The most difficult requirement to satisfy is WCS matching. Each image has to be in exactly the same pixel space in order to overlay them successfully in an image program. The process is generally to use Montage's mProject to project the images into the same plane, then mAdd with a blank map of a given size so that the dimensions in pixels are identical. Once that's done, I load the images into GIMP. However, GIMP reads .fits files as 256 bit data - which is essentially useless because most (interesting) images have a dynamical range >~1000. So I usually make images emphasizing the faint emission in log scale with the high and low ends cut off (I use DS9 to determine high/low). I make a second copy showing the details of the very bright regions, again in logscale but it ends up being a different log scale - essentially, my transfer function becomes a broken power law. The tricks in GIMP are numerous, but primarily two: 1. Rotate the color table ~60 degrees 2. Use images as "Layer Masks" (aka alpha layers) on a solid color background There's also the nice trick when using radio data of using optical or some other wavelength to provide the high-resolution details, while the radio emission provides the intensity.
IDL array indexing
array_indices(array, location) instead of that x mod n_e(), y / n_e() crap
IDL colors
To get IDL colors to 'work right' (i.e. a colortable has 255 colors etc), put this in a startup file:
device, true_color = 24, retain = 2, decompose = 0red = [0,1,1,0,0,1]green = [0,1,0,1,0,1]blue = [0,1,0,0,1,0]if not strcmp(getenv('DISPLAY'),'') then $ tvlct, 255*red, 255*green, 255*blueIDL string conversion
Just a reminder to me: to convert an IDL number to a string, use string! `` s = string(x,format='(F10.5)')`` Also, Julian Date conversion
IDL syntax highlighting in VIM
I've edited my idlang.vim to auto-identify files that start with a semicolon. Add Line 19: `` syn match idlangStatement "^s*;s"`` Line 61/2 (allow spaces before ;): syn match idlangComment "\s*[\;].*$" contains=idlangTodo AG
IDL-to-Python
astrobetter started up an idl-to-python guide on their wiki.
.inputrc
New unix stuff! This is, again, stuff I'd searched for forever but never found the right collection of terms. This is what bash readline is REALLY all about. if you make an inputrc file, you can get awesome readline capabilities (similar to ipython). This post at lifehacker showed me how to do it. This site has a more complete description of how to use readline/inputrc. Even better: VI command line editing. There's also something called magic space but I don't know what purpose it serves all the time... it will replace 'magic' characters like !* and !& and !! with whatever command they represent if you hit space immediately after typing them (explained better here). Wow. Awesome.
Installing 64 bit tcl/tk on Mac OS X
Everything is described in this post: http://www.nabble.com/Error-compiling-tk-8.5.7-on-Mac-OS-X-10.5-td23790967.html
But here's a script too: curl -O 'http://osdn.dl.sourceforge.net/sourceforge/tcl/t{cl,k}8.5.7-src.tar.gz'for f in t*8.5.7*.gz; do tar zxf $f; done cd tcl8.5.7/unix/./configure --enable-framework --enable-64-bitcd tk8.5.7/unix/./configure --enable-framework --enable-64-bitmake -j 4 -C tcl8.5.7/unix make -j 4 -C tk8.5.7/unixsudo make install -C tcl8.5.7/unix sudo make install -C tk8.5.7/unix
Concerns:
- might be necessary to do this in the macosx directory for some reason, though Aqua doesn't support 64 bits
- have to recompile python to get _tkinter to work (see a later post)
Installing Snow Leopard
I'm going to attempt to install snow leopard today. This post will serve as a record of the difficulties I run into. Things to install (and ensure they are 64-bit):
- ipython
- numpy
- scipy
- matplotlib
- stsci-python
- starlink
- gfortran
- latex
- idl (check)
Things that have happened:
- Had to restart again (twice) to install additional updates
- My bash command line looked funny - something about bash changed, but I don't know what. The fix was easy: commented out some code from http://pseudogreen.org/blog/set_tab_names_in_leopard_terminal.html that I had been using to set the tab title
- My locate db broke. Needed repair: sudo /usr/libexec/locate.updatedb
- numpy svn failed to build: `` python setup.py buildRunning from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'F2PY Version 2_8111numpy/core/setup_common.py:86: MismatchCAPIWarning: API mismatch detected, the C API version numbers have to be updated. Current C api version is 4, with checksum 59750b518272c8987f02d66445afd3f1, but recorded checksum for C API version 4 in codegen_dir/cversions.txt is 3d8940bf7b0d2a4e25be4338c14c3c85. If functions were added in the C API, you have to update C_API_VERSION in numpy/core/setup_common.pyc. MismatchCAPIWarning)blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec']running buildrunning config_ccunifing config_cc, config, build_clib, build_ext, build commands --compiler optionsrunning config_fcunifing config_fc, config, build_clib, build_ext, build commands --fcompiler optionsrunning build_srcbuild_srcbuilding py_modules sourcesbuilding library "npymath" sourcescustomize NAGFCompilerFound executable /usr/local/bin/f95customize AbsoftFCompilerCould not locate executable f90Found executable /usr/bin/f77absoft: no Fortran 90 compiler foundabsoft: no Fortran 90 compiler foundcustomize IBMFCompilerCould not locate executable xlf90Could not locate executable xlfcustomize IntelFCompilerCould not locate executable ifortCould not locate executable ifccustomize GnuFCompilerFound executable /usr/local/bin/g77gnu: no Fortran 90 compiler foundgnu: no Fortran 90 compiler foundcustomize Gnu95FCompilerFound executable /usr/local/bin/gfortrancustomize Gnu95FCompilercustomize Gnu95FCompiler using configC compiler: gcc -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypescompile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'gcc: _configtest.cgcc _configtest.o -o _configtestld: library not found for -lcrt1.10.5.ocollect2: ld returned 1 exit statusld: library not found for -lcrt1.10.5.ocollect2: ld returned 1 exit statusfailure.removing: _configtest.c _configtest.oTraceback (most recent call last): File "setup.py", line 210, in setup_package() File "setup.py", line 203, in setup_package configuration=configuration ) File "/Users/adam/repos/numpy-svn/numpy/distutils/core.py", line 186, in setup return old_setup(new_attr) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py", line 134, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 163, in build_sources self.build_library_sources(*libname_info) File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 298, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 670, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program")RuntimeError: Broken toolchain: cannot link a simple C program`` **SOLUTION: Use the Mac OS X 10.6 python (/usr/bin/python). I will do this until I run into another problem. Numpy build successfully
- Build/install matplotlib - failed! Completely!
- Acquired gcc/gfortran from hpc
- Followed instructions from hyperjeff on fortran install...
- Get rid of numpy 1.2.1: `` mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/.not_numpy.bak``
- Try to install scipy. Fail on missing umfpack, follow hyperjeff's instructions (but make sure to edit the site.cfg in scipy, not just the one in numpy). Had to add the following code: sudo cp AMD/Lib/libamd.a /System/Library/Frameworks/Python.framework/Versions/2.6/libsudo cp UMFPACK/Lib/libumfpack.a /System/Library/Frameworks/Python.framework/Versions/2.6/libsudo cp AMD/Include/amd.h /System/Library/Frameworks/Python.framework/Versions/2.6/includesudo cp UFconfig/UFconfig.h /System/Library/Frameworks/Python.framework/Versions/2.6/includesudo cp UMFPACK/Include/*.h /System/Library/Frameworks/Python.framework/Versions/2.6/include
- Installed fftw from fftw.org with simple ./configure, make, sudo make install - no compiler opts as they killed the install
- Get SoundSource from rogueamoeba
- Updated istatmenus
IRAF append/prepend/replace
IRAF has special syntax to append/replace, so you can do something like: imarith *.fits - dark.fits ds_//*.fits ...though I can't remember right now how to do replacement etc.