem.
I will look into the ResampleImageFilter (that so far I was
using only to adjust the resolution of different volumes
acquired with different scanners to a common one).</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Thanks a lot!</div>
<div class=""><br class="">
</div>
<div class="">Fausto Milletari<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 04 May 2016, at 20:36, Lowekamp, Bradley
(NIH/NLM/LHC) [C] <<a moz-do-not-send="true"
href="mailto:blowekamp@mail.nih.gov" class="">blowekamp@mail.nih.gov</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;"
class="">
Hello,
<div class=""><br class="">
</div>
<div class="">If I understand you correctly you want
to rotate the image and pad it for visualization
before exporting to numpy.</div>
<div class=""><br class="">
</div>
<div class="">Have you looked into the
ResampleImageFilter? It accepts a transform, along
with output image geometry so that you can readily
manipulate the image for display. You also may want
to scale the image’s intensity with a
WindowLevelImageFilter for better visualization of
the range of interest.</div>
<div class=""><br class="">
</div>
<div class="">HTH,</div>
<div class="">Brad</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On May 4, 2016, at 1:14 PM, fausto
milletarì <<a moz-do-not-send="true"
href="mailto:fausto.milletari@gmail.com"
class="">fausto.milletari@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;"
class="">
Hello everyone,
<div class=""><br class="">
<div class="">I have a probably naive
question about simpleITK. I find
simpleITK extremely useful to process
medical data such as MRI scans but I
would like also to enjoy being able to
convert my images in numpy format while
respecting the transformation of the
volume.</div>
</div>
<div class=""><br class="">
</div>
<div class="">In other words I would like to
get the MRI image in numpy rotated by the
correct amount around each axis with zero
padding for example.</div>
<div class=""><br class="">
</div>
<div class="">when i do simply <span
style="color: rgb(128, 128, 128);
font-style: italic; font-family: Menlo;
font-size: 9pt; background-color:
rgb(255, 255, 255);" class="">sitk.GetArrayFromImage(imgResampledCropped)</span>I
get back the raw data itself, but what I
would like to do is to have a numpy array
that contains the data “ready to
visualise” by simple slicing of the array
itself.</div>
<div class=""><br class="">
</div>
<div class="">Do you think this is doable?
Is there a standard way of doing it?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class=""><br class="">
</div>
<div class="">Fausto</div>
<div class=""><br class="">
</div>
</div>
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