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FixFITS

A program to find and fix bad columns and bad pixels in FITS files.

By Sander Pool, Tungsten Technologies.

This program may be freely distributed for private use but not for monetary gain. Contact the author for specifics.

Quick Start

Description

FixFITS is used to detect bad columns in raw FITS images. Once detected the user can instruct the program to fix them. In addition FixFITS can use a single dark frame to determine hot and cold pixels and apply those. FixFITS is a command line utility that can work on either a specified file or all FITS files found in the current directory.

Installation

Unzip the files into a directory of your choosing. Add the directory to your path if you'd like to run FixFITS without having to specify the entire path. The suggested path is c:\bin but any path can be used. In the following text it is assumed FixFITS is installed in c:\bin and that c:\bin is part of your path. Use windows help or your favorite search engine to find out how to add c:\bin to your path.

Typical usage

fixfits -a -fc

Find bad columns, use the default bad column percentage (25) and scan all FITS files in the current directory. Typical output:

C:\WD_Drive\AstroImaging\Captures\2009\2009-01-16\Markarian>fixfits -a -fc
Fixfits version 1.0.1.3
Markarian_001.fit Bad columns: 443 1544 2359 2716
Markarian_002.fit Bad columns: 443 1544 2359 2716
Markarian_003.fit Bad columns: 443 1544 2359 2716
Markarian_004.fit Bad columns: 443 1544 2359 2716
Markarian_005.fit Bad columns: 443 1544 2359 2716
Markarian_006.fit Bad columns: 443 1544 2359 2716
Markarian_007.fit Bad columns: 443 1544 2359 2716
Markarian_008.fit Bad columns: 443 1544 2359 2716
Markarian_009.fit Bad columns: 443 1544 2359 2716
Markarian_010.fit Bad columns: 443 472 1544 2359 2716
Markarian_011.fit Bad columns: 443 472 591 1544 2359 2716
Markarian_012.fit Bad columns: 443 591 1544 2359 2716
Markarian_013.fit Bad columns: 443 1544 2359 2716
Markarian_014.fit Bad columns: 443 1544 2359 2716
Markarian_015.fit Bad columns: 443 1544 2359 2716
Markarian_016.fit Bad columns: 443 1544 2359 2716
Markarian_017.fit Bad columns: 443 591 1544 2359 2716
Markarian_018.fit Bad columns: 443 591 1544 2359 2716
Markarian_019.fit Bad columns: 443 1544 2359 2716
Found the following bad columns:
443 : 19
472 : 2
591 : 4
1544 : 19
2359 : 19
2716 : 19

No files are actually written at this time. Note that files with fixfits in the name will not be scanned. For each file the bad columns are printed. Then a summary where each column that was found is followed by a count of how many times. This information can then be used for the following step which does the actual fixing. Note that I've left out 472 and 591:

fixfits -a -cc 443,1544,2359,2716 -d ≤path to dark file≥

Fix the specified columns in all images and use the specified dark file to find hot and cold pixels with the default sigma setting (30):


C:\WD_Drive\AstroImaging\Captures\2009\2009-01-16\Markarian>fixfits -a -f -c 443
,1544,2359,2716 -d c:\WD_Drive\AstroImaging\MasterFiles\Darks\Dark20F\Dark15m20F
B110G1_001.fit
Fixing columns: 443 1544 2359 2716
Fixfits version 1.0.1.4
Found 37 hot pixels (column, row):
26, 44
216, 63
1708, 108
1847, 288
2573, 291
2009, 322
1255, 325
1018, 361
2217, 365
85, 474
86, 474
1553, 480
828, 534
1177, 580
523, 699
1532, 740
1052, 782
3024, 786
147, 790
148, 790
1781, 796
1681, 869
1219, 1023
1855, 1225
442, 1265
443, 1265
441, 1266
1449, 1288
1059, 1382
402, 1414
1673, 1639
2714, 1758
2715, 1758
3000, 1812
3001, 1812
888, 1943
2090, 1971
Markarian_001.fit Markarian_002.fit Markarian_003.fit Markarian_004.fit Markaria
n_005.fit Markarian_006.fit Markarian_007.fit Markarian_008.fit Markarian_009.fi
t Markarian_010.fit Markarian_011.fit Markarian_012.fit Markarian_013.fit Markar
ian_014.fit Markarian_015.fit Markarian_016.fit Markarian_017.fit Markarian_018.
fit Markarian_019.fit
C:\WD_Drive\AstroImaging\Captures\2009\2009-01-16\Markarian>

At this point files have been created with fixfits in the name. Use these to stack.

Detailed usage

  • -m : monochrome image, use immediate neighbors for averaging default is OSC image, uses col-2 and col+2.
  • -fc : find bad columns
  • -fp : bad column threshold percentage (default 25)
  • -m : monochrome image, use immediate neighbors for averaging
  • -c columns : fix columns (comma separated list of up to 20 integers)
  • -dc : fix default columns (443,2359,2716,1534)
  • -a: : fix all .fts and .fit files in the current directory (except ones with 'fixfits' in the name) creates [filename]_fixfits.fts files, overwriting if they already exist
  • -i image: image to fix. Use -a to open all .FTS and .FIT files in the current working directory.
  • -d path : use path as dark frame to determine warm/hot pixels. See -s below.
  • -b int : skip int pixels around the border when determining warm/hot pixels. Default: 10
  • -s int : use int as sigma value to determine warm/hot pixels pixels outside the range of mean +/- sigma*stddev are considered warm/hot pixels default: 30. Averaging done like column fixing, depends on -m flag.

Release Notes

2/17/09

  • Removed the -f option
  • Added -dc option

1/17/09

  • First Release

      

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