| Title: | Omni Driver R wrapper |
|---|---|
| Description: | This package is a wrapper of the OmniDriver java driver for Ocean Optics spectrometers. |
| Authors: | Pedro J. Aphalo [aut, cre] |
| Maintainer: | Pedro J. Aphalo <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.1.20 |
| Built: | 2024-09-02 08:19:38 UTC |
| Source: | https://github.com/aphalo/rOmniDriver |
This package is a wrapper of the OmniDriver java driver for Ocean Optics spectrometers.
OmniDriver is a proprietary library provided by Ocean Insight to allow the control of the spectrometers they sell through third party software.
Although this package is under GPL, Omnidriver is not, it is copyrighted commercial software from Ocean Insight http://www.oceanoptics.com
Ocean Insight distributes the OmniDriver runtime free of charge. This can be downloaded from Ocean Insight web site. It can be used only with spectrometers sold by Ocean Insight. Ocean Insight has supported the development of this R package by providing a free licence to the OmniDriver SDP, which gave me access to documentation.
Ocean Insight will not provide support for the use of this package, unless the user buys a licence for OmniDriver SDP (spectroscopy development plattform). All support requests about this package should be addressed to the maintainer of the package or public R user forums.
We have access to only three spectrometers for testing, a Maya2000Pro, a two-chennal Jaz and a Flame. So, the software is supplied without any assurance that it will work with a particular model and configuration of spectrometer. Please, do report to the maintainer any problems and also if you encounter no problems when using this package. Always supply detailed information about the spectrometer used when contacting the maintainer of the package.
Many methods in OmniDriver are available in two versions, one for
multichannel spectrometers and one for single channels ones. In this
package each such pair of similar methods are wrapped into a single R
method. The default channel index, ch.index, in the R implementation
defaults to the first available channel, so it does not need to be
explicitly supplied for single channel instruments. The spectrometer index,
sr.index, in the R implementation defaults to the first available
spectrometer, so it does not need to be explicitly supplied when a single
instrument is connected to the host computer.
Maintainer: Pedro J. Aphalo [email protected] (ORCID)
http://www.oceanoptics.com/Products/omnidriver.asp
http://oceanoptics.com/api/omnidriver/overview-summary.html
Useful links:
Report bugs at https://github.com/aphalo/romnidriver/issues
close all open connections to spectrometers
close_all_spectrometers(jwrapper) srs_close(jwrapper)close_all_spectrometers(jwrapper) srs_close(jwrapper)
jwrapper |
a open Wrapper object from Omnidriver |
a numeric value
A function to query the version of OmniDriver.
get_api_version(jwrapper)get_api_version(jwrapper)
jwrapper |
an open Wrapper object from Omnidriver |
A character string value of form "1.01.01" or similar.
A function to query the characteristics of the optical bench from a spectrometer.
get_bench(jwrapper, sr.index = 0L, ch.index = 0L)get_bench(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a value
Function to query the boxcar width being used (the number of pixels averaged).
get_boxcar_width(jwrapper, sr.index = 0L, ch.index = 0L)get_boxcar_width(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Function to query calibration coefficients from memory buffer of a spectrometer.
get_calibration_coefficients_from_buffer( jwrapper, sr.index = 0L, ch.index = 0L )get_calibration_coefficients_from_buffer( jwrapper, sr.index = 0L, ch.index = 0L )
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
A Coefficients Java object containing all of the calibration
coefficients..
Function to query calibration coefficients from the EEPROM of a spectrometer.
get_calibration_coefficients_from_eeprom( jwrapper, sr.index = 0L, ch.index = 0L )get_calibration_coefficients_from_eeprom( jwrapper, sr.index = 0L, ch.index = 0L )
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
A Coefficients Java object containing all of the calibration
coefficients..
Get current setting of linearity correction (enabled or not)
get_correct_for_detector_nonlineary(jwrapper, sr.index = 0L, ch.index = 0L)get_correct_for_detector_nonlineary(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Get current setting for electrical dark correction
get_correct_for_electrical_dark(jwrapper, sr.index = 0L, ch.index = 0L)get_correct_for_electrical_dark(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Get current setting of stray light correction
get_correct_for_stray_light(jwrapper, sr.index = 0L, ch.index = 0L)get_correct_for_stray_light(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel |
Get description of detector
get_detector(jwrapper, sr.index = 0L, ch.index = 0L)get_detector(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a Detector object (Java)
This method seems to be only of use for multichannel spectrometers. It is not documented in the OmniDriver manual and the Java documentation is extremely terse so it is difficult to know what it does and/or how to use it.
A function to retrieve an interface that allows to control the saturation threshold.
get_feature_controller_saturation_threshold(jwrapper, sr.index = 0L)get_feature_controller_saturation_threshold(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling this function you first need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_saturation_threshold.
Get a wrapper for accessing this optional feature.
get_feature_I2C_bus(jwrapper, sr.index = 0L)get_feature_I2C_bus(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling this function you first need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_I2C_bus.
Other Spectrometer I2C- and SPI-bus functions.:
get_I2C_bus(),
get_SPI_bytes(),
get_feature_SPI_bus(),
is_feature_supported_I2C_bus(),
is_feature_supported_SPI_bus()
Obtain an inferface to the "pixel binning" function of a spectrometer if available.
get_feature_pixel_binning(jwrapper, sr.index = 0L)get_feature_pixel_binning(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling this function you first need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_pixel_binning.
Get a wrapper for accesing this optional feature.
get_feature_spectrum_type(jwrapper, sr.index = 0L)get_feature_spectrum_type(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling this function you first need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_spectrum_type.
Get a wrapper for accessing this optional feature.
get_feature_SPI_bus(jwrapper, sr.index = 0L)get_feature_SPI_bus(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling this function you first need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_SPI_bus.
Other Spectrometer I2C- and SPI-bus functions.:
get_I2C_bus(),
get_SPI_bytes(),
get_feature_I2C_bus(),
is_feature_supported_I2C_bus(),
is_feature_supported_SPI_bus()
A function to query the version of the firmware from a spectrometer.
get_firmware_model(jwrapper, sr.index = 0L)get_firmware_model(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
A character string value of form "USB2000" or similar.
Only supported in API version >= 2.40, in earlier API versions an error is triggered if use is attempted.
A function to query the version of the firmware from a spectrometer.
get_firmware_version(jwrapper, sr.index = 0L)get_firmware_version(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
A character string value of form "1.01.01" or similar.
Send a packet of bytes over the I2C bus and read the result, or simply read from an address.
get_I2C_bus(I2C.bus.wrapper, I2C.address, num.bytes) set_I2C_bus(I2C.bus.wrapper, I2C.address, num.bytes, message)get_I2C_bus(I2C.bus.wrapper, I2C.address, num.bytes) set_I2C_bus(I2C.bus.wrapper, I2C.address, num.bytes, message)
I2C.bus.wrapper |
feature wrapper as returned by function
|
I2C.address |
byte, address to select device in I2C bus. |
num.bytes |
numeric Number of bytes to be transferred or read, 1..61. |
message |
byte, array of bytes with maximum length of 61. |
Several spectrometers have an I2C bus accesible through the auxiliary connector which can be used to control accessories. The I2C bus in Ocean Insight spectrometers is not intended to be used to control the spectrometer or retrieve data but instead to control and access other accessories with the spectrometer acting as middle man.
Function get_I2C_bus() performs a general purpose read on the I2C
pins for interfacing to attached peripherals. The time to complete the
command is determined by the amount of data transferred and the response time
of the peripheral. The I2C bus runs at 400KHz. The maximum number of bytes
that can be read is 61.
Function set_I2C_bus() performs a general-purpose write on the I2C
pins for interfacing to attached peripherals. The time to complete the
command is determined by the amount of data transferred and the response time
of the peripheral. The I2C bus runs at 400KHz.
The result Array of bytes containing the read data. May be null.
The result of the write to the I2C device.
Other Spectrometer I2C- and SPI-bus functions.:
get_SPI_bytes(),
get_feature_I2C_bus(),
get_feature_SPI_bus(),
is_feature_supported_I2C_bus(),
is_feature_supported_SPI_bus()
A function to query the integration time in use from a spectrometer.
get_integration_time(jwrapper, sr.index = 0L, ch.index = 0L)get_integration_time(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
current integration time setting, in units of microseconds.
A function to retrieve the most recent Java exception triggered by OmniDrive as a character string.
get_last_exception(jwrapper)get_last_exception(jwrapper)
jwrapper |
an open Wrapper object from Omnidriver |
A character string String with a description of the most recent error exception, or "no exception" if no error has been encountered..
A function to query the maximum integration time that can be used from a spectrometer.
get_maximum_integration_time(jwrapper, sr.index = 0L)get_maximum_integration_time(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
maximum integration time setting, in units of microseconds.
A function to query the maximum integration time that can be used from a spectrometer.
get_maximum_intensity(jwrapper, sr.index = 0L)get_maximum_intensity(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
maximum value per pixel, in units of counts???.
A function to query the minimum integration time that can be used from a spectrometer.
get_minimum_integration_time(jwrapper, sr.index = 0L)get_minimum_integration_time(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
minimum integration time setting, in units of microseconds.
A function to query the name (e.g. USB2000) from a spectrometer.
get_name(jwrapper, sr.index = 0L)get_name(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a value
A function to query the number of channels from a spectrometer.
get_number_of_channels(jwrapper, sr.index = 0L)get_number_of_channels(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a numeric value
Function to query the number of pixels in the CCD array.
get_number_of_dark_pixels(jwrapper, sr.index = 0L, ch.index = 0L)get_number_of_dark_pixels(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value with the total number of pixels (ie. CCD elements) provided by this spectrometer, including any dark or bevel (unused) pixels.
A function to query the number of enabled channels from a spectrometer.
get_number_of_enabled_channels(jwrapper, sr.index = 0L)get_number_of_enabled_channels(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a numeric value
Function to query the total number of pixels in a spectrometer.
get_number_of_pixels(jwrapper, sr.index = 0L, ch.index = 0L)get_number_of_pixels(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value with the total number of pixels (ie. CCD elements) provided by this spectrometer, including any dark or bevel (unused) pixels.
Get the setting "number of scans to average" currently in use by the addressed spectrometer channel.
get_scans_to_average(jwrapper, sr.index = 0L, ch.index = 0L) get_scans_to_avg(jwrapper, sr.index = 0L, ch.index = 0L)get_scans_to_average(jwrapper, sr.index = 0L, ch.index = 0L) get_scans_to_avg(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Compute the time difference between two high speed time stamps.
get_seconds_time_delta(before, after) get_nano_time_delta(before, after) get_micro_time_delta(before, after) get_milli_time_delta(before, after)get_seconds_time_delta(before, after) get_nano_time_delta(before, after) get_micro_time_delta(before, after) get_milli_time_delta(before, after)
before, after
|
HighResTimeStamp defined in OmniDriver API and retrieved or constructed with other OmniDriver API methods. Not vectorized! |
a numeric vector of length one giving the time difference in seconds, milliseconds, microseconds or nanoseconds.
Nanosecond timing and normal timing are not coincident, but as both are stored in parallel, the differences should differ only in their resolution.
Other high speed acquisition functions:
get_seconds_time_delta_since(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_spectrum(),
highSpdAcq_get_time_stamp(),
highSpdAcq_start_acquisition(),
oo_timestamp_to_string()
Compute the time difference between a high speed time stamp and current time.
get_seconds_time_delta_since(then) get_nano_time_delta_since(then) get_micro_time_delta_since(then) get_milli_time_delta_since(then)get_seconds_time_delta_since(then) get_nano_time_delta_since(then) get_micro_time_delta_since(then) get_milli_time_delta_since(then)
then |
HighResTimeStamp defined in OmniDriver API and retrieved or constructed with other OmniDriver API methods. Not vectorized! |
a numeric vector of length one giving the time difference in seconds, milliseconds, microseconds or nanoseconds.
Nanosecond timing and normal timing are not coincident, but as both are stored in parallel, the differences should differ only in their resolution.
Other high speed acquisition functions:
get_seconds_time_delta(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_spectrum(),
highSpdAcq_get_time_stamp(),
highSpdAcq_start_acquisition(),
oo_timestamp_to_string()
A function to query the serial number from a spectrometer.
get_serial_number(jwrapper, sr.index = 0L)get_serial_number(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a value
Get a spectrum from the spectrometer
get_spectrum(jwrapper, sr.index = 0L, ch.index = 0L)get_spectrum(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Send a packet of bytes over the SPI bus and read the result.
get_SPI_bytes(SPI.bus.wrapper, message, num.bytes)get_SPI_bytes(SPI.bus.wrapper, message, num.bytes)
SPI.bus.wrapper |
feature wrapper as returned by function
|
message |
bytes, array of bytes with maximum length of 62. |
num.bytes |
numeric Number of bytes, 1..62. |
Several spectrometers have an I2C bus accesible through the auxiliary connector which can be used to control accesories. The I2C bus in Ocean Insight spectrometers is not intended to be used to control the spectrometer or retrieve data but instead to control and access other accessories with the spectrometer acting as middle man.
After writing to SPI, the spectrometer immediately reads from it. The resulting Byte array is returned.
Other Spectrometer I2C- and SPI-bus functions.:
get_I2C_bus(),
get_feature_I2C_bus(),
get_feature_SPI_bus(),
is_feature_supported_I2C_bus(),
is_feature_supported_SPI_bus()
Function to get wavelengths corresponding to the pixels in the CCD array.
get_wavelengths(jwrapper, sr.index = 0L, ch.index = 0L)get_wavelengths(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
A numeric (double) vector with the calculated wavelength at each pixel.
A function to query enable the WrapperExtensions class.
get_wrapper_extensions(jwrapper)get_wrapper_extensions(jwrapper)
jwrapper |
an open Wrapper object from Omnidriver |
A character string value of form "1.01.01" or similar.
Pre-allocates a buffer. A call to this function should always precede a call
to highSpdAcq_start_acquisition()
highSpdAcq_allocate_buffer(jwrapper, sr.index = 0L, number.of.spectra = 100L)highSpdAcq_allocate_buffer(jwrapper, sr.index = 0L, number.of.spectra = 100L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
number.of.spectra |
integer The number of spectra to be acquired. |
a numeric value
Other high speed acquisition functions:
get_seconds_time_delta(),
get_seconds_time_delta_since(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_spectrum(),
highSpdAcq_get_time_stamp(),
highSpdAcq_start_acquisition(),
oo_timestamp_to_string()
The number of spectra acquired can be smaller than the intended one, and
this function retrieved the true number of spectra available in the buffer
after the acquisition has finished. A call to this function can be used
after a call to highSpdAcq_start_acquisition() returns.
highSpdAcq_get_number_of_spectra_acquired(jwrapper)highSpdAcq_get_number_of_spectra_acquired(jwrapper)
jwrapper |
an open Wrapper object from Omnidriver |
a numeric value
Other high speed acquisition functions:
get_seconds_time_delta(),
get_seconds_time_delta_since(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_spectrum(),
highSpdAcq_get_time_stamp(),
highSpdAcq_start_acquisition(),
oo_timestamp_to_string()
Retrieve a single, previously measured, spectrum from the buffer. A call to
this function can be used after a call to
highSpdAcq_start_acquisition() returns.
highSpdAcq_get_spectrum(jwrapper, spectrum.number = 1)highSpdAcq_get_spectrum(jwrapper, spectrum.number = 1)
jwrapper |
an open Wrapper object from Omnidriver |
spectrum.number |
integer The index into the sequence of spectra most recently acquired at high speed and available in the memory buffer. |
a numeric vector
Other high speed acquisition functions:
get_seconds_time_delta(),
get_seconds_time_delta_since(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_time_stamp(),
highSpdAcq_start_acquisition(),
oo_timestamp_to_string()
Retrieve the time stamp for a single, previously measured, spectrum from the
buffer. A call to this function can be used after a call to
highSpdAcq_start_acquisition() returns.
highSpdAcq_get_time_stamp(jwrapper, spectrum.number = 1)highSpdAcq_get_time_stamp(jwrapper, spectrum.number = 1)
jwrapper |
an open Wrapper object from Omnidriver |
spectrum.number |
integer The index into the sequence of spectra most recently acquired at high speed and available in the memory buffer. |
A HighResTimeStamp object.
Other high speed acquisition functions:
get_seconds_time_delta(),
get_seconds_time_delta_since(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_spectrum(),
highSpdAcq_start_acquisition(),
oo_timestamp_to_string()
Acquires a series of spectra into a preallocated buffer. A call to this
function should be always preceded by a call to
highSpdAcq_allocate_buffer().
highSpdAcq_start_acquisition(jwrapper, sr.index = 0L)highSpdAcq_start_acquisition(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a numeric value
Other high speed acquisition functions:
get_seconds_time_delta(),
get_seconds_time_delta_since(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_spectrum(),
highSpdAcq_get_time_stamp(),
oo_timestamp_to_string()
Function init_api() (and its synonim init_srs())
create a Wrapper object for calling Omnidriver functions. This Java object of
class com.oceanoptics.omnidriver.api.wrapper.Wrapper is
later used by all other functions in the rOmniDriver to communicate with
the spectrometers through the OmniDriver API from Ocen Insight.
Only one wrapper object can be active at a time. You should call this
function only once and save the returned object as it is used to access the
methods implementing communication with the spectrometer. Clean up by use of
close_srs() before exiting or before initializing another wrapper to
the same driver.
Function is_api_enableb() tests if the argument passed to
jwrapper has been initialized and if it is connected to an active
instance of the Java wrapper class.
Function init_api_extensions() enables API extensions
and returns a wrapper that makes it possible to call additional
functions.
Function is_extended_api_enabled() tests if the argument passed to
jwrapperext has been initialized and if it is connected to an active
instance of the Java wrapper class.
Function init_api_extensions() enables API extensions
and returns a wrapper that makes it possible to call additional
functions.
Function is_highres_time_api_enabled() tests if
wrapper has been initialized and saved to a private environment of the
package.
init_api() init_srs() is_api_enabled(jwrapper) init_extended_api() is_extended_api_enabled(jwrapperext) init_highres_time_api() is_highres_time_api_enabled()init_api() init_srs() is_api_enabled(jwrapper) init_extended_api() is_extended_api_enabled(jwrapperext) init_highres_time_api() is_highres_time_api_enabled()
jwrapper |
jobjRef A Java Wrapper object from OmniDriver. |
jwrapperext |
jobjRef An "extension" Java Wrapper object from OmniDriver API. |
a wrapper to an instance of a Java object of class "wrapper"
logical
logical
Informs whether a channel of a multichannel spectrometer is enbled or not.
is_channel_enabled(jwrapper, sr.index = 0L, ch.index = 0L)is_channel_enabled(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Check whether feature "board temperature" is available in the spectrometer addressed. Construct a wrapper on the Java controller for the feature. Use a wrapped controller to query the temperature.
is_feature_supported_board_temperature(jwrapper, sr.index = 0L) get_feature_controller_board_temperature(jwrapper, sr.index = 0L) get_board_temperature(brd.wrapper)is_feature_supported_board_temperature(jwrapper, sr.index = 0L) get_feature_controller_board_temperature(jwrapper, sr.index = 0L) get_board_temperature(brd.wrapper)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
brd.wrapper |
an open controller wrapper object obtained with
|
a numeric value
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling get_feature_controller_board_temperature you f
irst need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_board_temperature.
Check whether feature "detector temperature" is available in the spectrometer addressed. Construct a wrapper on the Java controller for the feature. Use a wrapped controller to query the detector temperature.
is_feature_supported_detector_temperature(jwrapper, sr.index = 0L) get_feature_detector_temperature(jwrapper, sr.index = 0L) get_detector_temperature(dtr.wrapper)is_feature_supported_detector_temperature(jwrapper, sr.index = 0L) get_feature_detector_temperature(jwrapper, sr.index = 0L) get_detector_temperature(dtr.wrapper)
jwrapper |
an open Wrapper object from OmniDriver |
sr.index |
an index to address the spectrometer |
dtr.wrapper |
an open detector wrapper object obtained with
|
a numeric value
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
Before calling get_feature_detector_temperature you first need to check that the feature
is supported by the spectrometer in use#' by calling
is_feature_supported_detector_temperature.
Checks whether feature "I2C Bus" is available in the spectrometer addressed.
is_feature_supported_I2C_bus(jwrapper, sr.index = 0L)is_feature_supported_I2C_bus(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a logical value
Other Spectrometer I2C- and SPI-bus functions.:
get_I2C_bus(),
get_SPI_bytes(),
get_feature_I2C_bus(),
get_feature_SPI_bus(),
is_feature_supported_SPI_bus()
Check whether feature "ìnternal trigger" is available in the spectrometer addressed. Retrieve an interface that allows to control the ìnternal trigger. Control internal trigger of light sources such as Jaz PX.
is_feature_supported_internal_trigger(jwrapper, sr.index = 0L) get_feature_controller_internal_trigger(jwrapper, sr.index = 0L) get_trigger_period_valid_range(tgr.wrapper) get_trigger_period(tgr.wrapper) set_trigger_period(tgr.wrapper, period) set_trigger_source(tgr.wrapper, source) get_trigger_source(tgr.wrapper, char.out = TRUE)is_feature_supported_internal_trigger(jwrapper, sr.index = 0L) get_feature_controller_internal_trigger(jwrapper, sr.index = 0L) get_trigger_period_valid_range(tgr.wrapper) get_trigger_period(tgr.wrapper) set_trigger_period(tgr.wrapper, period) set_trigger_source(tgr.wrapper, source) get_trigger_source(tgr.wrapper, char.out = TRUE)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
tgr.wrapper |
feature wrapper as returned by function
|
period |
numeric Internal trigger period in seconds. |
source |
character, "on", "off", "external", "internal" or integer [0..3] or logical. |
char.out |
logical If TRUE return a character string, otherwise return integer as returned by the API call. |
an integer value
an object which provides the desired interface, or null if this feature is not available for this spectrometer.
numeric vector of length three with times in seconds for "min", "max" and "step".
Before calling get_feature_controller_internal_trigger you first need to check that the feature
is supported by the spectrometer in use by calling
is_feature_supported_internal_trigger.
Check whether feature "Irradiance Calibration Factor" is available in the spectrometer addressed. Construct a wrapper on the Java controller for the feature. Use a wrapped controller to retrieve the calibration factors.
is_feature_supported_irradiance_calibration_factor(jwrapper, sr.index = 0L) get_feature_irradiance_calibration_factor(jwrapper, sr.index = 0L) get_irradiance_calibration_factors(irrad.cal.wrapper)is_feature_supported_irradiance_calibration_factor(jwrapper, sr.index = 0L) get_feature_irradiance_calibration_factor(jwrapper, sr.index = 0L) get_irradiance_calibration_factors(irrad.cal.wrapper)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
irrad.cal.wrapper |
An open wrapper for the feature object. |
a logical value
A wrapper on a Java object which provides the interface, or null if this feature is not available for this spectrometer.
A numeric vector of calibration factors, as returned by the spectrometer.
Before calling get_feature_irradiance_calibration_factor you
first need to check that the feature is supported by the spectrometer in
use by calling is_feature_supported_irradiance_calibration_factor.
An attempt to retrieve calibration factors may fail and not return
unless a USB timeout is set with function set_USB_timeout().
Checks whether feature "pixel binning" is available in the spectrometer addressed.
is_feature_supported_pixel_binning(jwrapper, sr.index = 0L)is_feature_supported_pixel_binning(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a numeric value
Checks whether feature "saturation threshold" is available in the spectrometer addressed.
is_feature_supported_saturation_threshold(jwrapper, sr.index = 0L)is_feature_supported_saturation_threshold(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a logical? value
Checks whether feature "spectrum type" is available in the spectrometer addressed.
is_feature_supported_spectrum_type(jwrapper, sr.index = 0L)is_feature_supported_spectrum_type(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a logical value
Checks whether feature "SPI Bus" is available in the spectrometer addressed.
is_feature_supported_SPI_bus(jwrapper, sr.index = 0L)is_feature_supported_SPI_bus(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a logical value
Other Spectrometer I2C- and SPI-bus functions.:
get_I2C_bus(),
get_SPI_bytes(),
get_feature_I2C_bus(),
get_feature_SPI_bus(),
is_feature_supported_I2C_bus()
Checks whether the most recently acquired spectrum is saturated (= signal clipping occured).
is_saturated(jwrapper, sr.index = 0L, ch.index = 0L)is_saturated(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Be aware that clipping outside the wavelength range of interest for a given measuremt may not be important and can be ignored. This method tests for clipping at any pixel of the array.
Informs whether the most recently acquired spectrum is valid (no communication or similar errors have occurred during acquisition).
is_spectrum_valid(jwrapper, sr.index = 0L, ch.index = 0L)is_spectrum_valid(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Checks whether the last operation has timed out. This is useful when working with triggers together with signals used for triggering that may fail or be delayed.
is_timeout(jwrapper, sr.index = 0L)is_timeout(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a numeric value
Checks whether the last USB operation has timed out. This is useful when working with triggers together with signals used for triggering that may fail or be delayed.
is_USB_timeout(jwrapper, sr.index = 0L, ch.index = 0L)is_USB_timeout(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
Convert a time stamp into a character string. Times with millisecond resolution and nanosecond resolutions are separate, with the nanosecond component useful for computing time differences only.
oo_timestamp_to_string(jwrapper, oo_timestamp)oo_timestamp_to_string(jwrapper, oo_timestamp)
jwrapper |
an open Wrapper object from Omnidriver |
oo_timestamp |
HighResTimeStamp defined in OmniDriver API and retrieved or constructed with other OmniDriver API methods. Not vectorized! |
a character string.
Nanosecond timing and normal timing are not coincident.
Other high speed acquisition functions:
get_seconds_time_delta(),
get_seconds_time_delta_since(),
highSpdAcq_allocate_buffer(),
highSpdAcq_get_number_of_spectra_acquired(),
highSpdAcq_get_spectrum(),
highSpdAcq_get_time_stamp(),
highSpdAcq_start_acquisition()
Opens connections to communicate with all Ocean Insight spectrometers connected through USB and returns the number of spectrometers that can be addressed.
open_all_spectrometers(jwrapper) number_srs(jwrapper)open_all_spectrometers(jwrapper) number_srs(jwrapper)
jwrapper |
an open Wrapper object from Omnidriver |
A numeric value giving the number of USB-connected spectrometers.
Set setting "boxcar width" (the number of adjacent pixels averaged)
set_boxcar_width(jwrapper, half.width.px = 0L, sr.index = 0L, ch.index = 0L)set_boxcar_width(jwrapper, half.width.px = 0L, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
half.width.px |
the number of pixels in one half of the bocar window (an integer number) |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
The signature of this function is different to that of the Java equivalent, so that as with other functions in the package indexes for addressing spectrometer and channel can have default values.
Set setting "correct for detector nonlinearity" for the addressed spectrometer.
set_correct_for_detector_nonlinearity( jwrapper, correct = 0L, sr.index = 0L, ch.index = 0L )set_correct_for_detector_nonlinearity( jwrapper, correct = 0L, sr.index = 0L, ch.index = 0L )
jwrapper |
an open Wrapper object from Omnidriver |
correct |
integer or logical; 0, FALSE: apply correction; 1, TRUE: do not apply correction. |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a logical value that the user SHOULD test as the method may fail.
The signature of this function is different to that of the Java equivalent, so that as with other functions in the package indexes for addressing spectrometer and channel can have default values.
Set setting "correct for electrical dark signal" for the addressed spectrometer channel
set_correct_for_electrical_dark( jwrapper, enable = 0L, sr.index = 0L, ch.index = 0L )set_correct_for_electrical_dark( jwrapper, enable = 0L, sr.index = 0L, ch.index = 0L )
jwrapper |
an open Wrapper object from Omnidriver |
enable |
integer or logical; 0, FALSE: disable; 1, TRUE: enable. |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a logical value
The signature of this function is different to that of the Java equivalent, so that as with other functions in the package indexes for addressing spectrometer and channel can have default values.
Set "integration time" for the addressed spectrometer channel
set_integration_time(jwrapper, time.usec = 100L, sr.index = 0L, ch.index = 0L)set_integration_time(jwrapper, time.usec = 100L, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
time.usec |
integartion time in microseconds (an integer) |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
The signature of this function is different to that of the Java equivalent, so that as with other functions in the package indexes for addressing spectrometer and channel can have default values.
Set "number of scans to average"
set_scans_to_average(jwrapper, n.scans = 1L, sr.index = 0L, ch.index = 0L) set_scans_to_avg(jwrapper, n.scans = 1L, sr.index = 0L, ch.index = 0L)set_scans_to_average(jwrapper, n.scans = 1L, sr.index = 0L, ch.index = 0L) set_scans_to_avg(jwrapper, n.scans = 1L, sr.index = 0L, ch.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
n.scans |
number of scans (an integer) |
sr.index |
an index to address the spectrometer |
ch.index |
an index to address the channel in a spectrometer with more than one channel. |
a numeric value
The signature of this function is different to that of the Java equivalent, so that as with other functions in the package indexes for addressing spectrometer and channel can have default values.
Set the spectrum type to one of normal or raw.
set_spectrum_type(spct.type.wrapper, spct.type = "normal")set_spectrum_type(spct.type.wrapper, spct.type = "normal")
spct.type.wrapper |
feature wrapper as returned by function
|
spct.type |
character, "normal" or "raw" or interger, 0 or 1. |
logical TRUE = success, FALSE = failure.
Setting a "timeout" for the addressed spectrometer is useful when used together with triggers to avoid endless waiting in case the trigger input does not take place.
set_timeout(jwrapper, time.millisec = 1000L, sr.index = 0L)set_timeout(jwrapper, time.millisec = 1000L, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
time.millisec |
time to wait in milliseconds (an integer) |
sr.index |
an index to address the spectrometer |
a numeric value
This method is applied to all channels.
Setting a "timeout" for the addressed spectrometer is useful when used together with triggers to avoid endless waiting. This function is supported only by USB spectrometers. A time of 0L disables the timeout.
set_USB_timeout(jwrapper, time.millisec = 1000L, sr.index = 0L)set_USB_timeout(jwrapper, time.millisec = 1000L, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
time.millisec |
time to wait in milliseconds (an integer) |
sr.index |
an index to address the spectrometer |
a numeric value
This method is applied to all channels.
Flush the most recent spectrum acquired or currently being acquired
spectrum_flush(jwrapper, sr.index = 0L)spectrum_flush(jwrapper, sr.index = 0L)
jwrapper |
an open Wrapper object from Omnidriver |
sr.index |
an index to address the spectrometer |
a numeric value
Stop averaging for addressed spectrometer probably not very useful in "vanilla" R as this aborts the current averaging of spectra, but needs a multithreaded application to be able to call it before get.spectrum returns.
stop_averaging(jwrapper, sr.index = 0L, ch.index = 0L)stop_averaging(jwrapper, sr.index = 0L, ch.index = 0L)
jwrapper |
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. |
a numeric value
The signature of this function is different to that of the Java equivalent, so that as with other functions in the package indexes for addressing spectrometer and channel can have default values.