Always chdir into ij_dir on Mac OS X

[benwbooth]

See issue #17

[dscho]

Actually, the idea of chdiring into imagejDir only when the -psn flag was passed was carefully thought out (but not properly documented, as you found out to my chagrin): we use the launcher for many a use case, including running macros from the command line and launching the ImageJ.app from the icon. In the latter case, it is kind of okay to chdir into imagejDir (as a convenience for the user), but in the former case it would be a major bug to do so. Just imagine you want to run a macro in the current directory via

/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx this-here-macro.ijm

Currently, it is found correctly. Good. With the change in this PR, it would no longer be found correctly...

I agree I have to document this better.

But now I am curious: why do you need this change? Just for consistency, or do you have a concrete use case where you require this (e.g. because the file chooser refuses to let you switch into Fiji.app/ without jumping through hoops by drag-n-dropping files/folders from the Finder into the file chooser)?

[benwbooth]

I'm trying to run Micro-Manager as a Fiji plugin. Unfortunately, Micro-Manager looks for its plugins directory in the current working directory, so if the launcher doesn't chdir into the Fiji directory, then the Micro-Manager plugins don't appear in the UI. As a workaround I modified the JVM options in the Info.plist file to explicitly pass in the Micro-Manager plugin directories as property values. However, it would be nice if I didn't have to modify the Info.plist in order for everything to work.

[benwbooth]

In any case, the "-psn" flag is no longer passed in in Mavericks, so I guess you'll have to find another mechanism to determine if ImageJ was launched from the Finder

[dscho]

Unfortunately, Micro-Manager looks for its plugins directory in the current working directory

I guess that is the bug we have to address, then...

[dscho]

In any case, the "-psn" flag is no longer passed in in Mavericks

Oh, we can probably address this issue separately anyway. Since I am on Snow Leopard right now and have no easy access to a Mavericks installation, could you execute the following Beanshell in your Fiji.app (just hit [ to start the script editor, then select Language>Beanshell):

print(System.getenv());

If you compare the output between a Fiji.app started from the command-line vs the Dock icon, do you see a difference? We might use that as a better indicator than -psn.

[benwbooth]

Here is what I get when running from the Dock icon:

Started New_.bsh at Wed Jun 25 10:43:36 PDT 2014
{SHELL=/bin/bash, TMPDIR=/var/folders/sv/7m1mxyn90yv0gbjny6nn_4fm000xnk/T/, DYLD_LIBRARY_PATH=/Applications/Fiji.app/lib/macosx:/Applications/Fiji.app/mm/macosx, com.apple.java.jvmMode=client, APP_NAME_26504=ImageJ, __CF_USER_TEXT_ENCODING=0x76B2:0:0, PATH=/usr/bin:/bin:/usr/sbin:/sbin, APP_ICON_26504=/Applications/Fiji.app/Contents/Resources/Fiji.icns, DISPLAY=/tmp/launch-Lxczfb/org.macosforge.xquartz:0, USER=bbooth, com.apple.java.jvmTask=JNI, HOME=/Users/ben, LOGNAME=bbooth, Apple_PubSub_Socket_Render=/tmp/launch-kKtn34/Render, SSH_AUTH_SOCK=/tmp/launch-MjK7W2/Listeners, __CHECKFIX1436934=1}

And here is what I get from running on the command-line:

Started New_.bsh at Wed Jun 25 10:45:11 PDT 2014
{TERM=xterm-256color, DYLD_LIBRARY_PATH=/Applications/Fiji.app/lib/macosx:/Applications/Fiji.app/mm/macosx, JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_65-b14-462.jdk/Contents/Home, TERM_PROGRAM=iTerm.app, GENDATA=/data/GenData, PWD=/Applications/Fiji.app/Contents/MacOS, CONSED=/usr/local/bdgp/consed_mac-27.0/bin/consed, BC_ENV_ARGS=/Users/ben/.bc, MACHTYPE=x86_64, PS1=\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ , PERLBREW_PERL=perl-5.20.0, BLASTDB=/data/blast/db, PERLBREW_PATH=/Users/ben/.perlbrew/macair/root/bin:/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/bin, TMPDIR=/var/folders/sv/7m1mxyn90yv0gbjny6nn_4fm000xnk/T/, EDITOR=vim, BDGPCONF=/usr/local/bdgp/etc/conf, PATH=/Users/ben/.perlbrew/macair/root/bin:/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/bin:/Users/ben/bin:/usr/local/share/npm/bin:/Users/ben/.cabal/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/texbin:/sbin:/bin:/usr/bin/vendor_perl:/usr/bin/site_perl:/usr/bin:/bin:/usr/sbin:/sbin, LESS=-FMXSRi, PERLBREW_BASHRC_VERSION=0.69, PAGER=less, Apple_PubSub_Socket_Render=/tmp/launch-kKtn34/Render, LSCOLORS=ExGxcxdxCxcgcdabagacad, BDGPDATA=/usr/local/bdgp/data, PERLBREW_ROOT=/Users/ben/.perlbrew/macair/root, ITERM_PROFILE=Default, BLASTFILTER=/usr/local/bdgp/wublast/filter, com.apple.java.jvmMode=client, PERLDB_OPTS=ReadLine=1, SHLVL=1, NODE_PATH=:/usr/lib/node_modules, WINEARCH=win32, __CF_USER_TEXT_ENCODING=0x76B2:0:0, MANPATH=/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/man:/usr/local/share/man:/usr/share/man:/usr/texbin/man:/Applications/Xcode.app/Contents/Developer/usr/share/man:/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/share/man, CDNATERM=/opt/X11/bin/xterm, PERLBREW_MANPATH=/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/man, APP_NAME_26546=ImageJ, PHRAPVIEW_PARAMETERS=/usr/local/bdgp/etc/phrapview.dat, LOGNAME=bbooth, _=./ImageJ-macosx, __CHECKFIX1436934=1, SSH_AUTH_SOCK=/tmp/launch-MjK7W2/Listeners, BDGP=/usr/local/bdgp, ABIdata=/data/ABIdata, OLDPWD=/Applications/Fiji.app, SHELL=/bin/bash, ITERM_SESSION_ID=w0t1p0, PHRED_PARAMETER_FILE=/usr/local/bdgp/phrap/etc/phredpar.dat, BDGPBIN=/usr/local/bdgp/bin, PERLBREW_HOME=/Users/ben/.perlbrew/macair/home, BDGPLIB=/usr/local/bdgp/lib, DISPLAY=/tmp/launch-Lxczfb/org.macosforge.xquartz:0, USER=bbooth, PERLBREW_VERSION=0.69, com.apple.java.jvmTask=JNI, APP_ICON_26546=/Applications/Fiji.app/Contents/Resources/Fiji.icns, HOME=/Users/ben, HOMEBREW_CASK_OPTS=--appdir=/Applications, ABIDATA=/data/ABIdata, BDGPETC=/usr/local/bdgp/etc, CONSED_PARAMETERS=/usr/local/bdgp/etc/.consedrc, LANG=en_US.UTF-8}

[ctrueden]

Here's the diff:

diff --git a/dock.txt b/cli.txt
index c05b496..49e6da1 100644
--- a/dock.txt
+++ b/cli.txt
@@ -1,15 +1,60 @@
-APP_ICON_26504=/Applications/Fiji.app/Contents/Resources/Fiji.icns
-APP_NAME_26504=ImageJ
+ABIDATA=/data/ABIdata
+ABIdata=/data/ABIdata
+APP_ICON_26546=/Applications/Fiji.app/Contents/Resources/Fiji.icns
+APP_NAME_26546=ImageJ
 Apple_PubSub_Socket_Render=/tmp/launch-kKtn34/Render
+BC_ENV_ARGS=/Users/ben/.bc
+BDGP=/usr/local/bdgp
+BDGPBIN=/usr/local/bdgp/bin
+BDGPCONF=/usr/local/bdgp/etc/conf
+BDGPDATA=/usr/local/bdgp/data
+BDGPETC=/usr/local/bdgp/etc
+BDGPLIB=/usr/local/bdgp/lib
+BLASTDB=/data/blast/db
+BLASTFILTER=/usr/local/bdgp/wublast/filter
+CDNATERM=/opt/X11/bin/xterm
+CONSED=/usr/local/bdgp/consed_mac-27.0/bin/consed
+CONSED_PARAMETERS=/usr/local/bdgp/etc/.consedrc
 DISPLAY=/tmp/launch-Lxczfb/org.macosforge.xquartz:0
 DYLD_LIBRARY_PATH=/Applications/Fiji.app/lib/macosx:/Applications/Fiji.app/mm/macosx
+EDITOR=vim
+GENDATA=/data/GenData
 HOME=/Users/ben
+HOMEBREW_CASK_OPTS=--appdir=/Applications
+ITERM_PROFILE=Default
+ITERM_SESSION_ID=w0t1p0
+JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_65-b14-462.jdk/Contents/Home
+LANG=en_US.UTF-8
+LESS=-FMXSRi
 LOGNAME=bbooth
-PATH=/usr/bin:/bin:/usr/sbin:/sbin
+LSCOLORS=ExGxcxdxCxcgcdabagacad
+MACHTYPE=x86_64
+MANPATH=/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/man:/usr/local/share/man:/usr/share/man:/usr/texbin/man:/Applications/Xcode.app/Contents/Developer/usr/share/man:/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/share/man
+NODE_PATH=:/usr/lib/node_modules
+OLDPWD=/Applications/Fiji.app
+PAGER=less
+PATH=/Users/ben/.perlbrew/macair/root/bin:/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/bin:/Users/ben/bin:/usr/local/share/npm/bin:/Users/ben/.cabal/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/texbin:/sbin:/bin:/usr/bin/vendor_perl:/usr/bin/site_perl:/usr/bin:/bin:/usr:/sbin:/sbin
+PERLBREW_BASHRC_VERSION=0.69
+PERLBREW_HOME=/Users/ben/.perlbrew/macair/home
+PERLBREW_MANPATH=/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/man
+PERLBREW_PATH=/Users/ben/.perlbrew/macair/root/bin:/Users/ben/.perlbrew/macair/root/perls/perl-5.20.0/bin
+PERLBREW_PERL=perl-5.20.0
+PERLBREW_ROOT=/Users/ben/.perlbrew/macair/root
+PERLBREW_VERSION=0.69
+PERLDB_OPTS=ReadLine=1
+PHRAPVIEW_PARAMETERS=/usr/local/bdgp/etc/phrapview.dat
+PHRED_PARAMETER_FILE=/usr/local/bdgp/phrap/etc/phredpar.dat
+PS1=\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ 
+PWD=/Applications/Fiji.app/Contents/MacOS
 SHELL=/bin/bash
+SHLVL=1
 SSH_AUTH_SOCK=/tmp/launch-MjK7W2/Listeners
+TERM=xterm-256color
+TERM_PROGRAM=iTerm.app
 TMPDIR=/var/folders/sv/7m1mxyn90yv0gbjny6nn_4fm000xnk/T/
 USER=bbooth
+WINEARCH=win32
+_=./ImageJ-macosx
 __CF_USER_TEXT_ENCODING=0x76B2:0:0
 __CHECKFIX1436934=1
 com.apple.java.jvmMode=client

[dscho]

@benwbooth To be honest, I hoped for an analysis from your side...

[dscho]

Okay, after spending time on the analysis myself, I think that the PWD environment variable is a good tell-tale.

@benwbooth feel free to make up for it by updating your pull request ;-)

[benwbooth]

That's the same conclusion I just came to! You beat me to it :) I'll update pull request.

[dscho]

How about squashing those two commits? In general, we try to avoid to introduce flawed code in the same PR that fixes it. It is easy to fix, too: just call git rebase -i HEAD~2, add the line exec git reset --soft HEAD^^ && git commit -C HEAD@{1} after the two pick lines, save and quit the editor. That's it. Except for the forced push: git push origin +HEAD.

[benwbooth]

OK, I guess that should do it. Thanks!

[dscho]

Perfect! Thank you so much!