[ITK] image segmentation
Giuseppe Amatulli
giuseppe.amatulli at gmail.com
Thu Mar 9 11:32:21 EST 2017
Hi All,
after several try i was able to perform a good watershed delineation
wget https://www.dropbox.com/s/hky66n5ilhpy9k2/impervius_cost.tif
wget https://www.dropbox.com/s/vtumfmi9m5i9r4g/markers.tif
python <<EOF
import SimpleITK as sitk
img = sitk.ReadImage("impervius_cost.tif" , sitk.sitkFloat32 ) # 5
'32-bit unsigned integer' # to check img.GetPixelIDTypeAsString()
core = sitk.ReadImage("markers.tif")
marker_img = sitk.ConnectedComponent(core, fullyConnected=True)
ws_line = sitk.MorphologicalWatershedFromMarkers( img, marker_img,
markWatershedLine=True, fullyConnected=True)
ws_poly = sitk.MorphologicalWatershedFromMarkers( img, marker_img,
markWatershedLine=False, fullyConnected=True)
sitk.WriteImage( sitk.Cast( ws_line , sitk.sitkFloat32 ),
'watershed_line.tif' )
sitk.WriteImage( sitk.Cast( ws_poly , sitk.sitkFloat32 ),
'watershed_poly.tif' )
EOF
Thanks for the help
Giuseppe
[image: Inline images 1]
On 14 February 2017 at 17:14, Matt McCormick <matt.mccormick at kitware.com>
wrote:
> 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/
>>
>
>
--
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/
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