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When you're ready to get started, just go to the file menu, hit open, and browse to the file you want. Typically an input file for fitlc consists of any number of data lines with four columns of numeric data each, and any number of optional lines to specify your desired settings. The actual format of the numeric data can be whatever you want, as long as all four columns are separated by at least one space. The first column should be a flag specifying which filter the current line belongs to. The second column is the HJD of the observation, the third column is the magnitude, and the last column is the error. Below is an example that contains 23 data lines and 4 settings (also, click here to download this file). Every data line beginning with a '0' is a measurement in the 'B' filter, and the lines beginning with a '1' are a measurement in the 'V' filter. An explanation of all the settings you can use can be found here.
filtername[0] = 'B'
filtername[1] = 'V'
minday = 1494
maxday = 1495
0 1895.82250977 25.863 0.1270
0 1494.77758789 25.090 0.0810
0 1895.75512695 25.658 0.1100
0 1494.91149902 25.583 0.1160
0 1895.93774414 26.383 0.2040
0 1494.84423828 25.419 0.1030
0 1895.88916016 26.132 0.1550
0 1494.97888184 26.100 0.1720
0 1494.93029785 25.545 0.1160
0 1494.71020508 25.831 0.1400
0 1895.73632812 25.653 0.1180
0 1895.95654297 26.255 0.1690
0 1494.57617188 26.142 0.1800
0 1895.87036133 26.046 0.1590
0 1494.64355469 25.896 0.1480
0 1895.80371094 26.016 0.1540
1 1895.46984863 25.568 0.0980
1 1895.53515625 25.614 0.1040
1 1494.44152832 25.677 0.1010
1 1494.39428711 25.658 0.1070
1 1494.50817871 25.754 0.1080
1 1895.60180664 25.338 0.0850
1 1494.37622070 25.637 0.0990
This format is flexible. Settings can be located anywhere in this file, including in the middle of the data (as long as they are on a line by themselves). In a setting line, use a semi-colon to comment out a line or part of a line. Most importantly, you can include as many additional columns in the data section as you want, and these extra columns will be stored and later sent to the final output file along with everything else. There's a couple requirements about extra columns though. First, every data line must have the same number of extra columns. Second, these extra columns can only contain numeric data. If a line contains anything other than the characters 0-9, +, -, ., e, E, d, D, or whitespace the line will be assumed to be a comment and will be treated as such.