Additional functionality for use with fastai’s medical imaging module

Related tags

Deep Learning dicom medical-imaging
Overview

fmi

Adding additional functionality to fastai's medical imaging module

To learn more about medical imaging using Fastai you can view my blog

CI

fmi

Install

git clone https://github.com/asvcode/fmi.git

Tutorials

Medical Imaging Tutorial Updated

Bounding Box Generation

Explore & Preprocessing Tutorial

Dicom Splitter Examples

Signal Processing Tutorial Not Complete

Successfully merged updates with fastai.medical.imaging

Updates that have successfully merged with fastai.medical.imaging are displayed with:

merged

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Comments
  • Bump nokogiri from 1.10.8 to 1.11.4 in /docs

    Bump nokogiri from 1.10.8 to 1.11.4 in /docs

    Bumps nokogiri from 1.10.8 to 1.11.4.

    Release notes

    Sourced from nokogiri's releases.

    1.11.4 / 2021-05-14

    Security

    [CRuby] Vendored libxml2 upgraded to v2.9.12 which addresses:

    Note that two additional CVEs were addressed upstream but are not relevant to this release. CVE-2021-3516 via xmllint is not present in Nokogiri, and CVE-2020-7595 has been patched in Nokogiri since v1.10.8 (see #1992).

    Please see nokogiri/GHSA-7rrm-v45f-jp64 or #2233 for a more complete analysis of these CVEs and patches.

    Dependencies

    • [CRuby] vendored libxml2 is updated from 2.9.10 to 2.9.12. (Note that 2.9.11 was skipped because it was superseded by 2.9.12 a few hours after its release.)

    1.11.3 / 2021-04-07

    Fixed

    • [CRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this likely segfaulted. [#1900]
    • [JRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this raised a TypeError exception.
    • [CRuby] arm64/aarch64 systems (like Apple's M1) can now compile libxml2 and libxslt from source (though we continue to strongly advise users to install the native gems for the best possible experience)

    1.11.2 / 2021-03-11

    Fixed

    • [CRuby] NodeSet may now safely contain Node objects from multiple documents. Previously the GC lifecycle of the parent Document objects could lead to nodes being GCed while still in scope. [#1952]
    • [CRuby] Patch libxml2 to avoid "huge input lookup" errors on large CDATA elements. (See upstream GNOME/libxml2#200 and GNOME/libxml2!100.) [#2132].
    • [CRuby+Windows] Enable Nokogumbo (and other downstream gems) to compile and link against nokogiri.so by including LDFLAGS in Nokogiri::VERSION_INFO. [#2167]
    • [CRuby] {XML,HTML}::Document.parse now invokes #initialize exactly once. Previously #initialize was invoked twice on each object.
    • [JRuby] {XML,HTML}::Document.parse now invokes #initialize exactly once. Previously #initialize was not called, which was a problem for subclassing such as done by Loofah.

    Improved

    • Reduce the number of object allocations needed when parsing an HTML::DocumentFragment. [#2087] (Thanks, @​ashmaroli!)
    • [JRuby] Update the algorithm used to calculate Node#line to be wrong less-often. The underlying parser, Xerces, does not track line numbers, and so we've always used a hacky solution for this method. [#1223, #2177]
    • Introduce --enable-system-libraries and --disable-system-libraries flags to extconf.rb. These flags provide the same functionality as --use-system-libraries and the NOKOGIRI_USE_SYSTEM_LIBRARIES environment variable, but are more idiomatic. [#2193] (Thanks, @​eregon!)
    • [TruffleRuby] --disable-static is now the default on TruffleRuby when the packaged libraries are used. This is more flexible and compiles faster. (Note, though, that the default on TR is still to use system libraries.) [#2191, #2193] (Thanks, @​eregon!)

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.11.4 / 2021-05-14

    Security

    [CRuby] Vendored libxml2 upgraded to v2.9.12 which addresses:

    Note that two additional CVEs were addressed upstream but are not relevant to this release. CVE-2021-3516 via xmllint is not present in Nokogiri, and CVE-2020-7595 has been patched in Nokogiri since v1.10.8 (see #1992).

    Please see nokogiri/GHSA-7rrm-v45f-jp64 or #2233 for a more complete analysis of these CVEs and patches.

    Dependencies

    • [CRuby] vendored libxml2 is updated from 2.9.10 to 2.9.12. (Note that 2.9.11 was skipped because it was superseded by 2.9.12 a few hours after its release.)

    1.11.3 / 2021-04-07

    Fixed

    • [CRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this likely segfaulted. [#1900]
    • [JRuby] Passing non-Node objects to Document#root= now raises an ArgumentError exception. Previously this raised a TypeError exception.
    • [CRuby] arm64/aarch64 systems (like Apple's M1) can now compile libxml2 and libxslt from source (though we continue to strongly advise users to install the native gems for the best possible experience)

    1.11.2 / 2021-03-11

    Fixed

    • [CRuby] NodeSet may now safely contain Node objects from multiple documents. Previously the GC lifecycle of the parent Document objects could lead to nodes being GCed while still in scope. [#1952]
    • [CRuby] Patch libxml2 to avoid "huge input lookup" errors on large CDATA elements. (See upstream GNOME/libxml2#200 and GNOME/libxml2!100.) [#2132].
    • [CRuby+Windows] Enable Nokogumbo (and other downstream gems) to compile and link against nokogiri.so by including LDFLAGS in Nokogiri::VERSION_INFO. [#2167]
    • [CRuby] {XML,HTML}::Document.parse now invokes #initialize exactly once. Previously #initialize was invoked twice on each object.
    • [JRuby] {XML,HTML}::Document.parse now invokes #initialize exactly once. Previously #initialize was not called, which was a problem for subclassing such as done by Loofah.

    Improved

    • Reduce the number of object allocations needed when parsing an HTML::DocumentFragment. [#2087] (Thanks, @​ashmaroli!)
    • [JRuby] Update the algorithm used to calculate Node#line to be wrong less-often. The underlying parser, Xerces, does not track line numbers, and so we've always used a hacky solution for this method. [#1223, #2177]
    • Introduce --enable-system-libraries and --disable-system-libraries flags to extconf.rb. These flags provide the same functionality as --use-system-libraries and the NOKOGIRI_USE_SYSTEM_LIBRARIES environment variable, but are more idiomatic. [#2193] (Thanks, @​eregon!)
    • [TruffleRuby] --disable-static is now the default on TruffleRuby when the packaged libraries are used. This is more flexible and compiles faster. (Note, though, that the default on TR is still to use system libraries.) [#2191, #2193] (Thanks, @​eregon!)

    ... (truncated)

    Commits
    • 9d69b44 version bump to v1.11.4
    • 058e87f update CHANGELOG with complete CVE information
    • 9285251 Merge pull request #2234 from sparklemotion/2233-upgrade-to-libxml-2-9-12
    • 5436f61 update CHANGELOG
    • 761d320 patch: renumber libxml2 patches
    • 889ee2a test: update behavior of namespaces in HTML
    • 9751d85 test: remove low-value HTML::SAX::PushParser encoding test
    • 9fcb7d2 test: adjust xpath gc test to libxml2's max recursion depth
    • 1c99019 patch: backport libxslt configure.ac change for libxml2 config
    • 82a253f patch: fix isnan/isinf patch to apply cleanly to libxml 2.9.12
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump rexml from 3.2.4 to 3.2.5 in /docs

    Bump rexml from 3.2.4 to 3.2.5 in /docs

    Bumps rexml from 3.2.4 to 3.2.5.

    Changelog

    Sourced from rexml's changelog.

    3.2.5 - 2021-04-05 {#version-3-2-5}

    Improvements

    • Add more validations to XPath parser.

    • require "rexml/document" by default. [GitHub#36][Patch by Koichi ITO]

    • Don't add #dcloe method to core classes globally. [GitHub#37][Patch by Akira Matsuda]

    • Add more documentations. [Patch by Burdette Lamar]

    • Added REXML::Elements#parent. [GitHub#52][Patch by Burdette Lamar]

    Fixes

    Thanks

    • Koichi ITO

    • Akira Matsuda

    • Burdette Lamar

    • Juho Nurminen

    Commits
    • a622645 Add 3.2.5 entry
    • 3c137eb Fix a parser bug that some data may be ignored before DOCTYPE
    • 9b311e5 Fix a bug that invalid document declaration may be accepted
    • f9d88e4 Fix a bug that invalid document declaration may be generated
    • f7bab89 Fix a bug that invalid element end may be accepted
    • 6a250d2 Fix a bug that invalid element start may be accepted
    • 2fe62e2 Fix a bug that invalid notation declaration may be accepted
    • a659c63 Fix a bug that invalid notation declaration may be generated
    • 790dd11 Use ruby/setup-ruby (#66)
    • eda1b20 Clean up and enhance high-level RDoc (#65)
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 1
  • Bump nokogiri from 1.10.8 to 1.13.4 in /docs

    Bump nokogiri from 1.10.8 to 1.13.4 in /docs

    Bumps nokogiri from 1.10.8 to 1.13.4.

    Release notes

    Sourced from nokogiri's releases.

    1.13.4 / 2022-04-11

    Security

    Dependencies

    • [CRuby] Vendored zlib is updated from 1.2.11 to 1.2.12. (See LICENSE-DEPENDENCIES.md for details on which packages redistribute this library.)
    • [JRuby] Vendored Xerces-J (xerces:xercesImpl) is updated from 2.12.0 to 2.12.2.
    • [JRuby] Vendored nekohtml (org.cyberneko.html) is updated from a fork of 1.9.21 to 1.9.22.noko2. This fork is now publicly developed at https://github.com/sparklemotion/nekohtml

    sha256sum:

    095ff1995ed3dda3ea98a5f08bdc54bef02be1ce4e7c81034c4812e5e7c6e7e3  nokogiri-1.13.4-aarch64-linux.gem
7ebfc7415c819bcd4e849627e879cef2fb328bec90e802e50d74ccd13a60ec75  nokogiri-1.13.4-arm64-darwin.gem
41efd87c121991de26ef0393ac713d687e539813c3b79e454a2e3ffeecd107ea  nokogiri-1.13.4-java.gem
ab547504692ada0cec9d2e4e15afab659677c3f4c1ac3ea639bf5212b65246a1  nokogiri-1.13.4-x64-mingw-ucrt.gem
fa5c64cfdb71642ed647428e4d0d75ee0f4d189cfb63560c66fd8bdf99eb146b  nokogiri-1.13.4-x64-mingw32.gem
d6f07cbcbc28b75e8ac5d6e729ffba3602dffa0ad16ffac2322c9b4eb9b971fc  nokogiri-1.13.4-x86-linux.gem
0f7a4fd13e25abe3f98663fef0d115d58fdeff62cf23fef12d368e42adad2ce6  nokogiri-1.13.4-x86-mingw32.gem
3eef282f00ad360304fbcd5d72eb1710ff41138efda9513bb49eec832db5fa3e  nokogiri-1.13.4-x86_64-darwin.gem
3978610354ec67b59c128d23259c87b18374ee1f61cb9ed99de7143a88e70204  nokogiri-1.13.4-x86_64-linux.gem
0d46044eb39271e3360dae95ed6061ce17bc0028d475651dc48db393488c83bc  nokogiri-1.13.4.gem

    1.13.3 / 2022-02-21

    Fixed

    • [CRuby] Revert a HTML4 parser bug in libxml 2.9.13 (introduced in Nokogiri v1.13.2). The bug causes libxml2's HTML4 parser to fail to recover when encountering a bare < character in some contexts. This version of Nokogiri restores the earlier behavior, which is to recover from the parse error and treat the < as normal character data (which will be serialized as &lt; in a text node). The bug (and the fix) is only relevant when the RECOVER parse option is set, as it is by default. [#2461]

    SHA256 checksums:

    025a4e333f6f903072a919f5f75b03a8f70e4969dab4280375b73f9d8ff8d2c0  nokogiri-1.13.3-aarch64-linux.gem
b9cb59c6a6da8cf4dbee5dbb569c7cc95a6741392e69053544e0f40b15ab9ad5  nokogiri-1.13.3-arm64-darwin.gem
e55d18cee64c19d51d35ad80634e465dbcdd46ac4233cb42c1e410307244ebae  nokogiri-1.13.3-java.gem
53e2d68116cd00a873406b8bdb90c78a6f10e00df7ddf917a639ac137719b67b  nokogiri-1.13.3-x64-mingw-ucrt.gem
b5f39ebb662a1be7d1c61f8f0a2a683f1bb11690a6f00a99a1aa23a071f80145  nokogiri-1.13.3-x64-mingw32.gem
7c0de5863aace4bbbc73c4766cf084d1f0b7a495591e46d1666200cede404432  nokogiri-1.13.3-x86-linux.gem
</tr></table>

    ... (truncated)

    Changelog

    Sourced from nokogiri's changelog.

    1.13.4 / 2022-04-11

    Security

    Dependencies

    • [CRuby] Vendored zlib is updated from 1.2.11 to 1.2.12. (See LICENSE-DEPENDENCIES.md for details on which packages redistribute this library.)
    • [JRuby] Vendored Xerces-J (xerces:xercesImpl) is updated from 2.12.0 to 2.12.2.
    • [JRuby] Vendored nekohtml (org.cyberneko.html) is updated from a fork of 1.9.21 to 1.9.22.noko2. This fork is now publicly developed at https://github.com/sparklemotion/nekohtml

    1.13.3 / 2022-02-21

    Fixed

    • [CRuby] Revert a HTML4 parser bug in libxml 2.9.13 (introduced in Nokogiri v1.13.2). The bug causes libxml2's HTML4 parser to fail to recover when encountering a bare < character in some contexts. This version of Nokogiri restores the earlier behavior, which is to recover from the parse error and treat the < as normal character data (which will be serialized as &lt; in a text node). The bug (and the fix) is only relevant when the RECOVER parse option is set, as it is by default. [#2461]

    1.13.2 / 2022-02-21

    Security

    • [CRuby] Vendored libxml2 is updated from 2.9.12 to 2.9.13. This update addresses CVE-2022-23308.
    • [CRuby] Vendored libxslt is updated from 1.1.34 to 1.1.35. This update addresses CVE-2021-30560.

    Please see GHSA-fq42-c5rg-92c2 for more information about these CVEs.

    Dependencies

    1.13.1 / 2022-01-13

    Fixed

    • Fix Nokogiri::XSLT.quote_params regression in v1.13.0 that raised an exception when non-string stylesheet parameters were passed. Non-string parameters (e.g., integers and symbols) are now explicitly supported and both keys and values will be stringified with #to_s. [#2418]
    • Fix CSS selector query regression in v1.13.0 that raised an Nokogiri::XML::XPath::SyntaxError when parsing XPath attributes mixed into the CSS query. Although this mash-up of XPath and CSS syntax previously worked unintentionally, it is now an officially supported feature and is documented as such. [#2419]

    1.13.0 / 2022-01-06

    ... (truncated)

    Commits
    • 4e2c4b2 version bump to v1.13.4
    • 6a20ee4 Merge pull request #2510 from sparklemotion/flavorjones-encoding-reader-perfo...
    • b848031 Merge pull request #2509 from sparklemotion/flavorjones-parse-processing-inst...
    • c0ecf3b test: pend the LIBXML_LOADED_VERSION test on freebsd
    • e444525 fix(perf): HTML4::EncodingReader detection
    • 1eb5580 style(rubocop): allow intentional use of empty initializer
    • 0feac5a fix(dep): HTML parsing of processing instructions
    • db72b90 test: recent nekohtml versions do not consider 'a' to be inline
    • 2af2a87 style(rubocop): allow intentional use of empty initializer
    • ba7a28c Merge pull request #2499 from sparklemotion/2441-xerces-2.12.2-backport-v1.13.x
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 0
  • function

    function "check_duplicate", errors out in colab

    In colab, the file paths don't have "\", so in my case it is working now by replacing this line:

    fn = str(file).split('/')[-2], and

    ull = str(u).split('/')[-2]

    Kindly, update me about this.

    Thanks..

    enhancement 
    opened by m-ali-awan 1
Owner
Machine Learning Practitioner | Health Informatics | Advisor | Pharmacist
null
GitHub
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Pytorch Code for "Medical Transformer: Gated Axial-Attention for Medical Image Segmentation"

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The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

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