pyradiomics | source python package for the extraction of Radiomics | Machine Learning library
kandi X-RAY | pyradiomics Summary
kandi X-RAY | pyradiomics Summary
Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. Support:
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QUESTION
I have two files: one contains images, and the other includes segmentations. I could read both by running the following command:
...ANSWER
Answered 2021-Jul-01 at 19:46You have two file paths:
/Users/mostafa/Desktop/PyRadiomics/Labeled Segmentation/*
is the path for nrrd files.
/Users/mostafa/Desktop/PyRadiomics/Image/*
is the path for image files.
Your invalid path error is an nrrd file in the image directory, pyradiomics: error: unrecognized arguments: /Users/mostafa/Desktop/PyRadiomics/Image/CT_G0045.nrrd
An additional problem you may encounter is the space in your directory name. You should replace spaces with underscores or use quotes when constructing the command. Something like cmd='pyradiomics "'+file+'" "'+image_filenames[i]+'" -o results'+str(i)+'.csv -f csv'
should work.
QUESTION
I am trying to visualize features that were extracted from a dataset of CT-scans using radiomics. I extracted features using the Pyradiomics library, and now I have a few .csv
files.
I found this R Library which can read a dataset and generate images for it. Reading the dataset works according to plan using the input = import_pyradiomics(dir = "/path/to/datadir")
command, but when I try to visualize it using for instance plot_correlation_matrix(rdr = input, view_as = "heatmap")
, one of the visualization functions, I get the following error:
Error: $ operator not defined for this S4 class
I read about S3 and S4 classes, and I think that [line 160] in the library is where this error occurs first as it attempts to call this '$' operator. I am currently using R version 4.0.2. It seems to me like this issue is caused by this R library relying on an older version of R, but it is relatively up to date. What can I do to resolve this issue? Do I have to go in and manually change the code in the library? Or is there an easier fix, such as casting the S4 class to an S3 class? I feel like I'm missing an easy solution because I'm not familiar with R.
I found a similar question here, but it doesn't answer my specific question. Answers on other questions regarding this topic also do not work for me unfortunately.
...ANSWER
Answered 2020-Sep-08 at 21:04I am the developer of RadAR, thank you for your interest in our package. The issue was probably related to the use of a different version of the SummarizedExperiment R package. The bug has now been fixed. You can re-install the new version of RadAR from https://github.com/cgplab/RadAR. For any questions related to RadAR, please refer to the "issues" section of the RadAR github page.
QUESTION
I'm trying to install a package from Anaconda Cloud called pyradiomics. So I wrote this Dockerfile:
...ANSWER
Answered 2020-Aug-16 at 14:293.8 doesn't seem to be supportd as per https://pyradiomics.readthedocs.io/en/latest/installation.html#install-via-conda, though the 3.7 install conditions might contain an error.
In this case you can try to contact the authors or try with pip.
QUESTION
I'm trying to implement a GUI to assist some coworkers with image processing, but I am running into a problem with the Tkinter (ttk) progress bar, which keeps lagging while I execute work in another thread.
Basically, I want to have the progress bar run in indeterminate mode and bounce back and forth, as a kind of visual confirmation that things are still progressing (like the "working" circle in windows).
I set it up as follows:
...ANSWER
Answered 2020-Jan-24 at 20:27Okay, so after doing some research I found out that pyradiomics has a flag that prohibits this kind of rapid task switching, and therefore threading is not a viable solution. To solve the problem, as furas recommended, I implemented multiprocessing (pooling, in fact!). This not only allowed me to have the progress bar run without any lag, but also enabled dividing up the computation across cores, speeding up my implementation greatly. The syntax is very similar to that of threading, with one main exception that caused me a lot of grief before I figured it out. Variables are not inherited by child processes! Therefore, should I want to get a value from an Entry or something, I would have to explicitly pass it in to the child process. Past that, there really aren't that many changes. Instead of threading just use the associated process thing (Process instead of Thread, multiprocessing.Queue instead of queue). No lag, and greater efficiency!
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