FILE menu

NOTE:   LabAnalyst will open double-clicked data files of appropriate formats, or data files ‘dragged and dropped’ onto the LabAnalyst icon..

The program can have up to 20 data files open simultaneously, each in its own window.   You can switch between files either by clicking the appropriate window, or with the WINDOW menu.  Individual files can be closed either by clicking the standard 'close' button, or if the window of the file you want to close is active (in front), with the close file option in the FILE menu.
         If you have the maximum number files open and attempt to load another, you will be asked which of the currently open files you want to close to make room for the new file.

For any file format, you can automatically scan and fix large ‘spikes’ in the data by selecting the ‘Automatically Filter Newly-loaded Files’ option in the PREFERENCES/FileHandling menu.

  •    OPEN WARTHOG...  O         Loads data files produced by LabHelper or LabAnalyst.  There are four types (note:  icons may be 'lost' if files are sent across the Internet):

         Warthog-format text files
      (chart or oscilloscope)

      raw binary chart data

      raw binary scope data

        

      binary edited data

      (saved from LabAnalyst)

    The file opening box highlights only these types.  Two are binary formats, for LabHelper and edited LabAnalyst files:  the older Binary-Coded Decimal (BCD) and Floating-Point (FP).  LabAnalyst will transparently read either, but will write only in FP format.  The main difference is speed:   BCD files load more slowly (since they are read and converted one sample at a time), while FP files load quickly (since entire channels are read directly from disk into memory).

    BCD or binary files imported from 'Classic' Macs (OS8 or OS9) may look like this:  

    If you click the toolbar 'Open' or 'Append' or 'Stack' buttons, you will get this window if you've not specified in the 'Preferences' window that only Warthog files will be shown:

    This gives you the choice of Warthog (current OS X files or 'classic' files obtained on earlier Mac OS versions [OS8, OS9, etc]), ASCII (text) or Sable SSCF or ExpeData files (see below).

    Two of the buttons ('Warthog Only') and ('Sable or Warthog Binary') will only access files with the correct extensions (.whog,   .whsc,   .WHdata,   .ext,   .sabl,   .WHsable).   The 'Any Sable or Warthog File' button allows access to all file types, but only files in Warthog or Sable format will load properly.   If you attempt to load a file that isn't Warthog or Sable format, you'll get an error message.

  •    IMPORT       This submenu has three items:

  •    WARTHOG BINARY FROM 'CLASSIC' OS9...      For old Warthog binary files from prior to OS X.  WARNING:   only files with these formats will load properly.

  •    TEXT [ .csv, ASCII ] FILE...     This routine lets you load data in text (.csv) files, as long as:
    • data are in spreadsheet format with variables (columns) delimited by commas or tabs (spaces do not work as delimiters) and cases (rows) delimited by carriage returns
    • the data are numeric only (text data are ignored)
    • the input file may contain many variables but you must select a maximum of 40.
    • NOTE:  this will NOT import complex Excel worksheets (i.e., .xls; .xlsx).   If you want to load data in Excel format into LabAnalyst, save a copy as a tab-delimited text file (.txt) or .csv file, which LabAnalyst can read.

    Go to this page for more information on importing text files.

  •    SABLE FILE...     Loads Sable Systems data files in SSCF format or the similar but newer 'ExpeData' format.  Nearly all Sable files will load; those which have more than 40 variables will load the first 40 only.  The maximum number of markers in LabAnalyst is about 20,000; Sable files can (theoretically; extremely rarely in practice) exceed that limit.  The converter will read the first 20,000 markers only.  Older SSCF files do not include channel labels, so after the completion of file loading you are prompted to provide your own labels.  Also, the values for mass, flow rate, effective volume, and so forth are arbitrary and may have to be edited, and there is no information on voltage conversions.   The newer ExpeData files contain channel labels and many conversion factors.
    If you save Sable files from LabAnalyst or LabHelper, they will appear (on a Mac) with a custom icon:        

  • Back to top

  •    APPEND OR STACK       This submenu has 3 items:

  •   WARTHOG FILE...    
  •   SABLE FILE...      Merges a Warthog-format file (either text or binary) or a Sable SSCF file with the currently loaded file.   The new file can either be appended to the 'right' (i.e., adding new cases) of the current file, or stacked to the 'bottom' (i.e., adding new channels).

    Appending is much more common than adding channels.   In either case, the following window opens (appearance will vary depending on the number of channels and samples in the two files):

    The program checks to make sure the merged file will not exceed the current maximum file size -- unlikely unless one or both of the files are very large (a warning is shown if this is the case).   However, the program does not check to make sure the channel contents match in the current and new files.  Thus it is possible to create a new file that contains two (or more) types of data in a single channel (i.e., a set of temperature data from the initial file, then gas concentration data from a second file, then wind speed data from a third file, etc.).

    Needless to say, this can cause considerable confusion unless you are careful to avoid merging files with differing channel types.  To help avoid such mistakes, the computer provides a graphical display of the old and new data.  In this example, the file to be merged has 8 channels and the current file contains 9 channels.

    LabAnalyst will allow access to the maximum number of channels in either the current or new file.  Sable SSCF files don't contain channel labels, so if you merge them you HAVE to know ahead of time what the channel structure is.

  •   TIME SCALE ADJUSTMENT...      This is a specialized operation that has to be used with care.   It is primarily intended to equalize the effective sampling rates of two files that you want to merge or append.   This is done in one of two ways, depending on the old and new sampling rates.  It is important to note that even if you add points, you do NOT add information.   And if you make the file smaller, information will be LOST.   Therefore, it is a good idea to make a copy of the file before you perform this manipulation.

    • If the new rate is “faster” than the old rate (i.e., more samples per unit time), LabAnalyst will add the extra data points by interpolation.   For a simple example, if the original sample rate was one Hz (one sample per second) and you want to change that to two Hz (two samples per second), the program will fit one additional data point between each of two successive existing points.  The new point will have a value that is the mean of the two points surrounding it.   The operation is similar, but more complex, if the new and old sample rates are not integral multiples of each other.
         As mentioned earlier, don’t make the mistake of thinking that because you have added more data points, you somehow have added information content.

    • If the new rate is “slower” than the old rate (i.e., fewer samples per unit time), LabAnalyst will simply remove data points as appropriate.   It does not do any averaging.  Consequently, this operation reduces the amount of information in the file…. so use with care (and backup copies if you are wise).

    These operations are transient unless you save the file (or use the ‘Save as’ option to make a copy with a different name).   But if you save a time-adjusted file under its original name, the file is permanently changed. You cannot ‘undo’ time adjustment.   The time scale adjustment window looks like this:

    Back to top


         Screen display basics

    After a file is loaded, the 'plot area' in the top part of the screen displays either the first channel of the file (single channel mode) or several user-selected channels (multi-channel mode); see the VIEW menu for details.  The screen in single-channel mode looks approximately as shown below -- but note that immediately after loading, no block will be selected and no data will appear in the results or block windows.  The colors of the plot area and block window are user-selectable (VIEW menu) and may differ from this example.

    The major components are the plot area (top half of the screen), yellow data bar (upper left), screen selection slider (bottom edge of plot area), 'toolbar' menu buttons (across the center, just below the screen selection slider -- optionally, the toolbar can be above or to the left of the plot area), comments window (middle right), block window (lower right), and results window (lower left; this contains controls for EDIT menu operations as well as analysis results).  A selected block appears as a color-inverted segment of the plot area.   The small 'n' buttons along the bottom of the plot area indicate notes entered while gathering data; clicking one of these buttons brings up the note text (example):

             

    Note that in current versions, a small gray band between the data bar and the plot area shows marker labels (this doesn't appear in the image above).

    The appearance of the plot area depends on the screenwidth (the width of the screen in pixels) and the number of cases.  If the file contains <= screenwidth cases, data are plotted 1 pixel per case (if the number of cases is < 50% of screenwidth, the plot is expanded, with more than 1 pixel per case).  If the total number of cases is more than screenwidth, the X-axis will be scaled to fit within the screen dimensions.  'Screens' (consisting of screenwidth cases) are indicated by vertical lines, with a crossbar at the top of the active screen.  The example shows a file containing many screenwidths of data. 

    If there are more than screenwidth cases, the bottom of the plot area will show a screen selection slider. The currently 'active' segment of the file -- the active screen - is indicated by the slider position.  Use the slider or the left and right arrow keys to change the active screen.  To view the active screen only (necessary for some manipulation and analysis operations), hit the shift or return keys.  Do this again to go back to viewing the entire file (this example shows 'entire file' mode).  Any markers are shown as vertical dashed lines (this file contains numerous markers, but they are not shown; see the VIEW menu).  While in the plot area, the cursor is a cross-hair; out of the area it is an arrow.  The data bar has a readout of case number, elapsed time, and the value of the currently active channel at the cursor position. The time of day is shown (24-hour scale) along the bottom of the plot area, with optional hour indicators (vertical dotted lines).

    To perform analyses and some transformations, you need to select a data block. This can be done by the normal 'click-hold-and-drag' method (the cursor must be within the plot area).  A second method uses individual clicks: move the cursor to the desired start point and click once; repeat for the end point (which may be on either side of the start point).  Alternately, blocks of defined width can be selected with single clicks (see the BLOCK WIDTH option in the ANALYZE menu).  If there is sufficient space, you can 'shift' blocks to the left or right with the BLOCK SHIFT commands (also in the ANALYZE menu).
          You can select blocks in 'entire file' or in 'active screen only' mode, and blocks can include multiple screens.  If a single screen is shown, mark the start with a single click, then shift screens until the end can be marked.  A selected block is indicated as a color-inverted rectangle in the plot area, and is scaled to fit within the block window (discrete data points on the block window only appear if the number of included points is small).

    Back to top

    Note for file saving options:

    When you save a file in either Sable or Warthog binary format, with either the Save... or Save As... options, LabAnalyst will add a file extension ( .WHdata for Save...; .WHSable if you select Sable-format output in the Save As... option).   The new extension will replace any existing extension, which in effect creates a new file if the source file had a different extension (e.g, .whsc, .whog, .sabl, .ext) or no extension.

  •   SAVE...    S     Stores the current file including any modifications you made.  Note that binary files saved from LabAnalyst have different icons than the 'raw' data files generated by LabHelper

  •   SAVE AS...      Stores the current file -- or optionally a marked block -- with any modifications you made.  You may save all channels or a subset.  Files are stored in Warthog binary (file type 'WHog') format, in Sable format (ExpeData), or as ASCII text files. The 'standard format' button saves the existing file (with any modifications you have made with transformations, smoothing, etc.) under a new file name of your choice.    If 'standard format' was not clicked, after selecting the channels to save, the file format selection window appears, as shown below:

    If you save in Warthog text format, you retain most all of the data that can be contained in binary files.  The major exception is in the 'comment' text.  The floating-point binary format allows very extensive comments (up to 32K of text), and the comments can include carriage returns.  When saved in Warthog text format, comments are stripped of carriage returns (these are replaced with a single space) and limited to a total of 252 characters.
    As mentioned above, Sable ExpeData files do not include values for mass, flow rate, barometric pressure, temperature, and effective volume (unless written in the comments), and comments are limited to 240 characters.
    The 'time counter' option creates a variable that indicates elapsed time in hours.   For example, this variable would have the value of '1' for all data during the first hour, '2' for all data during the second hour, and so forth.
    If you are saving in Text format, you can save any markers in the file in a separate column.

    If you select the ASCII option, you have two formatting choices:

    The 'Conditional save' option lets you filter data case by case and save only the cases that meet the selection conditions. You need to specify which channel is to be tested (it is not necessary that the tested channel will be saved), one of five Boolean criteria (<, =<, =, >=, >), and a selection criterion (a number against which the individual case values in the tested channel are compared).
         In this example, only cases where the value of channel 13 (wheel#1 speed in RPM) is greater than 0.5 will be saved.

    Data files (other than ASCII) that have been saved by LabAnalyst have these icons:


    binary files

     
    Warthog text files


    Sable formats

    LabAnalyst saves some other file types, shown here (these may look different on your system, depending on what version of OS X is running):

      Preference files

      Script files

  •    SHOW FILE DATA     Opens a window below the plot area showing the labels of all the channels, the sample interval, the time and date of storage, etc., and the conversions used by the LabHelper acquisition program to change raw voltages into appropriate units (temperature, gas concentrations, speed, etc.).  The type of conversion equation ("transform") and the number of samples averaged for each recorded point ("N") are also shown.

    Note that a file loaded in Sable or ASCII format may not show all of the variables.

    The following example shows the file data for a 13 channel file.

    Conversion equations:

    Most conversion equations used by the Warthog acquisition program LabHelper are 2-order polynomials (shown as "poly" in the transform column):

    value = A + B*volts + C*volts2

    Note that a C of zero produces a linear conversion.  Occasionally a power function is used:

    value = A + B*voltsC

    Note that in a power function a non-integer C will produce meaningless data if the voltage is negative; in this condition, LabHelper sets the results to zero.  A C value of 1 produces a linear conversion.

    LabHelper allows use of the keyboard as an event recorder, and a single channel can use a 3-degree polynomial conversion.  If data have been transformed or copied into a new channel, no coefficients are shown.

    Back to top

  •    PRINT FILE IMAGE...     Sends an image of the file to the printer port (or a pdf file).   You can usually do this by hitting the 's' key.  If you have selected a block, you have the option of printing an image of the block or of the entire file.

    Before printing, you are presented with 'Page Setup' boxes for whatever printer driver is in use.  Note that for 'US LETTER' (or similar) sized paper, you should use landscape mode (maximum image sizes are about 70% for portrait mode and 80% for landscape mode).  If you use other paper sizes, the recommended image sizes may be too large to fit on the page or smaller than the available space.

    The printed output will match whatever is shown in the on-screen viewing mode (Entire File or Active Screen).  A file displayed in the "Compacted and Averaged" format will be printed in that format.  If a block has been selected, you have the option of printing only the block.

    You can select which features will appear in the printout, such as labeling, file information, comments, and markers.  If the file has more than one channel, you can print any subset of the channels.

    If you click the 'non-standard plot heights' button, a window will open to allow customization of the height of each printed channel:

    The window contains a diagram of the printed page.  You select the relative height of each channel in sequence by moving the cursor on the diagram to the desired height, and then clicking the mouse ONCE.  The channels will be redrawn one by one as their heights are selected.  Note that there is a fixed amount of room on the page, so that enlarging one channel requires shrinking one or more of the others.  Consequently, the computer reserves an amount of space necessary for plotting the remaining channels at the minimum possible height (and will not let you exceed that limit).  You must select plot heights for all the channels.  When done, you can accept the results, redo the plot height selection, or revert to the normal setting (all channels plotted with equal heights).

  •    FILE IMAGE PREVIEW... like the above routine, but it sends the image to the screen instead of directly to the printer (you can re-route the previewed image to the printer).

  • Back to top


  •    SEND RESULTS TO    This submenu has three items.

  •    PRINTER     This tells LabAnalyst to route the data in the Results Window to the temporary printer file 'printfile' whenever the 'P' or 'p' key is struck.  Printing occurs when you close this file with PRINT \ CLOSE FILE.  After printing the 'printfile' remains available (but it is overwritten if any additional printing is performed).

  •    SPREADSHEET...      Opens a spreadsheet-format text file for storing results generated by analysis menu operations.  Data are saved in a tab-delineated format readable by many spreadsheet programs or statistical packages.  Optionally, you can save results to an Excel-format file (double-clickable directly into Excel).  Besides the results data, the spreadsheet file also contains column labels.  Mean, SD, N, and variable name are always saved; other parameters (start of block, end of block, start and end time, elapsed time, analysis type, mass, and channel number and file name) are user-selectable.  You can also enter one or two user-typed 'notes' with each case (edit fields appear in a window over the COMMENTS window when the 'p' key is struck; hit 'return' or click the window close button when the values are correct).  Certain analyses, such as regressions, do not fit this format and cannot be put into spreadsheets.

    The default is one set of analysis results per line in the spreadsheet, but if you've selected Excel format you can use the 'Multiple results per line' option to save the results from two to 15 different analyses per line.  You need to specify how many results you want to save initially (you can't change this when the file is in use).  Therefore, you need to keep track of the order of analyses so as to avoid confusion later on.   If you use notes or store animal mass, these items are saved only once per spreadsheet line (not every time you save an analysis result).

    Here is a general format for one line from a file with 2 results per line, with both user notes selected and mass saved:

    Note1 · Note2 · M1 · SD1 · N1 · var1 · anal1 · mass · M2 · SD2 · N2 · var2 · anal2 <CR>

    where · is a tab character, <CR> is a carriage return character, M1 = mean of the first result, SD1 = SD of first result, N1 = sample size of first result, var1 = variable for first result, anal1 = analysis for first result, mass = body mass, M2 = mean of the second result, etc.

    Storage of results (in memory) occurs when you press the 'p' key (with the Results window open), or select OUTPUT RESULTS.  The spreadsheet file is not saved to disk until you exit from LabAnalyst or use the PRINT | CLOSE FILE option.

    Some additional considerations:

  •   TEXT FILE...     Opens a text file for storing the contents of the Results Window.  The format of the disk file is similar to that shown in the Results Window and is identical to the format of data sent to the printer.   These files are not formatted for use in spreadsheet-based applications, such as Excel.

  • Analysis results are transferred to temporary storage in a memory table when you press the 'P' or 'p' key, or select OUTPUT RESULTS.

    Real storage (writing data to disk) occurs when you select the PRINT | CLOSE FILE   ( J ) option. However, any temporary memory tables are automatically saved to disk if you quit the program.

    Back to top


    Other links: