LabAnalyst has six menus, plus on-line instructions in the "Help" menu (OS 8 and above), "Special" menu (OS X), or the Apple menu (earlier operating systems).
| FILE | EDIT | ANALYZE | VIEW | CHANNELS | SCRIPTS | HELP / SPECIAL |
This describes the portion of the EDIT menu covering topics other than respirometry. See the Respirometry submenu for gas exchange calculations.
For BASELINE, INTEGRATE, DERIVATIVE, SMOOTHING, GAS EXCHANGE, and some other EDIT menu calculations, clicking the plot window is equivalent to clicking a highlighted button.
To change channels, go to the CHANNELS menu, use the up and down arrow keys, or push the desired channel number on the keyboard ('0' for 10; for higher channel numbers push shift+number, i.e., shift-2 for channel 12).
UNDO
+Z Replaces
the most recently changed channel with its previous value.
This allows you to recover, without reloading the original file from disk,
if you make a mistake during a transformation or other manipulation.
When performing complex manipulations on data, remember that only one level of UNDO is available. |
CUT TEXT +X
COPY TEXT +C
PASTE
TEXT +V
CUT, COPY, and PASTE work like the normal Apple
operations, but only on text (not on items like data blocks.).
CLEAR BLOCK Clears
any currently selected block and closes the block window (if open).
Note: hitting the 'esc' or 'clear' key has the same
effect.
EDIT FILE DATA...
+E
Allows editing of channel labels (within the limit of 30 characters -- including
spaces -- per label), along with mass, barometric pressure, effective volume,
etc. The edit window looks like this:
By clicking one of the 'channel x' buttons, you can change to the selected channel. Comments can also be edited up to the maximum of 32K characters (255 charaters in non-FP versions; 240 characters if you want to save in Sable SSCF format).
Clicking on the 'comments' window in the main display takes you directly to the 'edit comments' window.
CORRECT BASELINE...
+B
(Active channel only) There
are six methods of baseline correction. You should select the one
most appropriate for your data set.
1. Automatic -- the program selects blocks at the start and/or end of the data and uses them in a regression to compute the baseline. You can change the number of cases in these blocks by editing the value in the box (the default is 15). Use the automatic method only if the beginning and end of the file contain nothing but true baseline values. If this condition is not met, use another method (such as #2, below).
2. Use the mouse to select a sequential series of baseline blocks (multiple points), starting from the 'left' end of the file and moving to the 'right' end. This method corrects the baseline in a series of segments (up to 40 in a given file; you can repeat the process if you need to handle more than 40). Alternately, you can click on single points (instead of selecting blocks).
3. Use the mouse to select beginning and ending blocks, which LabAnalyst then uses in a linear regression to compute the baseline. Alternately, you can click the single point button to pick baseline points (instead of selecting blocks).
4. Use the mouse to select a single block which the program uses to calculate a flat baseline. Alternately, you can click on a single point (instead of selecting a block).
5. Keyboard entry of beginning and ending baseline values.
6. Keyboard entry of a constant baseline value.
For all methods except #2 (multiple blocks), the baseline is drawn on-screen (if it fits within the current Y-axis scale) and you can cancel, reselect, or select it. The final baseline is drawn across the entire file.
See the Reference removal section for an easy method of eliminating baseline sections for analysis.
LAG CORRECTION...
(Active channel only). Asks for the number
of seconds of lag time (for example, if the response of one channel is delayed
relative to some other channel). The channel is 'left-shifted' (time
is advanced) by the chosen amount. On the right end of the trace,
a group of samples equal to the lag interval is set to zero.
The main goal of lag correction is usually to correctly synchronize two channels. To determine how much lag time to use, follow these steps:
INTEGRATE... +I 
Sequentially
adds all points from the first to the last to get a cumulative curve (this
is not 'true' mathematical integration). The window looks like the
example shown here (note that the program places an integral sign in front
of the original file label):
DERIVATIVE...
+D 
Goes from
the last point to the first point (right to left), computing and storing
the change between successive points (this is not 'true' mathematical
derivation). The derivation window is nearly identical to the one
shown at right for integration (and the program places a derivation symbol
in front of the original file label).
NOTE: Because numbers are stored in floating point format with 8-10 digit precision, integration may result in loss of least-significant digits, particularly if the numbers are large (i.e., if their cumulative sum contains more than 8-10 decimal digits). Thus integration followed by derivation of the same data will not necessarily produce a result identical to the original data. Normally this poses no problems to users. |
SMOOTHING...
+F 
(Active channel
only) Performs nearest-neighbor smoothing with a choice of 3, 5, 7, 9, 11,
15, 19, and 25- point averaging intervals with one or more smoothing repetitions
(the default is 1).
The program makes a memory
copy of the channel and uses it as its data source (this insures that within
a given smoothing iteration, previously smoothed data are not part of the
calculations). When smoothing is complete, the channel is redrawn.
If a block has been selected, you can smooth either all the data or just
within the block. You can also smooth conditionally, changing only
those data within a certain range (i.e., greater than or less than user-
specified values). If the file contains less than 14 channels, you
can copy the active channel to a new channel before smoothing.
This example shows 19-sample smoothing to be repeated over six cycles. Notice that the indicated smoothing interval (calculated from the sample interval and the averaging interval of 19 samples) is 90 seconds. Only data with values less than 1500 will be smoothed.
Smoothing can be repeated as often as necessary, but be very careful that you do not obliterate useful information from the data. For example, smoothing a high-frequency waveform may result in a substantial decrease in the peak amplitude, although this should not affect frequency calculations. Remember that you can undo only the last smoothing operation performed.
REMOVE SPIKES...
(Active
channel only) Allows you to remove voltage 'spikes' or other inaccurate
data, either automatically or interactively. There are several options
for removing spikes:
Automatic: . Single-point spikes that exceed a
user-defined amplitude are easily removed with the spike sweep operation.
However, this will not work effectively for multiple-sample spikes.
Spike sweep searches for single data points that differ from their nearest
neighbors by the threshold value or greater (in absolute units). Points
meeting these criteria are converted to the average of the two nearest neighbors.
Two options are available for sweeping: 'Single scan' makes a single pass through the data; 'Spike sweep' repeats scanning until all appropriate spikes are removed.
The trim data option searches for data points that are greater or less than preset limits; all data outside these limits are set to user-defined values. Both sweep and trim can be performed within blocks only (if a block has been selected).
In this example, the user has performed a spike sweep with a threshold value of .02, and the program found and removed 4 spikes. Also, the trim data options have been set such than any value exceeding .25 will be set to equal .25, and any value less than -.01 will be set to zero.
Interactive: In Spike mode, spikes are
selected by clicking on them with the crosshair cursor. The program
replaces the selected point with the average of the two values on either
side. This is most effective for spikes of short duration (optimally,
a single sample).
An alternate noise-removal method is 'Data Linearizing'. This mode linearizes all data points between two selected points (as shown schematically in the example plot).
You can alternate between spike removal mode and linearizing mode by first clicking in the lower left window, then clicking the desired mode button, and finally returning to the plot area. Accessing the 'Quit' button is done similarly.
If you are in multi-channel display mode, the program will shift to single-channel display (of the currently active channel) for spike removal operations. If the file contains more than screenwidth cases and you are in Entire File display mode, the program will shift to Active Screen mode when interactive spike removal is selected. Use the screen buttons to shift between screenfulls of data (note that the data linearizing option can work across screen boundaries).
REMOVE REFERENCES...
(Active channel only; FP and
X versions only) Reference readings are a common method of checking
measurements against a known value. Typically one reads sample data
for a certain period, after which the instrument is switched to read some
standard condition (perhaps a known temperature or gas concentration).
After the reference reading, more sample data are recorded, and the process
is repeated as necessary (the LabHelper program can do this automatically,
for example). References help insure accuracy, but may be inconvenient
during analyses. This routine lets you eliminate most kinds of reference
readings from a channel. The Remove references window is shown at
right. To use it you need to specify:
Reference removal is computed and the new values are displayed in the plot area when you click the 'Fix references' button. You can then undo the results, or exit the function.
RESPIROMETRY
In
the 'FP' and 'X' versions, this selection is a submenu. See the
Respirometry page for details for
both FP and older versions.
SIMPLE TRANSFORMATIONS...
+T 
This option
(called TRANSFORMATIONS in non-OS X versions) allows mathematical
manipulations such as logarithms (base e and base 10), inverses, exponentiation,
multiplication, division, square-roots, Q10 correction,
etc. Several cross-channel operations are also possible (addition,
subtraction, multiplication, division). A polynomial conversion with
one to nine degrees is available. Results are stored in the first
source channel, or optionally (if the number of channels is less than 16)
in a new channel.
This sample window shows the addition of two channels, with the result stored in a new channel. The multiply/divide option is set to 1 (meaning that no action is taken on the result of the addition operation). If you set this number to something other than 1.0 and click either of the multiply or divide buttons, the result of the 'main' operation will be adjusted accordingly.
Two buttons at left toggle between TRANSFORMATIONS and UNIT CONVERSIONS.
The operations for transformations are selected from the smaller
(left-most) of the two pop-up menus shown at near right. Note that
the last five transformations (addition, subtraction, multiplication, and
division with different channels, and Q10 correction
from a temperature channel) are only available if the file contains more
than one channel.
Alternately, you can use a range of unit conversions from the pop-up menu shown at far right. These pertain to commonly-used units of energy, flow rate, pressure, mass, speed, temperature, water vapor pressure, gas volume, and so forth. Conversion into mass-specific units is also available. The 'STP converter' option does not affect the channel data, but allows you to calculate an appropriate correction for temperature and pressure effects on gas volume (useful in respirometry).
For most of these operations, the conversion factors (i.e., the numerical coefficients in the conversion equations) can be edited as desired prior to actual calculations. For example, you may wish to adjust the conversion factor for the heat of vaporization of water (which is set for a default evaporative surface temperature of 37 °C) to a value accurate at some other temperature.
Many of the conversions will attempt to adjust the channel label as appropriate. For example, if you have chosen to convert a channel to mass-specific units, the program will append a "/g" or "/Kg" to the end of the current label. Similarly, if you are converting a channel with units of watts to units of KJ/day, the program will search the label for the word "watts" and replace it with "KJ/day". Keep in mind that automatic label modification is not always successful (depending on the format of your channel labels), so be sure to check.
Note that the transformations routines do not make any attempt to adjust labels to reflect changes. You should be diligent in correcting the file labels appropriately in order to avoid confusion later on.
During mathematically complex operations that are time-consuming (such as calculating logs or computing vapor pressure from temperature), a progress bar appears. This isn't shown for faster operations, since drawing the progress bar often is slower than the computations themselves!
Some special considerations for transformations and conversions:
The response correction option is similar to the 'effective volume' computation used for gas exchange. It compensates for capacitance-like characteristics that slow response times and obscure rapid changes in measured variables, using the "Z-transformation". The algorithm compares successive values and corrects them according to the following equation:
corrected value = [(value-last value)/Z factor] + last value
Typical Z factors are between 0.1 and 1.0 (other values are accepted). It is reasonable to determine the correct value by trial-and-error, if you have a recording that contains a known step change (or near-instantaneous change). Apply different Z factors until the results approximate a step change.
The breakpoint transforms option lets you use different transformation equations depending on whether data are less than or greater than a user-specified 'breakpoint' value. You enter the equations and the breakpoint in the following window (which appears whenever you select the breakpoint option):
After entering the breakpoint value, pick the type of equation for data below the breakpoint value, using the radio buttons at left. Then click the 'use this equation for data < breakpoint' button, and enter the a, b, and c values in the first set of edit fields at the bottom of the window. Then select the equation type for data equal to or greater than breakpoint, click the 'use this equation for data > breakpoint' button, and enter the a, b, and c values in the second set of edit fields. In this example, a 2-way polynomial will be applied to data < breakpoint, and an exponential equation will be applied to data > breakpoint. When all is correct, click the 'OK to transform' button to return to the main Transformations and Conversions window.
| NOTE: LabAnalyst does not allow invalid or meaningless mathematical operations, such as division by zero, taking the log of a negative number, or using a non-integer exponent on a negative number. If LabAnalyst encounters these situations during a transformation, the offending cases are set to zero, the computer beeps, and a warning message appears. At this point you can click the 'Cancel' button to discard the transformed data, or accept the (partially invalid) transformation. |
For related operations, see also the SCALE RESULTS option (ANALYZE menu).
EXPRESSION TRANSFORMS... (LabAnalyst
X only)
This routine lets you write a mathematical expression to transform a channel. The program parses the expression into components and performs the operations. The expression evaluator understands the following symbols (upper or lower case entries are OK):
Results are stored in the first of the source channels, or optionally (if the number of channels is less than 16) in a new channel (edit the file label as appropriate). If a data block has been selected, you can transform all the data or just within the block. A typical expression transforms window looks like this:
Some general considerations:
NOTE: This will only 'catch' errors in the basic numeric expression. It may not detect invalid or meaningless math operations that may be attempted when channel data are processed, such as division by zero, or taking the log or a non-integer exponent of a negative number. If such situations occur, results may be unpredicatable. The algorithm does find most such errors during processing, however.
| The underlying code for the expression evaluator was very largely developed by Robert Purves. I 'borrowed' it -- with his permission -- and made some modifications for LabAnalyst. But Robert P. deserves all the credit. |
SCALE TO BLOCK...
(LabAnalyst X only)
Resets the scale and range of the data to values specified by the user, based on a block of data. For example, you can rescale a block of data with an initial range of -.134 to .335 to a new range of zero to 100% (or any other upper and lower limits).
Note: although calculations are based on data within the selected block, the scale and range adjustment is applied to the entire file.
COMPACT &
AVERAGE... Makes a compact version of
the data by breaking it into a series of blocks of user-specified length,
and then computing a mean and S.D. for each of the blocks. Each
block contains a fixed number of cases, and the block duration (in time
units) depends on this number and the sample interval.
Compacted data can be
saved as tab-delineated text files containing both means and standard deviations.
It is also shown on-screen in the regular plot area. This can make
it easier to see trends in noisy data, and is also useful for preparing
data for publication -- a figure broken into a series of means and S.D.s
is frequently easier to read than a simple line plot (particularly if the
raw data are somewhat noisy).
NOTE: although the plot area on the screen shows the compacted version, any analyses are performed on the original data, which is shown as normal in the block window.
This example shows a 10-fold compaction, which equates to a 'block size' of 15 seconds for each mean and S.D. computation. The 'highlight data means' and 'show S.D.' options are selected; this will show the mean values as a dot, and the SDs as vertical lines in the plot area (in active screen mode only if there are more than screenwidth cases).
Some operations, like Baseline with user-selected points, are difficult to use if the data are shown in compacted form (although you can still read the uncompacted values for the cursor position in the data bar). It's probably best to shift to the regular display ('normal plot') for these operations.
CHANGE OR REMOVE
In
the 'FP' and 'X' versions, this selection is a submenu with three items:
DUPLICATE CHANNEL
Makes an identical copy of the currently active channel, and makes the
new copy the active channel (this only works if the number of channels is
less than 16).
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