From 68f4dfd963690061310440dbde5a7ed8e7ee90d1 Mon Sep 17 00:00:00 2001
From: "Eric A. Borisch" <eborisch@gmail.com>
Date: Wed, 31 Oct 2018 09:14:46 -0500
Subject: [PATCH] py-pydicom: New package.

---
 biology/py-pydicom/DESCR    |   6 +
 biology/py-pydicom/Makefile |  29 +++
 biology/py-pydicom/PLIST    | 424 ++++++++++++++++++++++++++++++++++++
 biology/py-pydicom/distinfo |   6 +
 4 files changed, 465 insertions(+)
 create mode 100644 biology/py-pydicom/DESCR
 create mode 100644 biology/py-pydicom/Makefile
 create mode 100644 biology/py-pydicom/PLIST
 create mode 100644 biology/py-pydicom/distinfo

diff --git a/biology/py-pydicom/DESCR b/biology/py-pydicom/DESCR
new file mode 100644
index 000000000000..4a6c78f99724
--- /dev/null
+++ b/biology/py-pydicom/DESCR
@@ -0,0 +1,6 @@
+Pydicom is a pure Python package for working with DICOM files such as medical
+images, reports, and radiotherapy objects.
+
+Pydicom makes it easy to read these complex files into natural pythonic
+structures for easy manipulation. Modified datasets can be written again to
+DICOM format files.
diff --git a/biology/py-pydicom/Makefile b/biology/py-pydicom/Makefile
new file mode 100644
index 000000000000..59d93ae52388
--- /dev/null
+++ b/biology/py-pydicom/Makefile
@@ -0,0 +1,29 @@
+# $NetBSD$
+
+DISTNAME=	pydicom-1.2.0
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_GITHUB:=pydicom/}
+GITHUB_PROJECT=	pydicom
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+MAINTAINER=	eborisch@gmail.com
+HOMEPAGE=	https://github.com/pydicom/pydicom/
+COMMENT=	Pure python package for working with DICOM files
+LICENSE=	modified-bsd AND mit
+
+USE_LANGUAGES=	# none
+
+DOCDIR=	share/doc/${PKGBASE}
+PLIST_SUBST+=	DOCDIR=${DOCDIR:Q}
+INSTALLATION_DIRS+= ${DOCDIR}
+
+post-extract:
+	chmod a-x ${WRKSRC}/pydicom/data/test_files/*.dcm
+
+post-install:
+	${INSTALL_DATA} ${WRKSRC}/LICENSE ${DESTDIR}${PREFIX}/${DOCDIR}
+	${INSTALL_DATA} ${WRKSRC}/README.md ${DESTDIR}${PREFIX}/${DOCDIR}
+
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/py-pydicom/PLIST b/biology/py-pydicom/PLIST
new file mode 100644
index 000000000000..9e146fd19873
--- /dev/null
+++ b/biology/py-pydicom/PLIST
@@ -0,0 +1,424 @@
+@comment $NetBSD$
+${PYSITELIB}/dicom.py
+${PYSITELIB}/dicom.pyc
+${PYSITELIB}/dicom.pyo
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/pydicom/__init__.py
+${PYSITELIB}/pydicom/__init__.pyc
+${PYSITELIB}/pydicom/__init__.pyo
+${PYSITELIB}/pydicom/_dicom_dict.py
+${PYSITELIB}/pydicom/_dicom_dict.pyc
+${PYSITELIB}/pydicom/_dicom_dict.pyo
+${PYSITELIB}/pydicom/_private_dict.py
+${PYSITELIB}/pydicom/_private_dict.pyc
+${PYSITELIB}/pydicom/_private_dict.pyo
+${PYSITELIB}/pydicom/_storage_sopclass_uids.py
+${PYSITELIB}/pydicom/_storage_sopclass_uids.pyc
+${PYSITELIB}/pydicom/_storage_sopclass_uids.pyo
+${PYSITELIB}/pydicom/_uid_dict.py
+${PYSITELIB}/pydicom/_uid_dict.pyc
+${PYSITELIB}/pydicom/_uid_dict.pyo
+${PYSITELIB}/pydicom/_version.py
+${PYSITELIB}/pydicom/_version.pyc
+${PYSITELIB}/pydicom/_version.pyo
+${PYSITELIB}/pydicom/benchmarks/__init__.py
+${PYSITELIB}/pydicom/benchmarks/__init__.pyc
+${PYSITELIB}/pydicom/benchmarks/__init__.pyo
+${PYSITELIB}/pydicom/benchmarks/bench_encaps.py
+${PYSITELIB}/pydicom/benchmarks/bench_encaps.pyc
+${PYSITELIB}/pydicom/benchmarks/bench_encaps.pyo
+${PYSITELIB}/pydicom/benchmarks/bench_handler_numpy.py
+${PYSITELIB}/pydicom/benchmarks/bench_handler_numpy.pyc
+${PYSITELIB}/pydicom/benchmarks/bench_handler_numpy.pyo
+${PYSITELIB}/pydicom/benchmarks/bench_handler_rle.py
+${PYSITELIB}/pydicom/benchmarks/bench_handler_rle.pyc
+${PYSITELIB}/pydicom/benchmarks/bench_handler_rle.pyo
+${PYSITELIB}/pydicom/charset.py
+${PYSITELIB}/pydicom/charset.pyc
+${PYSITELIB}/pydicom/charset.pyo
+${PYSITELIB}/pydicom/compat.py
+${PYSITELIB}/pydicom/compat.pyc
+${PYSITELIB}/pydicom/compat.pyo
+${PYSITELIB}/pydicom/config.py
+${PYSITELIB}/pydicom/config.pyc
+${PYSITELIB}/pydicom/config.pyo
+${PYSITELIB}/pydicom/data/__init__.py
+${PYSITELIB}/pydicom/data/__init__.pyc
+${PYSITELIB}/pydicom/data/__init__.pyo
+${PYSITELIB}/pydicom/data/charset_files/FileInfo.txt
+${PYSITELIB}/pydicom/data/charset_files/__init__.py
+${PYSITELIB}/pydicom/data/charset_files/__init__.pyc
+${PYSITELIB}/pydicom/data/charset_files/__init__.pyo
+${PYSITELIB}/pydicom/data/charset_files/charlist.py
+${PYSITELIB}/pydicom/data/charset_files/charlist.pyc
+${PYSITELIB}/pydicom/data/charset_files/charlist.pyo
+${PYSITELIB}/pydicom/data/charset_files/chrArab.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrFren.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrFrenMulti.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrGerm.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrGreek.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrH31.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrH32.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrHbrw.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrI2.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrJapMulti.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrJapMultiExplicitIR6.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrKoreanMulti.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrRuss.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrSQEncoding.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrSQEncoding1.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrX1.dcm
+${PYSITELIB}/pydicom/data/charset_files/chrX2.dcm
+${PYSITELIB}/pydicom/data/data_manager.py
+${PYSITELIB}/pydicom/data/data_manager.pyc
+${PYSITELIB}/pydicom/data/data_manager.pyo
+${PYSITELIB}/pydicom/data/test_files/CT_small.dcm
+${PYSITELIB}/pydicom/data/test_files/ExplVR_BigEnd.dcm
+${PYSITELIB}/pydicom/data/test_files/ExplVR_BigEndNoMeta.dcm
+${PYSITELIB}/pydicom/data/test_files/ExplVR_LitEndNoMeta.dcm
+${PYSITELIB}/pydicom/data/test_files/JPEG-LL.dcm
+${PYSITELIB}/pydicom/data/test_files/JPEG-lossy.dcm
+${PYSITELIB}/pydicom/data/test_files/JPEG2000.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small_RLE.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small_bigendian.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small_expb.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small_implicit.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small_jp2klossless.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_small_jpeg_ls_lossless.dcm
+${PYSITELIB}/pydicom/data/test_files/MR_truncated.dcm
+${PYSITELIB}/pydicom/data/test_files/OBXXXX1A.dcm
+${PYSITELIB}/pydicom/data/test_files/OBXXXX1A_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/OBXXXX1A_expb.dcm
+${PYSITELIB}/pydicom/data/test_files/OBXXXX1A_expb_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/OBXXXX1A_rle.dcm
+${PYSITELIB}/pydicom/data/test_files/OBXXXX1A_rle_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/OT-PAL-8-face.dcm
+${PYSITELIB}/pydicom/data/test_files/README.txt
+${PYSITELIB}/pydicom/data/test_files/SC_rgb.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_16bit.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_16bit_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_32bit.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_32bit_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_+eb+cr.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_+eb+cy+n1.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_+eb+cy+n2.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_+eb+cy+np.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_+eb+cy+s2.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_+eb+cy+s4.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_ebcr_dcmd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_ebcyn1_dcmd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_ebcyn2_dcmd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_ebcynp_dcmd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_ebcys2_dcmd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_dcmtk_ebcys4_dcmd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_expb.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_expb_16bit.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_expb_16bit_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_expb_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_expb_32bit.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_expb_32bit_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_gdcm2k_uncompressed.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_gdcm_KY.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_jpeg_dcmtk.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_jpeg_gdcm.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_jpeg_lossy_gdcm.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_rle.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_rle_16bit.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_rle_16bit_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_rle_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_rle_32bit.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_rle_32bit_2frame.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_small_odd.dcm
+${PYSITELIB}/pydicom/data/test_files/SC_rgb_small_odd_jpeg.dcm
+${PYSITELIB}/pydicom/data/test_files/__init__.py
+${PYSITELIB}/pydicom/data/test_files/__init__.pyc
+${PYSITELIB}/pydicom/data/test_files/__init__.pyo
+${PYSITELIB}/pydicom/data/test_files/badVR.dcm
+${PYSITELIB}/pydicom/data/test_files/color-pl.dcm
+${PYSITELIB}/pydicom/data/test_files/color-px.dcm
+${PYSITELIB}/pydicom/data/test_files/color3d_jpeg_baseline.dcm
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/77654033/CR1/6154
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/77654033/CR2/6247
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/77654033/CR3/6278
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+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/77654033/CT2/17166
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/77654033/CT2/17196
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892001/CT2N/6293
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892001/CT2N/6924
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892001/CT5N/2062
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892001/CT5N/2392
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892001/CT5N/2693
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+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892001/CT5N/3353
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR1/15820
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR1/4919
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+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR2/4950
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+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR2/6273
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+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR700/4528
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR700/4558
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR700/4588
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR700/4618
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR700/4648
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/98892003/MR700/4678
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/DICOMDIR
+${PYSITELIB}/pydicom/data/test_files/emri_small.dcm
+${PYSITELIB}/pydicom/data/test_files/emri_small_RLE.dcm
+${PYSITELIB}/pydicom/data/test_files/emri_small_big_endian.dcm
+${PYSITELIB}/pydicom/data/test_files/emri_small_jpeg_2k_lossless.dcm
+${PYSITELIB}/pydicom/data/test_files/emri_small_jpeg_ls_lossless.dcm
+${PYSITELIB}/pydicom/data/test_files/image_dfl.dcm
+${PYSITELIB}/pydicom/data/test_files/liver.dcm
+${PYSITELIB}/pydicom/data/test_files/liver_1frame.dcm
+${PYSITELIB}/pydicom/data/test_files/liver_expb.dcm
+${PYSITELIB}/pydicom/data/test_files/liver_expb_1frame.dcm
+${PYSITELIB}/pydicom/data/test_files/meta_missing_tsyntax.dcm
+${PYSITELIB}/pydicom/data/test_files/nested_priv_SQ.dcm
+${PYSITELIB}/pydicom/data/test_files/no_meta_group_length.dcm
+${PYSITELIB}/pydicom/data/test_files/priv_SQ.dcm
+${PYSITELIB}/pydicom/data/test_files/reportsi.dcm
+${PYSITELIB}/pydicom/data/test_files/reportsi_with_empty_number_tags.dcm
+${PYSITELIB}/pydicom/data/test_files/rtdose.dcm
+${PYSITELIB}/pydicom/data/test_files/rtdose_1frame.dcm
+${PYSITELIB}/pydicom/data/test_files/rtdose_expb.dcm
+${PYSITELIB}/pydicom/data/test_files/rtdose_expb_1frame.dcm
+${PYSITELIB}/pydicom/data/test_files/rtdose_rle.dcm
+${PYSITELIB}/pydicom/data/test_files/rtdose_rle_1frame.dcm
+${PYSITELIB}/pydicom/data/test_files/rtplan.dcm
+${PYSITELIB}/pydicom/data/test_files/rtplan.dump
+${PYSITELIB}/pydicom/data/test_files/rtplan_truncated.dcm
+${PYSITELIB}/pydicom/data/test_files/rtstruct.dcm
+${PYSITELIB}/pydicom/data/test_files/rtstruct.dump
+${PYSITELIB}/pydicom/data/test_files/test-SR.dcm
+${PYSITELIB}/pydicom/data/test_files/test.py
+${PYSITELIB}/pydicom/data/test_files/test.pyc
+${PYSITELIB}/pydicom/data/test_files/test.pyo
+${PYSITELIB}/pydicom/data/test_files/zipMR.gz
+${PYSITELIB}/pydicom/data/tests/__init__.py
+${PYSITELIB}/pydicom/data/tests/__init__.pyc
+${PYSITELIB}/pydicom/data/tests/__init__.pyo
+${PYSITELIB}/pydicom/data/tests/test_data_manager.py
+${PYSITELIB}/pydicom/data/tests/test_data_manager.pyc
+${PYSITELIB}/pydicom/data/tests/test_data_manager.pyo
+${PYSITELIB}/pydicom/datadict.py
+${PYSITELIB}/pydicom/datadict.pyc
+${PYSITELIB}/pydicom/datadict.pyo
+${PYSITELIB}/pydicom/dataelem.py
+${PYSITELIB}/pydicom/dataelem.pyc
+${PYSITELIB}/pydicom/dataelem.pyo
+${PYSITELIB}/pydicom/dataset.py
+${PYSITELIB}/pydicom/dataset.pyc
+${PYSITELIB}/pydicom/dataset.pyo
+${PYSITELIB}/pydicom/dicomdir.py
+${PYSITELIB}/pydicom/dicomdir.pyc
+${PYSITELIB}/pydicom/dicomdir.pyo
+${PYSITELIB}/pydicom/dicomio.py
+${PYSITELIB}/pydicom/dicomio.pyc
+${PYSITELIB}/pydicom/dicomio.pyo
+${PYSITELIB}/pydicom/encaps.py
+${PYSITELIB}/pydicom/encaps.pyc
+${PYSITELIB}/pydicom/encaps.pyo
+${PYSITELIB}/pydicom/errors.py
+${PYSITELIB}/pydicom/errors.pyc
+${PYSITELIB}/pydicom/errors.pyo
+${PYSITELIB}/pydicom/filebase.py
+${PYSITELIB}/pydicom/filebase.pyc
+${PYSITELIB}/pydicom/filebase.pyo
+${PYSITELIB}/pydicom/filereader.py
+${PYSITELIB}/pydicom/filereader.pyc
+${PYSITELIB}/pydicom/filereader.pyo
+${PYSITELIB}/pydicom/fileutil.py
+${PYSITELIB}/pydicom/fileutil.pyc
+${PYSITELIB}/pydicom/fileutil.pyo
+${PYSITELIB}/pydicom/filewriter.py
+${PYSITELIB}/pydicom/filewriter.pyc
+${PYSITELIB}/pydicom/filewriter.pyo
+${PYSITELIB}/pydicom/misc.py
+${PYSITELIB}/pydicom/misc.pyc
+${PYSITELIB}/pydicom/misc.pyo
+${PYSITELIB}/pydicom/multival.py
+${PYSITELIB}/pydicom/multival.pyc
+${PYSITELIB}/pydicom/multival.pyo
+${PYSITELIB}/pydicom/pixel_data_handlers/__init__.py
+${PYSITELIB}/pydicom/pixel_data_handlers/__init__.pyc
+${PYSITELIB}/pydicom/pixel_data_handlers/__init__.pyo
+${PYSITELIB}/pydicom/pixel_data_handlers/gdcm_handler.py
+${PYSITELIB}/pydicom/pixel_data_handlers/gdcm_handler.pyc
+${PYSITELIB}/pydicom/pixel_data_handlers/gdcm_handler.pyo
+${PYSITELIB}/pydicom/pixel_data_handlers/jpeg_ls_handler.py
+${PYSITELIB}/pydicom/pixel_data_handlers/jpeg_ls_handler.pyc
+${PYSITELIB}/pydicom/pixel_data_handlers/jpeg_ls_handler.pyo
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+${DOCDIR}/LICENSE
+${DOCDIR}/README.md
diff --git a/biology/py-pydicom/distinfo b/biology/py-pydicom/distinfo
new file mode 100644
index 000000000000..8880b4db1494
--- /dev/null
+++ b/biology/py-pydicom/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (pydicom-1.2.0.tar.gz) = dcc41a56d25322ba9326ed7431ee80c1125dd997
+RMD160 (pydicom-1.2.0.tar.gz) = 1ef6d7f68d5944c227cd80a8db38242630573fbc
+SHA512 (pydicom-1.2.0.tar.gz) = 8e5cf899509a9928b641e4db95f7731928823933d24b36daa6cb92fe27fd0d536bb7e32340559917a6ee98339582d06a3936b8e63bb2fa97d9c98b91c383fd88
+Size (pydicom-1.2.0.tar.gz) = 7041217 bytes