[bug#55989] [PATCH 1/2] gnu: Add python-pydicom.

[bug#55989] [PATCH 1/2] gnu: Add python-pydicom.

[Antero Mejr via Guix-patches via]

* gnu/packages/python-science.scm (python-pydicom): New variable.
---
 gnu/packages/python-science.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 0684826a6c..08359515d5 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -20,6 +20,7 @@
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
 ;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
+;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -46,6 +47,7 @@ (define-module (gnu packages python-science)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
@@ -1367,3 +1369,38 @@ (define-public python-gpy
 Python, from the Sheffield machine learning group.  GPy implements a range of
 machine learning algorithms based on GPs.")
     (license license:bsd-3)))
+
+(define-public python-pydicom
+  (package
+    (name "python-pydicom")
+    (version "2.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pydicom/pydicom")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      ;; 181 failed, 2235 pass. Pulls test datasets off the web, no-go for Guix
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (chdir "pydicom/tests")
+               (invoke "python3" "-m" "pytest")))))))
+    (native-inputs (list python-pytest))
+    (inputs (list gdcm libjpeg-turbo))
+    (propagated-inputs (list python-numpy python-pillow))
+    (home-page "https://github.com/pydicom/pydicom")
+    (synopsis "Pure Python package for reading and writing DICOM data")
+    (description "pydicom provides a pure Python package for reading and
+writing DICOM medical imaging data. It lets developers read, modify and write
+DICOM data in a pythonic way.")
+    (license license:expat)))
-- 
2.36.1

[bug#55988] [PATCH 2/2] gnu: Add gdcm.

[Antero Mejr via Guix-patches via]

* gnu/packages/bioinformatics.scm (gdcm): New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87df6c3515..d151172725 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23,6 +23,7 @@
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -15745,3 +15746,33 @@ (define-public wfmash
 module capable of computing base-level alignments for very large sequences.")
     (home-page "https://github.com/ekg/wfmash")
     (license license:expat)))
+
+(define-public gdcm
+  (package
+    (name "gdcm")
+    (version "2.8.9")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/malaterre/gdcm")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0v8ggym2kz26rwyvsyy3mg7j5jbvd1pz5cwchh29iyclagf0l9ry"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      ;; dev claims release branches (even numbered minor rev) don't need tests
+      ;; so the check step is not generated
+      #:tests? #f)) ;see CMakeLists.txt
+    (home-page "http://gdcm.sourceforge.net/wiki/index.php/Main_Page")
+    (synopsis "Grassroots DICOM library")
+    (description
+     "Grassroots DICOM (GDCM) is an implementation of the DICOM
+standard designed to be open source so that researchers may access clinical
+data directly. GDCM includes a file format definition and a network
+communications protocol, both of which should be extended to provide a full set
+of tools for a researcher or small medical imaging vendor to interface with an
+existing medical database.")
+    (license license:bsd-2)))
-- 
2.36.1

[bug#55989] [PATCH 1/2] gnu: Add python-pydicom.

[Maxime Devos]

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Antero Mejr via Guix-patches via schreef op wo 15-06-2022 om 01:27
[+0000]:
> +      ;; 181 failed, 2235 pass. Pulls test datasets off the web, no-go for Guix
> +      #:tests? #f

How about only disabling tests that download from the web?
Are all of these test failures due to downloading from the web or are
there some other tests too?

> +    (synopsis "Pure Python package for reading and writing DICOM data")

Unlike some language-specific package managers, Guix supports using dependents
from other languages without any complications, so no need to mention ‘Pure’
here.

> + pydicom provides a pure Python package

It doesn't provide a Python package, it is a Python package, especially if pydicom
is replaced by @code{python-pydicom}.

Greetings,
Maxime.
 

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[bug#55989] [PATCH 1/2] gnu: Add python-pydicom.

[Antero Mejr via Guix-patches via]

Maxime Devos <maximedevos@telenet.be> writes:

> How about only disabling tests that download from the web?
> Are all of these test failures due to downloading from the web or are
> there some other tests too?

Sure, see updated patch. I looked through the error log to confirm
that the tests were failing due to missing data. I also did an
end-to-end test of pydicom by importing it, then reading/writing
a DICOM file.

>
>> +    (synopsis "Pure Python package for reading and writing DICOM data")
>
> Unlike some language-specific package managers, Guix supports using dependents
> from other languages without any complications, so no need to mention ‘Pure’
> here.
>

OK, updated.

>> + pydicom provides a pure Python package
>
> It doesn't provide a Python package, it is a Python package, especially if pydicom
> is replaced by @code{python-pydicom}.
>

Updated.

[bug#55989] [PATCH 1/2] gnu: Add python-pydicom.

[Antero Mejr via Guix-patches via]

Updated to add tests that don't use web resources.
Tested using the example code, reading/writing a dicom file and accessing
the pixel_array using numpy.

* gnu/packages/python-science.scm (python-pydicom): New variable.
---
 gnu/packages/python-science.scm | 51 +++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 0684826a6c..d26d3bc9b4 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -20,6 +20,7 @@
 ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
 ;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
+;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -46,6 +47,7 @@ (define-module (gnu packages python-science)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
@@ -1367,3 +1369,52 @@ (define-public python-gpy
 Python, from the Sheffield machine learning group.  GPy implements a range of
 machine learning algorithms based on GPs.")
     (license license:bsd-3)))
+
+(define-public python-pydicom
+  (package
+    (name "python-pydicom")
+    (version "2.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pydicom/pydicom")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (chdir "pydicom/tests")
+               (invoke "python3" "-m" "pytest" "-k" ;skip tests using web data
+                       (string-append
+                        "not test_jpeg_ls_pixel_data.py"
+                        " and not test_gdcm_pixel_data.py"
+                        " and not test_pillow_pixel_data.py"
+                        " and not test_rle_pixel_data.py"
+                        " and not Test_JPEG_LS_Lossless_transfer_syntax"
+                        " and not test_numpy_pixel_data.py"
+                        " and not test_data_manager.py"
+                        " and not test_handler_util.py"
+                        " and not test_overlay_np.py"
+                        " and not test_encoders_pydicom.py"
+                        " and not test_encaps.py"
+                        " and not test_reading_ds_with_known_tags_with_UN_VR"
+                        " and not TestDatasetOverlayArray"
+                        " and not TestReader"
+                        " and not test_filewriter.py"))))))))
+    (native-inputs (list python-pytest))
+    (inputs (list gdcm libjpeg-turbo))
+    (propagated-inputs (list python-numpy python-pillow))
+    (home-page "https://github.com/pydicom/pydicom")
+    (synopsis "Python library for reading and writing DICOM data")
+    (description "@code{python-pydicom} is a Python library for reading
+and writing DICOM medical imaging data. It lets developers read, modify and
+write DICOM data in a pythonic way.")
+    (license license:expat)))
-- 
2.36.1

[bug#55989] [PATCH 2/2] gnu: Add gdcm.

[Antero Mejr via Guix-patches via]

Here's the updated GDCM patch, which is a dependency.

* gnu/packages/bioinformatics.scm (gdcm): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87df6c3515..2c9f3b4a6f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23,6 +23,7 @@
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -15745,3 +15746,39 @@ (define-public wfmash
 module capable of computing base-level alignments for very large sequences.")
     (home-page "https://github.com/ekg/wfmash")
     (license license:expat)))
+
+(define-public gdcm
+  (package
+    (name "gdcm")
+    (version "2.8.9")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/malaterre/gdcm")
+                    (commit (string-append "v" version))
+                    (recursive? #t)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0v8ggym2kz26rwyvsyy3mg7j5jbvd1pz5cwchh29iyclagf0l9ry"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DGDCM_BUILD_TESTING=true"
+              (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;"
+                             "'TestFileMetaInformation"
+                             "|TestElement2"
+                             "|TestSCUValidation"
+                             "|TestEcho"
+                             "|TestFind'"))))
+    (home-page "http://gdcm.sourceforge.net/wiki/index.php/Main_Page")
+    (synopsis "Grassroots DICOM library")
+    (description
+     "Grassroots DICOM (GDCM) is an implementation of the DICOM
+standard designed to be open source so that researchers may access clinical
+data directly. GDCM includes a file format definition and a network
+communications protocol, both of which should be extended to provide a full set
+of tools for a researcher or small medical imaging vendor to interface with an
+existing medical database.")
+    (license license:bsd-2)))
-- 
2.36.1

bug#55989: [PATCH 1/2] gnu: Add python-pydicom.

[Ludovic Courtès]

Hi,

Antero Mejr <antero@mailbox.org> skribis:

> Here's the updated GDCM patch, which is a dependency.
>
> * gnu/packages/bioinformatics.scm (gdcm): New variable.

I had to adjust the hash of the GDCM source (a typo?), but after that I
applied both the GDCM and pydicom patches.

Thanks, and apologies for the delay!

Ludo’.