jeremysanders / contbin Public
Contour binning code
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Contour binning and accumulative smoothing software version 1.6 ------------------------------------------------------------------------------ Copyright Jeremy Sanders <email@example.com> (2002-2016) The reference paper is Sanders (2006), MNRAS, 371, 829, http://adsabs.harvard.edu/abs/2006MNRAS.371..829S This software is licensed under the GNU Public License See the file included as LICENSE for details Development location and where to file bug reports: https://github.com/jeremysanders/contbin Changes: 1.4: 2010-12-07: Fixes to compile on new gcc versions 1.5: Compilation fixes 1.6: Warnings for invalid image sizes and invalid S/N ratios -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= How to build the software ------------------------- This software requires a fairly recent gcc C++ compiler (other C++ compilers haven't been tested) with c++0x support. I've currently tested it on gcc-4.6.3. The only other requirement is the CFITSIO library. When unpacked, it should be simply a matter of typing "make" on Linux systems. The program depends on CFITSIO being on the system library path. If this is not the case, then the Makefile should be edited to add the installed include location as -I/directory/path on CXXFLAGS and the library location as -L/directory/path at the start of linkflags. Several executables, including contbin, accumulate_smooth, make_region_files, paint_output_images and accumulate_smooth_expmap should be built. The files will be copied to "bindir" in the Makefile if "make install" is used. This is /usr/local/bin by default. You can copy them by hand if preferred. Please report any problems building to me via preferably the github tracker. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= How to use the software ----------------------- The programs all use GNU-style command line options (--something=foo). They also allow the parameters to be defined in text files, specified using "@" syntax, e.g. "program @myopts", which may can contain carriage returns, and unix-style comments using "#", Contour binning ^^^^^^^^^^^^^^^ The main contour binning program. The most useful outputs of the program are the binned image (conbin_out.fits), and the binmap (contbin_binmap.fits). The binmap is a FITS image where each pixel is numbered according to which bin it is in. Beware: all my programs count from 0, not 1! The binmap can be used to generate region files (see make_region_files below). Usage is as follows: contbin [OPTIONS] inimage.fits inimage.fits is a counts image to do the binning on. Optional arguments are as follows: --out=FILE Specify an output filename for the binned image. This is the input image binned with the generated bins. Default is contbin_out.fits --outsn=FILE Specify output image which shows the final signal to noise for each bin, in each pixel of each bin. --outbinmap=FILE This is a generated binmap. The binmap is a fits image, where each pixel in the input image has been replaced by a number specifying which bin that pixel is in. The bins are numbered from zero. Region files can be produced from this file by make_region_files. --bg=FILE This is a counts image with a background image to use for the signal to noise calculations. This can have a different exposure to the input image (make sure the EXPOSURE keyword is set correctly). If the input and background images have exposures varying as a function of position (e.g. they are the result of several images added together), the --expmap and --bgexpmap options can specify FITS images where the exposure of each pixel is given (in the same units). --mask=FILE An image to exclude certain regions of the image from binning (e.g. point sources, regions beyond the edge of the CCD). Pixels in the image should be 1 to be included, and 0 elsewhere. A good way of making the image is to take the input image and set each of the pixels to 1. farith (FTOOLS) could be used here. farith inimage.fits 0 temp.fits MUL farith temp.fits 1 allones.fits ADD rm temp.fits You would make a region file with ds9 to specify the included regions and make the mask using (CIAO): dmcopy "allones.fits[sky=region(myreg.reg)][opt full]" mask.fits Alternatively, ask me for a program to make them directly from region files. --smoothed=FILE Rather than accumulatively smoothing the input image with the background image in the program, an smoothed image can be specified here. For instance, this could be an csmooth output image, or a smoothed hardness map. accumulate_smooth_expmap or accumulate_smooth could be used to produce this (if you do a lot of binning, it helps to split the smoothing and binning operations timewise). --expmap=FILE --bgexpmap=FILE Specify exposure map foreground and background images (see the --bg option above for details) --noisemap=FILE Normally signal to noise is calculated from the input image and background images, with their respective exposure times. If this option is set, instead this image is used for signal to noise calculations. The noise in a bin is sqrt of the sum of the squares of this input image for the pixels considered. --sn=VAL Specify the minimum signal to noise of each bin. This is t_b in the paper. If there is no background, this is approximately the square root of the number of counts. --automask Automatically try to remove unused regions of the input image, so that a mask image does not need to be supplied. This works by removing 8x8 pixel regions from the input image which do not contain any counts. This option is designed for a "quick look" at the binning process, if you haven't made a mask image. --constrainfill Enable the geometric constraint in the binning process, as described in the paper. This ensures that the bins do not become too elongated. The constraint parameter should be set with --constrainval=X --constrainval=VAL Set the geometric constraint value. --constrainfill has to be specified for this to have any effect. If a bin currently has N pixels, the program calculates the radius of a circle (r) with that area. It will not add any new pixels greated than VAL*r away from the current flux-weighted centroid of the bin. If VAL is around 1 then the bins are approximately spherical. Typical values are 2-3. --smoothsn=VAL Signal to noise to smooth the image by before binning. This is 15 by default. Larger values make smoothed-edged bins, but may miss small features. --noscrub An option to leave out the scrubbing process which removes small bins below the signal to noise threshold. This is for testing purposes. --binup The program bins the image binning using the highest pixel in the smoothed map first. This reverses this, binning from the lowest pixel first. This is useful if binning using a colour map. --scrublarge=VAL Bins with a fractional area greater than this value are "scrubbed" - i.e. discarded from the output. --help Shows the various options --version Which version of the program this is Accumulative Smoothing ^^^^^^^^^^^^^^^^^^^^^^ The accumulate_smooth program implements accumulative smoothing. Its syntax is accumulate_smooth [OPTIONS] inimage.fits inimage.fits is the input counts fits image. The possible options are: --bg=back.fits Set a background counts fits image. This is taken into account for the signal to noise calculations. The image should be of the same size as the input image. The EXPOSURE keywords in the input foreground and background images both need to be correct for this to work. --mask=mask.fits Supply a mask image to specify which parts of the image should not be smoothed. This is useful if there are point sources to be removed, or there are large blank areas at the edges. The image should be 1 where you want to smooth, and 0 elsewhere. See the contbin command for a way of making these using CIAO. --out=out.fits Specify the output image filename (default acsmooth.fits) --sn=VAL Specify the signal to noise threshold of the smoothing (default 15) For example: accumulate_smooth --mask=mymask.fits.gz --sn=100 --out=myout.fits inimage.fits Accumulative smoothing (with exposure map) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ A version of the program which can take account of an exposure map of the image. You need to supply an exposure map and an exposure corrected image. These could be generated by CIAO's merge_all script. accumulate_smooth_expmap --sn=20 expcorrect.fits expmap.fits Optional arguments are --mask, --out and --sn as above. Accumulative smoothing (for counts) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ accumulative_counts measures the size (scale) of a top hat kernel containing a certain signal to noise ratio (square root of number of counts), writing to a scale file. The scale file can then be applied to the same or other data to use the same smoothing kernel. When applying either a top-hat or a Gaussian smoothing can be used. To make the scale file: accumulate_counts --sn=30 --mask=mask.fits --scale scale.fits input.fits To apply the scale file (add --gaussian for Gaussian scaling): accumulate_counts --apply --scale scale.fits --applied out.fits input.fits Note that the mask file should contain integer pixels containing positive values for valid regions. 0 pixels are invalid regions. A special value of -2 in the mask file indicates regions (e.g. point sources) which should be replaced by smoothed counts from neighbouring regions. This special value allows point sources to be removed from output images. Making region files ^^^^^^^^^^^^^^^^^^^ make_region_files converts the binmap generated by the binning program into region files compatible with CIAO (well hopefully). You will see the regions it produces are pretty brain-dead (everything is made out of boxes). A polygon edge-following algorithm is left as an exercise for the reader. Usage is pretty simple: make_region_files --minx=XXXX --miny=YYYY --bin=B --outdir=outdir binmap.fits This will write region files called xaf_A.reg in directory outdir, where A goes from 0 to the number of regions-1. The regions are in physical coordinates. To work out the coordinates the program needs to know the minimum X and Y coordinates of the original image that went into creating the binmap. It also needs to know the size of the bins in these units. If your image was created in CIAO using dmcopy "in_evt2.fits[bin x=1000:2000:2,1500:2500:2]" in_image.fits then XXXX is 1000, YYYY is 1500, and B is 2. Making images with calculated values ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ After spectral fitting you often want to make a map showing the value of each bin (temperature, metallicity, etc). This program takes the collected spectral fit results and creates a map for each parameter. The format is suited to my automated spectral fitting tool, so some adaptation is necessary if you want to use this program. Please contact me if you are interested in using my automated spectral fitting software (xaf3). The usage is paint_output_images --binmap=binmap.fits --input_dir=/some/input/directory or paint_output_images -n binmap.fits -i /some/input/directory (short forms are accepted for the other programs, see --help) The program reads a file called region_list.txt in the input directory. That file contains a list of region names and the (unused by this program) input spectrum. e.g. region_list.txt contains xaf_0 xaf_0_grp_spec.fits xaf_1 xaf_1_grp_spec.fits ... xaf_0 is the name of the zeroth region, and xaf_0_grp_spec.fits is the name of the input spectrum (this is unused, so this could be anything without a space). The program reads from files with the name appended by "_fit_out.txt" in the same directory as region_list.txt, for example xaf_0_fit_out.txt, xaf_1_fit_out.txt, ... These files contain a list of variable names and values, e.g. xaf_0_fit_out.txt could contain kT 3.0 Z 1.0 NH 0.1 The program will "paint" in the output files kT_out.fits, Z_out.fits, NH_out.fits the values specified for each bin. For example, the region where the pixels are 0 in the binmap file, will contain 3.0 in the output file kT_out.fits for this example.
Contour binning code
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