[ITK] image segmentation

[Matt McCormick]

Hi Giuseppe,

Not all file formats support all pixel types. One approach is to cast the
image to a different type.  See `help(sitk.Cast)`.

HTH,
Matt

On Tue, Feb 14, 2017 at 4:11 PM, Giuseppe Amatulli <
giuseppe.amatulli at gmail.com> wrote:

> Hi,
> thanks for the input.
> I try to follow your suggestion to build up a watershed segmentation image
> starting from external markers, but i get something strange.
>
> These are the files that i used
>
> wget  https://dl.dropboxusercontent.com/u/29337496/small_core.tif
> wget  https://dl.dropboxusercontent.com/u/29337496/cost_Int32.tif
>
> python
>
> import SimpleITK as sitk
>
> img  = sitk.ReadImage("cost_Int32.tif")
> core = sitk.ReadImage("small_core.tif")
>
> feature_img = sitk.GradientMagnitude(img)
> marker_img = sitk.ConnectedComponent(core, fullyConnected=False)
>
> ws = sitk.MorphologicalWatershedFromMarkers(feature_img, marker_img,
> markWatershedLine=True, fullyConnected=False)
>
> sitk.WriteImage(ws,  'watershed.jpg' )
>
>
> Moreover, I also try to save the final image as tiff, but i get the
> following error.
>
> sitk.WriteImage(ws,  'watershed.tif' )
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.7/dist-packages/SimpleITK/SimpleITK.py",
> line 7942, in WriteImage
>     return _SimpleITK.WriteImage(*args)
> RuntimeError: Exception thrown in SimpleITK WriteImage:
> /tmp/SimpleITK-build/ITK/Modules/IO/TIFF/src/itkTIFFImageIO.cxx:544:
> itk::ERROR: TIFFImageIO(0x2e6d880): TIFF supports unsigned/signed char,
> unsigned/signed short, and float
>
> seams to me the tiff is not supported or i miss some modules of ITK
>
> May anyone help me
>
> Thank you
> Best
> Giuseppe
>
>
>
>
>
> On 13 February 2017 at 16:15, Francois Budin <francois.budin at kitware.com>
> wrote:
>
>> Hello Giuseppe,
>>
>> Yes it is possible to create this type of segmentation with ITK.
>> The first step would be to convert your RGB(A) image into a grayscale
>> image using RGBToLuminanceImageFilter [1]. The second step would be to run
>> a watershed filter such as MorphologicalWatershedImageFilter [2]. If you
>> want to keep the lines, use "MarkWatershedLineOn()".
>>
>> Hope this helps,
>> Francois
>>
>> [1] https://itk.org/Doxygen/html/classitk_1_1RGBToLuminanceImage
>> Filter.html
>> [2] https://itk.org/Doxygen/html/classitk_1_1MorphologicalWaters
>> hedImageFilter.html
>>
>> On Mon, Feb 13, 2017 at 3:56 PM, Giuseppe Amatulli <
>> giuseppe.amatulli at gmail.com> wrote:
>>
>>>
>>> Hi,
>>> I'm new in ITK <https://itk.org/> and would like to have some
>>> directions/suggestions.
>>>
>>> I'm trying to segment the image in Figure 1 and be able to identify
>>> "valleys" between each one of the blue point.  In other words I
>>> would like to obtain a red-line on the valleys like the one show in Figure
>>> 2.
>>>
>>> Is this possible with ITK and if yes which are the commands/libraries
>>> that should use?
>>> Is there any python-itk example that I can use to obtain something
>>> similar.
>>>
>>> Thanks
>>> Best Giuseppe
>>>
>>>
>>> FIGURE 1
>>> [image: Inline images 2]
>>>
>>> FIGURE 2
>>>
>>> [image: Inline images 1]
>>>
>>>
>>>
>>> --
>>> Giuseppe Amatulli, Ph.D.
>>>
>>> Research scientist at
>>> Yale School of Forestry & Environmental Studies
>>> Yale Center for Research Computing
>>> Center for Science and Social Science Information
>>> New Haven, 06511
>>> Teaching: http://spatial-ecology.org
>>> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>>>
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>
>
>
> --
> Giuseppe Amatulli, Ph.D.
>
> Research scientist at
> Yale School of Forestry & Environmental Studies
> Yale Center for Research Computing
> Center for Science and Social Science Information
> New Haven, 06511
> Teaching: http://spatial-ecology.org
> Work:  https://environment.yale.edu/profile/giuseppe-amatulli/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20170214/07599631/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 114561 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/community/attachments/20170214/07599631/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 49430 bytes
Desc: not available
URL: <http://public.kitware.com/pipermail/community/attachments/20170214/07599631/attachment-0003.png>