pyradiomics | source python package for the extraction of Radiomics | Machine Learning library

 by   AIM-Harvard Jupyter Notebook Version: v3.0.1 License: BSD-3-Clause

kandi X-RAY | pyradiomics Summary

kandi X-RAY | pyradiomics Summary

pyradiomics is a Jupyter Notebook library typically used in Artificial Intelligence, Machine Learning, Deep Learning, Pytorch applications. pyradiomics has no bugs, it has no vulnerabilities, it has a Permissive License and it has medium support. You can download it from GitHub.

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. Support:
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            kandi-support Support

              pyradiomics has a medium active ecosystem.
              It has 892 star(s) with 439 fork(s). There are 48 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 87 open issues and 408 have been closed. On average issues are closed in 101 days. There are 7 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of pyradiomics is v3.0.1

            kandi-Quality Quality

              pyradiomics has 0 bugs and 0 code smells.

            kandi-Security Security

              pyradiomics has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              pyradiomics code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              pyradiomics is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              pyradiomics releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.
              It has 18422 lines of code, 412 functions and 44 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

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            pyradiomics Key Features

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            pyradiomics Examples and Code Snippets

            No Code Snippets are available at this moment for pyradiomics.

            Community Discussions

            QUESTION

            Loop for reading the content of two files
            Asked 2021-Jul-01 at 20:09

            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 19:46

            You 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.

            Source https://stackoverflow.com/questions/68215911

            QUESTION

            R: Error: $ operator not defined for this S4 class when using RadAR package
            Asked 2020-Sep-08 at 21:04

            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 21:04

            I 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.

            Source https://stackoverflow.com/questions/63269425

            QUESTION

            Why is conda rejecting every version of python I try?
            Asked 2020-Aug-16 at 14:29

            I'm trying to install a package from Anaconda Cloud called pyradiomics. So I wrote this Dockerfile:

            ...

            ANSWER

            Answered 2020-Aug-16 at 14:29

            3.8 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.

            Source https://stackoverflow.com/questions/63438022

            QUESTION

            Progress bar lagging with computationally intensive function on separate thread tkinter
            Asked 2020-Jan-24 at 20:27

            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 20:27

            Okay, 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!

            Source https://stackoverflow.com/questions/59867423

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install pyradiomics

            PyRadiomics is OS independent and compatible with Python >= 3.5. Pre-built binaries are available on PyPi and Conda. To install PyRadiomics, ensure you have python installed and run:. Detailed installation instructions, as well as instructions for building PyRadiomics from source, are available in the documentation.

            Support

            Please join the Radiomics community section of the 3D Slicer Discourse.
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            gh repo clone AIM-Harvard/pyradiomics

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