[med-svn] [Git][med-team/mricron][master] 2 commits: disable building/distribution of dcm2nii and npm
Yaroslav Halchenko
gitlab at salsa.debian.org
Tue Jan 19 00:17:35 GMT 2021
Yaroslav Halchenko pushed to branch master at Debian Med / mricron
Commits:
380db5e2 by Yaroslav Halchenko at 2021-01-18T18:54:38-05:00
disable building/distribution of dcm2nii and npm
See https://github.com/neurolabusc/MRIcron/issues/15 for a dialog
with upstream
- - - - -
e9fecd98 by Yaroslav Halchenko at 2021-01-18T19:17:22-05:00
Switch to qt5 from gtk2
upstream says that compatibility with gtk3 is untested
- - - - -
12 changed files:
- debian/changelog
- − debian/clean
- debian/control
- − debian/dcm2nii.1
- − debian/dcm2niigui.desktop
- debian/mricron-data.install
- debian/mricron.1
- debian/mricron.install
- debian/mricron.manpages
- − debian/patches/pigz_compat
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,15 +1,22 @@
mricron (1.0.20190902-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* New upstream version
* Standards-Version: 4.5.1 (routine-update)
* Add salsa-ci file (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
- TODO: Build error
- nifti_hdr.pas(1286) Fatal: (10026) There were 2 errors compiling module, stopping
- -- Andreas Tille <tille at debian.org> Sun, 17 Jan 2021 18:22:57 +0100
+ [ Yaroslav Halchenko ]
+ * Remove building/distribution of dcm2nii (superseded by dcm2niix,
+ developed and packaged independently), and npm (AKA mricron-npm):
+ niistat (not packaged) and PALM (3rd party, not packaged) are
+ recommended instead. Closes: #898842
+ * Added dcm2niix to Recommends
+ * Switch to build against qt5 instead of gtk2. Closes: #967644
+
+ -- Yaroslav Halchenko <debian at onerussian.com> Mon, 18 Jan 2021 19:03:52 -0500
mricron (0.20140804.1~dfsg.1-4) unstable; urgency=medium
=====================================
debian/clean deleted
=====================================
@@ -1 +0,0 @@
-dcm2nii/dcm2niigui.res
=====================================
debian/control
=====================================
@@ -7,10 +7,9 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
fp-units-misc,
imagemagick,
- lcl-gtk2,
+ lcl-qt5,
lcl-units,
lcl-utils,
- libgtk2.0-dev
Standards-Version: 4.5.1
Rules-Requires-Root: no
Vcs-Browser: https://salsa.debian.org/med-team/mricron
@@ -20,7 +19,7 @@ Homepage: https://www.nitrc.org/projects/mricron
Package: mricron
Architecture: any
Depends: mricron-data, ${misc:Depends}, ${shlibs:Depends}
-Recommends: pigz
+Recommends: pigz, dcm2niix
Suggests: fsl, mricron-doc
Description: magnetic resonance image conversion, viewing and analysis
This is a GUI-based visualization and analysis tool for (functional) magnetic
=====================================
debian/dcm2nii.1 deleted
=====================================
@@ -1,49 +0,0 @@
-.TH "DCM2NII" "1" "April 2010" "Michael Hanke" "User Commands"
-.SH NAME
-dcm2nii \- convert DICOM or PAR/REC image into the NIfTI format
-.SH SYNOPSIS
-\fBdcm2nii\fR <options> <sourcenames>
-.SH OPTIONS
-.TP
-\fB\-a\fR Anonymize [remove identifying information]: Y,N = Y
-.TP
-\fB\-b\fR load settings from specified inifile, e.g. '\-b /etc/mricron.ini'
-.TP
-\fB\-c\fR Collapse input folders: Y,N = N
-.TP
-\fB\-d\fR Date in filename [filename.dcm \-> 20061230122032.nii]: Y,N = Y
-.TP
-\fB\-e\fR events (series/acq) in filename [filename.dcm \-> s002a003.nii]: Y,N = Y
-.TP
-\fB\-f\fR Source filename [e.g. filename.par \-> filename.nii]: Y,N = Y
-.TP
-\fB\-g\fR gzip output, filename.nii.gz [ignored if '\-n n']: Y,N = Y
-.TP
-\fB\-i\fR ID in filename [filename.dcm \-> johndoe.nii]: Y,N = Y
-.TP
-\fB\-n\fR output .nii file [if no, create .hdr/.img pair]: Y,N = Y
-.TP
-\fB\-o\fR Output Directory, e.g. '/tmp' (if unspecified, source directory is used)
-.TP
-\fB\-p\fR Protocol in filename [filename.dcm \-> TFE_T1.nii]: Y,N = Y
-.TP
-\fB\-r\fR Reorient image to nearest orthogonal: Y,N
-.TP
-\fB\-s\fR SPM2/Analyze not SPM5/NIfTI [ignored if '\-n y']: Y,N = N
-.TP
-\fB\-v\fR Convert every image in the directory: Y,N = Y
-.TP
-\fB\-x\fR Reorient and crop 3D NIfTI images: Y,N = N
-.PP
-You can also set defaults by editing /home/michael/.dcm2nii/dcm2nii.ini
-.SH "EXAMPLES"
-dcm2nii -a y /home/joe/Documents/dcm/IM_0116
-.SH "AUTHOR"
-\fBdcm2nii\fR was written by Chris Rorden.
-.PP
-This manual page was written by Michael Hanke <michael.hanke at gmail.com>,
-for the Debian project (but may be used by others).
-.SH "SEE ALSO"
-.BR mricron "(1)"
-.TP
-\fBMRIcron Homepage:\fR http://www.cabiatl.com/mricro/mricron/
=====================================
debian/dcm2niigui.desktop deleted
=====================================
@@ -1,10 +0,0 @@
-[Desktop Entry]
-GenericName=DICOM to NIfTI Conversion
-GenericName[ru]=Конвертор из DICOM в NIfTI
-Name=dcm2nii
-Exec=dcm2niigui %F
-TryExec=dcm2niigui
-Type=Application
-Terminal=false
-Categories=Education;Graphics;Science;MedicalSoftware;GTK;
-Icon=/usr/share/pixmaps/mricron.xpm
=====================================
debian/mricron-data.install
=====================================
@@ -1,2 +1,2 @@
-lut usr/share/mricron
-templates usr/share/mricron
+Resources/lut usr/share/mricron
+Resources/templates usr/share/mricron
=====================================
debian/mricron.1
=====================================
@@ -8,16 +8,12 @@ of statistical overlay maps on brain anatomy images. Moreover, it aids drawing
anatomical regions-of-interest (ROI), or lesion mapping, as well as basic
analysis of functional timeseries (e.g. creating plots of peristimulus
signal-change).
-.PP
-In addition to 'mricron', this package also provides 'dcm2nii' that supports
-converting DICOM and PAR/REC images into the NIfTI format, and 'npm' for
-non-parametric data analysis.
.SH "AUTHOR"
\fBmricron\fR was written by Chris Rorden.
.PP
This manual page was written by Michael Hanke <michael.hanke at gmail.com>,
for the Debian project (but may be used by others).
.SH "SEE ALSO"
-.BR dcm2nii "(1)"
+.BR dcm2niix "(1)"
.TP
\fBMRIcron Homepage:\fR http://www.cabiatl.com/mricro/mricron/
=====================================
debian/mricron.install
=====================================
@@ -1,7 +1,4 @@
-dcm2nii/dcm2nii usr/bin
-dcm2nii/dcm2niigui usr/bin
debian/*.desktop usr/share/applications
debian/wrapper/mricron usr/bin
mricron usr/lib/mricron
mricron.xpm usr/share/pixmaps
-npm/mricron-npm usr/bin
=====================================
debian/mricron.manpages
=====================================
@@ -1,2 +1 @@
-debian/dcm2nii.1
debian/mricron.1
=====================================
debian/patches/pigz_compat deleted
=====================================
@@ -1,19 +0,0 @@
-From: Michael Hanke <michael.hanke at gmail.com>
-Subject: No exceptions for pigz
-
-In Debian it does exist on powerpc and other big-endian architectures.
-
---- a/dcm2nii/niftiutil.pas
-+++ b/dcm2nii/niftiutil.pas
-@@ -202,11 +202,6 @@
- exename: string;
- {$IFDEF DARWIN} temp: string;{$ENDIF}
- begin
-- {$IFDEF ENDIAN_BIG}
-- Msg('pigz not available with PowerPC computers');
-- result := '';
-- exit;
-- {$ENDIF}
- for i := 1 to 2 do begin
- {$IFDEF UNIX}
- if i = 1 then
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
-pigz_compat
lazarus_modern
debian_paths
stricter_fpc.patch
=====================================
debian/rules
=====================================
@@ -11,16 +11,10 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
override_dh_auto_build:
# first the non-gui parts
cp common/notgui.inc common/isgui.inc
- lazbuild --build-all --pcp=/etc/lazarus dcm2nii/dcm2nii.lpi
- # intermediate clean
- find $(CURDIR)/dcm2nii -name '*.o' -delete -o -name '*.ppu' -delete
# and now the gui parts
cp common/gui.inc common/isgui.inc
- lazbuild --build-all --ws=gtk2 --pcp=/etc/lazarus mricron.lpi
- lazbuild --build-all --ws=gtk2 --pcp=/etc/lazarus dcm2nii/dcm2niigui.lpi
- lazbuild --build-all --ws=gtk2 --pcp=/etc/lazarus npm/npm.lpi
- # rename npm to prevent conflict with npm package
- mv npm/npm npm/mricron-npm
+ lazbuild --build-all --ws=qt5 --pcp=/etc/lazarus mricron.lpi
+ mv ./MRIcron mricron
# build icon
convert iconfinal.ico -resize 32x32 iconfinal.xpm
mv iconfinal-0.xpm mricron.xpm || mv iconfinal.xpm mricron.xpm
@@ -40,9 +34,6 @@ override_dh_clean:
find . -name '*.compiled' -delete
find . -name '*.or' -delete
-rm mricron.rc mricron.lrs mricron
- -rm dcm2nii/dcm2nii
- -rm dcm2nii/dcm2niigui
- -rm npm/mricron-npm
-rm iconfinal*.xpm mricron.xpm
-rm text.lrs
dh_clean
View it on GitLab: https://salsa.debian.org/med-team/mricron/-/compare/8661bf14e00751d74d06a4e26e6bea19ad727e12...e9fecd985171dca1db2b42e2efd03f37370c9c1f
--
View it on GitLab: https://salsa.debian.org/med-team/mricron/-/compare/8661bf14e00751d74d06a4e26e6bea19ad727e12...e9fecd985171dca1db2b42e2efd03f37370c9c1f
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