Error during implementation

[pavi1303]

Hi,
I am running this in the Pycharm IDE. I created a collage object and then initialized an empty haralick image to then extract features from both angles using the calculate_haralick_textures function. But I'm not getting an ''Object has no attribute error" when initialising an empty variable. Then I had to proceed to get the statistics measure like mean, variance, skewness and kurtosis from these features. My image and mask files were in .mat (MATLAB) format and thus I imported them using the scipy.io library. Here is my code snippet,

import collageradiomics as crd
import numpy as np

Creating a collage object

collage = crd.Collage(vol_full, TI_mask)
collage.is_3D = True

Creating a haralick image variable

haralick_image = np.empty(collage.dominant_angles.shape + (13,))

Calculating features from both orientations

for angle in range(2):
haralick_image[:, :, :, angle, :] = collage.calculate_haralick_textures(collage.dominant_angles[:, :, :, angle])

It is showing me this error,
AttributeError: 'Collage' object has no attribute 'dominant_angles'

Where am I going wrong here? Any help would be highly appreciated.

[nathanhillyer]

@pavi1303 That method isn't intended to be used publicly. We will push out an update that prefixes the method with an underscore for clarity.

What are you trying to accomplish? If you just want to calculate the haralick textures, I'd suggest using the mahotas library: https://github.com/luispedro/mahotas

[satishev]

He’s trying to calculate COLLAGE feature for his image/ROI. @pavi1303 never checked — are you able to run the Jupyter notebook? The syntax should be in there (sample code to extract features from an image).

[nathanhillyer]

Here is a link to that notebook: https://github.com/radxtools/collageradiomics/blob/master/jupyter/examples/example.ipynb

In order to calculate the COLLAGE feature for the image, you can do this:

collage = crd.Collage(vol_full, TI_mask)
collage.execute()

We'll be able to detect whether or not it is 3D internally, so no need to set that.

[pavi1303]

I did check the sample jupyter notebook but did not implement it as a jupyter notebook, I did it in PyCharm. I'll check that out. Thanks.

[nathanhillyer]

You're welcome. If you experience any further difficulties, please reopen this ticket. We're happy to help.