Package: ooacquire 0.4.6

ooacquire: Acquire Data from OO Spectrometers

Functions to acquire data directly from Ocean Optics spectrometers, and functions to read similar data from files. Functions to convert raw-counts into counts-per-second and physical quantities. Data are saved in objects of classes defined in package 'photobiology'. The instrument settings, instrument description, date-time of acquisition and optionally goecode are stored as attributes.

Authors:Pedro J. Aphalo [aut, trl, cre], Lasse Ylianttila [aut], Titta K. Kotilainen [ctb]

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ooacquire.pdf |ooacquire.html✨
ooacquire/json (API)
NEWS

# Install 'ooacquire' in R:
install.packages('ooacquire', repos = c('https://aphalo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/aphalo/ooacquire/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

data-acquisitiondata-importr4photobiologyspectra

69 exports 1.51 score 66 dependencies

Last updated 21 days agofrom:519a3e7288

Exports:acq_fraction_interactiveacq_irrad_interactiveacq_raw_mspctacq_raw_spctacq_settingsbleed_nascheck_sn_matchchoose_ch_interactivechoose_sr_interactivecollect_spct_filescompute_irrad_calibrationend_sessionf.trigger.messagefilter_correctionget_oo_descriptorget_oo_settingshs_acq_raw_mspctirrad_summary_tablelinearize_countslist_instrumentslist_srs_interactivemap_oofile_header_rowsMAYP11278_tail_correctionMAYP112785_tail_correctionmerge_cpsmerge_raw_mspctnew_correction_methodno_filter_correctionoo_calib2irrad_multoofile_data_rowsplot_spct_fileprotocol_interactiveQC_darkraw2corr_cpsraw2cpsread_files2mspctread_oo_caldataread_oo_dataread_oo_ovdataread_oo_pidataread_oo_ssdataref_correctionrm_jwrappers_fraction_correcteds_irrad_correctedset_descriptor_bad_pixsset_descriptor_entrance_opticsset_descriptor_integ_timeset_descriptor_irrad_multset_descriptor_nlset_descriptor_wlset_folder_interactiveset_oo_ssdata_descriptorset_oo_ssdata_settingsset_seq_interactiveset_session_name_interactiveset_user_name_interactiveskip_bad_pixsslit_function_correctionstart_sessionTfr_summary_tabletrim_countstune_acq_settingstune_interactiveupdate_bad_pixsupdate_mspct_bad_pixsupdate_spct_bad_pixsuvb_correctionswhich_descriptor

Dependencies:anytimeBHbitbit64bitopscaToolscellrangerclicliprcolorspacecolorSpeccpp11crayondplyrfansifarvergenericsggplot2ggrepelggspectragluegtablehmsisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmephotobiologyphotobiologyInOutphotobiologyWavebandspillarpkgconfigplyrpolynomprettyunitsprogresspurrrR6RColorBrewerRcppreadrreadxlrematchrlangscalessplus2Rstringistringrtibbletidyrtidyselecttimechangetzdbutf8vctrsviridisLitevroomwithrzoo

Acquisition of Spectra

Pedro J. Aphalo

Rendered fromuserguide-acquisition.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-01-15
Started: 2021-01-16

Import and conversion

Pedro J. Aphalo

Rendered fromuserguide-import.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2021-01-16
Started: 2021-01-16

The R for Photobiology Suite

Pedro J. Aphalo

Rendered fromr4p-introduction.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2023-05-13
Started: 2021-01-16

User Guide

Pedro J. Aphalo

Rendered fromuserguide-introduction.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2023-12-20
Started: 2021-01-16

Readme and manuals

Help Manual

Help pageTopics
ooacquire: Acquire Data from OO Spectrometersooacquire-package ooacquire
Acquire spectral fractionacq_fraction_interactive
Acquire spectral irradiance or spectral fluenceacq_irrad_interactive
Take one set of spectral readingsacq_raw_mspct
Measure one raw spectrumacq_raw_spct
Settings for spectral measurementacq_settings tune_acq_settings
Expand NA's to neighbouring pixelsbleed_nas
Raw counts data for a filter measurementblue_filter.raw_mspct
Check consistency of serial numbercheck_sn_match
Interactively select a channelchoose_ch_interactive
Interactively select an instrumentchoose_sr_interactive
Collect spectra into a collectioncollect_spct_files
Compute calibration multipliers.compute_irrad_calibration
Disconnect from spectrometerend_session
Manual trigger pulses requestf.trigger.message
Correct for stray lightfilter_correction no_filter_correction
Flame S spectrometer s/n FLMS00416FLMS00416_cal.spct FLMS00416_calib_dates.df FLMS00416_descriptors FLMS00416_none.mthd FLMS00416_simple.mthd FLMS00416_sun.mthd FLMS00416_ylianttila.mthd
Flame S spectrometer s/n FLMS00440FLMS00440_cal.spct FLMS00440_calib_dates.df FLMS00440_descriptors FLMS00440_none.mthd FLMS00440_simple.mthd FLMS00440_sun.mthd FLMS00440_ylianttila.mthd
Flame S spectrometer s/n FLMS00673FLMS00673_cal.spct FLMS00673_calib_dates.df FLMS00673_descriptors FLMS00673_none.mthd FLMS00673_simple.mthd FLMS00673_sun.mthd FLMS00673_ylianttila.mthd
Flame S spectrometer s/n FLMS04133FLMS04133_cal.spct FLMS04133_calib_dates.df FLMS04133_descriptors FLMS04133_none.mthd FLMS04133_simple.mthd FLMS04133_sun.mthd FLMS04133_ylianttila.mthd
Get the instrument description and EEPROM dataget_oo_descriptor
Get the current values of instrument settingsget_oo_settings
Raw counts data for a lamp measurement.halogen.raw_mspct
Acquire spectra at high speedhs_acq_raw_mspct
Summarize spectral irradiance or fluenceirrad_summary_table
Jaz spectrometer s/n JAZA3098JAZA3098_calib_dates.df JAZA3098_ch1_descriptors JAZA3098_ch1_none.mthd JAZA3098_ch1_simple.mthd JAZA3098_ch1_sun.mthd JAZA3098_ch1_ylianttila.mthd JAZA3098_ch2_descriptors JAZA3098_ch2_none.mthd JAZA3098_ch2_simple.mthd JAZA3098_ch2_sun.mthd JAZA3098_ch2_ylianttila.mthd JAZA3098_descriptors
Function to apply linearization correction to raw counts data.linearize_counts
List connected spectrometerslist_instruments
Get list of connected instrumentslist_srs_interactive
Parse a file header to locate metadata itemsmap_oofile_header_rows
Maya2000 Pro spectrometer s/n MAYP11278MAYP11278_calib_dates.df MAYP11278_descriptors MAYP11278_short_flt_ref.mthd MAYP11278_simple.mthd MAYP11278_sun.mthd MAYP11278_ylianttila.mthd
Function to compute the tail correctionMAYP11278_tail_correction
Maya2000 Pro spectrometer s/n MAYP112785MAYP112785_calib_dates.df MAYP112785_descriptors MAYP112785_simple.mthd MAYP112785_sun.mthd MAYP112785_ylianttila.mthd
Function to compute the tail correctionMAYP112785_tail_correction
Maya2000 Pro spectrometer s/n MAYP114590MAYP114590_cal.spct MAYP114590_calib_dates.df MAYP114590_descriptors MAYP114590_none.mthd MAYP114590_simple.mthd MAYP114590_sun.mthd MAYP114590_ylianttila.mthd
Merge counts per second datamerge_cps
Merge raw spectra into a single multicolumn spectrummerge_raw_mspct
Make default method from descriptornew_correction_method
Convert an OO calibrationoo_calib2irrad_mult
Find range of lines in file containing spectral data.oofile_data_rows
Read a file and plot spectrumplot_spct_file
Interactively select a measurement protocolprotocol_interactive
Quality control of dark spectraQC_dark
Convert raw detector counts into counts-per-secondraw2corr_cps raw2corr_cps.default raw2corr_cps.raw_mspct raw2corr_cps.raw_spct
Convert raw detector counts into counts per second (cps).raw2cps raw2cps.default raw2cps.raw_mspct raw2cps.raw_spct
Read multiple files into raw_mspct objectread_files2mspct
Read OO irradiance calibration.read_oo_caldata
Read Files Saved by Ocean Optics' instruments or software.read_oo_data
Read File Saved by Ocean Optics' OceanView.read_oo_ovdata
Read File Saved by Ocean Optics' Raspberry Pi software.read_oo_pidata
Read File Saved by Ocean Optics' SpectraSuite.read_oo_ssdata
Raw counts data for a filter measurementred_filter.raw_mspct
Apply a correction to spectral data.ref_correction ref_correction.cps_mspct ref_correction.cps_spct ref_correction.default ref_correction.numeric ref_correction.raw_spct
Remove java wrapper from descriptorrm_jwrapper
Convert raw counts data into a spectral fractions_fraction_corrected s_fraction_corrected.default s_fraction_corrected.list s_fraction_corrected.raw_mspct
Convert raw counts data into spectral irradiance or fluences_irrad_corrected s_irrad_corrected.default s_irrad_corrected.list s_irrad_corrected.raw_mspct s_irrad_corrected.raw_spct
Interactively set user attributesset_attributes_interactive
Add bad pixel information to an instrument descriptionset_descriptor_bad_pixs update_mspct_bad_pixs update_spct_bad_pixs
Add or replace entrance optics data to descriptorset_descriptor_entrance_optics
Replace integration time limits in instrument descriptorset_descriptor_integ_time
Add spectral irradiance calibrationset_descriptor_irrad_mult
Replace linearization function in instrument description.set_descriptor_nl
Replace wavelength values in an instrument descriptionset_descriptor_wl
Interactively get folder to useset_folder_interactive
Set the instrument description.set_oo_ssdata_descriptor
Set the values of instrument settings from file headerset_oo_ssdata_settings
Interactively set sequential measurementsset_seq_interactive
Interactively get session name to setset_session_name_interactive
Interactively get user name to setset_user_name_interactive
Replace bad pixelsskip_bad_pixs
Connect to Maya spectrometerstart_session
Raw counts data for a lamp measurement.sun001.raw_mspct
Summarize spectral transmittanceTfr_summary_table
Replace out-of-range instrument countstrim_counts
Interactively adjust the integration time settingstune_interactive
Update bad-pixels in instrument descriptorupdate_bad_pixs
Apply filter-based stray-light correctionslit_function_correction uvb_corrections
Select which instrument descriptor to usewhich_descriptor
Raw counts data for a lamp measurement.white_LED.raw_mspct
Raw counts data for a lamp measurement.xenon_flash.raw_mspct