Running from the Command Line

Nifty is started with the runNifty command by specifying a pipeline or step with arguments and options.

The syntax used to start Nifty is:

runNifty <Pipeline or Step Name> <arguments>

To get help or list the available options, type the runNifty command without any arguments.

runNifty

Examples of Running from the Command Line

Starting a Data Reduction from the Beginning

To start the NIFS pipeline, populating a configuration file interactively:

runNifty nifsPipeline -i

To start the NIFS pipeline from a pre-built configuration file:

runNifty nifsPipeline config.cfg

To do a fully automatic data reduction, downloading raw data from the Gemini Public Archive (Eg: GN-2013A-Q-62):

runNifty nifsPipeline -f GN-2013A-Q-62

To do a fully automatic data reduction, using raw data from a local directory (Eg: /Users/ncomeau/data/TUTORIAL):

runNifty nifsPipeline /Users/ncomeau/data/TUTORIAL

Starting a Data Reduction from a Specified Point

You can run each step, one at a time, from the command line like so. You need a config.cfg file in your current working directory to run individual steps. Each step requires the general config section and its unique config section to be populated.

You can also run an individual step by turning them on or off in nifsPipeline config and running the nifsPipeline.

nifsSort: To only copy and sort NIFS raw data type:

runNifty nifsSort

Or use a config.cfg file like this:

# Nifty configuration file.
#
# Each section lists parameters required by a pipeline step.

manualMode = False
over = False
merge = True
scienceDirectoryList = []
telluricDirectoryList = []
calibrationDirectoryList = []

[nifsPipelineConfig]
sort = True
calibrationReduction = False
telluricReduction = False
scienceReduction = False

[sortConfig]
rawPath = ''
program = ''
skyThreshold = 2.0
sortTellurics = True
date = ''
copy = ''

[calibrationReductionConfig]
baselineCalibrationStart = 1
baselineCalibrationStop = 4

[telluricReductionConfig]
telStart = 1
telStop = 6
telluricSkySubtraction = True
spectemp = ''
mag = ''
hline_method = 'vega'
hlineinter = False
continuuminter = False

[scienceReductionConfig]
sciStart = 1
sciStop = 6
scienceSkySubtraction = True
telluricCorrectionMethod = ''
telinter = False
fluxCalibrationMethod = ''
use_pq_offsets = True
im3dtran = True

# Good luck with your Science!

And run the nifsPipeline with:

runNifty nifsPipeline config.cfg

nifsBaselineCalibration: To only reduce calibrations type:

runNifty nifsBaselineCalibration

Or use a config.cfg file like this:

# Nifty configuration file.
#
# Each section lists parameters required by a pipeline step.

manualMode = False
over = False
merge = True
scienceDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/obs28', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/obs55', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/obs44', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/obs75', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/obs83']
calibrationDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/Calibrations_H']
telluricDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs26', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs51', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs30', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/Tellurics/obs53', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/Tellurics/obs38', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/Tellurics/obs34', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/Tellurics/obs64', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/H/Tellurics/obs69', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/Tellurics/obs42', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/Tellurics/obs46', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/Tellurics/obs73', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/Tellurics/obs77', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/Tellurics/obs81', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/Tellurics/obs85']

[nifsPipelineConfig]
sort = False
calibrationReduction = True
telluricReduction = False
scienceReduction = False

[sortConfig]
rawPath = ''
program = ''
skyThreshold = 2.0
sortTellurics = True
date = ''
copy = ''

[calibrationReductionConfig]
baselineCalibrationStart = 1
baselineCalibrationStop = 4

[telluricReductionConfig]
telStart = 1
telStop = 6
telluricSkySubtraction = True
spectemp = ''
mag = ''
hline_method = 'vega'
hlineinter = False
continuuminter = False

[scienceReductionConfig]
sciStart = 1
sciStop = 6
scienceSkySubtraction = True
telluricCorrectionMethod = ''
telinter = False
fluxCalibrationMethod = ''
use_pq_offsets = True
im3dtran = True

# Good luck with your Science!

And run the nifsPipeline with:

runNifty nifsPipeline config.cfg

nifsReduce Telluric: To only reduce telluric data type:

runNifty nifsReduce Telluric

Or use a config.cfg file like this:

# Nifty configuration file.
#
# Each section lists parameters required by a pipeline step.

manualMode = False
over = False
merge = True
scienceDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/obs28', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/obs55', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/obs44', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/obs75', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/obs83']
calibrationDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/Calibrations_H']
telluricDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs26', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs51', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs30', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/Tellurics/obs53', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/Tellurics/obs38', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/Tellurics/obs34', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/Tellurics/obs64', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/H/Tellurics/obs69', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/Tellurics/obs42', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/Tellurics/obs46', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/Tellurics/obs73', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/Tellurics/obs77', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/Tellurics/obs81', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/Tellurics/obs85']

[nifsPipelineConfig]
sort = False
calibrationReduction = False
telluricReduction = True
scienceReduction = False

[sortConfig]
rawPath = ''
program = ''
skyThreshold = 2.0
sortTellurics = True
date = ''
copy = ''

[calibrationReductionConfig]
baselineCalibrationStart = 1
baselineCalibrationStop = 4

[telluricReductionConfig]
telStart = 1
telStop = 6
telluricSkySubtraction = True
spectemp = ''
mag = ''
hline_method = 'vega'
hlineinter = False
continuuminter = False

[scienceReductionConfig]
sciStart = 1
sciStop = 6
scienceSkySubtraction = True
telluricCorrectionMethod = ''
telinter = False
fluxCalibrationMethod = ''
use_pq_offsets = True
im3dtran = True

# Good luck with your Science!

And run the nifsPipeline with:

runNifty nifsPipeline config.cfg

nifsReduce Science: To only reduce science data type:

runNifty nifsReduce Science

Or use a config.cfg file like this:

# Nifty configuration file.
#
# Each section lists parameters required by a pipeline step.

manualMode = False
over = False
merge = True
scienceDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/obs28', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/obs55', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/H/obs36', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/obs44', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/obs75', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/obs83']
calibrationDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/Calibrations_H', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/Calibrations_H']
telluricDirectoryList = ['/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs26', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs51', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130527/H/Tellurics/obs30', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/Tellurics/obs53', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130530/H/Tellurics/obs38', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/Tellurics/obs34', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130531/H/Tellurics/obs64', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130621/H/Tellurics/obs69', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/Tellurics/obs42', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130622/H/Tellurics/obs46', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/Tellurics/obs73', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130624/H/Tellurics/obs77', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/Tellurics/obs81', '/Users/ncomeau/tests/newQ62/AEGISz1284/20130626/H/Tellurics/obs85']

[nifsPipelineConfig]
sort = False
calibrationReduction = False
telluricReduction = False
scienceReduction = True

[sortConfig]
rawPath = ''
program = ''
skyThreshold = 2.0
sortTellurics = True
date = ''
copy = ''

[calibrationReductionConfig]
baselineCalibrationStart = 1
baselineCalibrationStop = 4

[telluricReductionConfig]
telStart = 1
telStop = 6
telluricSkySubtraction = True
spectemp = ''
mag = ''
hline_method = 'vega'
hlineinter = False
continuuminter = False

[scienceReductionConfig]
sciStart = 1
sciStop = 6
scienceSkySubtraction = True
telluricCorrectionMethod = ''
telinter = False
fluxCalibrationMethod = ''
use_pq_offsets = True
im3dtran = True

# Good luck with your Science!

And run the nifsPipeline with:

runNifty nifsPipeline config.cfg