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Update to version 1.53u

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OBS-URL: https://build.opensuse.org/package/show/science/imagej?expand=0&rev=19
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Dmitry Roshchin 2024-11-26 14:23:39 +00:00 committed by Git OBS Bridge
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## Default LFS
*.7z filter=lfs diff=lfs merge=lfs -text
*.bsp filter=lfs diff=lfs merge=lfs -text
*.bz2 filter=lfs diff=lfs merge=lfs -text
*.gem filter=lfs diff=lfs merge=lfs -text
*.gz filter=lfs diff=lfs merge=lfs -text
*.jar filter=lfs diff=lfs merge=lfs -text
*.lz filter=lfs diff=lfs merge=lfs -text
*.lzma filter=lfs diff=lfs merge=lfs -text
*.obscpio filter=lfs diff=lfs merge=lfs -text
*.oxt filter=lfs diff=lfs merge=lfs -text
*.pdf filter=lfs diff=lfs merge=lfs -text
*.png filter=lfs diff=lfs merge=lfs -text
*.rpm filter=lfs diff=lfs merge=lfs -text
*.tbz filter=lfs diff=lfs merge=lfs -text
*.tbz2 filter=lfs diff=lfs merge=lfs -text
*.tgz filter=lfs diff=lfs merge=lfs -text
*.ttf filter=lfs diff=lfs merge=lfs -text
*.txz filter=lfs diff=lfs merge=lfs -text
*.whl filter=lfs diff=lfs merge=lfs -text
*.xz filter=lfs diff=lfs merge=lfs -text
*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text

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.osc

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version https://git-lfs.github.com/spec/v1
oid sha256:b311df5116b039d464e64336de746f7ec8a2911f6c2c874e15f10d9934b548ac
size 1549329

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version https://git-lfs.github.com/spec/v1
oid sha256:efae9ace32e8b54871cb1dfaf83f3c902d59385acddffbef881d64f509729a13
size 6001015

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Index: source/build.xml
===================================================================
--- source.orig/build.xml
+++ source/build.xml
@@ -14,7 +14,7 @@
<!-- First, ensure the build directory exists. -->
<mkdir dir="${build.dir}" />
<!-- Build everything; add debug="on" to debug -->
- <javac srcdir="./ij" destdir="${build.dir}" optimize="on" source="1.6" target="1.6" debug="on" includeantruntime="false" encoding="utf-8">
+ <javac srcdir="./ij" destdir="${build.dir}" optimize="on" debug="on" includeantruntime="false" encoding="utf-8">
</javac>
</target>

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-------------------------------------------------------------------
Tue Nov 26 06:20:54 UTC 2024 - ming li <mli@suse.com>
- update to 1.53u:
* the Image>Transform>Bin command now supports z-binning of 4D
hyperstacks.
* the Analyze>Plot Profile command works with rotated rectangles.
* The Edit>Selection>Line to Area command converts straight line
selections to rotated rectangle selections.
* improved recording of the Edit>Selection>Properties command and
added a comment to the Edit>Options>Line Width dialog to make
it clearer what the command does.
* the Selection Brush Tool is no longer disabled when activating a
selection in an overlay by double clicking on it.
* made GenericDialog.resetCounters() public so it can be called by
plugins using GenericDialog.addButton() (example).
* added the recordable Image.removeScale() macro function and the
ImagePlus.removeScale() method.
* Added the ImageProcessor.setColor(String) method.
* fixed a bug that caused toolbar contextual menus to ignore the
Edit>Options>Appearance "GUI scale" setting.
* fixed a bug that caused the "Results" menu in a table to
disappear if the table was renamed.
* fixed a bug that caused the File>Import>TIFF Virtual Stack
command to not correctly calibrate TIFF stacks that were not
created by ImageJ.
* fixed a bug that caused the Image>Overlay>From ROI Manager menu
command to not transfer the ROI positions.
* fixed a bug that caused the Edit>Selection>Straighten command
to change the global line selection width.
* fixed a bug that caused ROIs with x or y coordinates greater than
60,535 and less than 65,535 to be saved incorrectly.
* fixed a bug that caused ImageJ to create TIFF files with invalid
RowsPerStrip tags when the image height was greater than 65,535.
* fixed several bugs with Image>Stacks>Plot Z-axis Profile "Live"
plots.
* fixed a bug that caused the "CP" window to not be updated when
the Color Picker tool was used to pick new colors from the active
image.
* fixed a bug that caused the Opener.openAndAddToRecent() method to
return 'false' when the file was opened successfully.
* worked around a Java bug on Windows that caused the main menu bar
sub-menus to not scale to larger than 17 points. Unfortunately,
the main menu bar font size on Windows is still limited to 17
points regardless of the "GUI scale" setting.
* fixed a bug that caused the Roi.Paste macro function to not work
as expected.
* fixed a scale bar width rounding error.
* fixed a bug that caused the Edit>Selection>Rotate command to
convert Rotated Rectangle selections to Polygon selections.
* fixed bugs that caused the Scale and Rotate commands in the ROI
Manager to only work correctly when processing all the ROIs.
* fixed a 1.53t regression that caused the Image>Stacks>Z Project
command to ignore the last slice when doing "Average" projection
of 32-bit stacks.
* fixed a 1.53o regression that caused unexpected error messages
when double clicking on a line in a table or in the ROI Manager
when a custom action was not defined (example).
-------------------------------------------------------------------
Thu Feb 22 13:46:01 UTC 2024 - Dominique Leuenberger <dimstar@opensuse.org>
- Use %autosetup macro. Allows to eliminate the usage of deprecated
%patchN
-------------------------------------------------------------------
Tue Dec 6 20:53:06 UTC 2022 - Dirk Müller <dmueller@suse.com>
- update to 1.53v:
* too many changes to list here, see https://wsr.imagej.net/notes.html
-------------------------------------------------------------------
Fri Apr 8 13:44:13 UTC 2022 - Fridrich Strba <fstrba@suse.com>
- Build with java source and target levels 8
* Fixes build in Factory with jdk17
- Added patch:
* imagej-nosourcetarget.patch
+ Do not hardcode source and target levels, but allow them to
be specified on ant's command-line
-------------------------------------------------------------------
Wed Dec 2 18:37:15 UTC 2020 - andy great <andythe_great@pm.me>
- Update to version 1.53f.
* Added a popup menu to the magnifying glass tool icon.
* Added a popup menu triggered on a right click or long press
inside a selection.
* Updated the built in toolbar "Dev" menu.
* The text in a text selection can be edited in the
Edit>Selection>Properties dialog.
* The File>Import>Image Sequence dialog is used when drag and
dropping a folder on the "ImageJ" window.
* Undo works with overlays when translating and rotating images,
and the "Overlay only" checkbox is only shown in the Translate
dialog when there is an overlay.
* Added the Edit>Options>Fresh Start command, which closes all
images, empties the ROI Manager, clears the Results table and
enables the "Black background" option.
* The Reslice command is faster on Windows when re-slicing from
"Left" or "Right" and it uses an ordinary progress bar when
run from a macro.
* Added an "Open as separate images" checkbox to the
File>Import>Image Sequence dialog.
* Added "Foreground..." and "Background..." entries to the color
picker tool popup menu.
* Added the Image.width, Image.height, Image.copy and
Image.paste(x,y) macro functions (example).
* Added the Array.filter(arr,str), Math.toRadians(degrees) and
Math.toDegrees(radians) functions.
* Added the ResultsTable.addRow() method. For an example, run
Help>Examples>JavaScript>Sine/Cosine Table.
* Fixed a bug that caused the RoiManager.getSelectedIndexes()
method to sometimes not work as expected.
* Fixed a bug that slowed saving of virtual stacks in TIFF
format.
* Fixed a bug that caused the dynamic "Value" and "Count" values
in HIstogram windows to sometimes not be displayed correctly.
* Fixed a bug that caused the Ctrl+F (Edit>Fill) keyboard
shortcut on Windows, when used on a stack, to not display the
"Proces Stack?" dialog.
* Fixed a 1.53e regression that caused the imageCaculator() macro
function do somethimes not work as expected.
* Fixed a 1.52 regression that caused the Analyze Skeleton plugin
to output incorrect Results tables.
* Fixed a regression that caused the Edit>Copy to Image Info
command in the text editor to fail.
* Fixed a 1.53c regression in the AVI Reader that caused it to
throw a null pointer exception.
* Fixed a 1.52 regression that caused the IJ.getImage() method to
sometimes display model error dialogs.
* Many bugfixes and usability improvements
-------------------------------------------------------------------
Sun Feb 18 11:36:26 UTC 2018 - jengelh@inai.de
- Wrap and compact description.
-------------------------------------------------------------------
Thu Feb 15 11:38:49 UTC 2018 - robby.engelmann@igfs-ev.de
- Update to 1.51u
* possible to run on Java 9
* Java plugins can now iterate over the points contained in a selection
* added support for diamond symbols to the Plot class
* many more bugfixes and usability improvements
-------------------------------------------------------------------
Tue Mar 8 17:11:26 UTC 2016 - bwiedemann@suse.com
- drop build time from png file to fix build-compare
-------------------------------------------------------------------
Tue Apr 09 08:16:45 UTC 2013 - lumnis@opensuse.org
- Update to version 1.47n
* see included release-notes.html
-------------------------------------------------------------------
Sun Dec 23 18:21:46 UTC 2012 - dmitry_r@opensuse.org
- Remove _service for downloading files
- Use ImageMagick for icon converting
- Update to version 1.47g
* see included release-notes.html
-------------------------------------------------------------------
Fri Sep 14 06:53:45 UTC 2012 - lumnis@opensuse.org
- startup script fix (in spec file)
-------------------------------------------------------------------
Thu Sep 13 15:28:52 UTC 2012 - dmitry_r@opensuse.org
- Various spec file cleanups
-------------------------------------------------------------------
Wed Sep 12 15:32:07 UTC 2012 - lumnis@opensuse.org
- vers update 1.47c
* Added a "Source" (display source code of selected command) button to Plugins>Utilities>Find Commands.
* Dorai Iyer added a "Bar" option to the arrow tool.
* Bill Mohler modified the ROI Manager to use a JList instead of a List, which makes loading and sorting the large (>10,000) ROI sets faster.
* Added an "Append results" checkbox to the ROI Manager's "Multi Measure" command.
* When opening images, the transfer rate in MB/sec is displayed in the status bar.
* Thanks to Sébastien Tosi, opening TIFF files using File>Import>URL is faster and requires less memory.
* Thanks to Jan Eglinger, fixed a bug that caused incorrect recording of commands implemented in JavaScript when the recorder was in "JavaScript" mode.
* Thanks to Sébastien Tosi, fixed a bug that caused File>Import>URL to not correctly read TIFF files larger than 2GB.
* Fixed a bug in the Analyze>Tools>Synchronize Windows command that caused it to not work as expected when changing the channel of composite color images.
* Thanks to Christoph Deil, fixed a bug in Plugins>Utilities>Find Commands that caused esc and ctrl-w key presses to not close the window after "Show full information" was enabled.
* Thanks to Christoph Deil, fixed bugs in the "Save changes?" dialog that caused it to not work as expected after the focus was changed (by tabbing) to the "Don't Save" or "Cancel" buttons.
1.47b 12 August 2012
* Added the Image>Stacks>Statistics command.
* Thanks to Michael Schmid, the built in brush, pencil and overlay brush tools draw using the background color when alt key is down, are constrained to draw horizontally when shift is down, are resized when shift&control are down (shift&cmd on Macs), and "pick up" the foreground color when control is down (cmd on Macs).
* Added a "16 bit range" choice to the Edit>Options>Appearance dialog box. This is the same as the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog.
* Thanks to Olivio Donati, File>Import>Image Sequence opens any associated ROIs that are in a file named RoiSet.zip.
* Thanks to David Knecht, added a "sum" option to Image>Transform>Bin.
* The getHistogram() macro function no longer limits the number of bins to 256 with 8-bit and RGB images.
* Added the IJ.createHyperStack(title,width,height,channels,slices,frames,bitdepth) method, where 'bitdepth' is 8, 16, 24 (rgb), or 32 (float).
* Thanks to Qingzong Tseng, fixed a bug that caused overlays to be lost when converting composite stacks to RGB.
* Thanks to Jan Eglinger, fixed a bug that caused images created by the particle analyzer's "Show:" option to not use the calibration of the original image.
* Thanks to Guenter Giese, fixed bugs that caused the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog to not work as expected with multi-channel images.
* Thanks to Barry DeZonia, fixed a bug that caused the command recorder to not work with Image>Stacks>3D Project when processing 16 and 32 bit images.
* Thanks to William Edwards, fixed a bug that sometimes caused the median of 32-bit float images to be calculated incorrectly.
* Thanks to Michael Cammer, worked around a bug that could cause commands in the Image>Type submenu to not work as expected in non-batch-mode macros.
1.47a 17 July 2012
* Thanks to Thomas Boudier, added five new 3D filters (Median, Mean, Minimum, Maximum and Variance) to the Process>Filters submenu.
* Added the "Restore Startup Tools" command to the toolbar's >> menu.
* Thanks to Tiago Ferreira, built-in and plugin tools can be added to toolsets and the startup macros (example).
* Michael Schmid modified the Overlay Brush tool for constrained motion (vertical or horizontal) with shift and resizing with ctrl-shift (cmd-shift on Macs).
* Thomas Tongue added support for the CDELT and CTYPE headers to the FITS Reader.
* Added the getinfo("selection.color") and getValue("selection.width") macro functions.
* Thanks to Simon Roussel, fixed a bug that could cause overlays to not be displayed on virtual stacks.
* Fixed a bug that caused the brush and pencil tools to activate overlay selections.
* Michael Schmid fixed a bug that sometimes caused Preview to not work correctly with commands in the Process>Filters submenu.
* Fixed a 1.46 regression that caused the ROI Manager to generate incorrect ROI labels when the Associate 'Show All" ROIs with Slices" option was not enabled.
* Thanks to Stephan Semmler, fixed a regression that caused the ImagePlus.getNDimensions() method to sometimes return the wrong value.
* Thanks to Glen MacDonald, fixed a 1.46 regression that caused the setOption("Show All",boolean) macro function to not work.
-------------------------------------------------------------------
Fri Jun 1 10:32:47 UTC 2012 - lumnis@opensuse.org
- version update 1.46o 18 May 2012
* Set the stroke width to 0 in the Edit>Selection>Properties,
Image>Overlay>Overlay Options and ROI ManagerProperties dialogs
to have selections drawn using a width of one pixel
regardless of the image magnification.
* Fixed a bug that could cause selections being moved to not be
displayed correctly when the "Use ROI names as labels" option in
the ROI Manager was enabled.
* Fixed a bug that caused Analyze>Plot Profile to fail with line
selections with widths less than 1.0.
* Thanks to Franklin Shaffer, fixed a bug that sometimes a caused a
stack overflow error when importing large image sequences.
* Thanks to Tiago Ferreira, fixed a 1.46n regression that caused overlay
items to be removed when toggling the ROI Manager "Show All" checkbox.
- changes in 1.46n 11 May 2012
* In "Show All" mode, the ROI Manager now uses an overlay to
display the selections.
* Added the More>>Labels... command to the ROI Manager, as a
shortcut to Image>Overlay>Labels.
* Add a "Show plot" checkbox to the Analyze>Calibrate dialog box.
* File>Save As>XY Coordinates now correctly saves subpixel resolution
selections, and it works with more kinds of selections.
* Tiago Ferreira added a list of valid factors to the
Image>Stacks>Tools>GroupedZProjector dialog.
* Made the IJ.runPlugIn(String,String,String) method public.
* Added the IJ.getFullVersion() method.
* Thanks to Burri Olivier, fixed a bug that caused Image>Adjust>Threshold,
when the "Stack histogram" option was enabled, to use the histogram of
all channels instead of only the current channel.
* Tiago Ferreira fixed a bug that caused stacks binned with
Image>Stacks>Tools>GroupedZProjector to loose spatial calibration.
* Thanks to Burri Olivier, fixed a bug that caused incorrect auto stack
thresholds when "Limit to threshold was enabled in Analyze>Set Measurements.
* Thanks to Thomas Boudier and Michael Schmid, fixed a bug that caused
the Analyze>Summarize command to not work correctly on reopened results tables.
* Thanks to Jim Passmore, fixed a bug that caused NonBlockingDialogs to
not handle the yes/no/cancel option.
* Thanks to Norbert Vischer, fixed a bug that caused Image>Show Info to
incorrectly display the selection location when the image origin was not (0,0).
-------------------------------------------------------------------
Wed May 2 13:10:47 UTC 2012 - lumnis@opensuse.org
- vers update 1.46m
* ROIs in an overlay can be activated by alt-clicking, control-clicking or long-pressing.
* Thanks to Gabriel Landini, the Brush and Pencil tools installed from the toolbar's >> menu can be resized by shift-dragging.
* The icons for drawing tools installed from the toolbar's >> menu reflect the foreground color and are updated when the foreground color changes.
* Commands in the Edit>Selection submenu that modify the selection now support Undo and Redo and transfer color and line width properties.
* Fiji saves and loads custom tool configurations.
* Thanks to Ved Sharma, removed the restriction in Image>Stacks>Tools>Insert that the destination must be a stack.
* Thanks to Richie Mort, fixed a bug that could cause the contents of multiple custom results tables created by plugins to be invalid.
-------------------------------------------------------------------
Thu Mar 29 11:21:24 UTC 2012 - lumnis@opensuse.org
- vers update 1.46j
-------------------------------------------------------------------
Wed Feb 22 07:21:24 UTC 2012 - lumnis@opensuse.org
- vers update 1.45g
-------------------------------------------------------------------
Mon Feb 13 12:21:24 UTC 2012 - lumnis@opensuse.org
- vers update 1.45f
- ant build target set to : build
-------------------------------------------------------------------
Mon Sep 5 13:21:24 UTC 2011 - lumnis@opensuse.org
- vers update 1.45m
-------------------------------------------------------------------
Fri Jul 22 08:33:01 UTC 2011 - lumnis@opensuse.org
- vers update 1.45l
-------------------------------------------------------------------
Fri Jun 10 10:14:00 UTC 2011 - lumnis@opensuse.org
- vers update 1.45i
-------------------------------------------------------------------
Thu May 5 11:31:51 UTC 2011 - lumnis@opensuse.org
- update vers 1.45
Fri Jan 14 09:00:00 UTC 2010 - lumnis@opensuse.org
- copy from home:martin_ginkel
- updated version 1.44
- package cleanup e.g. changelog

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[Desktop Entry]
Name=ImageJ
GenericName="ImageJ public domain Java image processing program"
GenericName[DE]="Wissenschaftliches Bildbearbeitungsprogramm"
Type=Application
Comment=Image Processing
Comment[DE]=Bildverarbeitung
Exec=imagej
TryExec=imagej
Icon=imagej
Terminal=false
Categories=Graphics;2DGraphics;
X-SuSE-translation=true

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#!/bin/sh
#set -x
JAVA_HOME=@JAVA_HOME@
call=$0
if [ "`uname -s`" = "Linux" ]; then
awk=awk
else
awk=nawk
fi
if ls -l $call|grep -q ^l; then
# Symlink
call=`ls -l $call|$awk '{sub(/^.*-> /,"");print}'`
if [ -z "`echo $call|grep '^/'`" ]; then
#relative Symlink
call="`dirname $0`/$call"
fi
exec $call "$@"
else
# real file
dir=`dirname $call`
fi
export PATH=${JAVA_HOME}/bin:$PATH
exec java -Xmx512m -cp ${dir}/ij.jar:${JAVA_HOME}/lib/tools.jar ij.ImageJ -ijpath ${dir} "$@"

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#
# spec file for package imagej
#
# Copyright (c) 2024 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
%define SrcVersion 153u
Name: imagej
Version: 1.53u
Release: 0
Summary: A Java image processing program
License: SUSE-Public-Domain
Group: Productivity/Graphics/Convertors
URL: https://rsbweb.nih.gov/ij/
Source: https://rsbweb.nih.gov/ij/download/src/ij%{SrcVersion}-src.zip
Source1: %{name}.in
Source2: %{name}.desktop
Patch0: imagej-nosourcetarget.patch
BuildRequires: ImageMagick
BuildRequires: ant
BuildRequires: java-devel >= 1.8
BuildRequires: unzip
BuildRequires: update-desktop-files
Requires: java >= 1.8
BuildArch: noarch
%description
ImageJ is a multithreaded image processing program inspired by NIH
Image for the Macintosh, running either as an applet or as a
standalone program.
It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM,
FITS and "raw", and display, edit, anazlye, process and print
8/16/32-bit images. It supports "stacks", a series of images that
share a single window. It can calculate area and pixel value
statistics of user-defined selections, measure distances and angles,
create density histograms and line profile plots, supports standard
image processing functions such as contrast manipulation, sharpening,
smoothing, edge detection and median filtering. It does geometric
transformations such as scaling, rotation and flips. Zoom in/out up
to 32:1/1:32. Spatial calibration is available to provide real-world
dimensional measurements in units such as millimeters. Density or
gray scale calibration is also available.
ImageJ can be extended via Java plugins, and has a built-in editor and
compiler.
%prep
%autosetup -p1 -n source
%build
%{ant} -Dant.build.javac.source=1.8 -Dant.build.javac.target=1.8 build
%install
install -d -m 755 %{buildroot}%{_datadir}/%{name}
install -m 755 ij.jar %{buildroot}%{_datadir}/%{name}/%{name}.jar
# startscript
cat > %{name} << 'EOF'
#!/bin/sh
#
# imagej startscript
#
# Source functions library
echo Starting %{name} version %{version} ...
echo with options : ${@}
java -jar %{_datadir}/%{name}/imagej.jar ${@}
EOF
install -d -m 755 %{buildroot}%{_bindir}
install -m 755 %{name} %{buildroot}%{_bindir}/
# Icon
convert -strip build/microscope.gif build/%{name}.png
install -Dm 644 build/%{name}.png %{buildroot}%{_datadir}/pixmaps/%{name}.png
# Desktop menu entry
install -d -m 755 %{buildroot}%{_datadir}/applications
install -m 644 %{SOURCE2} %{buildroot}%{_datadir}/applications/%{name}.desktop
%suse_update_desktop_file %{name}
%files
%doc release-notes.html
%{_bindir}/*
%{_datadir}/%{name}
%{_datadir}/%{name}/*.jar
#%{_datadir}/%{name}/lib/*
%{_datadir}/applications/%{name}.desktop
%{_datadir}/pixmaps/%{name}.png
%changelog