Package overview

ooacquire-package

ooacquire: Acquire Data from OO Spectrometers

Interactive data acquisition functions

Functions for direct acquisition of spectral data from array spectrometers.

acq_irrad_interactive() acq_fraction_interactive() acq_rfr_tfr_interactive()

Acquire spectra interactively

acq_fluence_interactive() acq_fraction_pulsed_interactive()

Acquire flash spectra interactively

Interactive data acquisition utility utility functions

Functions useful for development of user defined interactive functions. Used for the implementation of the functions in the previous section.

choose_ch_interactive()

Interactively select a channel

list_srs_interactive()

Get list of conencted instruments

choose_sr_interactive()

Interactively select an instrument

protocol_interactive()

Interactively select a measurement protocol

set_attributes_interactive()

Interactively set user attributes

set_folder_interactive()

Interactively get folder to use

set_seq_interactive()

Interactively set sequential measurements

tune_interactive()

Interactively adjust the integration time settings

f.trigger.message()

Manual trigger pulses request

Utility functions for data acquisition from spectrometers

Low level functions useful for development of both of user defined scripts and interactive functions.

start_session()

Connect to Maya spectrometer

end_session()

Disconnect from spectrometer

list_instruments()

List connected spectrometers

get_oo_descriptor()

Get the instrument description and EEPROM data

set_descriptor_wl()

Replace wavelength values in an instrument description

set_descriptor_bad_pixs()

Add bad pixel information to an instrument description

set_descriptor_nl()

Replace linearization function in instrument description.

set_descriptor_irrad_mult()

Add spectral irradiance calibration

set_descriptor_integ_time()

Replace integration time limits in instrument descriptor

get_oo_settings()

Get the current values of instrument settings

acq_settings() tune_acq_settings()

Settings for spectral measurement

acq_raw_spct()

Measure one raw spectrum

acq_raw_mspct()

Take one set of spectral readings

Read raw-counts data from files

Functions for reading raw-counts and metadata from output files from OceanView, SpectraSuite, Raspberry Pi software and the inbuilt-firmware of the Jaz modular spectrometer.

read_oo_data()

Read Files Saved by Ocean Optics' instruments or software.

read_oo_ssdata()

Read File Saved by Ocean Optics' SpectraSuite.

read_oo_ovdata()

Read File Saved by Ocean Optics' OceanView.

read_oo_pidata()

Read File Saved by Ocean Optics' Raspberry Pi software.

read_oo_caldata()

Read OO irradiance calibration.

read_files2mspct()

Read multiple files into raw_mspct object

Utility functions for reading data from files

Utility functions for reading raw-counts and metadata from output files from OceanView, SpectraSuite, Raspberry Pi software and the inbuilt-firmware of the Jaz modular spectrometer.

map_oofile_header_rows()

Set the instrument description.

oofile_data_rows()

Find range of lines in file containing spectral data.

set_oo_ssdata_settings()

Set the values of instrument settings from file header

set_oo_ssdata_descriptor()

Set the instrument description.

High level conversion functions and methods.

Functions related to conversion of raw detector counts into counts-per-second and physical quantities.

raw2corr_cps()

Convert raw detector counts into counts-per-second and correct

raw2cps()

Convert raw detector counts into counts per second (cps).

s_irrad_corrected()

Convert raw counts data into spectral irradiance or fluence

s_fraction_corrected()

Convert raw counts data into a spectral fraction

which_descriptor()

Select which instrument descriptor to use

Low level conversion functions and methods.

Individual functions implementing different steps in the conversion of raw-counts data.

merge_raw_mspct()

Merge raw spectra into a single multicolumn spectrum

trim_counts()

Replace out-of-range instrument counts

bleed_nas()

Expand NA's to neighbouring pixels

linearize_counts()

Function to apply linearization correction to raw counts data.

ref_correction()

Apply a correction to spectral data.

filter_correction() no_filter_correction()

Correct for stray light

uvb_corrections() slit_function_correction()

Apply filter-based stray-light correction

raw2cps()

Convert raw detector counts into counts per second (cps).

merge_cps()

Merge counts per second data

new_correction_method()

Make default method from descriptor

skip_bad_pixs()

Replace bad pixels

Computation of calibration coefficients

Compute a calibration coefficients.

compute_irrad_calibration()

Compute calibration multipliers.

oo_calib2irrad_mult()

Convert an OO calibration

Raw spectral data examples

Collections of raw-counts spectra stored as R objects of class raw_mspct defined in package ‘photobiology’.

blue_filter.raw_mspct

Raw counts data for a filter measurement

red_filter.raw_mspct

Raw counts data for a filter measurement

white_LED.raw_mspct

Raw counts data for a lamp measurement.

white_LED_2min.raw_mspct

Raw counts data for a lamp measurement.

halogen.raw_mspct

Raw counts data for a lamp measurement.

xenon_flash.raw_mspct

Raw counts data for a lamp measurement.

Calibration data examples

Examples of individual instrument calibrations as used by the functions in this package, serving only as examples. Not all listed methods are currently implemented.

MAYP11278_calib_dates.df

Dates for which the different descriptors conatin valid calibrations.

MAYP11278_descriptors

Instrument descriptors for a Maya2000 Pro spectrometer

MAYP11278_ylianttila.mthd

Correction method definition

MAYP11278_tail_correction()

Function to compute the tail correction

MAYP11278_simple.mthd

Correction method definition

MAYP11278_sun.mthd

Correction method definition

MAYP112785_calib_dates.df

Dates for which the different descriptors conatin valid calibrations.

MAYP112785_descriptors

Instrument descriptors for a Maya2000 Pro spectrometer

MAYP112785_ylianttila.mthd

Correction method definition

MAYP112785_tail_correction()

Function to compute the tail correction

MAYP112785_simple.mthd

Correction method definition

MAYP112785_sun.mthd

Correction method definition

JAZA3098_calib_dates.df

Dates for which the different descriptors contain valid calibrations.

JAZA3098_ch1_descriptors

Instrument descriptors for a JAZ spectrometer

JAZA3098_ch1_ylianttila.mthd

Correction method definition

JAZA3098_ch1_none.mthd

Correction method definition

JAZA3098_ch1_simple.mthd

Correction method definition

JAZA3098_ch1_sun.mthd

Correction method definition

JAZA3098_ch2_descriptors

Instrument descriptors for a JAZ spectrometer

JAZA3098_ch2_ylianttila.mthd

Correction method definition

JAZA3098_ch2_none.mthd

Correction method definition

JAZA3098_ch2_simple.mthd

Correction method definition

JAZA3098_ch2_sun.mthd

Correction method definition

FLMS00416_calib_dates.df

Dates for which the different descriptors conatin valid calibrations.

FLMS00416_descriptors

Instrument descriptors for a Flame S spectrometer

FLMS00416_none.mthd

Correction method definition

FLMS00416_cal.spct

Instrument calibration for a Flame S spectrometer

FLMS00416_simple.mthd

Correction method definition

FLMS00416_sun.mthd

Correction method definition

FLMS00416_ylianttila.mthd

Correction method definition

FLMS00440_calib_dates.df

Dates for which the different descriptors conatin valid calibrations.

FLMS00440_descriptors

Instrument descriptors for a Flame S spectrometer

FLMS00440_none.mthd

Correction method definition

FLMS00440_cal.spct

Instrument calibration for a Flame S spectrometer

FLMS00440_simple.mthd

Correction method definition

FLMS00440_sun.mthd

Correction method definition

FLMS00440_ylianttila.mthd

Correction method definition

FLMS00673_calib_dates.df

Dates for which the different descriptors conatin valid calibrations.

FLMS00673_descriptors

Instrument descriptors for a Flame S spectrometer

FLMS00673_none.mthd

Correction method definition

FLMS00673_cal.spct

Instrument calibration for a Flame S spectrometer

FLMS00673_simple.mthd

Correction method definition

FLMS00673_sun.mthd

Correction method definition

FLMS00673_ylianttila.mthd

Correction method definition

FLMS04133_cal.spct

Instrument calibration for a Flame S spectrometer

FLMS04133_calib_dates.df

Dates for which the different descriptors conatin valid calibrations.

FLMS04133_descriptors

Instrument descriptors for a Flame S spectrometer

FLMS04133_none.mthd

Correction method definition

FLMS04133_simple.mthd

Correction method definition

FLMS04133_sun.mthd

Correction method definition

FLMS04133_ylianttila.mthd

Correction method definition