Backport fix for agilent data conversion

Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 60 insertions, 18 deletions

diff --git a/sci-chemistry/nmrglue/ChangeLog b/sci-chemistry/nmrglue/ChangeLog
index f09722ee8f4a..ec1161cd75cf 100644
--- a/sci-chemistry/nmrglue/ChangeLog
+++ b/sci-chemistry/nmrglue/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/nmrglue
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/ChangeLog,v 1.2 2015/02/20 08:54:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/ChangeLog,v 1.3 2015/03/04 08:17:14 jlec Exp $
+
+*nmrglue-0.5-r1 (04 Mar 2015)
+
+  04 Mar 2015; Justin Lecher <jlec@gentoo.org> +files/nmrglue-0.5-nohyper.patch,
+  +nmrglue-0.5-r1.ebuild, -nmrglue-0.5.ebuild:
+  Backport fix for agilent data conversion
 
 *nmrglue-0.5 (20 Feb 2015)
 
diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest
index 6830f6a75316..21cc53ca6483 100644
--- a/sci-chemistry/nmrglue/Manifest
+++ b/sci-chemistry/nmrglue/Manifest
@@ -1,28 +1,29 @@
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 Hash: SHA512
 
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 DIST nmrglue-0.4-corrected.tar.gz 128298 SHA256 85c45750aef431f2c1326a9f4856eeac4da8aedbc94c6255de6e08e3ea35f316 SHA512 c2376ba8e8f993e6e4b536d67d4a780087ac8f811b2d5a846ff8b4785b02c0a4e86956c4205f90a17c5c0a2dc620d75fb7886fbad9cca314b548e3368137eda0 WHIRLPOOL eb8a2a5064b5fa5b60d16a70cf51667daa55f1584ed9d0ca3092af4672ed2c5cef56d135e82b35c107856d338fb0893248a1719b673a4e96c1edb2fb75243d08
 DIST nmrglue-0.5.tar.gz 142604 SHA256 a05c880bd0d5f0b388156409e18a5618742f829f2532d19970d05b11bfcc6103 SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 WHIRLPOOL 78f9d094a2ab1ebc01f452717fdc1cdeccc27951195c9dd6e97069a575722acf25442009b4ccede03ad728b0767fced4a2220a8072ccc1d604a9f62e9c45af4a
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+MISC ChangeLog 689 SHA256 26d93992a39ef4db578883a615b7fbce1285e1e8fddc5cf04a4173563c18f131 SHA512 70d1328005577e4eb76ddec29f84ace2bdcafe8e9219ebd203be0e2aa15ee4f77d7de2d688000edf83c6fb20325ec79ad6c99a2b55c70fc15cc91086844ad054 WHIRLPOOL 12d264ee1a48880d27f85ea5ece5c2c52768785bcebc3c31b5f25dad3c1e147ead8d2934ab3c97ee7e95393cde8381195dc0dc22cd25bc65aa50d638459ab9fd
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diff --git a/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch
new file mode 100644
index 000000000000..103f5b154d0b
--- /dev/null
+++ b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch
@@ -0,0 +1,33 @@
+From ba1eee9e71623110511545c058afe2a92e139aa5 Mon Sep 17 00:00:00 2001
+From: Jonathan Helmus <jjhelmus@gmail.com>
+Date: Tue, 3 Mar 2015 19:47:05 -0600
+Subject: [PATCH] pipe_proc.py tp function correctly sets FDSIZE.
+
+Fixes issue #27
+---
+ nmrglue/process/pipe_proc.py | 7 +++++--
+ 1 file changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/nmrglue/process/pipe_proc.py b/nmrglue/process/pipe_proc.py
+index 79b6303..8c1271c 100644
+--- a/nmrglue/process/pipe_proc.py
++++ b/nmrglue/process/pipe_proc.py
+@@ -1527,13 +1527,16 @@ def tp(dic, data, hyper=False, nohyper=False, auto=False, nohdr=False):
+         data = np.array(p.tp_hyper(data), dtype="complex64")
+     else:
+         data = p.tp(data)
+-        if dic[fn2 + "QUADFLAG"] != 1 and nohyper is not True:
++        if dic[fn2 + "QUADFLAG"] != 1 and nohyper is False:
+             # unpack complex as needed
+             data = np.array(p.c2ri(data), dtype="complex64")
+ 
+     # update the dimentionality and order
+     dic["FDSLICECOUNT"] = data.shape[0]
+-    if data.dtype == 'float32':
++    if (data.dtype == 'float32') and (nohyper is True):
++        # when nohyper is True and the new last dimension was complex
++        # prior to transposing then FDSIZE is set as if the dimension was
++        # converted to complex data, that is half the actual size.
+         dic["FDSIZE"] = data.shape[1] / 2
+     else:
+         dic["FDSIZE"] = data.shape[1]
diff --git a/sci-chemistry/nmrglue/nmrglue-0.5.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
index 256c2ac94ad7..f408354620a7 100644
--- a/sci-chemistry/nmrglue/nmrglue-0.5.ebuild
+++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/nmrglue-0.5.ebuild,v 1.1 2015/02/20 08:54:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild,v 1.1 2015/03/04 08:17:14 jlec Exp $
 
 EAPI=5
 
@@ -29,6 +29,8 @@ DEPEND="
 	)
 "
 
+PATCHES=( "${FILESDIR}"/${P}-nohyper.patch )
+
 python_test() {
 	nosetests --verbosity=3 || die
 }