* [bug#55989] [PATCH 1/2] gnu: Add python-pydicom.
@ 2022-06-15 1:27 Antero Mejr via Guix-patches via
2022-06-15 1:27 ` [bug#55988] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
` (2 more replies)
0 siblings, 3 replies; 7+ messages in thread
From: Antero Mejr via Guix-patches via @ 2022-06-15 1:27 UTC (permalink / raw)
To: 55989
* 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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#55988] [PATCH 2/2] gnu: Add gdcm.
2022-06-15 1:27 [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Antero Mejr via Guix-patches via
@ 2022-06-15 1:27 ` Antero Mejr via Guix-patches via
2022-06-15 7:59 ` [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Maxime Devos
2022-06-15 15:39 ` Antero Mejr via Guix-patches via
2 siblings, 0 replies; 7+ messages in thread
From: Antero Mejr via Guix-patches via @ 2022-06-15 1:27 UTC (permalink / raw)
To: 55988
* 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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#55989] [PATCH 1/2] gnu: Add python-pydicom.
2022-06-15 1:27 [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Antero Mejr via Guix-patches via
2022-06-15 1:27 ` [bug#55988] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
@ 2022-06-15 7:59 ` Maxime Devos
2022-06-15 15:40 ` Antero Mejr via Guix-patches via
2022-06-15 15:39 ` Antero Mejr via Guix-patches via
2 siblings, 1 reply; 7+ messages in thread
From: Maxime Devos @ 2022-06-15 7:59 UTC (permalink / raw)
To: Antero Mejr, 55989
[-- Attachment #1: Type: text/plain, Size: 802 bytes --]
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.
[-- Attachment #2: This is a digitally signed message part --]
[-- Type: application/pgp-signature, Size: 260 bytes --]
^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#55989] [PATCH 1/2] gnu: Add python-pydicom.
2022-06-15 7:59 ` [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Maxime Devos
@ 2022-06-15 15:40 ` Antero Mejr via Guix-patches via
0 siblings, 0 replies; 7+ messages in thread
From: Antero Mejr via Guix-patches via @ 2022-06-15 15:40 UTC (permalink / raw)
To: Maxime Devos; +Cc: 55989
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.
^ permalink raw reply [flat|nested] 7+ messages in thread
* [bug#55989] [PATCH 1/2] gnu: Add python-pydicom.
2022-06-15 1:27 [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Antero Mejr via Guix-patches via
2022-06-15 1:27 ` [bug#55988] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
2022-06-15 7:59 ` [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Maxime Devos
@ 2022-06-15 15:39 ` Antero Mejr via Guix-patches via
2022-06-15 15:39 ` [bug#55989] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
2 siblings, 1 reply; 7+ messages in thread
From: Antero Mejr via Guix-patches via @ 2022-06-15 15:39 UTC (permalink / raw)
To: 55989
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
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [bug#55989] [PATCH 2/2] gnu: Add gdcm.
2022-06-15 15:39 ` Antero Mejr via Guix-patches via
@ 2022-06-15 15:39 ` Antero Mejr via Guix-patches via
2023-01-08 15:06 ` bug#55989: [PATCH 1/2] gnu: Add python-pydicom Ludovic Courtès
0 siblings, 1 reply; 7+ messages in thread
From: Antero Mejr via Guix-patches via @ 2022-06-15 15:39 UTC (permalink / raw)
To: 55989
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
^ permalink raw reply related [flat|nested] 7+ messages in thread
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2022-06-15 1:27 [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Antero Mejr via Guix-patches via
2022-06-15 1:27 ` [bug#55988] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
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2022-06-15 15:39 ` Antero Mejr via Guix-patches via
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2023-01-08 15:06 ` bug#55989: [PATCH 1/2] gnu: Add python-pydicom Ludovic Courtès
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