Package overview

ooacquire ooacquire-package

ooacquire: Acquire Data from OO Spectrometers

Data acquisition from spectrometers

Interactive data acquisition

Functions for direct acquisition of spectral data from array spectrometers.

acq_irrad_interactive()

Acquire spectral irradiance or spectral fluence

acq_fraction_interactive()

Acquire spectral fraction

plot_spct_file()

Read a file and plot spectrum

collect_spct_files()

Collect spectra into a collection

Interactive 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 connected 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

set_session_name_interactive()

Interactively get session name to set

set_user_name_interactive()

Interactively get user name to set

Low level functions

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() update_spct_bad_pixs() update_mspct_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

set_descriptor_entrance_optics()

Add or replace entrance optics data to 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

hs_acq_raw_mspct()

Acquire spectra at high speed

check_sn_match()

Check consistency of serial number

QC_dark()

Quality control of dark spectra

rm_jwrapper()

Remove java wrapper from descriptor

update_bad_pixs()

Update bad-pixels in instrument descriptor

Data import from text files

Read data

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

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.

irrad_summary_table()

Summarize spectral irradiance or fluence

Tfr_summary_table()

Summarize spectral transmittance

map_oofile_header_rows()

Parse a file header to locate metadata items

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.

format_idx()

Format index with enough leading zeros

Conversion of raw-counts into physical quantities

High level 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

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 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

Example data

Raw-counts data

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.

sun001.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.

Spectrometers

Instrument calibration data and instrument-specific functions.

MAYP11278_descriptors MAYP11278_calib_dates.df MAYP11278_ylianttila.mthd MAYP11278_short_flt_ref.mthd MAYP11278_sun.mthd MAYP11278_simple.mthd

Maya2000 Pro spectrometer s/n MAYP11278

MAYP11278_tail_correction()

Function to compute the tail correction

MAYP112785_descriptors MAYP112785_calib_dates.df MAYP112785_ylianttila.mthd MAYP112785_sun.mthd MAYP112785_simple.mthd

Maya2000 Pro spectrometer s/n MAYP112785

MAYP112785_tail_correction()

Function to compute the tail correction

MAYP114590_descriptors MAYP114590_cal.spct MAYP114590_calib_dates.df MAYP114590_ylianttila.mthd MAYP114590_sun.mthd MAYP114590_simple.mthd MAYP114590_none.mthd

Maya2000 Pro spectrometer s/n MAYP114590

JAZA3098_calib_dates.df JAZA3098_ch1_descriptors JAZA3098_ch1_ylianttila.mthd JAZA3098_ch1_sun.mthd JAZA3098_ch1_simple.mthd JAZA3098_ch1_none.mthd JAZA3098_ch2_descriptors JAZA3098_ch2_ylianttila.mthd JAZA3098_ch2_sun.mthd JAZA3098_ch2_simple.mthd JAZA3098_ch2_none.mthd

Jaz spectrometer s/n JAZA3098

FLMS00416_descriptors FLMS00416_cal.spct FLMS00416_calib_dates.df FLMS00416_ylianttila.mthd FLMS00416_sun.mthd FLMS00416_simple.mthd FLMS00416_none.mthd

Flame S spectrometer s/n FLMS00416

FLMS00440_descriptors FLMS00440_cal.spct FLMS00440_calib_dates.df FLMS00440_ylianttila.mthd FLMS00440_sun.mthd FLMS00440_simple.mthd FLMS00440_none.mthd

Flame S spectrometer s/n FLMS00440

FLMS00673_descriptors FLMS00673_cal.spct FLMS00673_calib_dates.df FLMS00673_ylianttila.mthd FLMS00673_sun.mthd FLMS00673_simple.mthd FLMS00673_none.mthd

Flame S spectrometer s/n FLMS00673

FLMS04133_descriptors FLMS04133_cal.spct FLMS04133_calib_dates.df FLMS04133_ylianttila.mthd FLMS04133_sun.mthd FLMS04133_simple.mthd FLMS04133_none.mthd

Flame S spectrometer s/n FLMS04133