| contsub.threshold | float | ≥ 0.0 | 2.0 | Relative clipping threshold. All channels with a flux density > `contsub.threshold` times the noise will be clipped and excluded from the polynomial fit. |
| flag.auto | string | true, false, channels, pixels | false | If set to `true`, SoFiA will attempt to automatically flag spectral channels and spatial pixels affected by interference or artefacts based on their RMS noise level. If set to `channels`, only spectral channels will be flagged. If set to `pixels`, only spatial pixels will be flagged. If set to `false`, auto-flagging will be disabled. Please see the user manual for details. |
| flag.catalog | string | | | Path to a catalogue file containing two columns that specify the longitude and latitude coordinates of sky positions to be flagged in the native coordinate system and units of the input data cube. The two columns can be separated by spaces, tabulators or commas. Also see `flag.radius`. |
| flag.cube | string | | | Optional path to a data cube containing flagging information. All pixels with a value greater than 0 in the flagging data cube will be flagged in the input data cube. The flagging cube must be of integer type and must have the same dimensions as the input data cube. |
| flag.log | bool | true, false | false | If set to `true`, write a list of the channels and pixels flagged by the auto-flagger to a log file. Note that if no channels or pixels were found to be in need of flagging, then the log file will not be written irrespective of the value of `flag.log`. |
| flag.radius | int | ≥ 0 | 5 | Radius around the sky positions listed in the catalogue provided by `flag.catalog` that should be flagged. If `0`, then only the nearest pixel to the position will be flagged. Otherwise, pixels within the specified radius around the nearest pixel will be flagged. |
| flag.region | list | | | Region(s) to be flagged in the input data cube prior to processing. The flagging region must contain a multiple of six comma-separated integer values of the following format: `x_min`, `x_max`, `y_min`, `y_max`, `z_min`, `z_max`, ... (all in units of pixels and 0-based). Pixels within those regions will be set to blank in the input cube. If unset, no flagging will occur. |
