haralick 3D

[ritasimoes]

Hi all,

I am computing the Haralick features of 3D images. The "haralick"
function returns a 4x13 array, but for 3D data shouldn't this be
13x13? It seems that only the first four directions are being computed
(as in the 2D case) - line 86 in texture.py. Is this a bug or am I
missing something?

Thanks in advance!

Rita

[Luis Pedro Coelho]

Hi Rita,

You're right, of course.

I will fix it in the next release.

Thank you,
Luis

--
Luis Pedro Coelho | Carnegie Mellon University | http://luispedro.org

[Sun]

Hi Luis,

I'm trying to read 3D png image and it reads as 2D image and gives 4x13 Haralick feature vectors.

Could you let me know if this issue has been fixed, or some pointers in that direction?

Thanks,

Sundar

[Luis Pedro Coelho]

On Sunday, April 29, 2012 06:44:20 PM Sun wrote:
> I'm trying to read 3D png image and it reads as 2D image and gives 4x13
> Haralick feature vectors.

Are you sure this is being correctly read? I wasn't even aware that you could
have 3D PNGs.

HTH
--
Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org

[Sundaresan R]

Hi Luis,

Thats where it fails. I tried reading 3D png and tiff using the following code and it reads as 2D image. 

I installed mahotas 0.7.3  and freeimage.

********************************

import numpy as np

from scipy import ndimage

import pylab

import mahotas

from mahotas import freeimage

from mahotas import imread,imsave

img = mahotas.imread('myuchar.tiff')

print img.ndim

print img

*********************************

It gives the following:

2

[[0 0 0 ..., 0 0 0]

 [0 0 0 ..., 0 0 0]

 [0 0 0 ..., 0 0 0]

 ..., 

 [0 0 0 ..., 0 0 0]

 [0 0 0 ..., 0 0 0]

 [0 0 0 ..., 0 0 0]]

I'm unsure why it fails while reading the 3D image. Does the imread package also needs to be installed separately?  

(there was a dependency issue for libwebp-dev in ubuntu 10.10, python 2.6).

Thanks,

Sundar

[Sun]

Hi all,

Could anyone tell me how could I read a 3D image in python?

Thanks
Sundar

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[Luis Pedro Coelho]

On Thursday, May 17, 2012 02:18:53 PM Sun wrote:
> Could anyone tell me how could I read a 3D image in python?

The same way you read a 2D image.

What is the format this image is in?

If you have tried imread (http://pypi.python.org/pypi/imread/0.2.1) and it
does not open it correctly, send the image file (per personal email) and I will
look into it.

Good luck

--
Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org

LxMLS 2012: Lisbon Machine Learning School
http://lxmls.it.pt

[Sundaresan R]

It works after I convert the image into a numpy array before computing the features.

Thanks Luis.

Sundar