How should I set /examples/exampleSettings/Params.yaml to use all filters？

[guangzhaohui]

Hi everyone!
Since I am about to begin a radiomic study ex novo, I just wanted to extract images with all filters.
Now
How should I set /examples/exampleSettings/Params.yaml？

Settings to use, possible settings are listed in the documentation (section "Customizing the extraction").

setting:
binWidth: 25
label: 1
interpolator: 'sitkBSpline' # This is an enumerated value, here None is not allowed
resampledPixelSpacing: # This disables resampling, as it is interpreted as None, to enable it, specify spacing in x, y, z as [x, y , z]
weightingNorm: # If no value is specified, it is interpreted as None

Image types to use: "Original" for unfiltered image, for possible filters, see documentation.

imageType:
Original: {} # for dictionaries / mappings, None values are not allowed, '{}' is interpreted as an empty dictionary
LoG: {'sigma' : [1.0,2.0,3.0,4.0,5.0]}
Wavelet:
Square:
SquareRoot:
Logarithm:
Exponential:

Thank you very much in advance,
Guangzhaohui

[JoostJM]

There is no way to specify "all filters", but the are all listed in the documentation and you can enable them all by specifying the in your parameter file as follows:

imageType:
  Original: {}  # no custom settings
  LoG: {sigma: (0.5, 1.0, 2.0)}  # custom settings defined in-line
  Wavelet: {}
  LBP3D:
    binWidth: 1.0  # Customized settings defined in tree-structure
  # (...) add the other filters here

The name (case-sensitive) of the filter is specified by the function name implementing that filter:
get<Filter>Image(), e.g. getLoGImage is enabled by specifying LoG. All filters are implemented here.

N.B. For local binary pattern there are separate implementations for 2D and 3D, so ensure you have the one that matches you extraction type.

[guangzhaohui]

How kind are you！ Could you add the other filters here：

[guangzhaohui]

imageType:
Original: {} # no custom settings
LoG: {sigma: (0.5, 1.0, 2.0)} # custom settings defined in-line
Wavelet: {}
LBP3D:
binWidth: 1.0 # Customized settings defined in tree-structure
Square:
SquareRoot:
Logarithm:
Exponential:
Thank you very much!!!

[JoostJM]

looks good, but mind the meaningfull white-space (i.e. your indentation). Also Don't forget the empty dictionary ({}), as otherwise the value is interpreted as None, which currently breaks the validation

imageType:
  Original: {} # no custom settings
  LoG: {sigma: (0.5, 1.0, 2.0)} # custom settings defined in-line
  Wavelet: {}
  LBP3D:
    binWidth: 1.0 # Customized settings defined in tree-structure
  Square: {}
  SquareRoot: {}
  Logarithm: {}
  Exponential: {}

[guangzhaohui]

LoG: 、Wavelet: have examples.
How cloud i run ：
LBP3D:
binWidth: 1.0 # Customized settings defined in tree-structure
Square: {}
SquareRoot: {}
Logarithm: {}
Exponential: {}
Could you give examples？
Thank you very much!!!

[JoostJM]

@guangzhaohui, see the example above, or the examples in the repository (examples/exampleSettings)
Customized settings defined in the tree structure means that for that specific filter, those settings override the default or global defined settings. (The sigma setting in LoG is can also be set globally)

[guangzhaohui]

yeah，i have solved it! Thank you very much!!!
But, LBP3D: i can set it as above examples,it can not work.

AttributeError: module 'radiomics.imageoperations' has no attribute 'getLBP3DImage'

[guangzhaohui]

But, LBP3D: i can set it as above examples,it can not work.

AttributeError: module 'radiomics.imageoperations' has no attribute 'getLBP3DImage'

How can i set it?
Thank you.

[JoostJM]

Which version of PyRadiomics are you using?

If you look up your image operations module (from radiomics import imageoperations; print(imageoperations.__file__)), are you able to find the getLBP3DImage function?

[guangzhaohui]

Sorry ！I don't hnow Which version of PyRadiomics
I get this：
D:\PYTHON\Lib\site-packages\pyradiomics-master\pyradiomics-master\radiomics\imageoperations.py

[JoostJM]

You can get the version by running (in cmd): pyradiomics --version

[guangzhaohui]

Could you please give me an example for LBP3D?
I really cant do it for many times。
Thanks very much！

[guangzhaohui]

python version 3.5.4

[guangzhaohui]

radiomics 0.1

[guangzhaohui]

and How can i upgrade most newer pyradiomic?

[guangzhaohui]

[JoostJM]

Currently, PyRadiomics is not yet on pypi (#335), but has to be installed from source.
You can install using pip with the following command:"

pip install git+https://github.com/Radiomics/pyradiomics (it is possible that this requires git to be installed on your pc)

[guangzhaohui]

Thank you for your time!
I have install as above.
and get it below in D:\PYTHON\Scripts
but, i open jupyter notebook it remain older one, why?

[JoostJM]

you mean that you have both pyradiomics.exe and pyradiomicsbatch.exe?
It is still the new one, pyradiomicsbatch is in there for backwards compatibility and will display a deprecation warning if used.

[guangzhaohui]

yes it both in D:\PYTHON\Scripts

[guangzhaohui]

usage : pyradiomics image:batch [mask] [Options]
pyradiomics: error:the followingarguments are required:< Image.Batch>FILE

[JoostJM]

@guangzhaohui that's the new one yes

[JoostJM]

run pyradiomics -h to get the help message detailing the usage.

[guangzhaohui]

oh,let me try.
thank you very much!

[guangzhaohui]

How can i run pyradiomics.exe by jupyter notebook?

[guangzhaohui]

i open jupyter notebook it was the older one

[JoostJM]

See this section in the documentation on interactive usage