A-D menu

  •   CONVERSION EQUATIONS        These submenus allow you to change one channel's voltage conversion and labeling from the regular voltage conversion window, instead of editing a series of values in different edit fields.  NOTE: oscilloscope channels are not accessible to such manipulations, since they record raw voltages only.

  •   CONVERSION OPTIONS       This selection opens a window to let you further modify one channel's signals (after voltage conversions).  This is mainly used in respirometry (calculation of gas exchange), but can also help correct for buffered responses.

  •    UI2 SERIAL INSTRUMENTS     Lets you control how LabHelper reads data strings from Sable Systems instruments with serial output.  These devices produce complex streams of data that usually contain several variables (see the Channel selection window for more detail).

    Since a single instrument usually provides several kinds of data (in the above example, a humidity analyzer provides humidity, dew point, vapor pressure, and temperature), you can read more than one variable from a single device.  However, at this time you can use only one serial instrument at a time.

  •   EXTERNAL A-D DEVICE         The options that appear in this submenu depend on the type of A-D converter in use.

    For a Sable UI2 or UI3, you will see these options:

  •   SABLE TEMPERATURE CHANNELS     Lets you control how the four temperature channels are used:

  •    Sable FIRMWARE      Shows the firmware version of the UI2 or UI3 (some early UI2 versions had voltage limits of ±5.00 volts; newer ones go to ± ~5.16 volts (LabHelper checks this at startup and adjusts accordingly).

  • For Datatakers, you will see these options (the exact menu labels on model):

  •   DATATAKER INPUTS     Allows use of the DataTaker's ability to return temperatures (instead of microvoltages) from thermocouples (note that the default setting is for copper-constantan thermocouples).  It also allows selection of differential or single-ended inputs for voltage measurements, or use of the high-speed counter:

    In this example, there are 6 channels in use.  Two channels (#5 and #6) use copper-constantan thermocouples.  The remaining channels read voltages; two are connected as single-ended inputs and two as differential inputs.

  •   DT800 ACQUISITION MODE     Lets you set the DT800 for sampling speed (slower with less noise versus faster with more noise) and mains power noise rejection (50 or 60 hz).

  •   RESET DATATAKER     Resets the DataTaker to base mode.   You should not have to do this often but if you do, a 5-second countdown timer shows you when it is safe to proceed after the reset.

  •   DT800 (or DT500, or DT50) FIRMWARE     Shows the firmware version; with a DT800 you can also click a button to get a complete internal diagnostic report.

  • For an ADAM-4019,you will see these options:

  •   ADAM-4019 INPUTS     Allows use of the ADAM's ability to return temperatures (instead of voltages) from thermocouples.  The three thermocouple types are J (iron-constantan), K (cromel-alumel), and T (copper-constantan); these are the most common types used in physiology.  The window also allows selection of several voltage ranges:

    If you have a second ADAM A-D module connected (4017 or 4019), you will see another 8 inputs, numbered 9 - 16.

  •   ADAM FIRMWARE     Shows ADAM module's name (should be '4019x'), firmware version, and the temperature of the internal CJC (cold junction compensator).   The CJC is necessary for correct thermocouple readings but also shows the unit's internal temperature.  The CJC value is updated continuously as long as the window is open; it will warm up after the unit is powered up and then should stabilize.
  •   CONFIGURE SERIAL PORT...   This option lets you may override the default serial port and baud rate if using an external A-D device.

    Make sure you set the same baud rate on both the computer and the external A-D device.  Note that LabHelper assumes that any external A-D device (Sable UI2 or UI3, or DataTaker) is set to run with no parity, 8 data bits, and 2 stop bits.  If you chose to change the serial port, make this selection immediately after launching the program.  DO NOT switch between serial ports during a run, as this will probably crash the program (maybe even the computer -- even in macOS!).

  •   TEST MODE (DEMO)     ⌘F      This option uses a random number generator to allow program setup and experimentation without connection to an actual analog-to-digital converter.  All aspects of the program are "operational," including analog output and oscilloscope sampling.

  •   SAMPLE AVERAGING       This submenu has three choices (all of which apply only in Chart mode):

  •   NORMAL   Data from each channel is averaged over a user-set number of readings (which may be different for each channel).  All readings for a given channel are made before proceeding to the next channel.  If any time is left until the time for the next sample, the computer idles.  If the total time necessary to make the pre-set number of readings exceeds the sample interval, the computer will not be able to keep up with the requested sampling rate.

  •   CONTINUOUS, LAST CHANNEL   In this mode, the first channels are averaged over a user-set number of readings and the final channel is then scanned continually for the remainder of the sample interval.  This mode provides more continuous monitoring of the last channel than is possible in 'normal' mode.

  •   CONTINUOUS, ALL CHANNELS   In this mode, all channels are scanned sequentially and continually throughout the sample interval.  The Averaging window is not available, and differences in the number of averaged readings between channels are not possible.  This mode provides a more continuous sampling of each channel than in the 'normal' averaging mode, wherein each channel is sampled for a predefined number of readings before proceeding to the next channel.

    In continuous scanning mode (for either one or all channels), the number of averaged readings per recorded sample depends on the number of channels, the sample interval, and the speed of the computer and the A-D converter.

  •    SPIKE FILTER     This option uses a sample-comparison algorithm to attempt to find and remove 'spikes' as data are acquired.   'Spikes' are single-point (i.e., one sample) aberrant readings that may represent electrical noise or some other instrumentation fault instead of real data.   The spike filter compares the current data value for a given channel with the previous value for that channel.   If the current value is sufficiently different from the previous value, it is resampled (resampled twice if you select the 'use double filtration' option), and the two 'new' samples are compared with the previous sample to determine which is aberrant.   Obviously it can't function for the first few data points in a recording (since it doesn't have any previous values for comparison).

    The 'difference' between current and previous readings is computed as a ratio, or fold-difference factor (e.g., 2X larger or smaller than previous data).   A ratio of 1.1 means that a reading 10% or more different from the mean of the two previous values is interpreted as a spike.   You can set the fold-factor in the edit field; only positive values greater than 1.0 are acceptable.   Larger fold-factors increase the factorial change between successive readings that will be accepted as valid data.  After recording is stopped, a report of the number of spikes removed is saved in the file comments.

    • The spike filter tests raw input values (voltage, resistance, etc.), not the final values after conversion factors have been applied.

    • Spike filtration is a compromise between sampling speed and spike discrimination ability.   The 'use double filtration' option will improve the algorithm's ability to find and discard spikes, but can slow sampling when sample rates are high.

    • The fold-factor should be determined from the noise level in the system and the necessary accuracy and speed.

    • The spike filter is not perfect and may sometimes reject valid data, especially when input data are close to zero and have some variance.   Therefore it should be used with care, and only for data containing considerable noise. Note that the spike filter does not function for data read as text from a serial-stream input.

  •   AUDIBLE EVENT TIMER     This option lets you use audible cues to time external events.  For example, if you need to perform a timed experimental manipulation and you do not want to look at a clock or watch, the program will provide you with an aural cue on a preset schedule.  You can adjust each sound (several spoken words, recorded from my "dulcet" (ahem...) voice, along with some standard computer sounds), when it occurs (in relation to elapsed time or elapsed samples), and when it starts and stops.  These settings are saved in 'setup' files.

    In this example, audible timing will commence with the spoken word "start" when the first marker is struck.  The alert "now" will sound every minute for 6.5 minutes, at which point the "stop" sound will occur.

  •   The BEEP AT SAMPLE option toggles an audible signal (a quiet 'peep' sound) when a sample is recorded.  This item is available if the sample rate is slower than 10 samples/second, and for the most part is really only useful for semple intervals of several seconds.

  •   SET ALARMS...      W      Opens a window (shown in the following example) that allows you to set up the alarm status for each channel.  An alarm is triggered whenever the input to that channel violates certain conditions -- some fixed, some user-specified.  If alarms are set, warnings of alarm conditions appear in the upper right corner of chart output during data gathering.  Optionally, an audible buzzer can be triggered by an alarm condition.  Finally, a summary of alarms can be called up from the Options window at the end of a data run.  Note that alarms do not function with oscilloscope channels.

    Three types of alarms are possible:

    • Overrange (over-voltage) alarms are triggered when the input voltage exceeds the capacity of the A-D converter in use (plus or minus 5 or 5.12 volts with the Sable UI2 or UI3, or plus or minus 3.5 volts with current DataTakers, etc.).  Optionally, the computer will sound an audible alarm when it encounters an overrange condition (note that this will slow acquisition when sampling at high rates).

    • Upper limit alarms occur whenever values (after conversion, NOT input volts) exceed a user-set limit.

    • Lower limit alarms occur whenever values (after conversion, NOT input volts) fall below a user-set limit. 

    Note that using alarms can slow the maximum possible sampling rate.  However, for most sampling rates, use of alarms has no effect on performance.

  •   AUTOREPEAT or AUTOMARKERS...      This selection depends on the recording mode in use:

    In chart mode, the Autorepeat option allows LabHelper to automatically save data when the maximum number of samples has been recorded, and then automatically restart data gathering.  If this option is selected, a standard Mac file opening dialog will appear, requesting a file root name.  Saved files will have a name consisting of the root (e.g., 'bird data') plus a suffix corresponding to the sequence number (e.g., 'bird data 1', then 'bird data 2', then 'bird data 3', etc.) of the file.

     WARNING:    if you selected a large number of samples, be sure you have plenty of disk space available to save the expected number of files!

    After the file root is selected, LabHelper presents a window for entering a comment string and data for gas exchange calculations (body mass, flow rate, barometric pressure, etc.).

    In scope + chart mode, the Automarkers option will place a marker in the chart channels whenever a scope file is saved with the 'tab' key.  These markers start with 0 and increment to 9, and then repeat. 

  •   CUT CHANNELS...     ⌘K      Opens a window that lets you selectively remove channels.  This is only available if at least two chart channels are available (it will not let you reduce the number of chart or scope channels to zero).

  •   ADD A CHANNEL...     Adds a single channel to the current acquisition setup.  This menu is available only in certain conditions:

    • chart or scope plus chart mode

    • accessible from the Show Setup or Options windows only

    • there must be less than the maximum number of channels selected (<16 in chart mode, <5 in scope plus chart mode)

    This selection opens a series of windows that request the A-D input, conversions, scaling, etc..

  • 2 - CHANNEL X-Y PLOTS...     This option lets you view a real-time scatterplot display of interactions between any two channels as data are being acquired. The interaction is shown as a bicoordinate plot of the corresponding values, with one data channel used for the X-axis and one channel for the Y-axis. A small window appears at the upper right of the main plot area, with data shown as yellow dots (one per sample) on a red background. The axes are scaled the same as they are for the corresponding channels in the main data display (you can change this scaling from the Show Setup window).

    If you are trying to sample very rapidly, an X-Y plot will slightly slow the maximum sample rate, but for most sample protocols it will make little or no difference.

    During a run, you can press the 'option-c' key combination to clear the X-Y plot screen of data.

    NOTE: The X-Y plot window will not open if there is insufficient space between the right edge of the main data plot and the right edge of the screen. At least 100 'spare' horizontal pixels are needed; more will be used (up to about 300) if available. Use the ' Set Window Area' option in the VIEW menu to select a smaller plot area, if necessary (this will be difficult to accomplish on a small screen, and the X-Y plot option is not available on a low-resolution 640 X 480 pixel screen).

  • EXTRA ZERO LINKAGES...     Zero linking is an option for periodic references, when one external device switches two logical channels. In this situation it is useful for the second channel to record zero when not 'connected' to the switched instrument. Zeroing helps to avoid confusion during analysis -- it's less likely that an incorrect assignment of data to animal will occur (the 'primary' channel automatically records zero when not 'connected'). To 'link' another channel to a primary channel, click the appropriate button to the right of the primary channel's label; when everything is appropriate, click the 'OK' button.
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