PyNOT : init

This task creates the file classification table and initiates the default parameter file for either the spectroscopic or photometric pipeline. The task takes two positional arguments mode (either spex or phot) and path which points to the directory holding the raw data files to be processed.

File classification

The classification task analyzes each image header and assigns an image type based on a set of pre-defined rules. The files are then sorted alphabetically for each type and saved as a PyNOT File Classification table (pfc). The filename is by default 'dataset.pfc'.

The file classification table is a plain text file, and can be edited for fast and flexible adjustments to the pipeline. For instance, any file that should be ignored by the pipeline can simply be commented out (by use of the '#' symbol). The file can also be used to create sublists for running individual tasks. One example would be to copy the full PFC table to a new file called 'bias.list' and remove all files that are not bias files. This list of bias images can then be passed to the task pynot bias.

Default options

The default options are generated based on the first argument: either 'spex'/'spec' or 'phot'. The filename of the PFC file created by the subtask above is inserted to the options file for easy execution of the pipeline afterwards. The options file is a YAML file and is sensitive to the indenting. Any changes to parameters should therefore maintain the same indent structure, otherwise the pipeline might not function as intended.

Note: An overview of the options for individual tasks can be shown by running the command line help function:
pynot init -h will show the available parameters for the init task.

Example Syntax

pynot init {spec,spex,phot} path


Full example of command line syntax:

pynot init [-h] [-p PARS] [-o OUTPUT] [-s] {spec,spex,phot} path [path ...]



Overview of parameters

mode
Create parameter file for spectroscopy or imaging?
path
Path (or paths) to raw data to be classified
Optional Arguments:
--pars (-p): 'options.yml'
Filename of parameter file, default = options.yml
--output (-o): 'dataset.pfc'
Filename of file classification table (*.pfc)
--silent (-s): True
Minimze the output to terminal