Title: | Acquire Data from OO Spectrometers |
---|---|
Description: | 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] |
Maintainer: | Pedro J. Aphalo <[email protected]> |
License: | GPL (>= 2) |
Version: | 0.5.1-1 |
Built: | 2024-12-01 04:57:09 UTC |
Source: | https://github.com/aphalo/ooacquire |
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.
Processing of raw-counts data acquired following different protocols and corrections including integration-time bracketing and merging, slit function corrections, subtraction of stray light and adaptive smoothing corrections.
Acquisition of raw-counts spectra directly from Ocean Optics' spectrometers. A high level interface to the OmniDriver library for spectrometer control and data acquisition provided by Ocean Optics for their instruments. Built on top of the 'rOmniDriver' package which provides a very thin wrapper on the Java functions giving access to the proprietary driver.
Reading of raw-counts spectra from files saved by Ocean Optics' software: OceanView, SpectraSuite, Raspberry Pi SDK, and Jaz firmware.
This package is provided without any warranty of suitability for any specific purpose or instrument as it has been tested with only three different models of Ocean Optics spectrometers, each with one or two of many available hardware configurations.
Maintainer: Pedro J. Aphalo [email protected] [translator]
Authors:
Lasse Ylianttila
Other contributors:
Titta K. Kotilainen [contributor]
Useful links:
Report bugs at https://github.com/aphalo/ooacquire/issues
Interactive front-end allowing acquisition of spectral fractions using Ocean Optics spectrometers. Output of spectral data in R data files stored in objects suitable for use with packages 'photobiology' and 'ggspectra' as well as plots as PDF files and summaries as comma separated files.
acq_fraction_interactive( tot.time.range = c(5, 15), target.margin = 0.1, HDR.mult = if (light.source == "pulsed") c(short = 1) else c(short = 1, long = 10), protocols = NULL, correction.method = NA, descriptors = NA, stray.light.method = "simple", seq.settings = NULL, light.source = "continuous", ref.value = 1, qty.out = "Tfr", type = "total", plot.lines.max = 11, summary.type = "VIS", save.pdfs = TRUE, save.summaries = !interface.mode %in% c("series", "series-attr"), save.collections = !interface.mode %in% c("simple", "series", "series-attr"), async.saves = FALSE, show.figs = TRUE, interface.mode = ifelse(light.source == "pulsed", "manual", "auto"), num.exposures = ifelse(light.source == "pulsed", 1L, -1L), f.trigger.init = NULL, f.trigger.on = f.trigger.message, f.trigger.off = NULL, triggers.enabled = c("sample", "reference"), folder.name = paste("acq", qty.out, lubridate::today(tzone = "UTC"), sep = "-"), user.name = Sys.info()[["user"]], session.name = paste(user.name, strftime(lubridate::now(tzone = "UTC"), "%Y.%b.%d_%H.%M.%S"), sep = "_"), verbose = getOption("photobiology.verbose", default = FALSE), QC.enabled = TRUE )
acq_fraction_interactive( tot.time.range = c(5, 15), target.margin = 0.1, HDR.mult = if (light.source == "pulsed") c(short = 1) else c(short = 1, long = 10), protocols = NULL, correction.method = NA, descriptors = NA, stray.light.method = "simple", seq.settings = NULL, light.source = "continuous", ref.value = 1, qty.out = "Tfr", type = "total", plot.lines.max = 11, summary.type = "VIS", save.pdfs = TRUE, save.summaries = !interface.mode %in% c("series", "series-attr"), save.collections = !interface.mode %in% c("simple", "series", "series-attr"), async.saves = FALSE, show.figs = TRUE, interface.mode = ifelse(light.source == "pulsed", "manual", "auto"), num.exposures = ifelse(light.source == "pulsed", 1L, -1L), f.trigger.init = NULL, f.trigger.on = f.trigger.message, f.trigger.off = NULL, triggers.enabled = c("sample", "reference"), folder.name = paste("acq", qty.out, lubridate::today(tzone = "UTC"), sep = "-"), user.name = Sys.info()[["user"]], session.name = paste(user.name, strftime(lubridate::now(tzone = "UTC"), "%Y.%b.%d_%H.%M.%S"), sep = "_"), verbose = getOption("photobiology.verbose", default = FALSE), QC.enabled = TRUE )
tot.time.range |
numeric vector Range of total times for a measurement in seconds. |
target.margin |
numeric (0..1) when tuning integration time, how big a head space to leave. |
HDR.mult |
numeric the integration time for each bracketed integration as a multiplier of the set or tuned integration time. |
protocols |
named list of character vectors, or a character vector with names of at least one member of the default list of protocols. |
correction.method |
list The method to use when applying the calibration |
descriptors |
list A list of instrument descriptors containing calibration data. |
stray.light.method |
character Used only when the correction method is created on-the-fly. |
seq.settings |
named list with numeric members |
light.source |
character One of "continuous", "pulsed". |
ref.value |
numeric or filter_spct/reflector_spct object. |
qty.out |
character One of "Tfr" (spectral transmittance as a fraction of one), "cps" (counts per second), or "raw" (raw sensor counts). |
type |
character Type of transmittance or reflectance measured. |
plot.lines.max |
integer Maximum number of spectra to plot as individual
lines. Random sampling is used if number of spectra exceeds
|
summary.type |
character One of "plant", "PAR" or "VIS". |
save.pdfs , save.summaries , save.collections
|
logical Whether to save plots to PDFs files or not, and collection summaries to csv files or not, enable collections user interface or not. |
async.saves |
logical A flag enabling or disabling the use of concurrent processes to save data to files. Package 'mirai' must be installed before enabling this feature. |
show.figs |
logical Default for flag enabling display plots of acquired spectra. |
interface.mode |
character One of "auto", "simple", "manual", "full", "series", "auto-attr", "simple-attr", "manual-attr", "full-atr", and "series-attr". |
num.exposures |
integer Number or light pulses (flashes) per scan. Set
to |
f.trigger.on , f.trigger.off , f.trigger.init
|
function Functions to be
called immediately before and immediately after a measurement, and any
initialization code needed before a repeat. See |
triggers.enabled |
character vector Names of protocol steps during which trigger functions should be called. |
folder.name , session.name , user.name
|
character Default name of the folder used for output, and session and user names. |
verbose |
logical If TRUE additional messages are emitted, including report on memory usage. |
QC.enabled |
logical If FALSE return NA skipping QC. |
This function can be used to acquire spectral reflectance, spectral transmittance and/or spectral absorptance using different protocols for acquisition and stray light and dark corrections. Depending on the optical setup, solid or liquid samples can be measured. The kinetics of changes in optical properties can be captured as a time series of spectra, using 'interface.mode = "series"'.
The protocols are described in the vignettes and in the help for the lower level functions called, also from this same package.
Using this function only requires an Ocean Optics spectrometer to be connected to the computer where R is running and the OmniDriver runtime from Ocean Insight installed. The connection to the spectrometer and selection of channel, when relevant, is done from within these functions. A stable and continuous source of light is also needed as well as black, white and possibly grey reflectance patches.
The calculations for reflectance and transmittance are very similar, so we provide a single function capable of handling both. For transmittance the reference is usually direct exposure to radiation but for reflectance a white reference patch is normally used. In some cases one may want to use a grey reference. We provide an argument that allows the user to supply a constant or a spectrum describing the properties of the reference. It is also important to distinguish between total and internal transmittance, and between total and specular reflectance. In both cases which of these is measured depends on the measuring protocol (condition used as reference, use of an integrating sphere versus use of a probe with a narrow angle of aperture, etc.) and consequently the correct value should be entered to ensure that data are correctly tagged and later computations valid.
A wavelength calibration is needed, but being the measurements relative, no calibration of pixel responsiveness is required. A known linearization function is also needed.
Some protocols are available by default. They differ in the additional measurements done to correct for stray light and dark noise. The default protocols are usually suitable, if new protocols are passed, each character vector must contain strings "light", "filter" and "dark".
By default the integration time is set automatically so that the number of
counts at the highest peak is close to 1 - target.margin
times the
maximum of the range of the instrument detector (retrieved from the
calibration or the instrument memory). The minimum tot.time
is
obtained by increasing the number of scans. The maximum integration time
supported by the spectrometer is not exceeded.
Plots are produced with functions from package 'ggspectra' and respect the
default annotations set with function set_annotations_default()
,
and default wavebands set with function set_w.band_default()
.
The different interface modes available are suitable for different types of measurements.
These functions return the acquired spectra through "side effects" as
each spectrum is saved, both as raw counts data and optionally as spectral
transmittance or counts-per-second data in an .rda
file as
objects of the classes defined in package 'photobiology'. Optionally, the
plot for each spectrum is saved as a .pdf
file. At any time, the
current group of spectra can be saved as a collection. When a collection is
created, spectral data for several spectra are saved together.
Summaries are saved to a CSV file and joint plots to a .pdf
file.
The value returned by the function is that from closing the connection to
the spectrometer.
Calibration data needs in most cases to be imported into R and parameters entered for the special correction algorithms into a correction method descriptor. The corrections are skipped if the needed information is missing. If no wavelength calibration is available and attempt is made to retrieve it from the spectrometer.
The function is composed in a modular way from functions that can be reshuffled and combined with other functions to define new variations possibly better suited to users' needs and tastes. Even easier is to simply change the default arguments in a wrapper function or in a script.
This function calls functions tune_interactive
,
protocol_interactive
and
set_attributes_interactive
.
Other interactive acquisition functions:
acq_irrad_interactive()
# please, see also the example scripts installed with the package ## Not run: # requires an Ocean Insight (former Ocean Optics) spectrometer to be # connected via USB acq_fraction_interactive() ## End(Not run)
# please, see also the example scripts installed with the package ## Not run: # requires an Ocean Insight (former Ocean Optics) spectrometer to be # connected via USB acq_fraction_interactive() ## End(Not run)
Interactive front-end allowing acquisition of spectral irradiance and spectral fluence using Ocean Optics spectrometers. Output of spectral data in R data files stored in objects suitable for use with packages 'photobiology' and 'ggspectra' as well as plots as PDF files and summaries as comma separated files and R objects.
acq_irrad_interactive( tot.time.range = if (qty.out == "fluence") 5 else c(5, 15), target.margin = 0.1, HDR.mult = if (qty.out == "fluence") c(short = 1) else c(short = 1, long = 10), protocols = NULL, correction.method = NA, descriptors = NA, entrance.optics = NULL, stray.light.method = "none", seq.settings = NULL, area = NULL, diff.type = NULL, qty.out = "irrad", plot.lines.max = 11, summary.type = "plant", save.pdfs = TRUE, save.summaries = !interface.mode %in% c("series", "series-attr"), save.collections = !interface.mode %in% c("simple", "series", "series-attr"), async.saves = FALSE, show.figs = TRUE, interface.mode = ifelse(qty.out == "fluence", "manual", "auto"), num.exposures = ifelse(qty.out == "fluence", 1L, -1L), f.trigger.init = NULL, f.trigger.on = ifelse(qty.out == "fluence", f.trigger.message, NULL), f.trigger.off = NULL, triggers.enabled = c("light", "filter"), folder.name = paste("acq", qty.out, lubridate::today(tzone = "UTC"), sep = "-"), user.name = Sys.info()[["user"]], session.name = paste(user.name, strftime(lubridate::now(tzone = "UTC"), "%Y.%b.%d_%H.%M.%S"), sep = "_"), verbose = getOption("photobiology.verbose", default = FALSE), QC.enabled = TRUE )
acq_irrad_interactive( tot.time.range = if (qty.out == "fluence") 5 else c(5, 15), target.margin = 0.1, HDR.mult = if (qty.out == "fluence") c(short = 1) else c(short = 1, long = 10), protocols = NULL, correction.method = NA, descriptors = NA, entrance.optics = NULL, stray.light.method = "none", seq.settings = NULL, area = NULL, diff.type = NULL, qty.out = "irrad", plot.lines.max = 11, summary.type = "plant", save.pdfs = TRUE, save.summaries = !interface.mode %in% c("series", "series-attr"), save.collections = !interface.mode %in% c("simple", "series", "series-attr"), async.saves = FALSE, show.figs = TRUE, interface.mode = ifelse(qty.out == "fluence", "manual", "auto"), num.exposures = ifelse(qty.out == "fluence", 1L, -1L), f.trigger.init = NULL, f.trigger.on = ifelse(qty.out == "fluence", f.trigger.message, NULL), f.trigger.off = NULL, triggers.enabled = c("light", "filter"), folder.name = paste("acq", qty.out, lubridate::today(tzone = "UTC"), sep = "-"), user.name = Sys.info()[["user"]], session.name = paste(user.name, strftime(lubridate::now(tzone = "UTC"), "%Y.%b.%d_%H.%M.%S"), sep = "_"), verbose = getOption("photobiology.verbose", default = FALSE), QC.enabled = TRUE )
tot.time.range |
numeric vector Range of total times for a measurement in seconds. |
target.margin |
numeric (0..1) when tuning integration time, how big a head space to leave. |
HDR.mult |
numeric the integration time for each bracketed integration as a multiplier of the set or tuned integration time. |
protocols |
named list of character vectors, or a character vector with names of at least one member of the default list of protocols. |
correction.method |
list The method to use when applying the calibration |
descriptors |
list A list of instrument descriptors containing calibration data. |
entrance.optics |
character, name or geometry of diffuser, needed only if there is more than one for the same instrument. |
stray.light.method |
character Used only when the correction method is created on-the-fly. |
seq.settings |
named list with numeric members |
area |
numeric Passed to |
diff.type |
character Passed to |
qty.out |
character One of "irrad" (spectral irradiance), "fluence" (spectral fluence), "cps" (counts per second), or "raw" (raw sensor counts). |
plot.lines.max |
integer Maximum number of spectra to plot as individual
lines. Random sampling is used if number of spectra exceeds
|
summary.type |
character One of "plant", "PAR" or "VIS". |
save.pdfs , save.summaries , save.collections
|
logical Whether to save plots to PDFs files or not, and collection summaries to csv files or not, enable collections user interface or not. |
async.saves |
logical A flag enabling or disabling the use of concurrent processes to save data to files. Package 'mirai' must be installed before enabling this feature. |
show.figs |
logical Default for flag enabling display plots of acquired spectra. |
interface.mode |
character One of "auto", "simple", "manual", "full", "series", "auto-attr", "simple-attr", "manual-attr", "full-atr", and "series-attr". |
num.exposures |
integer Number or light pulses (flashes) per scan. Set
to |
f.trigger.on , f.trigger.off , f.trigger.init
|
function Functions to be
called immediately before and immediately after a measurement, and any
initialization code needed before a repeat. See |
triggers.enabled |
character vector Names of protocol steps during which trigger functions should be called. |
folder.name , session.name , user.name
|
character Default name of the folder used for output, and session and user names. |
verbose |
logical If TRUE additional messages are emitted, including report on memory usage. |
QC.enabled |
logical If FALSE return NA skipping QC. |
Function acq_irrad_interactive()
supports measurement of
spectral irradiance from continuous light sources and spectral fluence
from discontinuous ones. For spectral irradiance it assumes that the
duration of the measurement event is the relevant time base for expression
of the flux of radiation. For spectral fluence the flux of radiation is
expressed per pulse of illumination. The acquisition of both individual
spectra and time series of spectra are supported.
A tutorial guiding on the use of this function, illustrated with diagrams, is available at https://www.r4photobiology.info/pages/acq-irrad-tutorial.html. A summary is provided below.
Different arguments passed to interface.mode
modify which aspects
of the user interface are available through menues, without altering
the ability to control the behaviour through arguments passed to formal
parameters when calling the function (see section Interface Modes for
details).
This function can acquire spectra using different protocols for acquisition and stray light and dark corrections. The protocols are described in the vignettes and in the help for the low-level functions called by this function, also from this same package.
Opening the connection to the spectrometer and selection of the channel, when relevant, is done from within this function.
The irradiance calibration is retrieved from the spectrometer memory
as a last resource if not supplied in any other way. Given that the factors
are stored by Ocean Optics in a format that ignores the entrance optics,
either the effective cosine diffuser area in xxx should be passed to
parameter area
or a character string with the type of the diffuser
passed to diff.type
. If no irradiance calibration is available,
counts per second (cps) or raw counts are the only options available for
the returned spectral data.
Three main protocols and two variations are available by default. They differ in the additional measurements done to correct for stray light and dark noise and in the sequence in which they are acquired. In most situations, at least one of the default protocols is suitable.
In the case of spectral irradiance, the default is to set the integration
time automatically so that the number of counts at the highest peak is
close to 1 - target.margin
times the maximum raw-counts of the
instrument detector (retrieved from the calibration or the instrument
memory). The minimum tot.time
is obtained by increasing the number
of scans. The maximum integration time supported by the spectrometer cannot
be exceeded but multiple scans can be averaged.
In the case of spectral fluence the default is for the integration time to be set manually and for a message to be displayed asking for the light pulse to be manually triggered. It is possible to override the default function by one that triggers the light source automatically when suitable hardware is available.
Repeated measurements are converted into physical units immediately after
acquisition and saved to file on disk. Each repeated measurement can be
either a single spectrum or a time series of spectra. To avoid long delays
caused by saving large files, async.saves
can be enabled.
Time series of spectra are acquired as fast as possible, converted into
physical units after the acquisition of all individual raw-counts spectra
and saved as a single cps_spct
or source_spct
in long form.
Time series of light measurements using single "dark" and "filter"
measurements are scheduled by setting four members of the named list
passed as argument to seq.settings
, or interactively through the
user interface.
The initial.delay
is numeric and gives a minimum delay in
seconds before the start of measurements with a default of 0s.
The step.delay
is numeric and gives the length of time between
successive "light" measurements. The value entered by the user is adjusted
based on the estimated duration of individual spectrum acquisition. In most
cases a vector of length one is used as time step lengths in seconds. Any vector
shorter than the number of steps will be extended with rep_len()
,
and the values interpreted as the time increment in seconds between the
start of successive measurements. If the length is the same as "num.steps",
and the values are monotonically increasing, they are interpreted as time
offsets from the start of the sequence. Member
The start.boundary
must be set to a character string, wither "none",
or a number of seconds, minutes or hours indicated by a number followed by
S, M, or H (capital letters) the round value of the current time at which
the measurement event will start. For example,1H
indicates that
measurements should be scheduled to start exactly at the hour, and
5M
at the next time the minutes in the current time are divisible by
5.
The num.steps
must be an integer between 1 and an 100000
indicating the number of time points at which spectra should be acquired
for the time series. The maximum value depends on the available memory and
in many computers 5000 spectra is a more realistic limit than 100000.
Applying corrections and applying the calibration are computation intensive,
consequently for long series is wise to set 'qty.out = "raw"' to speed up
the measurement session.
Plots are produced with functions from package 'ggspectra' and respect the
defaults for plot annotations set in R options. The options can be easily
set with functions set_annotations_default()
,
set_w.band_default()
, photon_as_default()
, and
energy_as_default()
. The ggplots are not saved as 'gg' objects as
they contain redundant copies of the spectral data. They can be easily
recreated using function autoplot()
after attaching package
'ggspectra'.
The screen display of plots can be disabled, as in some cases the delay
introduced by rendering can be a nuisance. Alternatively, the value of
plot.lines.max
can be changes from its default.
This function returns the acquired spectra through "side effects" as
each spectrum is saved, both as raw counts data and optionally as spectral
irradiance, spectral fluence or counts-per-second spectral data in an
.rda
(R data) file as objects of the classes defined in package
'photobiology'. Optionally, the plot for each spectrum or a time series of
spectra is saved as a .pdf
file. At any time, the current group of
spectra can be saved as a collection. When a collection is created, all
recently measured spectra are saved together, decreasing the number of
files and keeping related spectra in the same files. Summaries of the
spectra in a collection are additionally saved to a CSV file and a plot of
the collected spectra saved to a .pdf
file.
The value returned by the function is that from closing the connection to the spectrometer.
Mode simple displays a simplified user interface, supporting the acquisition of individual irradiance spectra. Integration time is adjusted automatically.
Mode auto displays a user interface supporting the acquisition of individual irradiance spectra and creation of collections of spectra. Integration time is adjusted automatically.
Mode manual displays a user interface supporting the acquisition of individual fluence or irradiance spectra and creation of collections of spectra. Integration time can adjusted automatically but also set manually.
Mode series displays a user interface supporting the acquisition of individual spectra and time series of irradiance spectra. Integration time can adjusted automatically but also set manually.
All these modes with -attr appended, enable a menu and dialogues
that make it possible to set the values stored in attributes comment
and what.measure
interactively.
All modes support repeated measurements with unchanged acquisition settings reusing the reference spectra ('dark' and 'filter') from the most recent previous measurement.
Object names entered interactively are sanitized if necessary. Sequentially numbered object names are enabled by appending "#" to the desired base name. As long as no new name is entered, the sequence continues. If a new name is entered, numbering restarts at 001 or stops depending on whether the new name ends in "#" or not. In the case of repeated measurements, sequential numbering is enforced to ensure unique names.
Calibration data needs in most cases to be imported into R and
parameters entered for the special correction algorithms into a correction
method descriptor. The corrections are skipped if the needed information is
missing. If no spectral irradiance calibration is available and attempt is
made to retrieve it from the spectrometer, but given the format used by
Ocean Optics/Ocean Insight, in this case the effective area
of the
cosine diffuser used (or the model name if from Ocean Optics) should be
supplied by the user.
Disabling the quality control with QC.enabled = FALSE
is necessary
when the "dark" reference is a measurement of ambient light instead of true
darkness; i.e., when the irradiance of one light source is measured as the
difference between background illumination and background illumination
plus the target light source.
The function is composed in a modular way from functions defined in this some package, R or imported packages. The code of the function can be reshuffled combining the functions used here with other functions to create new variations, possibly better suited to users' needs and tastes.
A "light-weight" approach to tweaking the user interface is to implement new modes by simply changing which of the logical flags that control the display of menus are enabled or not. And even easier approach is to create a simple script that passes suitable arguments to the different formal parameters.
This function calls functions tune_interactive
,
protocol_interactive
, set_seq_interactive
and
set_attributes_interactive
. If irradiance calibration is
retrieved from the instrument, functions get_oo_descriptor
and oo_calib2irrad_mult
are also called.
Other interactive acquisition functions:
acq_fraction_interactive()
# please, see also the example scripts installed with the package ## Not run: # requires an Ocean Optics spectrometer to be connected via USB acq_irrad_interactive() acq_irrad_interactive(qty.out = "cps") ## End(Not run)
# please, see also the example scripts installed with the package ## Not run: # requires an Ocean Optics spectrometer to be connected via USB acq_irrad_interactive() acq_irrad_interactive(qty.out = "cps") ## End(Not run)
Take readings according to parameters from a list of settings and a protocol defined by a vector of names.
acq_raw_mspct( descriptor, acq.settings, f.trigger.on = f.trigger.message, f.trigger.off = NULL, triggers.enabled = character(), seq.settings = list(initial.delay = 0, start.boundary = "none", step.delay = 0, num.steps = 1L), protocol = c("light", "filter", "dark"), user.label = "", where.measured = data.frame(lon = NA_real_, lat = NA_real_), pause.fun = NULL, verbose = TRUE, ... )
acq_raw_mspct( descriptor, acq.settings, f.trigger.on = f.trigger.message, f.trigger.off = NULL, triggers.enabled = character(), seq.settings = list(initial.delay = 0, start.boundary = "none", step.delay = 0, num.steps = 1L), protocol = c("light", "filter", "dark"), user.label = "", where.measured = data.frame(lon = NA_real_, lat = NA_real_), pause.fun = NULL, verbose = TRUE, ... )
descriptor |
list as returned by function |
acq.settings |
list as returned by functions |
f.trigger.on , f.trigger.off
|
function Functions to be called
immediately before and immediately after a measurement. See
|
triggers.enabled |
character vector Names of protocol steps during which trigger functions should be called. |
seq.settings |
list with members "initial.delay", "step,delay" numeric values in seconds, "num.steps" integer. |
protocol |
vector of character strings. |
user.label |
character string to set as label. |
where.measured |
data.frame with at least columns "lon" and "lat"
compatible with value returned by |
pause.fun |
function used for handling protocol transitions. |
verbose |
ogical to enable or disable warnings. |
... |
passed to |
Function acq_raw_mspct
acquires directly from a spectrometer
a collection of spectra. The settings used for the acquisition of each
member spectrum are the same, and are given by the argument passed to
acq.settings
. The number of numbers and their names are given by the
argument passed to protocol
.
Two types of light sources can be measured, for continuous-emission light
sources, the integration time can at later steps used to compute irradiance.
In the case of flashes, the duration of the exposure is unknown and
irradiance cannot be computed, while spectral energy per flash can be
computed if the number of flashes is known. The argument to
num.exposures
must be set to the number of flashes.
Two parameters accept functions as arguments, and default to functions that
request the operator to trigger the flash or change the light conditions
according to the names of the steps in the argument to protocol
.
Sequences of light measurements using single "dark" and "filter"
measurements are scheduled by setting the four members of the named list
passed as argument to seq.settings
. The member initial.delay
is numeric and gives a minimum delay in seconds before the start of
measurements with a default of 0s. Member step.delay
is numeric and
gives the delay in seconds between successive "light" measurements. In
most cases a vector of length one is used as time delta in seconds. Any
vector shorter than the number of steps will be extended with
rep_len()
, and the values interpreted as the time increment
in seconds between the start of successive measurements. If the length is
the same as "num.steps", and the values are monotonically increasing, they
are interpreted as time offsets from the start of the sequence. Member
start.boundary
can take one of "none", "second", "minute" or "hour"
indicating the unit to which the start of the series should be scheduled,
e.g. the next minute and 0s, for "minute". Member num.steps
must
be an integer between 1 and small thousands indicating the number of time
steps in the series.
A raw_mspct object. The names and number of member spectra are
determined by protocol
, and the number of columns in each member
spectrum is determined by acq.settings
.
Obviously the duration of the time steps must be longer than the time that a measurement takes. This time can be significantly more than the sum of integration times, as there is considerable overhead in both the OmniDriver Java code, in USB communication, in the spectrometer itself and in R. The overhead depends strongly on the model of spectrometer.
No multitasking is used or supported, so R waits for the spectrometer to answer. The operating system and other programs are not blocked, but the current R instance is.
acq_raw_spct
which is used to acquire each member
spectrum. Computations on date times are done with
lubridate
.
Other raw-counts-spectra acquisition functions:
acq_raw_spct()
,
hs_acq_raw_mspct()
Take one spectral measurement which depending on the settings can consist in multiple raw spectra meant to represent a SINGLE observation after conversion into calibrated data, such as in the case of bracketing of integration time for HDR.
acq_raw_spct( descriptor, acq.settings, f.trigger.on = f.trigger.message, f.trigger.off = NULL, what.measured = NA, where.measured = data.frame(lon = NA_real_, lat = NA_real_), set.all = TRUE, verbose = TRUE )
acq_raw_spct( descriptor, acq.settings, f.trigger.on = f.trigger.message, f.trigger.off = NULL, what.measured = NA, where.measured = data.frame(lon = NA_real_, lat = NA_real_), set.all = TRUE, verbose = TRUE )
descriptor |
list as returned by function |
acq.settings |
list as returned by functions |
f.trigger.on , f.trigger.off
|
function Functions to be called immediately before and immediately after a measurement. |
what.measured |
value used to set attribute. |
where.measured |
data.frame with at least columns "lon" and "lat"
compatible with value returned by |
set.all |
logical resend or not all instrument settings. |
verbose |
logical to enable or disable warnings. |
This function acquires one raw-detector-counts spectrum from a spectrometer,
using the descriptor
to connect to the spectrum and retrieve the
valid range for settings. The settings in acq.settings
are first
sent to the spectrometer and the values retrieved in case the spectrometer
has overridden the requested settings. Subsequently a spectrum, possibly
obtained by averaging multiple spectra in the spectrometer is acquired, and
the spectrometer queried on whether data are valid or not.
Function acq_raw_spct()
can optionally call two functions, one at the
start of the measurement and another one after it ends. f.trigger.on()
can be used for example when measuring the output from a xenon flash lamp, to
trigger a given number of light flashes. In other cases f.trigger.on()
and f.trigger.off()
can be used together to start and end a concurrent
measurement or any other action using a relay controlled by code in a
function defined by the user.
The functions passed as arguments to f.trigger.on()
and
f.trigger.off()
should return very quickly when called, so as not to
disturb the timing of the measurements of spectra as these start only after
f.trigger.on()
returns to the caller.
The first formal parameter of f.trigger.on()
should handle as input
an integer value indicating the number of events to trigger and a second
argument giving the delay in seconds between pulses. Of course the arguments
can be ignored if not needed, but should accepted. f.trigger.off()
currently expects no arguments. Example scripts are provided for YoctoPuce
USB modules.
The default function, displays a message asking the user to manually trigger
the flash a number of times that depends on the settings in
acq.settings
.
A raw_spct
object with one column w.length
and one
column counts
, or two or more columns counts1, counts2, ...
containing raw counts data. The number of columns with raw counts is
determined by acq.settings
, with multiple columns in the case of
integration time bracketing or HDR.
acq_raw_mspct
which can be used to acquire multiple
spectra according to a user defined protocol.
Other raw-counts-spectra acquisition functions:
acq_raw_mspct()
,
hs_acq_raw_mspct()
Validate parameters for spectral measurements and return a list of values
usable as input for functions retune_acq_settings()
, acq_sptc()
,
and acq_mspct()
.
Find optimal settings for spectral measurements under a given measurement protocol.
acq_settings( descriptor, integ.time = 0.01, num.scans = 10L, min.integ.time = -Inf, max.integ.time = Inf, tot.time.range = c(0, Inf), HDR.mult = ifelse(any(num.exposures != -1L), rep(1, length(num.exposures)), c(short = 1, long = 10)), target.margin = 0.1, pix.selector = TRUE, corr.elect.dark = 0L, corr.sensor.nl = 0L, boxcar.width = 0L, force.valid = FALSE, num.exposures = -1L, verbose = TRUE ) tune_acq_settings(descriptor, acq.settings, verbose = TRUE)
acq_settings( descriptor, integ.time = 0.01, num.scans = 10L, min.integ.time = -Inf, max.integ.time = Inf, tot.time.range = c(0, Inf), HDR.mult = ifelse(any(num.exposures != -1L), rep(1, length(num.exposures)), c(short = 1, long = 10)), target.margin = 0.1, pix.selector = TRUE, corr.elect.dark = 0L, corr.sensor.nl = 0L, boxcar.width = 0L, force.valid = FALSE, num.exposures = -1L, verbose = TRUE ) tune_acq_settings(descriptor, acq.settings, verbose = TRUE)
descriptor |
list as returned by function |
integ.time |
numeric vaue in seconds |
num.scans |
integer |
min.integ.time |
numeric vaue in seconds |
max.integ.time |
numeric vaue in seconds |
tot.time.range |
numeric vector of length two with values in seconds |
HDR.mult |
a numeric vector with integ.time multipliers to be used for "bracketing". |
target.margin |
numeric (0..1) |
pix.selector |
a logical or numeric vector used as subscript to select pixels |
corr.elect.dark , corr.sensor.nl
|
integer 0L (FALSE) or 1L (TRUE) |
boxcar.width |
integer Number of pixels to average |
force.valid |
logical Accept all spectra as valid, for example do not treat clipping as an error condition. |
num.exposures |
integer Number of flashes triggered per scan. |
verbose |
a logical to enable or disable warnings |
acq.settings |
list as returned by a previous call to
|
acq_settings()
is used to create a complete set of
instrument settings in a way that they can be reused as needed for repated
acquisition of spectra. acq_settings()
is an object constructor and
tune_acq_settings()
takes as argument a stored object containing
settings and tunes them to optimize them for the measurement of the current
spectral irradiance.
This function searches for the optimal integration time for a given condition by trial and error helped by interpolation and extrapolation when readings are not saturated. In the case of clipping or sensor signal saturation the integration time is decreased until clipping is avoided and then it is increased until optimal.
a list.
a list Containing the tuned settings.
pixel.selector
can be used for two different purposes: to
ignore bad pixels and to restrict integration-time tuning to the response
from a range of pixels. The interpretation of tot.time.range
is
as follows: first value is minimum time, second value is maximum time.
If both values are the same, then an exact measurement time is computed.
Ocean Optics spectrometers can be queried for the maximum and minimum
supported integration times. This function modifies the user supplied
values if outside these bounds. The defaults of -Inf and Inf force the use
of the whole valid range of integration time supported by the connected
intrument. pixel.selector
can be used for two different purposes: to
ignore bad pixels and to restrict integration-time tuning to the response
from a range of pixels.
The returned value can be used as argument to acq.settings
in
other functions like acq_raw_spct
and
acq_raw_mspct
Other acquisition-settings related functions:
set_integ_time()
,
set_linearized()
,
set_num_exposures()
Replace "good" data from pixels adjacent to NAs with NAs as data from pixels not saturated but located in the neighbourhood of saturated pixels can return unreliable data. This correction is needed by a phenomenon similar to "blooming" in camera sensors whereby when a sensor well gets saturated some of the charge migrates to adjacent wells in the detector increasing their readings.
bleed_nas(x, n = 10)
bleed_nas(x, n = 10)
x |
raw_spct object |
n |
integer Number of pixels to set to NAs. |
a copy of x with values replaced by NAs as needed in all counts columns present.
Avoid using very large n values as n pixels at each end of the array are assumed not to be ever saturated. The value of n needed for each detector type/instrument needs to be found through testing. As rule of thumb use 5 < n < 10 for Sony's ILxxx and 8 < n < 14 for Hamamatsu xxxx. At the moment we use a symmetric window although "blooming" could be asymmetric.
A blue interference filter from UQG measured using a household incandescent lamp as light source. The spectrometer used was an Ocean Optics Maya2000 Pro.
blue_filter.raw_mspct
blue_filter.raw_mspct
A raw_mspct
Other objects containing example raw-counts data:
halogen.raw_mspct
,
red_filter.raw_mspct
,
sun001.raw_mspct
,
white_LED.raw_mspct
,
xenon_flash.raw_mspct
This method checks that the sn of the instrument used to acquire the raw counts matches that in the definition of a correction method.
check_sn_match(x, correction.method, missmatch.action = stop)
check_sn_match(x, correction.method, missmatch.action = stop)
x |
a generic_mspct object, in normal use a raw_mspct object. |
correction.method |
a list describing the correction method. Must
incluse a member named |
missmatch.action |
a function, in practice one of |
A logical vector of length one, with FALSE
indicating a
missmatch.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
linearize_counts()
,
merge_raw_mspct()
,
new_correction_method()
,
ref_correction()
,
trim_counts()
,
uvb_corrections()
Choice of channel to be used if spectrometer has more than one channel.
choose_ch_interactive( instruments, sr.index = 0L, prompt.text = "Channels available: " )
choose_ch_interactive( instruments, sr.index = 0L, prompt.text = "Channels available: " )
instruments |
the returm value of |
sr.index |
integer The index to the spectrometer, starting from zero, following Omni Driver indexing conventions. |
prompt.text |
character string to use as prompt. |
A numeric index suitable for use in calls to functions defined in package 'rOmniDriver' based on which package 'ooacquire' is coded.
Other interactive acquisition utility functions:
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Choice of spectrometer from a list of serial numbers, allowing the user to correct the selection if needed.
choose_sr_interactive(instruments)
choose_sr_interactive(instruments)
instruments |
the returm value of |
A numeric index suitable for use in calls to functions defined in package 'rOmniDriver' based on which package 'ooacquire' is coded.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Read .Rda files as saved during data acquisition and build a collection with the spectra read, possibly first trimming the range of wavelengths and/or smoothing the spectral data.
collect_spct_files( path = ".", range = NULL, method = NULL, strength = 0, name.root = "", na.rm = FALSE )
collect_spct_files( path = ".", range = NULL, method = NULL, strength = 0, name.root = "", na.rm = FALSE )
path |
a character string giving the name of the folder from wich to load .Rda files containing spectra. |
range |
a numeric vector of length two, or any other object for which function range() will return two. |
method |
a character vector of length 1 or 2, containing the smoothing method to use, one of "custom", "lowess", or "supsmu". |
strength |
numeric value to adjust the degree of smoothing. |
name.root |
character string to prepend to the name of the spectra in the collection. |
na.rm |
a logical value indicating whether NA values should be stripped before the computation proceeds. |
If the argument passed to method
is of length 2, the first
member will apply to source_spct
objects and the second one to
filter_spct
and reflector_spct
objects. A numeric vector
of length 2 passed to strength
is treated in the same way. This
is only relevant when we are collecting spectra belonging to different
classes and need to treat them differently with respect to smoohting. It
also allows different defaults, as transmittance spectra tend to lack
the fine structure of some emission spectra.
Function trim_wl
is used to trim the
range of the data to plot, and function
smooth_spct
is used for smoothing, and
prameters range
, and strength
and method
are passed to
them, respectively.
Other functions for importing spectral data from files:
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Function to calculate from a set of three (or optionally five or two) output files from the spectrometer, as produced by SpectraSuite, for each of two calibration lamps (D2 and FEL), and calibration data for the lamps, a set of calibration multipliers for the instrument. This function applies a non-linearity correction, an slit-function correction, and stray-light correction, and optionally smoothing by means of process_maya_arrays(). Optionaly a HDR ("high dynamic range") merging of spectra (based on integration time bracketing) using two different integration times is done.
compute_irrad_calibration( FEL.raw.counts, D2.raw.counts, pix.wavelengths = NULL, wl.range = c(250, 900), FEL.k, D2.k, method, verbose = getOption("photobiology.verbose", default = FALSE) )
compute_irrad_calibration( FEL.raw.counts, D2.raw.counts, pix.wavelengths = NULL, wl.range = c(250, 900), FEL.k, D2.k, method, verbose = getOption("photobiology.verbose", default = FALSE) )
FEL.raw.counts |
source_mscpt The raw counts and integration time data for the FEL light source. |
D2.raw.counts |
source_mscpt The raw counts and integration time data for the D2 light source. |
pix.wavelengths |
numeric vector The "true" wavelengths in nanometres at each pixel in the detector array. |
wl.range |
numeric vector of length two Range of wavelengths for which to compute the calibration. |
FEL.k |
numeric vector a numeric vector with n constants for the polynomial for the FEL lamp. |
D2.k |
numeric vector a numeric vector with n constants for the polynomial for the D2 lamp. |
method |
list Method variant to be used. |
verbose |
Logical indicating the level of warnings wanted. Defaults to
|
An instrument descriptor as a list containing the updated wavelengths and multipliers from the calibration.
To calculate new multipliers we set the calibration multipliers equal to 1. Do the calculations as usual and calculate new multipliers based on the known spectral irradiance for the calibration lamps.
Close the connection to the spectrometer pointed
at by the Java object referenced in x
.
end_session(w)
end_session(w)
w |
a java wrapper as returned by |
Other spectrometer-connection functions:
list_instruments()
,
start_session()
This function is used by default. It prints a message asking the operator to manually trigger a flash. A more elaborate function, using specific hardware can be used to automatically trigger a light source or some other synchronized event such as releasing the shutter of a camera.
f.trigger.message(n = 1L, delay = 0)
f.trigger.message(n = 1L, delay = 0)
n |
integer Number of pulses (flashes) to trigger per call. |
delay |
numeric Time in seconds to wait before displaying the message. |
When using this function, set an integration time that gives enough time for the manual triggering of the flash to reliably fall within the integration.
Sys.sleep
for a description of the variation
in the effective duration of the delay
.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Correct cps readings for stray light, using either measured stray light, or using a non-excited region of the detector array.
filter_correction( x, flt, stray.light.method = "original", stray.light.wl = c(218.5, 228.5), flt.dark.wl = c(193, 209.5), flt.ref.wl = c(360, 379.5), flt.Tfr = 1, trim = 0.05, filter.nir.adjust = FALSE, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.1), verbose = getOption("photobiology.verbose", default = FALSE) ) no_filter_correction( x, stray.light.wl = c(218.5, 228.5), flt.dark.wl = c(193, 209.5), flt.ref.wl = NULL, flt.Tfr = 1, trim = 0, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.1), verbose = getOption("photobiology.verbose", default = FALSE) )
filter_correction( x, flt, stray.light.method = "original", stray.light.wl = c(218.5, 228.5), flt.dark.wl = c(193, 209.5), flt.ref.wl = c(360, 379.5), flt.Tfr = 1, trim = 0.05, filter.nir.adjust = FALSE, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.1), verbose = getOption("photobiology.verbose", default = FALSE) ) no_filter_correction( x, stray.light.wl = c(218.5, 228.5), flt.dark.wl = c(193, 209.5), flt.ref.wl = NULL, flt.Tfr = 1, trim = 0, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.1), verbose = getOption("photobiology.verbose", default = FALSE) )
x , flt
|
cps_spct objects, containing spectral data from which to subtract stray light, and measured stray light, respectively. |
stray.light.method |
Method variant used, "original" (Ylianttila), "simple", "full", "sun", "raw", "none". |
stray.light.wl |
numeric vector of length 2 giving the range of wavelengths to use for the final stray light correction. |
flt.dark.wl , flt.ref.wl
|
numeric vectors of length 2 giving the ranges of wavelengths to use for the "dark" and "illuminated" regions of the array in the filter correction. |
flt.Tfr |
numeric fractional transmittance of the filter to the source of stray light, used only for method "simple". |
trim |
a numeric value to be used as argument for mean |
filter.nir.adjust |
logical Flag indicating if the cps in the "filter" reference spectrum need to be adjust based on NIR region cps in the "light" spectrum. EXPERIMENTAL!! |
hdr.tolerance |
numeric Tolerance for mean deviation among cps columns as a fraction of one. Used in check of HDR consistency. |
verbose |
Logical indicating the level of warnings wanted. |
Calibration data, descriptors and methods for correction of stray light and high dynamic range based on multiple integrations times per spectrum.
FLMS00416_descriptors FLMS00416_cal.spct FLMS00416_calib_dates.df FLMS00416_ylianttila.mthd FLMS00416_sun.mthd FLMS00416_simple.mthd FLMS00416_none.mthd
FLMS00416_descriptors FLMS00416_cal.spct FLMS00416_calib_dates.df FLMS00416_ylianttila.mthd FLMS00416_sun.mthd FLMS00416_simple.mthd FLMS00416_none.mthd
Lists and data frames.
An object of class calibration_spct
(inherits from generic_spct
, tbl_df
, tbl
, data.frame
) with 2048 rows and 2 columns.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 1 rows and 6 columns.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 10.
Some of the method definitions are fill-ins for methods not implemented. In this case no characterizations of the slit function are available.
Other objects containing instrument-specific data:
FLMS00440_descriptors
,
FLMS00673_descriptors
,
FLMS04133_descriptors
,
JAZA3098_calib_dates.df
,
MAYP112785_descriptors
,
MAYP11278_descriptors
,
MAYP114590_descriptors
Calibration data, descriptors and methods for correction of stray light and high dynamic range based on multiple integrations times per spectrum.
FLMS00440_descriptors FLMS00440_cal.spct FLMS00440_calib_dates.df FLMS00440_ylianttila.mthd FLMS00440_sun.mthd FLMS00440_simple.mthd FLMS00440_none.mthd
FLMS00440_descriptors FLMS00440_cal.spct FLMS00440_calib_dates.df FLMS00440_ylianttila.mthd FLMS00440_sun.mthd FLMS00440_simple.mthd FLMS00440_none.mthd
Lists and data frames.
An object of class calibration_spct
(inherits from generic_spct
, tbl_df
, tbl
, data.frame
) with 2048 rows and 2 columns.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 1 rows and 6 columns.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 10.
Some of the method definitions are fill-ins for methods not implemented. In this case no characterizations of the slit function are available.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00673_descriptors
,
FLMS04133_descriptors
,
JAZA3098_calib_dates.df
,
MAYP112785_descriptors
,
MAYP11278_descriptors
,
MAYP114590_descriptors
Calibration data, descriptors and methods for correction of stray light and high dynamic range based on multiple integrations times per spectrum.
FLMS00673_descriptors FLMS00673_cal.spct FLMS00673_calib_dates.df FLMS00673_ylianttila.mthd FLMS00673_sun.mthd FLMS00673_simple.mthd FLMS00673_none.mthd
FLMS00673_descriptors FLMS00673_cal.spct FLMS00673_calib_dates.df FLMS00673_ylianttila.mthd FLMS00673_sun.mthd FLMS00673_simple.mthd FLMS00673_none.mthd
Lists and data frames.
An object of class calibration_spct
(inherits from generic_spct
, tbl_df
, tbl
, data.frame
) with 2048 rows and 2 columns.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 1 rows and 6 columns.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 10.
Some of the method definitions are fill-ins for methods not implemented. In this case no characterizations of the slit function are available.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00440_descriptors
,
FLMS04133_descriptors
,
JAZA3098_calib_dates.df
,
MAYP112785_descriptors
,
MAYP11278_descriptors
,
MAYP114590_descriptors
Calibration data, descriptors and methods for correction of stray light and high dynamic range based on multiple integrations times per spectrum.
FLMS04133_descriptors FLMS04133_cal.spct FLMS04133_calib_dates.df FLMS04133_ylianttila.mthd FLMS04133_sun.mthd FLMS04133_simple.mthd FLMS04133_none.mthd
FLMS04133_descriptors FLMS04133_cal.spct FLMS04133_calib_dates.df FLMS04133_ylianttila.mthd FLMS04133_sun.mthd FLMS04133_simple.mthd FLMS04133_none.mthd
Lists and data frames.
An object of class calibration_spct
(inherits from generic_spct
, spec_tbl_df
, tbl_df
, tbl
, data.frame
) with 2048 rows and 2 columns.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 1 rows and 6 columns.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 10.
An object of class list
of length 10.
Some of the method definitions are fill-ins for methods not implemented. In this case no characterizations of the slit function are available.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00440_descriptors
,
FLMS00673_descriptors
,
JAZA3098_calib_dates.df
,
MAYP112785_descriptors
,
MAYP11278_descriptors
,
MAYP114590_descriptors
Model, configuration, serial number, and calibration data stored in the EEPROM of an Ocean Optics spectrometer are retrieved and returned in a list.
get_oo_descriptor( w, sr.index = 0L, ch.index = 0L, area = NULL, diff.type = NULL )
get_oo_descriptor( w, sr.index = 0L, ch.index = 0L, area = NULL, diff.type = NULL )
w |
an open Wrapper object from OmniDriver. |
sr.index |
an index to address the spectrometer for the time being not exported. |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
area |
numeric Passed to |
diff.type |
character Passed to |
a list
One and only one of area
or diff.type
is needed if an
irradiance calibration stored in the EEPROM is to be retrieved. If both
are null, as by default, the irradiance calibration factors will not be
retireved even if present in the EEPROM.
Query the spectrometer for the settings currently in use for corrections, smotthing and acquisition parameters integration time and number of scans.
get_oo_settings(descriptor)
get_oo_settings(descriptor)
descriptor |
list as returned by function |
a list
A household Osram tungsten halogen 25W E27 lamp measured at short distance. The spectrometer used was an Ocean Optics Maya2000 Pro.
halogen.raw_mspct
halogen.raw_mspct
A raw_mspct
Other objects containing example raw-counts data:
blue_filter.raw_mspct
,
red_filter.raw_mspct
,
sun001.raw_mspct
,
white_LED.raw_mspct
,
xenon_flash.raw_mspct
Take one set of spectra at high speed using unchanged instrument settings special OmniDriver API functions for buffered acquisition. No HDR bracketing is possible, and synchronization with a pulsed light source is not supported.
hs_acq_raw_mspct( descriptor, acq.settings, num.spectra = 100L, base.name = NULL, f.trigger.on = f.trigger.message, f.trigger.off = NULL, what.measured = NA, where.measured = data.frame(lon = NA_real_, lat = NA_real_), set.all = TRUE, verbose = TRUE, return.list = FALSE )
hs_acq_raw_mspct( descriptor, acq.settings, num.spectra = 100L, base.name = NULL, f.trigger.on = f.trigger.message, f.trigger.off = NULL, what.measured = NA, where.measured = data.frame(lon = NA_real_, lat = NA_real_), set.all = TRUE, verbose = TRUE, return.list = FALSE )
descriptor |
list as returned by function |
acq.settings |
list as returned by functions |
num.spectra |
integer Number of individual spectra to acquire. |
base.name |
character The name given to individual spectra is formed by this string followed by a sequential numeric index. |
f.trigger.on , f.trigger.off
|
function Functions to be called
immediately before and immediately after a measurement. See
|
what.measured |
value used to set attribute. |
where.measured |
data.frame with at least columns "lon" and "lat"
compatible with value returned by |
set.all |
logical resend or not all instrument settings. |
verbose |
logical to enable or disable warnings. |
return.list |
logical Return a |
A raw_mspct
containing one raw_spct
object with one
column w.length
and one column counts
for each spectrum. The
number of columns with raw counts is always one and integration time
bracketing or HDR values in acq.settings
are ignored except for the
smallest value.
For normal speed acquisition of a single spectrum and multiple
spectra according to a user defined protocol see acq_raw_spct
and acq_raw_mspct
.
Other raw-counts-spectra acquisition functions:
acq_raw_mspct()
,
acq_raw_spct()
Compute irradiance or fluence by waveband and energy or photon ratios between wavebands of interest to plants' and human visual responses to light.
irrad_summary_table( mspct, unit.out = getOption("photobiology.radiation.unit", default = "energy"), scale.factor = ifelse(unit.out == "photon", 1e+06, 1), attr2tb = "when.measured", summary.type = "plant", digits = 3L )
irrad_summary_table( mspct, unit.out = getOption("photobiology.radiation.unit", default = "energy"), scale.factor = ifelse(unit.out == "photon", 1e+06, 1), attr2tb = "when.measured", summary.type = "plant", digits = 3L )
mspct |
A source_mspct, or a source_spct object containing spectral irradiance for one or more sources. |
unit.out |
character One of "photon" or "energy". |
scale.factor |
numeric A multiplicative factor used to rescale data. |
attr2tb |
character Vector with one or more of "when.measured", "what.measured", "where.measured", "how.measured" and "comment". |
summary.type |
character One of "plant", "PAR" or "VIS". |
digits |
integer The number of significant digits in the output. |
This function packages different functions from pacakge 'photobiology' and returns a typical set of summaries for different purposes.
A tibble with one row per spectrum and one column per summary quantity and attribute and a column with the names of the spectra.
See the documentation for functions
irrad
,
q_ratio
, e_ratio
,
add_attr2tb
,
spct_CRI
,
spct_CCT
and signif
which are called to build
the summary table.
irrad_summary_table(sun.spct) irrad_summary_table(sun.spct, attr2tb = c("what.measured", "where.measured")) irrad_summary_table(sun.spct, summary.type = "plant", unit.out = "photon") irrad_summary_table(sun.spct, summary.type = "PAR", unit.out = "photon") # temporary kludge until fixed in photobiologyInOut # irrad_summary_table(sun.spct, summary.type = "VIS", unit.out = "energy")
irrad_summary_table(sun.spct) irrad_summary_table(sun.spct, attr2tb = c("what.measured", "where.measured")) irrad_summary_table(sun.spct, summary.type = "plant", unit.out = "photon") irrad_summary_table(sun.spct, summary.type = "PAR", unit.out = "photon") # temporary kludge until fixed in photobiologyInOut # irrad_summary_table(sun.spct, summary.type = "VIS", unit.out = "energy")
Calibration data, descriptors and methods for correction of stray light and high dynamic range based on multiple integrations times per spectrum.
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
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
Lists and data frames.
An object of class list
of length 1.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 9.
An object of class list
of length 9.
An object of class list
of length 1.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 9.
An object of class list
of length 9.
Some of the method definitions are fill-ins for methods not implemented. In this case no calibration for spectral irradiance or characterizations of the slit function are available.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00440_descriptors
,
FLMS00673_descriptors
,
FLMS04133_descriptors
,
MAYP112785_descriptors
,
MAYP11278_descriptors
,
MAYP114590_descriptors
Uses a function stored as an attribute of x
, by default retrieved
from the instrument's firmware at the time of data acquisition or possibly
a replacement set by the user.
linearize_counts( x, force.zero = TRUE, verbose = getOption("photobiology.verbose", default = FALSE) )
linearize_counts( x, force.zero = TRUE, verbose = getOption("photobiology.verbose", default = FALSE) )
x |
raw_spct object. |
force.zero |
A logical indicating whether to change negative count values to zero. |
verbose |
Logical Currently ignored. |
A raw_spct object containing the adjusted values, still as uncalibrated counts. The object is tagged with the with attribute "linearized" set to the function used for linearization.
In contrast to other classes defined in package 'photobiology', class "raw_spct" can have more than one column of raw counts in cases where the intention is to merge these values as part of the processing at the time the calibration is applied. In other words these columns are not separate observations but instrumental replicates or bracketing readings part of the same "logical" or "effective" observation. The contents of any column whose name starts with "counts" will have the intrument response linearization function applied.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
check_sn_match()
,
merge_raw_mspct()
,
new_correction_method()
,
ref_correction()
,
trim_counts()
,
uvb_corrections()
List all connected spectrometers by model name and serial number, plus the number of channels in each of them.
list_instruments(w)
list_instruments(w)
w |
an open Wrapper object from Omnidriver |
a list
Other spectrometer-connection functions:
end_session()
,
start_session()
Get list of spectrometers requesting user to connect one or abort if none found.
list_srs_interactive(w)
list_srs_interactive(w)
w |
handle to Omni Driver, used to test if an spectrometer is still connected. |
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Locate in which lines of the file header different metadata features are located. Parsing is needed because the format used varies with among Ocean Optics programs and instruments. Even the number of lines in the header, and the position of the first line with spectral data vary.
map_oofile_header_rows(lines, header.end = NULL, grammar = oo.minimum.gr)
map_oofile_header_rows(lines, header.end = NULL, grammar = oo.minimum.gr)
lines |
character The data file read line by line. |
header.end |
integer The index to the last line of the longest header expected. |
grammar |
data.frame With character variables "feature" and "pattern" that will be used to locate the lines containing each type of metadata. |
A data frame with two variables, "feature" of class character, and "line.idx" of class integer.
Other functions for importing spectral data from files:
collect_spct_files()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
List of instrument descriptors, each one containing the calibration data needed to convert raw data acquired on different dates. Calibration data from STUK's non-ionising radiation laboratory. Correction method algorithms for stray light and slit function by Lasse Ylianttila, and variations by Pedro J. Aphalo..
MAYP11278_descriptors MAYP11278_calib_dates.df MAYP11278_ylianttila.mthd MAYP11278_short_flt_ref.mthd MAYP11278_sun.mthd MAYP11278_simple.mthd
MAYP11278_descriptors MAYP11278_calib_dates.df MAYP11278_ylianttila.mthd MAYP11278_short_flt_ref.mthd MAYP11278_sun.mthd MAYP11278_simple.mthd
Lists and data frames.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 9 rows and 8 columns.
An object of class list
of length 10.
An object of class list
of length 10.
An object of class list
of length 10.
An object of class list
of length 10.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00440_descriptors
,
FLMS00673_descriptors
,
FLMS04133_descriptors
,
JAZA3098_calib_dates.df
,
MAYP112785_descriptors
,
MAYP114590_descriptors
Function to compute the tail correction
MAYP11278_tail_correction(w_length, cts_second)
MAYP11278_tail_correction(w_length, cts_second)
w_length |
numeric vector of wavelengths in nanometres (nm). |
cts_second |
numeric vector of counts per second (stray-light corrected). |
tail returned as numeric vector within a list.
Tail correction is a reimplementation of the calculations developed by Lasse Ylianttila (STUK, Finland), originally in Excel.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
merge_raw_mspct()
,
new_correction_method()
,
ref_correction()
,
trim_counts()
,
uvb_corrections()
List of instrument descriptors, each one containing the calibration data needed to convert raw data acquired on different dates. Calibration data from STUK's non-ionising radiation laboratory. Correction method algorithms for stray light and slit function by Lasse Ylianttila, and variations by Pedro J. Aphalo..
MAYP112785_descriptors MAYP112785_calib_dates.df MAYP112785_ylianttila.mthd MAYP112785_sun.mthd MAYP112785_simple.mthd
MAYP112785_descriptors MAYP112785_calib_dates.df MAYP112785_ylianttila.mthd MAYP112785_sun.mthd MAYP112785_simple.mthd
Lists and data frames.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 4 rows and 8 columns.
An object of class list
of length 10.
An object of class list
of length 10.
An object of class list
of length 10.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00440_descriptors
,
FLMS00673_descriptors
,
FLMS04133_descriptors
,
JAZA3098_calib_dates.df
,
MAYP11278_descriptors
,
MAYP114590_descriptors
Function to compute the tail correction
MAYP112785_tail_correction(w_length, cts_second)
MAYP112785_tail_correction(w_length, cts_second)
w_length |
numeric vector of wavelengths in nm. |
cts_second |
numeric vector of counts per second (stray-light corrected). |
tail returned as numeric vector within a list.
Tail correction is a reimplementation of the calculations developed by Lasse Ylianttila (STUK, Finland), originally in Excel.
Other spectral data-processing functions:
MAYP11278_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
merge_raw_mspct()
,
new_correction_method()
,
ref_correction()
,
trim_counts()
,
uvb_corrections()
List of instrument descriptors, each one containing the calibration data needed to convert raw data acquired on different dates. Calibration data from STUK's non-ionising radiation laboratory. Correction method algorithms for stray light and slit function by Lasse Ylianttila, and variations by Pedro J. Aphalo..
MAYP114590_descriptors MAYP114590_cal.spct MAYP114590_calib_dates.df MAYP114590_ylianttila.mthd MAYP114590_sun.mthd MAYP114590_simple.mthd MAYP114590_none.mthd
MAYP114590_descriptors MAYP114590_cal.spct MAYP114590_calib_dates.df MAYP114590_ylianttila.mthd MAYP114590_sun.mthd MAYP114590_simple.mthd MAYP114590_none.mthd
Lists and data frames.
An object of class calibration_spct
(inherits from generic_spct
, spec_tbl_df
, tbl_df
, tbl
, data.frame
) with 2068 rows and 2 columns.
An object of class spec_tbl_df
(inherits from tbl_df
, tbl
, data.frame
) with 1 rows and 6 columns.
An object of class list
of length 0.
An object of class list
of length 0.
An object of class list
of length 10.
An object of class list
of length 10.
Some of the method definitions are fill-ins for methods not implemented. In this case no characterization of the slit function is available.
Other objects containing instrument-specific data:
FLMS00416_descriptors
,
FLMS00440_descriptors
,
FLMS00673_descriptors
,
FLMS04133_descriptors
,
JAZA3098_calib_dates.df
,
MAYP112785_descriptors
,
MAYP11278_descriptors
In a cps_spct
object with multiple columns of CPS data, each acquired
using a different integration time, merge columns into a single column.
merge_cps( x, tolerance = 0.05, verbose = getOption("photobiology.verbose", default = FALSE) )
merge_cps( x, tolerance = 0.05, verbose = getOption("photobiology.verbose", default = FALSE) )
x |
cps_spct object |
tolerance |
numeric Tolerance for mean deviation among cps columns as a fraction of one. |
verbose |
Logical indicating the level of warnings and messages wanted. |
Pixels affected directly, or by neighbourhood, by clipping, should
be set to NA
in each variable of CPS values, before passing the
spectrum as argument to parameter x
of this function.
The merging of the CPS variables starts from the one corresponding to the
longest integration time, expected to contain the largest number of NA
values, by replacing NA values by cps values from the variable
corresponding to the next shorter integration. The procedure is repeated
until no NA
remains or until no shorter integration time data are
available. The process stops when all NAs have been replaced, and,
even when available, CPS values for unnecesarilly short integration times
discarded.
When measuring daylight different exposures for HDR are taken sequentially, and if light conditions change rapidly the cps values may be inconsistent. If the mean ratio of cps values is outside plus/minus the tolerance, instead of merging, the data for the longer of the two exposures is discarded instead of merged (or spliced) with the longer exposure, in which case a message is emitted. Ratio is computed after discarding low signal pixels as these readings are affected by noise, distorting the ratio when the light source-spectrum has only narrow peaks of emission.
a copy of x with values replaced as needed in all counts columns present.
Member spectra are sorted according to integration time stored in the
inst.settings
attribute and merged into a single raw_spct
object with raw counts variables named counts_1
, counts_2
,
etc.
merge_raw_mspct(x)
merge_raw_mspct(x)
x |
raw_mspct |
The individual raw_spct
objects contained in x
must have
identical values in w.length
.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
new_correction_method()
,
ref_correction()
,
trim_counts()
,
uvb_corrections()
A function that builds a default method from an instrument descriptor.
Useful when the spectrometers has not been characterized as needed for
the more sofisticated methods. Can use stray light correction
but not slit function correction. Stray light correction is valid
only if it was also used during irradiance callibration. Suitablity
of wavelengths and method depends on the instrument configuration so
they are set to NA
as default..
new_correction_method( descriptor, stray.light.method = "none", stray.light.wl = c(NA_real_, NA_real_), flt.dark.wl = c(NA_real_, NA_real_), flt.ref.wl = c(NA_real_, NA_real_), flt.Tfr = NA_real_ )
new_correction_method( descriptor, stray.light.method = "none", stray.light.wl = c(NA_real_, NA_real_), flt.dark.wl = c(NA_real_, NA_real_), flt.ref.wl = c(NA_real_, NA_real_), flt.Tfr = NA_real_ )
descriptor |
list, as returned by |
stray.light.method |
character Name of method. |
stray.light.wl , flt.dark.wl , flt.ref.wl
|
numeric vector with wavelengths (nm). |
flt.Tfr |
numeric Transmittance of filter as a fraction (0...1). |
The currently recognized methods for stray-light correction are
"none"
, "original"
, "sun"
, and "simple"
. With
the default method "none"
, the values of the remaining parameters
are ignored.
a list
Defaults for indexes are for the first channel of the first spectrometer currently connected.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
merge_raw_mspct()
,
ref_correction()
,
trim_counts()
,
uvb_corrections()
Convert irradiance calibration values as supplied by Ocean Optics into multipliers expressed in the units and format expected by the functions in this package.
oo_calib2irrad_mult( x, area = NULL, diff.type = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
oo_calib2irrad_mult( x, area = NULL, diff.type = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
x |
generic_spct object with variables |
area |
numeric Area of the cosine diffuser (mm2). |
diff.type |
character Value giving type of diffuser as in OO's
documents, case insensitive. Ignored unless |
verbose |
Logical indicating the level of warnings wanted. |
a calibration_spct
object of the same number of rows as
x
containing wavelengths in varable w.length
and the
re-scaled calibration factors in variable irrad.mult
.
Ocean Optics files can have varying numbers of rows containing spectral data, but these rows are fenced between two lines containing recognizable character strings. This function, detects these strings.
oofile_data_rows(lines)
oofile_data_rows(lines)
lines |
character The data file read line by line. |
integer vector of length two, containing the indexes to the first last rows containing spectral data.
This is a rather slow operation, so if all files to be read have the same format, it is inefficient to call this function for each file.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Read an .Rda file as saved during data acquisition and plot it, possibly first trimming the range of wavelengths and/or smoothing the spectral data.
plot_spct_file(file, range = NULL, method = NULL, strength = 0, na.rm = FALSE)
plot_spct_file(file, range = NULL, method = NULL, strength = 0, na.rm = FALSE)
file |
a (readable binary-mode) connection or a character string giving the name of the file to load (when tilde expansion is done). |
range |
a numeric vector of length two, or any other object for which function range() will return two. |
method |
a character string "custom", "lowess", "supsmu". |
strength |
numeric value to adjust the degree of smoothing. |
na.rm |
a logical value indicating whether NA values should be stripped before the computation proceeds. |
If the argument passed to method
is of length 2, the first
member will apply to source_spct
objects and the second one to
filter_spct
and reflector_spct
objects. A numeric vector
of length 2 passed to strength
is treated in the same way. This
is only relevant when we are collecting spectra belonging to different
classes and need to treat them differently with respect to smoohting. It
also allows different defaults, as transmittance spectra tend to lack
the fine structure of some emission spectra.
Function trim_wl
is used to trim the
range of the data to plot, and function
smooth_spct
is used for smoothing, and
prameters range
, and strength
and method
are passed to
them, respectively.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Choose a protocol by name from a list of protocols, allowing the user to
correct the selection if needed. Protocols are not hard-wired, but instead
defined by the list passed as argument to protocols
.
protocol_interactive(protocols, default = names(protocols)[[1]])
protocol_interactive(protocols, default = names(protocols)[[1]])
protocols |
named list Measuring protocol defifinitions and names. |
default |
character Name of the default protocol. |
A protocol is defined as a named list of character strings, and consist in
multiple acquisition of spectra contributing to the same logical measurement.
The name of the list member is the name of the protocol, while the members
of each character vector correspond to spectra to be acquired, after some
change in the measurement conditions. For example the list
list(rsd = c("reference", "sample", "dark"), rs = c("reference", "sample"))
defines two protocols.
The member vector corresponding to the protocol selected by the user.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Function used to check the number of pixels that deviate from the median.
QC_dark( x, range = NULL, tol.margin = 1, max.hot = 60, max.cold = 20, spct.label = "Spectrum", verbose = getOption("photobiology.verbose", default = TRUE), QC.enabled = getOption("ooacquire.qc.enabled", default = TRUE) )
QC_dark( x, range = NULL, tol.margin = 1, max.hot = 60, max.cold = 20, spct.label = "Spectrum", verbose = getOption("photobiology.verbose", default = TRUE), QC.enabled = getOption("ooacquire.qc.enabled", default = TRUE) )
x |
cps_spct or raw_spct A spectrum measured in darkness. |
range |
numeric A wavelength range [nm]. |
tol.margin |
numeric A multiplier applied to MAD, the default 1 corresponds to 1 pixel per 1000 pixels as the expected random Normal noise. |
max.hot , max.cold
|
integer Maximum number of hot and cold pixels exceeding the tolerance per 1000 array pixels. |
spct.label |
character A character string to use in message. |
verbose |
logical If true a message is emitted in addition to returning the outcome. |
QC.enabled |
logical If FALSE return NA skipping QC. |
The expectation is that in a spectrum measured in the dark, to be
used as a reference, the variation among pixel counts is small. This also
applies in some cases to ranges of pixels protected from radiation by a
long pass or short pass filter. By default the whole spectrum is included
in the QC check, but if needed an argument can be passed to range
to select a smaller region.
A logical value.
Disabling the quality control is necessary when the "dark" reference is a measurement of ambient light instead of true darkness; i.e., when the irradiance of one light source is measured as the difference between background illumination and background illuminations plus the target light source.
Replace data from bad pixels with interpolated values, replace data from saturated and nearby pixels withs NAs, apply linearization function if data is not already linearized, optionally use a range of pixels as dark reference, convert the raw counts for each integration time used into counts-per-second, if data from bracketed intergartion times is available, splice the different spectra.
raw2corr_cps(x, ref.pixs.range, ...) ## Default S3 method: raw2corr_cps(x, ref.pixs.range = NULL, ...) ## S3 method for class 'raw_spct' raw2corr_cps( x, ref.pixs.range = c(1, 100), despike = FALSE, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), ... ) ## S3 method for class 'raw_mspct' raw2corr_cps(x, ref.pixs.range = c(1, 100), despike = FALSE, ...)
raw2corr_cps(x, ref.pixs.range, ...) ## Default S3 method: raw2corr_cps(x, ref.pixs.range = NULL, ...) ## S3 method for class 'raw_spct' raw2corr_cps( x, ref.pixs.range = c(1, 100), despike = FALSE, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), ... ) ## S3 method for class 'raw_mspct' raw2corr_cps(x, ref.pixs.range = c(1, 100), despike = FALSE, ...)
x |
raw_spct object. |
ref.pixs.range |
integer vector of length 2. |
... |
passed to |
despike |
logical flag, if TRUE despiking will be attempted. |
hdr.tolerance |
numeric Passed as tolerance argument to merge_cps(). |
a cps_spct object with one spectrum preserving the metadata present in
x
.
raw2corr_cps(default)
: Default method
raw2corr_cps(raw_spct)
: raw_spct method
raw2corr_cps(raw_mspct)
: raw_spct method
Other functions for conversion of raw-counts data:
raw2cps()
,
s_fraction_corrected()
,
s_irrad_corrected()
These functions simply divide "raw counts" by the integration time used for acquisition.
raw2cps(x, ...) ## Default S3 method: raw2cps(x, ...) ## S3 method for class 'raw_spct' raw2cps(x, ...) ## S3 method for class 'raw_mspct' raw2cps(x, ...)
raw2cps(x, ...) ## Default S3 method: raw2cps(x, ...) ## S3 method for class 'raw_spct' raw2cps(x, ...) ## S3 method for class 'raw_mspct' raw2cps(x, ...)
x |
an R object |
... |
not used in current version |
an object of class "cps_spct"
an object of class "cps_mspct"
raw2cps(default)
: Default method
raw2cps(raw_spct)
: Method for spectral data expressed as raw instrument counts.
raw2cps(raw_mspct)
: Method for collections of raw-counts spectra
In the case of objects of class "raw_spct" the columns with names starting with "counts" are processed and renamed to columns with names starting with "cps". All other columns are left unchanded.
Other functions for conversion of raw-counts data:
raw2corr_cps()
,
s_fraction_corrected()
,
s_irrad_corrected()
Read multiple files and return a collection of raw spectra as a raw_spct object.
read_files2mspct(files, read.f = ooacquire::read_oo_data, ...)
read_files2mspct(files, read.f = ooacquire::read_oo_data, ...)
files |
a named list of character strings of file names |
read.f |
a function which expects in its first parameter a file name or file path |
... |
additional arguments passed by name to the function passed as
argument to |
Depending of the function passed to read.f
more or less complete
metadata information will be stored as attributes in the raw_spct objects.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Reads a calibration data file as supplied by Ocean Optics. Wavelength and calibration values are stored as data and the metadata parsed from the header or supplied as arguments as attributes of the same object, including the time and date of the calibration. The whole file header is in addition stored as a comment.
read_oo_caldata( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
read_oo_caldata( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
file |
character string Path or file to read. |
time |
a |
geocode |
A one row data frame with numeric columns |
label |
character string, but if |
descriptor |
list A list describing the instrument, used to set
attribute |
tz |
character Time zone is by default read from the file. |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
verbose |
Logical indicating the level of warnings wanted. |
A generic_spct object, with columns w.length
and
oo.cal
.
Reads and parses the header of a processed data file as output by SpectraSuite to extract the whole header remark field. The time field is retrieved and decoded.
read_oo_data( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
read_oo_data( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
file |
character string |
time |
a |
geocode |
A data frame with columns |
label |
character string, but if |
descriptor |
list A list describing the instrument used. |
tz |
character Time zone is by default read from the file. |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
verbose |
Logical indicating the level of warnings wanted. |
A raw_spct object.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Reads and parses the header of a processed data file as output by OceanView to extract the whole header remark field. The time field is retrieved and decoded.
read_oo_ovdata( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
read_oo_ovdata( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
file |
character string |
time |
a |
geocode |
A data frame with columns |
label |
character string, but if |
descriptor |
list A list describing the instrument used. |
tz |
character Time zone is by default read from the file. |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
verbose |
Logical indicating the level of warnings wanted. |
A raw_spct object.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Reads and parses the header of a raw data file as output by the server running on a Raspberry Pi board to extract the whole header remark field. The time field is retrieved and decoded.
read_oo_pidata( file, date = NULL, geocode = NULL, label = NULL, tz = NULL, locale = readr::default_locale(), descriptor = NULL, corr.sensor.nl = FALSE, spectrometer.name = "Unknown via Raspberry Pi", spectrometer.sn = "Unknown via Raspberry Pi", npixels = 2048 )
read_oo_pidata( file, date = NULL, geocode = NULL, label = NULL, tz = NULL, locale = readr::default_locale(), descriptor = NULL, corr.sensor.nl = FALSE, spectrometer.name = "Unknown via Raspberry Pi", spectrometer.sn = "Unknown via Raspberry Pi", npixels = 2048 )
file |
character string |
date |
a |
geocode |
A data frame with columns |
label |
character string, but if |
tz |
character Time zone is not saved to the file. |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
descriptor |
list as returned by function |
corr.sensor.nl |
logical, indicating if spectral data is already linearized. If TRUE the spectrum is marked as linearized, and linearization skipped during processing. |
spectrometer.name , spectrometer.sn
|
character. |
npixels |
integer Number of pixels in spectral data. |
A raw_spct object.
The header in these files has very little information, so the user needs to supply the number of pixels in the array as well as the date-time. The file contains a date in milliseconds but as the Raspberry Pi board contains no real-time clock, it seems to default to number of milliseconds since the Pi was switched on.
http://www.r4photobiology.info
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
Reads and parses the header of a processed data file as output by SpectraSuite to extract the whole header remark field. The time field is retrieved and decoded.
read_oo_ssdata( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
read_oo_ssdata( file, time = NULL, geocode = NULL, label = NULL, descriptor = NULL, tz = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE) )
file |
character string |
time |
a |
geocode |
A data frame with columns |
label |
character string, but if |
descriptor |
list A list describing the instrument used. |
tz |
character Time zone is by default read from the file. |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
verbose |
Logical indicating the level of warnings wanted. |
A raw_spct object.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
set_oo_ssdata_descriptor()
,
set_oo_ssdata_settings()
A red long-pass filter from Heliopan (695 nm) measured using a household incandescent lamp as light source. The spectrometer used was an Ocean Optics Maya2000 Pro.
red_filter.raw_mspct
red_filter.raw_mspct
A raw_mspct
Other objects containing example raw-counts data:
blue_filter.raw_mspct
,
halogen.raw_mspct
,
sun001.raw_mspct
,
white_LED.raw_mspct
,
xenon_flash.raw_mspct
These functions simply subtract (by default) detector counts data (raw or cps) of one spectrum by the corresponding columns in another spectrum, or apply a user supplied operator or function to them.
ref_correction(x, y, .oper, ...) ## Default S3 method: ref_correction(x, y, .oper, ...) ## S3 method for class 'numeric' ref_correction(x, y, .oper = `-`, ...) ## S3 method for class 'raw_spct' ref_correction(x, y, .oper = `-`, ...) ## S3 method for class 'cps_spct' ref_correction(x, y, .oper = `-`, ...) ## S3 method for class 'cps_mspct' ref_correction(x, y = x, .oper = `-`, ref_name = "dark", ...)
ref_correction(x, y, .oper, ...) ## Default S3 method: ref_correction(x, y, .oper, ...) ## S3 method for class 'numeric' ref_correction(x, y, .oper = `-`, ...) ## S3 method for class 'raw_spct' ref_correction(x, y, .oper = `-`, ...) ## S3 method for class 'cps_spct' ref_correction(x, y, .oper = `-`, ...) ## S3 method for class 'cps_mspct' ref_correction(x, y = x, .oper = `-`, ref_name = "dark", ...)
x , y
|
R objects |
.oper |
a function with its first two formal parameters accepting numerical vectors of equal length (e.g. a binary numerical operator). |
... |
not used in current version |
ref_name |
character Name of variable to substract from all other columns. |
a numeric vector of the same length as x
an object of class "cps_spct"
an object of class "cps_spct"
an object of class "cps_mspct"
ref_correction(default)
: Default method
ref_correction(numeric)
: Numeric method
ref_correction(raw_spct)
: Method for spectral data expressed as raw
instrument counts.
ref_correction(cps_spct)
: Method for spectral data expressed as
counts per second.
ref_correction(cps_mspct)
: Method for collections of spectral data objects
containing data expressed as counts per second.
In the case of objects of class "raw_spct" the columns with names starting with "counts" are processed. All other columns are left unchanded.
If x
and y
are both cps_mspct objects,
y[[ref_name]]
will be used as reference, otherwise y
itself
should be a cps_spct and will be used as is. In all cases variables in
ref.name will be skipped in x
.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
merge_raw_mspct()
,
new_correction_method()
,
trim_counts()
,
uvb_corrections()
Clean up left-behind wrappers used to communicate with Java code using 'rJava'.
rm_jwrapper(x)
rm_jwrapper(x)
x |
raw_spct or raw_mspct object with attribute |
Field w
contains a wrapper on a Java object used to communicate with
the OmniDriver driver during data acquisition. Once the current connection
between R and a spectrometer ends, these wrappers are invalidated, becoming
useless. However, if present they create a dependency on 'rJava', possibly
triggering errors. In recent versions of 'ooacquire' this wrapper is removed
immediately after acquisition. However, the instrument descriptor of spectral
objects created with versions of 'ooacquire' for some years ago can contain a
member storing a useless Java wrapper. This function removes this field if
present.
a copy of x
possibly with an updated
instr.desc
attribute embedded.
Method getInstrDesc()
removes member field w
from the returned
value but does not modify its argument.
Convert raw counts data into spectral transmittance or spectral reflectance.
s_fraction_corrected(x, ...) ## Default S3 method: s_fraction_corrected(x, ...) ## S3 method for class 'list' s_fraction_corrected( x, reference.value = 1, type = "internal", time = NULL, correction.method, qty.out = "Tfr", descriptor = NULL, dyn.range = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE), ... ) ## S3 method for class 'raw_mspct' s_fraction_corrected( x, spct.names = c(sample = "sample", reference = "reference", dark = "dark"), reference.value = 1, type = switch(qty.out, Tfr = "internal", Rfr = "total"), correction.method, dyn.range = NULL, qty.out = "Tfr", verbose = getOption("photobiology.verbose", default = FALSE), ... )
s_fraction_corrected(x, ...) ## Default S3 method: s_fraction_corrected(x, ...) ## S3 method for class 'list' s_fraction_corrected( x, reference.value = 1, type = "internal", time = NULL, correction.method, qty.out = "Tfr", descriptor = NULL, dyn.range = NULL, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE), ... ) ## S3 method for class 'raw_mspct' s_fraction_corrected( x, spct.names = c(sample = "sample", reference = "reference", dark = "dark"), reference.value = 1, type = switch(qty.out, Tfr = "internal", Rfr = "total"), correction.method, dyn.range = NULL, qty.out = "Tfr", verbose = getOption("photobiology.verbose", default = FALSE), ... )
x |
A named list of one to three vectors of file names, with names "sample", "reference", and "dark". Or a raw_mspt object, or a raw_spct object. |
... |
Named argument passed to |
reference.value |
numeric or filter_spct or reflector_spct object, with the fractional transmittance or reflectance of the reference. |
type |
character One of "internal" or "total". |
time |
a |
correction.method |
A named list of constants and functions defining the method to be sued for stray light and dark signal corrections. |
qty.out |
character, one of "Tfr", "Rfr". |
descriptor |
A named list with a descriptor of the characteristics of the spectrometer (if serial number does not agree an error is triggered). |
dyn.range |
numeric Effective dynamic range of the spectrometer. |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
verbose |
Logical indicating the level of warnings wanted. |
spct.names |
named character vector of length three, to map names in
|
s_fraction_corrected(default)
: Default for generic function.
s_fraction_corrected(list)
: Default for generic function.
s_fraction_corrected(raw_mspct)
: Default for generic function.
Currently s_fraction_corrected.list
allows processing of files
written by OceanOptics' SpectraSuite software, from protocols with
integration-time bracketing or not, with a dark reference measurement or
not. Four measurements components are recognized: a "sample" measurement,
a "referenece" measurement using a clear or white, a "filter" measurement
with a UV-blocking filter in the light pass, and a "dark" measurement.
Only "sample" and "reference" are mandatory. Data should be raw counts,
either corrected for detector non-linearity or not. All three spectra
should be acquired using the same instrument settings to achieve good
accuracy.
Other functions for conversion of raw-counts data:
raw2corr_cps()
,
raw2cps()
,
s_irrad_corrected()
Convert raw counts data into spectral irradiance or fluence
s_irrad_corrected(x, ...) ## Default S3 method: s_irrad_corrected(x, ...) ## S3 method for class 'list' s_irrad_corrected( x, time = NULL, correction.method, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), return.cps = FALSE, trim.descriptor = !return.cps, descriptor, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE), ... ) ## S3 method for class 'raw_mspct' s_irrad_corrected( x, spct.names = c(light = "light", filter = "filter", dark = "dark"), correction.method, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), return.cps = FALSE, trim.descriptor = !return.cps, verbose = getOption("photobiology.verbose", default = FALSE), ... ) ## S3 method for class 'raw_spct' s_irrad_corrected( x, time = NULL, correction.method, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), return.cps = FALSE, trim.descriptor = !return.cps, verbose = getOption("photobiology.verbose", default = FALSE), ... )
s_irrad_corrected(x, ...) ## Default S3 method: s_irrad_corrected(x, ...) ## S3 method for class 'list' s_irrad_corrected( x, time = NULL, correction.method, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), return.cps = FALSE, trim.descriptor = !return.cps, descriptor, locale = NULL, verbose = getOption("photobiology.verbose", default = FALSE), ... ) ## S3 method for class 'raw_mspct' s_irrad_corrected( x, spct.names = c(light = "light", filter = "filter", dark = "dark"), correction.method, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), return.cps = FALSE, trim.descriptor = !return.cps, verbose = getOption("photobiology.verbose", default = FALSE), ... ) ## S3 method for class 'raw_spct' s_irrad_corrected( x, time = NULL, correction.method, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), return.cps = FALSE, trim.descriptor = !return.cps, verbose = getOption("photobiology.verbose", default = FALSE), ... )
x |
A named list of one to three vectors of file names, with names "light", "filter", and "dark". Or a raw_mspt object, or a raw_spct object. |
... |
Named arguments passed to |
time |
a |
correction.method |
A named list of constants and functions defining the method to be used for stray light and dark signal corrections. |
hdr.tolerance |
numeric Tolerance for mean deviation among cps columns as a fraction of one. Used in check of HDR consistency. A negative value disables merging using only the data for the shortest integration time. |
return.cps |
logical Useful when there is no need to apply a calibration, such as when computing new calibration multipliers. |
trim.descriptor |
logical If |
descriptor |
A named list with a descriptor of the characteristics of the spectrometer (if serial number does not agree an error is triggered). |
locale |
The locale controls defaults that vary from place to place. The
default locale is US-centric (like R), but you can use
|
verbose |
Logical indicating the level of warnings and messages wanted. |
spct.names |
named character vector of length three, to map names in
|
s_irrad_corrected(default)
: Default for generic function.
s_irrad_corrected(list)
: Default for generic function.
s_irrad_corrected(raw_mspct)
: Default for generic function.
s_irrad_corrected(raw_spct)
: Default for generic function.
Currently s_irrad_corrected.list
allows processing of files
written by OceanOptics' SpectraSuite software, from protocols with
integration-time bracketing or not, with a dark reference measurement or
not. Three measurements components are recognized: a "light" measurement, a
"filter" measurement using a polycarbonate filter and a dark measurement.
Only "light" is mandatory. Data should be raw counts, either corrected for
detector non-linearity or not. All three spectra should be acquired using
the same instrument settings to achieve good accuracy.
Enabling trim.descriptor
ensures that the data objects are
free of references to code in 'ooacquire', which is crucial for the
portability of the spectral data.
Other functions for conversion of raw-counts data:
raw2corr_cps()
,
raw2cps()
,
s_fraction_corrected()
Allow user to provide values for "user supplied" attribute values
"comment"
and "what.measured"
.
set_attributes_interactive( user.attrs = list(what.measured = "", comment.text = "") )
set_attributes_interactive( user.attrs = list(what.measured = "", comment.text = "") )
user.attrs |
character Default values for the attributes. |
a named list of character vectors.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
A integer vector of indexes to bad pixels in the instrument array. Data from these array pixels will be discarded.
set_descriptor_bad_pixs(descriptor, bad.pixs) update_spct_bad_pixs(spct, bad.pixs) update_mspct_bad_pixs(mspct, bad.pixs)
set_descriptor_bad_pixs(descriptor, bad.pixs) update_spct_bad_pixs(spct, bad.pixs) update_mspct_bad_pixs(mspct, bad.pixs)
descriptor |
list as returned by function |
bad.pixs |
numeric vector of positional indexes corresponding to
individual pixels in the instrument array, or an object of class
|
spct |
an object of class |
mspct |
an object of class |
A copy of the argument passed to descriptor
, spct
or
mspct
with the descriptor with indexes to bad pixels set to the
new values.
Following R's syntax the first pixel in the detector array has index 1.
Replace or add a description of the fibre and diffuser or other entrance optics to the instrument descriptor.
set_descriptor_entrance_optics( descriptor, make = NA_character_, model = NA_character_, geometry = NA_character_, serial.number = NA_character_, area = NA_real_ )
set_descriptor_entrance_optics( descriptor, make = NA_character_, model = NA_character_, geometry = NA_character_, serial.number = NA_character_, area = NA_real_ )
descriptor |
list as returned by function |
make , model , geometry , serial.number
|
character. |
area |
numeric ( |
a copy of the argument passed for oo_descriptor
with the
entrance.optics
field of the calibration data adde or replace
by the new list.
This function can be needed in exceptional cases such as when the limits stored in the intrument's persistent memory are wrong. In other cases in can be used to restrict the range of values allowed to be set to a smaller range than natively supported by the spectrometer.
set_descriptor_integ_time( descriptor, min.integ.time = NA_integer_, max.integ.time = NA_integer_, force.change = FALSE )
set_descriptor_integ_time( descriptor, min.integ.time = NA_integer_, max.integ.time = NA_integer_, force.change = FALSE )
descriptor |
list as returned by function |
min.integ.time , max.integ.time
|
numeric values in seconds in seconds. |
force.change |
If FALSE values outside the range returned by a query to the instrument trigger an error. If TRUE this test is overriden. |
a copy of the argument passed for oo_descriptor
with the
integration time fields of the descriptor modified.
This function should not be needed, but for some instruments the query may fail or return the wrong value. Values should be within the range in the instrument's specifications. Setting wrong values can result in invalid data without an error being triggered.
Adds calibration data expressed as multipliers for each pixel stores in a numeric vector.
set_descriptor_irrad_mult( descriptor, irrad.mult, wl.range = NULL, start.date = lubridate::today(tzone = "UTC") - lubridate::days(1), end.date = lubridate::today(tzone = "UTC") + lubridate::days(1), cal.source = "unknown" )
set_descriptor_irrad_mult( descriptor, irrad.mult, wl.range = NULL, start.date = lubridate::today(tzone = "UTC") - lubridate::days(1), end.date = lubridate::today(tzone = "UTC") + lubridate::days(1), cal.source = "unknown" )
descriptor |
list as returned by function |
irrad.mult |
numeric vector of the same length as the number of pixels or of length one. |
wl.range |
numeric Range of wavelengths for which the calibration is valid. |
start.date , end.date
|
range of dates when calibration is valid. |
cal.source |
character Identifier or source of the calibration data, used for traceability. |
A copy of the argument passed for oo_descriptor
with the
irrad.mult field of the calibration data replaced by the new values.
Uses a user supplied function, possibly that supplied by a manufacturer like Ocean Optics stored in firmware or in any other form.
set_descriptor_nl(descriptor, nl.coeff = NA_real_, nl.fun = NULL)
set_descriptor_nl(descriptor, nl.coeff = NA_real_, nl.fun = NULL)
descriptor |
list as returned by function |
nl.coeff |
numeric vector, if nl.fun is missing, assumed to be a polynomial. |
nl.fun |
A function or a polynom::polynomial object containing the linearization to be applied. |
A copy of the argument passed for oo_descriptor
with the
wavelengths field of the calibration data replaced by the new values.
Replace wavelength values in an instrument descriptor for an Ocean Optics spectrometer with new values. (e.g. when wavelngth calibration is not stored in firmware).
set_descriptor_wl(descriptor, wl)
set_descriptor_wl(descriptor, wl)
descriptor |
list as returned by function |
wl |
numeric vector of sorted wavelengths values corresponding to each pixel in the instrument array. |
a copy of the argument passed for oo_descriptor
with the
wavelengths field of the calibration data replaced by the new values.
Enter values for "user supplied" folder.
set_folder_interactive(folder.name = NULL)
set_folder_interactive(folder.name = NULL)
folder.name |
character Default name of the folder. |
If the requested folder does not already exist it will be created. The name of the folder is returned, but NOT set as working directory.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Model and serial number are retrieved from the file header, the remaining
unknown parameter values are set to NA. These values are used to set
the "inst.desc" atrribute of x
.
set_oo_ssdata_descriptor( x, file.header = comment(x), descriptor = photobiology::getInstrDesc(x), action = "merge" )
set_oo_ssdata_descriptor( x, file.header = comment(x), descriptor = photobiology::getInstrDesc(x), action = "merge" )
x |
generic_spct, although with defaults only raw_spct. |
file.header |
character string The header of the file output by SpectraSuite. |
descriptor |
list An already built instrument descriptor, to be
used as basis when action == "merge" or action == "keep". Defaults,
to that stored in |
action |
character A flag indicating if an existing instrument
descriptor in |
A copy of x
with updated attributes.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_settings()
Parse the header of the file returned by SpectraSuite for corrections,
smotthing and acquisition parameters used. These values are used to set
the "inst.settings" atrribute of x
.
set_oo_ssdata_settings(x, file.header = comment(x), overwrite = TRUE)
set_oo_ssdata_settings(x, file.header = comment(x), overwrite = TRUE)
x |
generic_spct, although with defaults only raw_spct. |
file.header |
character string The header of the file output by SpectraSuite. |
overwrite |
logical A flag indicating if an existing valid instrument
descriptor in |
A copy of x
with updated attributes.
Other functions for importing spectral data from files:
collect_spct_files()
,
map_oofile_header_rows()
,
oofile_data_rows()
,
plot_spct_file()
,
read_files2mspct()
,
read_oo_data()
,
read_oo_ovdata()
,
read_oo_pidata()
,
read_oo_ssdata()
,
set_oo_ssdata_descriptor()
Enter settings defining a sequence of spectra to be measured as a time series.
set_seq_interactive( seq.settings = list(start.boundary = "second", initial.delay = 0, step.delay = 0, num.steps = 1), measurement.duration = 0, minimum.step.delay = measurement.duration, time.division = 0 )
set_seq_interactive( seq.settings = list(start.boundary = "second", initial.delay = 0, step.delay = 0, num.steps = 1), measurement.duration = 0, minimum.step.delay = measurement.duration, time.division = 0 )
seq.settings |
numeric Definition of time steps for a sequence of
repeated measurements. Named vector with member named
|
measurement.duration |
numeric Duration of one measurement event (s). |
minimum.step.delay |
numeric Minimum duration of |
time.division |
numeric The step is forced to be a multiple of this time duration, because spectrometers normally are constantly acquiring spectra and thbey return the most recently acquired one. Should be set to the integration time plus a very small overhead (s). |
Function seq.settings()
allows users to enter values needed
to define a sequence of spectral acquisitions. These are the time unit
boundary to synchronize to, the delay or duration of the time
step between successive acquisitions and the number of acquisitions in the
series. The measurement.time
determines the minimum length for
"step"
.
A sequence of measurements are expected to share a single reference or dark scan, and be done as a sequence. With a single time point, the initial delay or time unit boundary can be used to schedule a single timed measurement.
A named numeric vector of length two.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Enter values for "session" name.
set_session_name_interactive(session.name = NULL)
set_session_name_interactive(session.name = NULL)
session.name |
character Default name of the folder. |
Validate seesionr name, and allow user to change the default.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_user_name_interactive()
,
tune_interactive()
Enter values for "user supplied" name.
set_user_name_interactive(user.name = NULL)
set_user_name_interactive(user.name = NULL)
user.name |
character Default name of the folder. |
Validate user name, and allow user to change the default.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
tune_interactive()
Replace bad pixels with the average of the counts from the two neighbouring pixels.
skip_bad_pixs(x)
skip_bad_pixs(x)
x |
raw_spct object |
a copy of x with values replaced as needed in all counts columns present.
Open a connection to the first spectrometer found and initialize an object with a reference to the Java object returned by Omni Driver.
start_session(error.action = stop)
start_session(error.action = stop)
error.action |
function, usually one of |
On success a java wrapper which allows access to the driver with an open connection to the instrument.
Other spectrometer-connection functions:
end_session()
,
list_instruments()
Solar radiation at ground level measured in Helsinki Finland. The spectrometer used was an Ocean Optics Maya2000 Pro.
sun001.raw_mspct
sun001.raw_mspct
A raw_mspct
Other objects containing example raw-counts data:
blue_filter.raw_mspct
,
halogen.raw_mspct
,
red_filter.raw_mspct
,
white_LED.raw_mspct
,
xenon_flash.raw_mspct
Compute transmittance by waveband of interest to plants' and human visual responses to light.
Tfr_summary_table( mspct, quantity = "average", attr2tb = "when.measured", summary.type = "VIS", digits = 3L )
Tfr_summary_table( mspct, quantity = "average", attr2tb = "when.measured", summary.type = "VIS", digits = 3L )
mspct |
A filter_mspct, or a filter_spct object containing spectral transmittance for one or more sources. |
quantity |
character Passed to |
attr2tb |
character Vector with one or more of "when.measured", "what.measured", "where.measured", "how.measured" and "comment". |
summary.type |
character One of "plant", "PAR" or "VIS". |
digits |
integer The number of significant digits in the output. |
This function calls different functions from package 'photobiology' and returns a typical set of summaries.
A tibble with one row per spectrum and one column per summary quantity and attribute and a column with the names of the spectra.
See the documentation for functions
transmittance
,
add_attr2tb
and signif
which are called to build
the summary table.
Tfr_summary_table(yellow_gel.spct) Tfr_summary_table(yellow_gel.spct, attr2tb = c("what.measured", "where.measured")) Tfr_summary_table(yellow_gel.spct, summary.type = "plant") Tfr_summary_table(yellow_gel.spct, summary.type = "PAR") Tfr_summary_table(yellow_gel.spct, summary.type = "VIS")
Tfr_summary_table(yellow_gel.spct) Tfr_summary_table(yellow_gel.spct, attr2tb = c("what.measured", "where.measured")) Tfr_summary_table(yellow_gel.spct, summary.type = "plant") Tfr_summary_table(yellow_gel.spct, summary.type = "PAR") Tfr_summary_table(yellow_gel.spct, summary.type = "VIS")
Trim out-of-range counts values in data stored in a "raw_spct" object. The
values are replaced with the supplied fill
value.
trim_counts(x, range = c(NA, getInstrDesc(x)[["max.counts"]] - 1), fill = NA)
trim_counts(x, range = c(NA, getInstrDesc(x)[["max.counts"]] - 1), fill = NA)
x |
raw_spct object |
range |
integer vector of length two |
fill |
an integer value (including NA) to be used to replace the values that are outside range. |
a copy of x with values replaced as needed in all counts columns present.
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
merge_raw_mspct()
,
new_correction_method()
,
ref_correction()
,
uvb_corrections()
Adjust integration time settings, allowing the user to repeat the tuning, and to change some of the parameters used for tuning such as total compound integration time and integration time bracketing.
tune_interactive( descriptor, acq.settings, start.int.time = 0.1, interface.mode = "auto" )
tune_interactive( descriptor, acq.settings, start.int.time = 0.1, interface.mode = "auto" )
descriptor |
list Descriptor of the instrument, including wrapper to Java object used to access the instrument. |
acq.settings |
list containing starting values for instrument settings. |
start.int.time |
numeric Integration time to use as starting guess when tuning the settings. |
interface.mode |
character One of "simple", "auto", or "manual". |
This function implements three different user interfaces: 1) "simple" is an interface suitable for the most usual measurements using automatic tuning of integration time and hides some of the less frequently used options, 2) "auto" gives access to all available options offering maximum flexibility when using automatic tuning of integration time, and 3) "manual" supports use of fixed integration times directly entered by the user.
Tuning of the integration time takes into account the range of times
supported by the connected instrument, read from the instrument descriptor.
The algorithm also makes use of the linearisation function when extrapolating
to guess the integration time needed. Initial (default) values are read from
acq.settings
while start.int.time
provides a default starting
value for integration time for tuning when the user chooses not to use the
value stored in acq.settings
.
Other interactive acquisition utility functions:
choose_ch_interactive()
,
choose_sr_interactive()
,
f.trigger.message()
,
list_srs_interactive()
,
protocol_interactive()
,
set_attributes_interactive()
,
set_folder_interactive()
,
set_seq_interactive()
,
set_session_name_interactive()
,
set_user_name_interactive()
Update field bad.pixs
of the instrument descriptor embedded in
raw_spct
and raw_mspct
objects.
update_bad_pixs(x, bad.pixs = NULL, action = "replace")
update_bad_pixs(x, bad.pixs = NULL, action = "replace")
x |
raw_spct or raw_mspct object with attribute |
bad.pixs |
numeric New vector of indexes to bad pixels in the detector
array. If |
action |
character One of "replace" or "add". |
Spectral objects, including those with raw counts data can contain an
instrument descriptor. One member of this attribute is a vector of indexes to
bad pixels. New bad pixels can be identified in some cases after data are
acquired. Recomputing of physical quantities from raw counts normally reuses
the embedded calibration data. Function update_bad_pixs()
makes it
possible to update the embedded bad pixels information before recomputing
derived quantities. This function can be applied only to
raw_spct
objects created with functions from package 'ooacquire'.
With defaults arguments for formal parameters bad.pixs
and
action
, the bad.pixs
field of the descriptor is updated to
match that in the matching calibration data in the version of 'ooacquire'
currently loaded. However, if a numeric vector to positions in the detector
array is passed as argument, depending on the argument passed to
action
, this vector will be used either to replace the existing one,
or the indexes in the vector "added" to those already stored, using
union()
.
a copy of x
with an updated instr.desc
attribute
embedded.
Only objects of class raw_spct
, individually or as members of a
raw_mspct
object, are supported as the update must precede any
conversion into physical units, and will propagate to returned values when
computations are applied to the updated raw_spct
objects.
Apply to a counts-per-second spectrum corrections based of a paired reading obtained with a polycarbonate filter (long-pass with cut-in at 400 nm). This is a bit more sophisticated than simple subtracting the filter reading from the measurement as the effect of the filter itself on stray light is corrected for.
uvb_corrections( x, spct.names = c(light = "light", filter = "filter", dark = "dark"), stray.light.method = "original", stray.light.wl = c(218.5, 228.5), flt.dark.wl = c(193, 209.5), flt.ref.wl = c(360, 379.5), flt.Tfr = 0.9, inst.dark.pixs = 1:4, worker.fun = NULL, trim = 0.05, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), verbose = getOption("photobiology.verbose", default = FALSE), ... ) slit_function_correction( x, worker.fun = NULL, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), verbose = getOption("photobiology.verbose", default = FALSE), ... )
uvb_corrections( x, spct.names = c(light = "light", filter = "filter", dark = "dark"), stray.light.method = "original", stray.light.wl = c(218.5, 228.5), flt.dark.wl = c(193, 209.5), flt.ref.wl = c(360, 379.5), flt.Tfr = 0.9, inst.dark.pixs = 1:4, worker.fun = NULL, trim = 0.05, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), verbose = getOption("photobiology.verbose", default = FALSE), ... ) slit_function_correction( x, worker.fun = NULL, hdr.tolerance = getOption("ooacquire.hdr.tolerance", default = 0.05), verbose = getOption("photobiology.verbose", default = FALSE), ... )
x |
|
spct.names |
named character vector of length three. |
stray.light.method |
Method variant used, "original" (Ylianttila), "simple", "full", "sun", "raw", "none". |
stray.light.wl |
numeric vector of length 2 giving the range of wavelengths to use for the final stray light correction. |
flt.dark.wl , flt.ref.wl
|
numeric vectors of length 2 giving the ranges of wavelengths to use for the "dark" and "illuminated" regions of the array in the filter correction. |
flt.Tfr |
numeric fractional transmittance of the filter to the source of stray light, used only for method "simple". |
inst.dark.pixs |
numeric vector with indexes to array pixels that are in full darkness by instrument design. |
worker.fun |
function actually doing the correction on the w.lengths and counts per second vectors, or the name of the function as a character string. |
trim |
a numeric value to be used as argument for mean |
hdr.tolerance |
numeric Tolerance for mean deviation among cps columns as a fraction of one. Used in check of HDR consistency. |
verbose |
Logical indicating the level of warnings wanted. |
... |
additional parameters passed to worker.fun. |
A cps_spct
object with the corrected count-per-second values
in coulmn "cps".
stray.light.method = "none"
is a valid argument only for
function uvb_corrections()
. The default worker.fun
is just an
example. Corrections are specific to each individual spectrometer unit (not
just type or configuration) and code needs to be written for most
individual use cases. The slit function tail correction requires the
characterization of the shape of the slit function by measuring one or more
laser beams at suitable wavelengths.
Algorithm for method "original" developed by Lasse Ylianttila. Other methods are modified from Ylianttila's method by Pedro J. Aphalo.
http://www.r4photobiology.info
Other spectral data-processing functions:
MAYP112785_tail_correction()
,
MAYP11278_tail_correction()
,
check_sn_match()
,
linearize_counts()
,
merge_raw_mspct()
,
new_correction_method()
,
ref_correction()
,
trim_counts()
Select from a list of instrument descriptors which one to use based on date of measurement.
which_descriptor( date = lubridate::now(tzone = "UTC"), descriptors = ooacquire::MAYP11278_descriptors, verbose = getOption("photobiology.verbose", TRUE), strict.calib = getOption("photobiology.strict.calib", FALSE), entrance.optics = NULL, ... )
which_descriptor( date = lubridate::now(tzone = "UTC"), descriptors = ooacquire::MAYP11278_descriptors, verbose = getOption("photobiology.verbose", TRUE), strict.calib = getOption("photobiology.strict.calib", FALSE), entrance.optics = NULL, ... )
date |
Any object that |
descriptors |
A named list of descriptors of the characteristics of the spectrometer including calibration data. |
verbose |
Logical indicating the level of warnings wanted. |
strict.calib |
Logical indicating the level of validity checks. |
entrance.optics |
character The name or geometry of the diffuser or entrance optics to select. Only required when there are calibration with multiple entrance optics for the same spectrometer. |
... |
Currently ignored. |
Calibrations for instruments stored in a list and passed as argument
to descriptors
, also store the dates between which they are valid.
This function walks the list searching for a calibration valid for
date
. If no valid calibration is found and strict.calib =
FALSE
, the calibration valid closest in time is returned with a warning
while if no valid calibration is found and strict.calib = TRUE
an
error is triggered.
If a character string is passed as argument to date
, it must be
in a format suitable for anytime::anydate()
. One needs to be
careful with months and days of the month when supplying them as numbers,
so using months names or their abbreviations can be safer.
The default argument for verbose
is for this function
TRUE
as conversion of other objects to a date may fail.
A zhaga standard module with Nichia "horticulture" LEDs measured at short distance. The spectrometer used was an Ocean Optics Maya2000 Pro.
white_LED.raw_mspct
white_LED.raw_mspct
A raw_mspct
Other objects containing example raw-counts data:
blue_filter.raw_mspct
,
halogen.raw_mspct
,
red_filter.raw_mspct
,
sun001.raw_mspct
,
xenon_flash.raw_mspct
A photography flash Godox AD200 with a bare lamp in a head with a reflector fitted. The spectrometer used was an Ocean Optics Maya2000 Pro.
xenon_flash.raw_mspct
xenon_flash.raw_mspct
A raw_mspct
Other objects containing example raw-counts data:
blue_filter.raw_mspct
,
halogen.raw_mspct
,
red_filter.raw_mspct
,
sun001.raw_mspct
,
white_LED.raw_mspct