Normally, image data is calibrated and bad pixels are edited out during the process of data collection; alternatively, you can use applycal to perform these operations after data collection.
applycal is a command-line application. There's a graphical front-end, applycal_i, which will generate a suitable command file for running applycal. Options for specifying the region to process and aspects of the graphical front-end are the same for applycal as for many other applications. See BatchRegion.html for a description of these common elements.
Overview | Calibration/bad pixel files | Forcing floating-point output
For each wave processed, applycal takes the name of a calibration file for that wave and the name of a file containing a list of pixels which should be edited out. For any wave, the calibration file can be omitted and no calibration will be performed on that wave's data; similarly, you can omit the bad pixel list for any wave so that pixel editing isn't applied to the data in that wave.
In the graphical front-end for applycal, the calibration file and bad pixel list are grouped by wave. Next to each is a toggle which when on indicates that that file should be used in the processing; you can select a file by entering its name directly or by pressing a Calibration file or Bad pixels file button to launch a file selection dialog. Selecting a file with the file selection dialog will automatically set the toggle to indicate that file will be used in processing.
On the command-line, the calibration files are specified by an argument of the form
-calfiles=file_1:file_2:file_3:file_4:file_5
where file_x is the calibration file for the xth wave in the input file. Any of the files can be omitted (the separating colons must still be included), or you can omit one or more entries from the end. For instance,
-calfiles=/usr/tmp/dapi_480x480.CAL
specifies that wave one in the input file will be calibrated with /usr/tmp/dapi_480x480.CAL and that no other waves will be calibrated.
-calfiles=:/usr/tmp/dapi_480x480.CAL:/usr/tmp/rhod_480x480.CAL::
specifies that wave one won't be calibrated, wave two will be calibrated with /usr/tmp/dapi_480x480.CAL, wave three will be calibrated with /usr/tmp/rhod_480x480.CAL, and no other waves will be calibrated. The argument
-calfiles=:/usr/tmp/dapi_480x480.CAL:/usr/tmp/rhod_480x480.CAL
has the same effect.
If no -calfiles argument appears on the command-line, applycal will prompt for the filenames and read them from standard input.
The bad pixel lists are specified with
-pixfiles=file_1:file_2:file_3:file_4:file_5
Such an argument (or its absence) is handled just as -calfiles is handled.
Overview | Calibration/bad pixel files | Forcing floating-point output
By default, applycal uses the same representation (byte, short, float) for an output pixel's data as was used for an input pixel. Setting the Force floating-point output toggle in the graphical front-end or specifyging -float on the command-line will cause applycal to use a floating-point representation for the output data.
applycal's internal calculations are always done in floating-point arithmetic regardless of the format of the input or output.
Overview | Calibration/bad pixel files | Forcing floating-point output