Package: ooacquire 0.5.1-1
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:
ooacquire_0.5.1-1.tar.gz
ooacquire_0.5.1-1.zip(r-4.5)ooacquire_0.5.1-1.zip(r-4.4)ooacquire_0.5.1-1.zip(r-4.3)
ooacquire_0.5.1-1.tgz(r-4.4-x86_64)ooacquire_0.5.1-1.tgz(r-4.4-arm64)ooacquire_0.5.1-1.tgz(r-4.3-x86_64)ooacquire_0.5.1-1.tgz(r-4.3-arm64)
ooacquire_0.5.1-1.tar.gz(r-4.5-noble)ooacquire_0.5.1-1.tar.gz(r-4.4-noble)
ooacquire_0.5.1-1.tgz(r-4.4-emscripten)ooacquire_0.5.1-1.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/aphalo/ooacquire/issues
- FLMS00416_cal.spct - Flame S spectrometer s/n FLMS00416
- FLMS00416_calib_dates.df - Flame S spectrometer s/n FLMS00416
- FLMS00416_descriptors - Flame S spectrometer s/n FLMS00416
- FLMS00416_none.mthd - Flame S spectrometer s/n FLMS00416
- FLMS00416_simple.mthd - Flame S spectrometer s/n FLMS00416
- FLMS00416_sun.mthd - Flame S spectrometer s/n FLMS00416
- FLMS00416_ylianttila.mthd - Flame S spectrometer s/n FLMS00416
- FLMS00440_cal.spct - Flame S spectrometer s/n FLMS00440
- FLMS00440_calib_dates.df - Flame S spectrometer s/n FLMS00440
- FLMS00440_descriptors - Flame S spectrometer s/n FLMS00440
- FLMS00440_none.mthd - Flame S spectrometer s/n FLMS00440
- FLMS00440_simple.mthd - Flame S spectrometer s/n FLMS00440
- FLMS00440_sun.mthd - Flame S spectrometer s/n FLMS00440
- FLMS00440_ylianttila.mthd - Flame S spectrometer s/n FLMS00440
- FLMS00673_cal.spct - Flame S spectrometer s/n FLMS00673
- FLMS00673_calib_dates.df - Flame S spectrometer s/n FLMS00673
- FLMS00673_descriptors - Flame S spectrometer s/n FLMS00673
- FLMS00673_none.mthd - Flame S spectrometer s/n FLMS00673
- FLMS00673_simple.mthd - Flame S spectrometer s/n FLMS00673
- FLMS00673_sun.mthd - Flame S spectrometer s/n FLMS00673
- FLMS00673_ylianttila.mthd - Flame S spectrometer s/n FLMS00673
- FLMS04133_cal.spct - Flame S spectrometer s/n FLMS04133
- FLMS04133_calib_dates.df - Flame S spectrometer s/n FLMS04133
- FLMS04133_descriptors - Flame S spectrometer s/n FLMS04133
- FLMS04133_none.mthd - Flame S spectrometer s/n FLMS04133
- FLMS04133_simple.mthd - Flame S spectrometer s/n FLMS04133
- FLMS04133_sun.mthd - Flame S spectrometer s/n FLMS04133
- FLMS04133_ylianttila.mthd - Flame S spectrometer s/n FLMS04133
- JAZA3098_calib_dates.df - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch1_descriptors - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch1_none.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch1_simple.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch1_sun.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch1_ylianttila.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch2_descriptors - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch2_none.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch2_simple.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch2_sun.mthd - Jaz spectrometer s/n JAZA3098
- JAZA3098_ch2_ylianttila.mthd - Jaz spectrometer s/n JAZA3098
- MAYP112785_calib_dates.df - Maya2000 Pro spectrometer s/n MAYP112785
- MAYP112785_descriptors - Maya2000 Pro spectrometer s/n MAYP112785
- MAYP112785_simple.mthd - Maya2000 Pro spectrometer s/n MAYP112785
- MAYP112785_sun.mthd - Maya2000 Pro spectrometer s/n MAYP112785
- MAYP112785_ylianttila.mthd - Maya2000 Pro spectrometer s/n MAYP112785
- MAYP11278_calib_dates.df - Maya2000 Pro spectrometer s/n MAYP11278
- MAYP11278_descriptors - Maya2000 Pro spectrometer s/n MAYP11278
- MAYP11278_short_flt_ref.mthd - Maya2000 Pro spectrometer s/n MAYP11278
- MAYP11278_simple.mthd - Maya2000 Pro spectrometer s/n MAYP11278
- MAYP11278_sun.mthd - Maya2000 Pro spectrometer s/n MAYP11278
- MAYP11278_ylianttila.mthd - Maya2000 Pro spectrometer s/n MAYP11278
- MAYP114590_cal.spct - Maya2000 Pro spectrometer s/n MAYP114590
- MAYP114590_calib_dates.df - Maya2000 Pro spectrometer s/n MAYP114590
- MAYP114590_descriptors - Maya2000 Pro spectrometer s/n MAYP114590
- MAYP114590_none.mthd - Maya2000 Pro spectrometer s/n MAYP114590
- MAYP114590_simple.mthd - Maya2000 Pro spectrometer s/n MAYP114590
- MAYP114590_sun.mthd - Maya2000 Pro spectrometer s/n MAYP114590
- MAYP114590_ylianttila.mthd - Maya2000 Pro spectrometer s/n MAYP114590
- blue_filter.raw_mspct - Raw counts data for a filter measurement
- halogen.raw_mspct - Raw counts data for a lamp measurement.
- red_filter.raw_mspct - Raw counts data for a filter measurement
- sun001.raw_mspct - Raw counts data for a lamp measurement.
- white_LED.raw_mspct - Raw counts data for a lamp measurement.
- xenon_flash.raw_mspct - Raw counts data for a lamp measurement.
data-acquisitiondata-importr4photobiologyspectra
Last updated 3 months agofrom:ae99731711. Checks:OK: 8 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win-x86_64 | OK | Nov 01 2024 |
| R-4.5-linux-x86_64 | OK | Nov 01 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 01 2024 |
| R-4.4-mac-x86_64 | OK | Nov 01 2024 |
| R-4.4-mac-aarch64 | OK | Nov 01 2024 |
| R-4.3-win-x86_64 | OK | Nov 01 2024 |
| R-4.3-mac-x86_64 | OK | Nov 01 2024 |
| R-4.3-mac-aarch64 | OK | Nov 01 2024 |
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:anytimeBHbitbit64bitopscaToolscellrangerclicliprcolorspacecolorSpeccpp11crayondplyrfansifarvergenericsggplot2ggrepelggspectragluegtablehmsisobandjsonlitelabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmephotobiologyphotobiologyInOutphotobiologyWavebandspillarpkgconfigplyrpolynomprettyunitsprogresspurrrR6RColorBrewerRcppreadrreadxlrematchrlangscalessplus2Rstringistringrtibbletidyrtidyselecttimechangetzdbutf8vctrsviridisLitevroomwithrzoo
Acquisition of Spectra
Rendered fromuserguide-acquisition.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-08-02
Started: 2021-01-16
Import and conversion
Rendered fromuserguide-import.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-08-02
Started: 2021-01-16
The R for Photobiology Suite
Rendered fromr4p-introduction.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2023-05-13
Started: 2021-01-16
User Guide
Rendered fromuserguide-introduction.Rmdusingknitr::rmarkdownon Nov 01 2024.Last update: 2024-08-02
Started: 2021-01-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ooacquire: Acquire Data from OO Spectrometers | ooacquire-package ooacquire |
| Acquire spectral fraction | acq_fraction_interactive |
| Acquire spectral irradiance or spectral fluence | acq_irrad_interactive |
| Take one set of spectral readings | acq_raw_mspct |
| Measure one raw spectrum | acq_raw_spct |
| Settings for spectral measurement | acq_settings tune_acq_settings |
| Expand NA's to neighbouring pixels | bleed_nas |
| Raw counts data for a filter measurement | blue_filter.raw_mspct |
| Check consistency of serial number | check_sn_match |
| Interactively select a channel | choose_ch_interactive |
| Interactively select an instrument | choose_sr_interactive |
| Collect spectra into a collection | collect_spct_files |
| Compute calibration multipliers. | compute_irrad_calibration |
| Disconnect from spectrometer | end_session |
| Manual trigger request | f.trigger.message |
| Correct for stray light | filter_correction no_filter_correction |
| Flame S spectrometer s/n FLMS00416 | FLMS00416_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 FLMS00440 | FLMS00440_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 FLMS00673 | FLMS00673_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 FLMS04133 | FLMS04133_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 data | get_oo_descriptor |
| Get the current values of instrument settings | get_oo_settings |
| Raw counts data for a lamp measurement. | halogen.raw_mspct |
| Acquire spectra at high speed | hs_acq_raw_mspct |
| Summarize spectral irradiance or fluence | irrad_summary_table |
| Jaz spectrometer s/n JAZA3098 | JAZA3098_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 spectrometers | list_instruments |
| Get list of connected instruments | list_srs_interactive |
| Parse a file header to locate metadata items | map_oofile_header_rows |
| Maya2000 Pro spectrometer s/n MAYP11278 | MAYP11278_calib_dates.df MAYP11278_descriptors MAYP11278_short_flt_ref.mthd MAYP11278_simple.mthd MAYP11278_sun.mthd MAYP11278_ylianttila.mthd |
| Function to compute the tail correction | MAYP11278_tail_correction |
| Maya2000 Pro spectrometer s/n MAYP112785 | MAYP112785_calib_dates.df MAYP112785_descriptors MAYP112785_simple.mthd MAYP112785_sun.mthd MAYP112785_ylianttila.mthd |
| Function to compute the tail correction | MAYP112785_tail_correction |
| Maya2000 Pro spectrometer s/n MAYP114590 | MAYP114590_cal.spct MAYP114590_calib_dates.df MAYP114590_descriptors MAYP114590_none.mthd MAYP114590_simple.mthd MAYP114590_sun.mthd MAYP114590_ylianttila.mthd |
| Merge counts per second data | merge_cps |
| Merge raw spectra into a single multicolumn spectrum | merge_raw_mspct |
| Make default method from descriptor | new_correction_method |
| Convert an OO calibration | oo_calib2irrad_mult |
| Find range of lines in file containing spectral data. | oofile_data_rows |
| Read a file and plot spectrum | plot_spct_file |
| Interactively select a measurement protocol | protocol_interactive |
| Quality control of dark spectra | QC_dark |
| Convert raw detector counts into counts-per-second | raw2corr_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 object | read_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 measurement | red_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 descriptor | rm_jwrapper |
| Convert raw counts data into a spectral fraction | s_fraction_corrected s_fraction_corrected.default s_fraction_corrected.list s_fraction_corrected.raw_mspct |
| Convert raw counts data into spectral irradiance or fluence | s_irrad_corrected s_irrad_corrected.default s_irrad_corrected.list s_irrad_corrected.raw_mspct s_irrad_corrected.raw_spct |
| Interactively set user attributes | set_attributes_interactive |
| Add bad pixel information to an instrument description | set_descriptor_bad_pixs update_mspct_bad_pixs update_spct_bad_pixs |
| Add or replace entrance optics data to descriptor | set_descriptor_entrance_optics |
| Replace integration time limits in instrument descriptor | set_descriptor_integ_time |
| Add spectral irradiance calibration | set_descriptor_irrad_mult |
| Replace linearization function in instrument description. | set_descriptor_nl |
| Replace wavelength values in an instrument description | set_descriptor_wl |
| Interactively get folder to use | set_folder_interactive |
| Set the instrument description. | set_oo_ssdata_descriptor |
| Set the values of instrument settings from file header | set_oo_ssdata_settings |
| Interactively set sequential measurements | set_seq_interactive |
| Interactively get session name to set | set_session_name_interactive |
| Interactively get user name to set | set_user_name_interactive |
| Replace bad pixels | skip_bad_pixs |
| Connect to Maya spectrometer | start_session |
| Raw counts data for a lamp measurement. | sun001.raw_mspct |
| Summarize spectral transmittance | Tfr_summary_table |
| Replace out-of-range instrument counts | trim_counts |
| Interactively adjust the integration time settings | tune_interactive |
| Update bad-pixels in instrument descriptor | update_bad_pixs |
| Apply filter-based stray-light correction | slit_function_correction uvb_corrections |
| Select which instrument descriptor to use | which_descriptor |
| Raw counts data for a lamp measurement. | white_LED.raw_mspct |
| Raw counts data for a lamp measurement. | xenon_flash.raw_mspct |
