MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data.

Center for Computational Imaging and Personalized Diagnostics

Last update: Dec 2, 2022

Related tags

Deep Learning python machine-learning quality-control mri medical-imaging quality-assurance imaging quality-metrics medical-image-processing medical-physics

Overview

Front-end View

Backend View

Description
Prerequisites
Running
Basic Information
- Measurements
- User Interface
Feedback and usage

Description

This tool takes MRI datasets in the file formats (.dcm, .nii, .nii.gz or .mha) as the input.
Two Python scripts (QC.py and QCF.py) are used to generate several tags and noise/information measurements for quality assessment. These scripts save the calculated measures in a .tsv file as well as generate .png thumbnails for all images in a subject volume. These are then fed to .js scripts to create the user interface (index.html) output. A schematic illustrating the framework of the tool is as follows.

Prerequisites

The current version of the tool has been tested on the Python 3.6+
You must have pipenv installed on your environment to run MRQy locally. It will pull all the dependencies listed in the diagram.

You can also likely install the python requirements using something like:

pip3 install -r requirements.txt

Running

For local development, test that the code is functional

MRQy % pipenv shell
(mrqy) MRQy% pipenv install .
(mrqy) MRQy% python -m mrqy.QC --help

The output should be

usage: QC.py [-h] output_folder_name [inputdir [inputdir ...]]

positional arguments:
  output_folder_name  the subfolder name on the
                      '...\UserInterface\Data\output_folder_name' directory.
  inputdir            input foldername consists of *.mha (*.nii or *.dcm)
                      files. For example: 'E:\Data\Rectal\input_data_folder'

optional arguments:
  -h, --help          show this help message and exit

Standard usage is to run QC.py output_folder_name “input directory” i.e.

python QC.py output_folder_name "E:\Data\Rectal\RectalCancer_Multisite\input_data_folder"

There is no need to make a subfolder in the Data directory, just specify its name in the command as in the above code.
Every action will be printed in the output console.
The thumbnail images in the format of .png will be saved in "...\UserInterface\Data\output_folder_name" with its original filename as the subfolder name. Afterward, double click "index.html" (on e.g. "D:\Downloads\MRQy-master\UserInterface") to open front-end user interface, and select the respective results.tsv file from the correct location e.g. "D:\Downloads\MRQy-master\UserInterface\Data\output_folder_name" directory.

Contribution guidelines

Testing

MRQy % pipenv shell
(mrqy) MRQy% pipenv install .
(mrqy) MRQY% pipenv run -m pytest tests/

Building on Travis

The recommended path is to follow the Forking Workflow. Create a Travis CI build for your github fork to validate your fork before pushing a merge request to master.

Basic Information

Measurements

The measures of the MRQy tool are listed in the following table.

User Interface

The following figures show the user interface of the tool (index.html).

Feedback and usage

Please report and issues, bugfixes, ideas for enhancements via the "Issues" tab.

Detailed usage instructions and an example of using MRQy to analyze TCIA datasets are in the Wiki.

You can cite this in any associated publication as:
Sadri, AR, Janowczyk, A, Zou, R, Verma, R, Antunes, J, Madabhushi, A, Tiwari, P, Viswanath, SE, "MRQy: An Open-Source Tool for Quality Control of MR Imaging Data", https://arxiv.org/abs/2004.04871, 2020

If you do use the tool in your own work, please drop us a line to let us know.

Comments

ModuleNotFoundError: No module named 'QCF'

Hello,

I was getting the ModuleNotFoundError: No module named 'QCF' issue when running the test example python -m mrqy.QC --help.

I solved this by going into the virtual environment site-packages and editing line 11 on the QC.py to import mrqy.QCF as QCF, which solved my issue. I don't know if you ever run into anything like this. The package mrqy included both files, but I had to point it to the package itself to import QCF it looks like. I'm on python 3.6.8.

Cheers, Vasco

opened by vascosa 9
Parallel

In our study we have thousands of scan sessions and I would like to run these in parallel. It seems though that the results.tsv file gets newly remade with every parallel run of the program. Is there a way to append to it while running it simultaneously? it seems that in the participant folder only the png files are saved and not any participant data that can be extracted afterwards in one go. Thanks.

opened by kJONN 5
Front-end View Problem Loading Images

Hello,

It seems like the front-end view is only able to load images that are stored in the UserInterface subdirectory of the main MRQy directory. Is the front-end view supposed to be capable of loading images stored outside the UserInterface subdirectory, and if it is then how can those images be loaded?

Thanks, Josh

opened by jgilberstadt 4

DLL load failed while importing _remap - module not found

Hi!

While testing whether the code is functional (python -m mrqy.QC --help) I have run into a few problems.

The first error was "ModuleNotFoundError: No module named 'skimage' - Subsequently I ran pipenv install scikit-image
After installing the scikit-image package I received the error: ImportError: DLL load failed while importing _remap: the specified module could not be found. Based on this post: https://github.com/scikit-image/scikit-image/issues/4780 I ran pipenv install msvc-runtime, but am still getting the following error:

PS C:\Users\Mattea\MDACC\MRQy> pipenv install .
Installing ....
Adding mrqy to Pipfile's [packages]...
Installation Succeeded
Installing dependencies from Pipfile.lock (fd82fb)...
 ================================ 1/1 - 00:00:00
PS C:\Users\Mattea\MDACC\MRQy> python -m mrqy.QC --help
Traceback (most recent call last):
 File "C:\Users\Mattea\anaconda3\lib\runpy.py", line 194, in _run_module_as_main
   return _run_code(code, main_globals, None,
 File "C:\Users\Mattea\anaconda3\lib\runpy.py", line 87, in _run_code
   exec(code, run_globals)
 File "C:\Users\Mattea\.virtualenvs\MRQy-0a-sfUiD\lib\site-packages\mrqy\QC.py", line 11, in <module>
   import mrqy.QCF as QCF ## import QCF
 File "C:\Users\Mattea\.virtualenvs\MRQy-0a-sfUiD\lib\site-packages\mrqy\QCF.py", line 17, in <module>
   from skimage.filters import threshold_otsu
 File "C:\Users\Mattea\.virtualenvs\MRQy-0a-sfUiD\lib\site-packages\skimage\__init__.py", line 127, in <module>
   from .util.dtype import (img_as_float32,
 File "C:\Users\Mattea\.virtualenvs\MRQy-0a-sfUiD\lib\site-packages\skimage\util\__init__.py", line 17, in <module>
   from ._map_array import map_array
 File "C:\Users\Mattea\.virtualenvs\MRQy-0a-sfUiD\lib\site-packages\skimage\util\_map_array.py", line 2, in <module>
   from ._remap import _map_array
ImportError: DLL load failed while importing _remap: The specified module could not be found.

Any tips or suggestions would be greatly appreciated! Thanks, Mattea

opened by matteawelch 4

sample_size error

Hello everyone, I was trying to use your tool to analize some data but it seems I can't make it work. I have followed the steps in the wiki but theese are the outputs. I have also tried to manually insert the sample size value but the output is the same.

Python version is 3.6.9

Do you have any idea of what can it be? Thank you for your help.

opened by RiccardoPederzolli 3

File exists error when saving the thumbnails

Hi, I'm testing this tool in a folder structure organized as follows:

.
├── ID1
│   ├── CT1.nii
│   └── FLAIR.nii
└── ID2
    ├── CT1.nii
    └── FLAIR.nii

And I'm getting this error:

Traceback (most recent call last):
  File "QC.py", line 359, in <module>
    saveThumbnails_nondicom(v,fname_outdir)
  File "QC.py", line 181, in saveThumbnails_nondicom
    os.makedirs(output + os.sep + v[1])
  File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
FileExistsError: [Errno 17] File exists: '/Users/censored/mrqy/MRQy/src/mrqy/UserInterface/Data/Jun24test/CT1'

I believe the issue is that when saving the thumbnails, these are stored in a single, flat folder that doesn't follow the original tree structure, so the program finds that the "CT1" folder already exists:

.
├── CT1
│   ├── CT1(1).png
│   ├── CT1(10).png
│   ├── CT1(11).png
│   ├── CT1(12).png
│   ├── CT1(13).png
│   ├── CT1(14).png
│   ├── CT1(15).png
│   ├── CT1(16).png
│   ├── CT1(17).png
│   ├── CT1(18).png
│   ├── CT1(19).png
│   ├── CT1(2).png
│   ├── CT1(20).png
│   ├── CT1(21).png
│   ├── CT1(22).png
│   ├── CT1(23).png
│   ├── CT1(24).png
│   ├── CT1(25).png
│   ├── CT1(26).png
│   ├── CT1(27).png
│   ├── CT1(28).png
│   ├── CT1(29).png
│   ├── CT1(3).png
│   ├── CT1(4).png
│   ├── CT1(5).png
│   ├── CT1(6).png
│   ├── CT1(7).png
│   ├── CT1(8).png
│   └── CT1(9).png
├── FLAIR
│   ├── FLAIR(1).png
│   ├── FLAIR(10).png
│   ├── FLAIR(11).png
│   ├── FLAIR(12).png
│   ├── FLAIR(13).png
│   ├── FLAIR(14).png
│   ├── FLAIR(15).png
│   ├── FLAIR(16).png
│   ├── FLAIR(17).png
│   ├── FLAIR(18).png
│   ├── FLAIR(19).png
│   ├── FLAIR(2).png
│   ├── FLAIR(20).png
│   ├── FLAIR(21).png
│   ├── FLAIR(22).png
│   ├── FLAIR(23).png
│   ├── FLAIR(24).png
│   ├── FLAIR(25).png
│   ├── FLAIR(26).png
│   ├── FLAIR(27).png
│   ├── FLAIR(28).png
│   ├── FLAIR(29).png
│   ├── FLAIR(3).png
│   ├── FLAIR(4).png
│   ├── FLAIR(5).png
│   ├── FLAIR(6).png
│   ├── FLAIR(7).png
│   ├── FLAIR(8).png
│   └── FLAIR(9).png
└── results.tsv

Did you ever run into this issue? And, in general, what tree structure MRQy expects to work correctly? Is there an option to avoid saving the thumbnails?

Also, as a minor comment, the first lines in the output in this case reads:

MRQy is starting....
The number of patients is 4

But in reality, the number of patients is 2, while 4 is the number of series.

Thanks!

opened by giemmecci 2

Pipfile Typo

Hello,

I noticed that there is a single quote on line 17 of the pipfile that is supposed to be a double quote. I received an error message when running the original pipfile, but everything seems to work if the single quote is changed to a double quote.

Thanks, Josh

opened by jgilberstadt 2

Error running QC.py on brain scan.

Summary

Getting a value error when running QC.py on a sample brain scan.

Output

(MRQy-irixV0Tq) lodge@DESKTOP-TBEVFI2:~/code/MRQy$ python src/mrqy/QC.py ~/code/MRQy/output ~/code/MRQy/input
MRQy is starting....
The number of patients is 1
The number of 22 images are saved to /home/lodge/code/MRQy/UserInterface/Data//home/lodge/code/MRQy/output/Output_3D_File
1-1. The VRX of the patient with the name of <Output_3D_File> is 0.47
1-2. The VRY of the patient with the name of <Output_3D_File> is 0.47
1-3. The VRZ of the patient with the name of <Output_3D_File> is 5.00
1-4. The ROWS of the patient with the name of <Output_3D_File> is 512
1-5. The COLS of the patient with the name of <Output_3D_File> is 512
1-6. The NUM of the patient with the name of <Output_3D_File> is 22
1-7. The MEAN of the patient with the name of <Output_3D_File> is 264.68047264391714
1-8. The RNG of the patient with the name of <Output_3D_File> is 1217.0
1-9. The VAR of the patient with the name of <Output_3D_File> is 26972.86366286672
1-10. The CV of the patient with the name of <Output_3D_File> is 60.56001727509839
1-11. The CPP of the patient with the name of <Output_3D_File> is 0.0
1-12. The PSNR of the patient with the name of <Output_3D_File> is 16.035276287657798
1-13. The SNR1 of the patient with the name of <Output_3D_File> is 21.97046333358044
1-14. The SNR2 of the patient with the name of <Output_3D_File> is 115.58171760174017
1-15. The SNR3 of the patient with the name of <Output_3D_File> is 4.875157085735123
1-16. The SNR4 of the patient with the name of <Output_3D_File> is 16.6181236994002
1-17. The CNR of the patient with the name of <Output_3D_File> is 15.726563711378503
1-18. The CVP of the patient with the name of <Output_3D_File> is 0.2720244069104087
1-19. The CJV of the patient with the name of <Output_3D_File> is 0.6383621489661986
1-20. The EFC of the patient with the name of <Output_3D_File> is 2.1080743214048123
1-21. The FBER of the patient with the name of <Output_3D_File> is 0.0
The results are updated.
Traceback (most recent call last):
  File "src/mrqy/QC.py", line 369, in <module>
    df = cleanup(address, 30)
  File "src/mrqy/QC.py", line 228, in cleanup
    tsne_umap(df, per)
  File "src/mrqy/QC.py", line 217, in tsne_umap
    tsne_obj = tsne.fit_transform(ds)
  File "/home/lodge/.local/share/virtualenvs/MRQy-irixV0Tq/lib/python3.8/site-packages/sklearn/manifold/_t_sne.py", line 932, in fit_transform
    embedding = self._fit(X)
  File "/home/lodge/.local/share/virtualenvs/MRQy-irixV0Tq/lib/python3.8/site-packages/sklearn/manifold/_t_sne.py", line 702, in _fit
    X = self._validate_data(X, accept_sparse=['csr'],
  File "/home/lodge/.local/share/virtualenvs/MRQy-irixV0Tq/lib/python3.8/site-packages/sklearn/base.py", line 421, in _validate_data
    X = check_array(X, **check_params)
  File "/home/lodge/.local/share/virtualenvs/MRQy-irixV0Tq/lib/python3.8/site-packages/sklearn/utils/validation.py", line 63, in inner_f
    return f(*args, **kwargs)
  File "/home/lodge/.local/share/virtualenvs/MRQy-irixV0Tq/lib/python3.8/site-packages/sklearn/utils/validation.py", line 726, in check_array
    raise ValueError("Found array with %d sample(s) (shape=%s) while a"
ValueError: Found array with 1 sample(s) (shape=(1, 21)) while a minimum of 2 is required.

Sample Data

This is the image upon which it fails: Output_3D_File.nii.gz

opened by nathanhillyer 2

Lung MRI project

Hello

I am trying to apply your tool for the Lung MR imaging. I has been looking for a tool to get some quantitative values such as SNR, CNR from the before and after denoising to Lung MR images. And finally, your MRQy gives me what I've been looking for. Yes, it works very successfully. ( thank you again for your great work!!) But I think I'd better to check (because it's Lung MR , zero TE image) whether it selects lung correctly. I just want to see overlay mask to see what's selected for foreground iamges because...the Lung itself has lower signal compare to the other surrounding muscle and fat. Please check the Lung MR images if you want, "Comparison of lung imaging using three-dimensional ultrashort echo time and zero echo time sequences: preliminary study"

At this point, I wonder if there is any way to extract the"selected foreground and background boundary, overlay mask" , Also, can I extract "MEAN of background" with MEAN of foreground , together ? Those two information will be important to check whether it successfully worked to the Lung MR or not.

Any comment and advice would be very appreciated. best regards Moonjung

opened by aranmaro 2
Bump numpy from 1.20.1 to 1.21.0
Bumps numpy from 1.20.1 to 1.21.0.

Release notes

Sourced from numpy's releases.

v1.21.0

NumPy 1.21.0 Release Notes

The NumPy 1.21.0 release highlights are

continued SIMD work covering more functions and platforms,

initial work on the new dtype infrastructure and casting,

universal2 wheels for Python 3.8 and Python 3.9 on Mac,

improved documentation,

improved annotations,

new PCG64DXSM bitgenerator for random numbers.

In addition there are the usual large number of bug fixes and other improvements.

The Python versions supported for this release are 3.7-3.9. Official support for Python 3.10 will be added when it is released.

:warning: Warning: there are unresolved problems compiling NumPy 1.21.0 with gcc-11.1 .

Optimization level -O3 results in many wrong warnings when running the tests.

On some hardware NumPy will hang in an infinite loop.

New functions

Add PCG64DXSM BitGenerator

Uses of the PCG64 BitGenerator in a massively-parallel context have been shown to have statistical weaknesses that were not apparent at the first release in numpy 1.17. Most users will never observe this weakness and are safe to continue to use PCG64. We have introduced a new PCG64DXSM BitGenerator that will eventually become the new default BitGenerator implementation used by default_rng in future releases. PCG64DXSM solves the statistical weakness while preserving the performance and the features of PCG64.

See upgrading-pcg64 for more details.

(gh-18906)

Expired deprecations

The shape argument numpy.unravel_index cannot be passed as dims keyword argument anymore. (Was deprecated in NumPy 1.16.)

... (truncated)

Commits

b235f9e Merge pull request #19283 from charris/prepare-1.21.0-release

34aebc2 MAINT: Update 1.21.0-notes.rst

493b64b MAINT: Update 1.21.0-changelog.rst

07d7e72 MAINT: Remove accidentally created directory.

032fca5 Merge pull request #19280 from charris/backport-19277

7d25b81 BUG: Fix refcount leak in ResultType

fa5754e BUG: Add missing DECREF in new path

61127bb Merge pull request #19268 from charris/backport-19264

143d45f Merge pull request #19269 from charris/backport-19228

d80e473 BUG: Removed typing for == and != in dtypes

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dependencies
opened by dependabot[bot] 1
Bump pillow from 8.2.0 to 9.0.0
Bumps pillow from 8.2.0 to 9.0.0.

Release notes

Sourced from pillow's releases.

9.0.0

https://pillow.readthedocs.io/en/stable/releasenotes/9.0.0.html

Changes

Restrict builtins for ImageMath.eval() #5923 [@radarhere]

Ensure JpegImagePlugin stops at the end of a truncated file #5921 [@radarhere]

Fixed ImagePath.Path array handling #5920 [@radarhere]

Remove consecutive duplicate tiles that only differ by their offset #5919 [@radarhere]

Removed redundant part of condition #5915 [@radarhere]

Explicitly enable strip chopping for large uncompressed TIFFs #5517 [@kmilos]

Use the Windows method to get TCL functions on Cygwin #5807 [@DWesl]

Changed error type to allow for incremental WebP parsing #5404 [@radarhere]

Improved I;16 operations on big endian #5901 [@radarhere]

Ensure that BMP pixel data offset does not ignore palette #5899 [@radarhere]

Limit quantized palette to number of colors #5879 [@radarhere]

Use latin1 encoding to decode bytes #5870 [@radarhere]

Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [@radarhere]

When saving RGBA to GIF, make use of first transparent palette entry #5859 [@radarhere]

Pass SAMPLEFORMAT to libtiff #5848 [@radarhere]

Added rounding when converting P and PA #5824 [@radarhere]

Improved putdata() documentation and data handling #5910 [@radarhere]

Exclude carriage return in PDF regex to help prevent ReDoS #5912 [@radarhere]

Image.NONE is only used for resampling and dithers #5908 [@radarhere]

Fixed freeing pointer in ImageDraw.Outline.transform #5909 [@radarhere]

Add Tidelift alignment action and badge #5763 [@aclark4life]

Replaced further direct invocations of setup.py #5906 [@radarhere]

Added ImageShow support for xdg-open #5897 [@m-shinder]

Fixed typo #5902 [@radarhere]

Switched from deprecated "setup.py install" to "pip install ." #5896 [@radarhere]

Support 16-bit grayscale ImageQt conversion #5856 [@cmbruns]

Fixed raising OSError in _safe_read when size is greater than SAFEBLOCK #5872 [@radarhere]

Convert subsequent GIF frames to RGB or RGBA #5857 [@radarhere]

WebP: Fix memory leak during decoding on failure #5798 [@ilai-deutel]

Do not prematurely return in ImageFile when saving to stdout #5665 [@infmagic2047]

Added support for top right and bottom right TGA orientations #5829 [@radarhere]

Corrected ICNS file length in header #5845 [@radarhere]

Block tile TIFF tags when saving #5839 [@radarhere]

Added line width argument to ImageDraw polygon #5694 [@radarhere]

Do not redeclare class each time when converting to NumPy #5844 [@radarhere]

Only prevent repeated polygon pixels when drawing with transparency #5835 [@radarhere]

Fix pushes_fd method signature #5833 [@hoodmane]

Add support for pickling TrueType fonts #5826 [@hugovk]

Only prefer command line tools SDK on macOS over default MacOSX SDK #5828 [@radarhere]

Fix compilation on 64-bit Termux #5793 [@landfillbaby]

Replace 'setup.py sdist' with '-m build --sdist' #5785 [@hugovk]

Use declarative package configuration #5784 [@hugovk]

Use title for display in ImageShow #5788 [@radarhere]

Fix for PyQt6 #5775 [@hugovk]

... (truncated)

Changelog

Sourced from pillow's changelog.

9.0.0 (2022-01-02)

Restrict builtins for ImageMath.eval(). CVE-2022-22817 #5923 [radarhere]

Ensure JpegImagePlugin stops at the end of a truncated file #5921 [radarhere]

Fixed ImagePath.Path array handling. CVE-2022-22815, CVE-2022-22816 #5920 [radarhere]

Remove consecutive duplicate tiles that only differ by their offset #5919 [radarhere]

Improved I;16 operations on big endian #5901 [radarhere]

Limit quantized palette to number of colors #5879 [radarhere]

Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [radarhere]

When saving RGBA to GIF, make use of first transparent palette entry #5859 [radarhere]

Pass SAMPLEFORMAT to libtiff #5848 [radarhere]

Added rounding when converting P and PA #5824 [radarhere]

Improved putdata() documentation and data handling #5910 [radarhere]

Exclude carriage return in PDF regex to help prevent ReDoS #5912 [hugovk]

Fixed freeing pointer in ImageDraw.Outline.transform #5909 [radarhere]

Added ImageShow support for xdg-open #5897 [m-shinder, radarhere]

Support 16-bit grayscale ImageQt conversion #5856 [cmbruns, radarhere]

Convert subsequent GIF frames to RGB or RGBA #5857 [radarhere]

... (truncated)

Commits

82541b6 9.0.0 version bump

cae5ac4 Merge pull request #5924 from radarhere/cves

ed4cf78 CVEs TBD

d7f60d1 Merge pull request #5923 from radarhere/imagemath_eval

8531b01 Restrict builtins for ImageMath.eval

1efb1d9 Merge pull request #5922 from radarhere/releasenotes

f6c7871 Added release notes for #5919, #5920 and #5921

032d2dc Update CHANGES.rst [ci skip]

baae9ec Merge pull request #5921 from radarhere/jpeg_eoi

1059eb5 If appended EOI did not work, do not keep trying

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dependencies
opened by dependabot[bot] 1
Bump setuptools from 60.9.3 to 65.5.1
Bumps setuptools from 60.9.3 to 65.5.1.

Release notes

Sourced from setuptools's releases.

v65.5.1

No release notes provided.

v65.5.0

No release notes provided.

v65.4.1

No release notes provided.

v65.4.0

No release notes provided.

v65.3.0

No release notes provided.

v65.2.0

No release notes provided.

v65.1.1

No release notes provided.

v65.1.0

No release notes provided.

v65.0.2

No release notes provided.

v65.0.1

No release notes provided.

v65.0.0

No release notes provided.

v64.0.3

No release notes provided.

v64.0.2

No release notes provided.

v64.0.1

No release notes provided.

v64.0.0

No release notes provided.

v63.4.3

No release notes provided.

v63.4.2

No release notes provided.

... (truncated)

Changelog

Sourced from setuptools's changelog.

v65.5.1

Misc ^^^^

#3638: Drop a test dependency on the mock package, always use :external+python:py:mod:unittest.mock -- by :user:hroncok

#3659: Fixed REDoS vector in package_index.

v65.5.0

Changes ^^^^^^^

#3624: Fixed editable install for multi-module/no-package src-layout projects.

#3626: Minor refactorings to support distutils using stdlib logging module.

Documentation changes ^^^^^^^^^^^^^^^^^^^^^

#3419: Updated the example version numbers to be compliant with PEP-440 on the "Specifying Your Project’s Version" page of the user guide.

Misc ^^^^

#3569: Improved information about conflicting entries in the current working directory and editable install (in documentation and as an informational warning).

#3576: Updated version of validate_pyproject.

v65.4.1

Misc ^^^^

#3613: Fixed encoding errors in expand.StaticModule when system default encoding doesn't match expectations for source files.

#3617: Merge with pypa/distutils@6852b20 including fix for pypa/distutils#181.

v65.4.0

Changes ^^^^^^^

#3609: Merge with pypa/distutils@d82d926 including support for DIST_EXTRA_CONFIG in pypa/distutils#177.

v65.3.0

... (truncated)

Commits

a462cb5 Bump version: 65.5.0 → 65.5.1

de35d8b Merge pull request #3656 from bmorris3/typos

58e23de Update changelog. Ref #3659.

43a9c9b Limit the amount of whitespace to search/backtrack. Fixes #3659.

5791343 Add test capturing failed expectation. Ref #3659.

1f97905 ⚫ Fade to black.

6254567 Remove workaround for emacs.

729b180 ⚫ Fade to black.

c068081 Typo corrections

f777a40 Suppress deprecation warning in --rsyncdir. Workaround for #3655.

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dependencies
opened by dependabot[bot] 0
Bump pillow from 9.0.1 to 9.3.0
Bumps pillow from 9.0.1 to 9.3.0.

Release notes

Sourced from pillow's releases.

9.3.0

https://pillow.readthedocs.io/en/stable/releasenotes/9.3.0.html

Changes

Initialize libtiff buffer when saving #6699 [@radarhere]

Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [@wiredfool]

Inline fname2char to fix memory leak #6329 [@nulano]

Fix memory leaks related to text features #6330 [@nulano]

Use double quotes for version check on old CPython on Windows #6695 [@hugovk]

GHA: replace deprecated set-output command with GITHUB_OUTPUT file #6697 [@nulano]

Remove backup implementation of Round for Windows platforms #6693 [@cgohlke]

Upload fribidi.dll to GitHub Actions #6532 [@nulano]

Fixed set_variation_by_name offset #6445 [@radarhere]

Windows build improvements #6562 [@nulano]

Fix malloc in _imagingft.c:font_setvaraxes #6690 [@cgohlke]

Only use ASCII characters in C source file #6691 [@cgohlke]

Release Python GIL when converting images using matrix operations #6418 [@hmaarrfk]

Added ExifTags enums #6630 [@radarhere]

Do not modify previous frame when calculating delta in PNG #6683 [@radarhere]

Added support for reading BMP images with RLE4 compression #6674 [@npjg]

Decode JPEG compressed BLP1 data in original mode #6678 [@radarhere]

pylint warnings #6659 [@marksmayo]

Added GPS TIFF tag info #6661 [@radarhere]

Added conversion between RGB/RGBA/RGBX and LAB #6647 [@radarhere]

Do not attempt normalization if mode is already normal #6644 [@radarhere]

Fixed seeking to an L frame in a GIF #6576 [@radarhere]

Consider all frames when selecting mode for PNG save_all #6610 [@radarhere]

Don't reassign crc on ChunkStream close #6627 [@radarhere]

Raise a warning if NumPy failed to raise an error during conversion #6594 [@radarhere]

Only read a maximum of 100 bytes at a time in IMT header #6623 [@radarhere]

Show all frames in ImageShow #6611 [@radarhere]

Allow FLI palette chunk to not be first #6626 [@radarhere]

If first GIF frame has transparency for RGB_ALWAYS loading strategy, use RGBA mode #6592 [@radarhere]

Round box position to integer when pasting embedded color #6517 [@radarhere]

Removed EXIF prefix when saving WebP #6582 [@radarhere]

Pad IM palette to 768 bytes when saving #6579 [@radarhere]

Added DDS BC6H reading #6449 [@ShadelessFox]

Added support for opening WhiteIsZero 16-bit integer TIFF images #6642 [@JayWiz]

Raise an error when allocating translucent color to RGB palette #6654 [@jsbueno]

Moved mode check outside of loops #6650 [@radarhere]

Added reading of TIFF child images #6569 [@radarhere]

Improved ImageOps palette handling #6596 [@PososikTeam]

Defer parsing of palette into colors #6567 [@radarhere]

Apply transparency to P images in ImageTk.PhotoImage #6559 [@radarhere]

Use rounding in ImageOps contain() and pad() #6522 [@bibinhashley]

Fixed GIF remapping to palette with duplicate entries #6548 [@radarhere]

Allow remap_palette() to return an image with less than 256 palette entries #6543 [@radarhere]

Corrected BMP and TGA palette size when saving #6500 [@radarhere]

... (truncated)

Changelog

Sourced from pillow's changelog.

9.3.0 (2022-10-29)

Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [wiredfool]

Initialize libtiff buffer when saving #6699 [radarhere]

Inline fname2char to fix memory leak #6329 [nulano]

Fix memory leaks related to text features #6330 [nulano]

Use double quotes for version check on old CPython on Windows #6695 [hugovk]

Remove backup implementation of Round for Windows platforms #6693 [cgohlke]

Fixed set_variation_by_name offset #6445 [radarhere]

Fix malloc in _imagingft.c:font_setvaraxes #6690 [cgohlke]

Release Python GIL when converting images using matrix operations #6418 [hmaarrfk]

Added ExifTags enums #6630 [radarhere]

Do not modify previous frame when calculating delta in PNG #6683 [radarhere]

Added support for reading BMP images with RLE4 compression #6674 [npjg, radarhere]

Decode JPEG compressed BLP1 data in original mode #6678 [radarhere]

Added GPS TIFF tag info #6661 [radarhere]

Added conversion between RGB/RGBA/RGBX and LAB #6647 [radarhere]

Do not attempt normalization if mode is already normal #6644 [radarhere]

... (truncated)

Commits

d594f4c Update CHANGES.rst [ci skip]

909dc64 9.3.0 version bump

1a51ce7 Merge pull request #6699 from hugovk/security-libtiff_buffer

2444cdd Merge pull request #6700 from hugovk/security-samples_per_pixel-sec

744f455 Added release notes

0846bfa Add to release notes

799a6a0 Fix linting

00b25fd Hide UserWarning in logs

05b175e Tighter test case

13f2c5a Prevent DOS with large SAMPLESPERPIXEL in Tiff IFD

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dependencies
opened by dependabot[bot] 0
QC.py npt recognized

This looks great and exactly what I need, but can't get past the install. I'm using Ubuntu 20.04, python 3.8

I followed the README instructions and I can launch the shell - setting up in my home .local directory .local/share/virtualenvs/MRQy-yxYQvYdT/bin/activate

I can install mrqy pipenv install . Installing .... Adding mrqy to Pipfile's [packages]... ✔ Installation Succeeded Installing dependencies from Pipfile.lock (829554)...

and I can get the help to output to the screen python -m mrqy.QC --help usage: QC.py [-h] [-r R] [-s S] [-b B] [-u U] [-t T] [-c C] output_folder_name [inputdir [inputdir ...]]

But, when I try to run "pipenv run -m pytest tests/" I get "Error: the command -m could not be found within PATH or Pipfile's [scripts]."

What PATH variable is it looking for? There seems to be a PATH that was created in the .local/share/virtualenvs directory

Any help would be greatly appreciated. And, yes, I did pip install the requirements.txt without issue.

opened by drkitty28 18
Bump joblib from 1.1.0 to 1.2.0
Bumps joblib from 1.1.0 to 1.2.0.

Changelog

Sourced from joblib's changelog.

Release 1.2.0

Fix a security issue where eval(pre_dispatch) could potentially run arbitrary code. Now only basic numerics are supported. joblib/joblib#1327

Make sure that joblib works even when multiprocessing is not available, for instance with Pyodide joblib/joblib#1256

Avoid unnecessary warnings when workers and main process delete the temporary memmap folder contents concurrently. joblib/joblib#1263

Fix memory alignment bug for pickles containing numpy arrays. This is especially important when loading the pickle with mmap_mode != None as the resulting numpy.memmap object would not be able to correct the misalignment without performing a memory copy. This bug would cause invalid computation and segmentation faults with native code that would directly access the underlying data buffer of a numpy array, for instance C/C++/Cython code compiled with older GCC versions or some old OpenBLAS written in platform specific assembly. joblib/joblib#1254

Vendor cloudpickle 2.2.0 which adds support for PyPy 3.8+.

Vendor loky 3.3.0 which fixes several bugs including:

robustly forcibly terminating worker processes in case of a crash (joblib/joblib#1269);

avoiding leaking worker processes in case of nested loky parallel calls;

reliability spawn the correct number of reusable workers.

Commits

5991350 Release 1.2.0

3fa2188 MAINT cleanup numpy warnings related to np.matrix in tests (#1340)

cea26ff CI test the future loky-3.3.0 branch (#1338)

8aca6f4 MAINT: remove pytest.warns(None) warnings in pytest 7 (#1264)

067ed4f XFAIL test_child_raises_parent_exits_cleanly with multiprocessing (#1339)

ac4ebd5 MAINT add back pytest warnings plugin (#1337)

a23427d Test child raises parent exits cleanly more reliable on macos (#1335)

ac09691 [MAINT] various test updates (#1334)

4a314b1 Vendor loky 3.2.0 (#1333)

bdf47e9 Make test_parallel_with_interactively_defined_functions_default_backend timeo...

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dependencies
opened by dependabot[bot] 0
Bump numpy from 1.20.1 to 1.22.0
Bumps numpy from 1.20.1 to 1.22.0.

Release notes

Sourced from numpy's releases.

v1.22.0

NumPy 1.22.0 Release Notes

NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.

A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.

NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.

New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.

A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

Expired deprecations

Deprecated numeric style dtype strings have been removed

Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

(gh-19539)

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

(gh-19615)

... (truncated)

Commits

4adc87d Merge pull request #20685 from charris/prepare-for-1.22.0-release

fd66547 REL: Prepare for the NumPy 1.22.0 release.

125304b wip

c283859 Merge pull request #20682 from charris/backport-20416

5399c03 Merge pull request #20681 from charris/backport-20954

f9c45f8 Merge pull request #20680 from charris/backport-20663

794b36f Update armccompiler.py

d93b14e Update test_public_api.py

7662c07 Update init.py

311ab52 Update armccompiler.py

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dependencies
opened by dependabot[bot] 0
4D datasets

Hi Amir,

Can the tool also deal with 4D datasets (e.g. fMRI)? I find that matplotlib returns an error ('Third dimension must be 3 or 4') when the input is 4D.

Am I missing something here?

Thanks!

opened by fotaras-github 6

Releases(v2022.04)

v2022.04(Apr 13, 2022)

Updating release to latest version of MRQy source.
Source code(tar.gz)
Source code(zip)
v2021.05(May 11, 2021)

Generating an initial release based on current working version of MRQy tool.
Source code(tar.gz)
Source code(zip)