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  • AfterMath: Overlaying Traces from Several Plots

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    When you need to create a plot which overlays traces from other plots, first create a new (empty) plot. Then, use either the copy-and-paste or drag-and-drop methods to copy all of the traces in question on to the new plot.

    If you want one of the traces on your overlay plot to be created directly from some experimental data (rather than copied from an existing plot), then use the “Add Trace” menu option (click here for details) to create a new trace.

    aftermath_overlay_example.jpg

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  • AfterMath: Changing the Appearance of Individual Points

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    Point Properties

    Unless otherwise specified, all of the data points in a given trace a drawn in exactly the same way. However, there are times when it is useful to highlight one or even a few particular data points on a trace. AfterMath allows individual data points on a trace to have their own specific and unique appearance.

    To change the appearance of a particular data point, use the point selection tool to select the point in question. Then double-click on the point to activate the Point Properties box (see example below).

    aftermath_point_property.jpg

    When the Point Properties box first appears, you should notice that all of the various properties are set to “none” or “unspecified”. This means that the point does not have any unique properties and that it should be drawn the same way as all the other points on the trace.

    However, if you change one of the various properties (color, marker shape, marker size, etc.), then the particular data point is drawn in a unique way which can distinguish it from the rest of the data points on the plot.

    aftermath_trace_point_unique.jpg

    Note that the choice of marker size and line width is somewhat limited when marking a particular data point with a unique marker.

    Point Labels

    Sometimes it is useful to show the actual value of a data point directly on the plot (either the “x” or “y” value). To do this, use either the point selection tool or the segment selection tool to choose the points to be labeled.

    Then, right-click on the selected point(s) and choose the “Properties” choice from the popup menu. The “Point Properties” box appears, and near the bottom of this box is a section called “Display Data Values”. In this section, you may activate the labels for the selected point(s). Either the “x” or “y” value or both may be displayed. These values may be displayed horizontally or vertically next to the data point(s).

    In the following example, two data points have been labeled with their “y” values.

    aftermath_point_labels.jpg

    Hiding Individual Data Points

    If you wish to hide one or more data points on a trace, select the points and bring up the “Point Properties” box (as described above). Then, select the “Hidden” option near the bottom of the “Point Properties” box. This will prevent the selected data points from appearing when the trace is drawn on the plot.

    Note that the data points are not deleted; they are simply hidden from view. You can show the hidden points again by right-clicking on the trace and choosing the “Show all hidden points” option from the popup menu.

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  • AfterMath: Changing the Appearance of a Trace

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    Setting the Line Segment Properties

    aftermath_trace_properties.jpgTo change the appearance of a trace on a plot, double-click on the trace to activate the “Trace Properties” box. This box gives you control over the colors, linewidths, and markers used to draw the trace on the plot.

    Traces which contain a large number of data points are usually represented by drawing lines between adjacent points. In the example to the right, the trace is represented by connecting adjacent data points with a blue line segments.

    By changing the “Width” of the line segments, it is possible to make the line segments appear much thicker, or to make the line segments disappear entirely (by setting the width equal to zero).

    You can also change the color of the line segments. If you double-click on the color box (which is a blue rectangle in the example to the right), another color selection box appears, and you can choose just about any color you wish for the line segments.

    Note that the data points themselves are not represented by markers in the example to the right. This is because the “Marker Size” has been set equal to zero. Because this trace has so many data points, it is a good idea not to use markers to represent all of the individual data points.

    In the examples shown below, there are fewer data points on the plot. With this few data points on the plot, it makes more sense to mark the individual data points with a symbol. The example shows each point marked with a filled red circle, but other markers are also available.

    The examples shown below also illustrate two different line segment styles. The example on the left shows the “straight” line style, where a single, straight line segment connects adjacent data points. The example on the right shows the “staircase” line style, where two line segments (one horizontal and one vertical) are used to create a more rectangular, stair step appearance for the trace.

    aftermath_trace_line_style_straight.jpg aftermath_trace_line_style_staircase.jpg

    Selecting a Point Marker

    aftermath_trace_point_marker.jpgThere are seven different symbols available for marking individual data points (see menu to left). The first three markers (circle, square, and diamond) have outlines which can be drawn with one color and internal areas that can be filled with the same or another color. The remaining markers do not have a fill area.

    You may select the overall size of the marker. You may also change the linewidth used to draw the outline of the marker.

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  • AfterMath: Duplicating Traces on a Plot

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    The easiest way to create an exact copy of a trace on a plot is to perform a copy-and-paste operation in the archive tree. In the archive tree, expand the plot so that you can see the traces which belong to the plot. Then, copy the trace of interest. Then, paste it right back on to the very same plot. AfterMath will automatically give a new name to the duplicate trace.

      It may be difficult to see the duplicate trace because it is sitting right on top of the previous trace.

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  • AfterMath: Deleting Data and Traces from a Plot

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    Deleting an Entire Trace

    To delete an entire trace from a plot, simply select the trace by clicking on it, and then press the Delete Key on your keyboard. You will be prompted to make sure you really want to delete the trace. If you agree, then then the trace is permanently deleted from the plot.

    Deleting Individual Data Points

    To delete one or more data points from a trace on a plot, simply select the points to be deleted using the point selection tool, and then press the Delete Key on your keyboard. You will be prompted to make sure you really want to delete the points. If you agree, then then the points are permanently deleted from the trace.

    Deleting Trace Segments

    To delete one or more trace segments from a trace on a plot, simply select the segments to be deleted using the segment selection tool, and then press the Delete Key on your keyboard. You will be prompted to make sure you really want to delete the segments. If you agree, then then the segments are permanently deleted from the trace.

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  • AfterMath: Dragging Traces

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    Placing Traces on a Plot

    There are a variety of ways to put a trace on a plot, and you should take the time to learn about all of them. Here is a list of some of the ways to do this:

    Drag a Trace from an Existing Plot

    AfterMath makes it very easy for you to move or copy traces from one plot to another plot. This portion of the User’s Guide describes how to do this using drag-and-drop mouse actions. Traces may also be moved or copied between plots using traditional copy and paste operations.

    As an example for illustrating how to drag a trace from one plot to another, consider the archive shown below. This archive contains two plots. One plot is called “Activation Barrier” and the other plot is called “Potential Well”. Note that the figure below shows two views of the same archive so that you can see how each plot appears initially.

    aftermath_blue_and_orange.jpg


    Note that by fully expanding the archive tree (on the left side of the screen) to reveal all levels of the archive hierarchy, it is possible to see the individual traces in the tree. One trace is named “blue trace” and the other trace is named “orange trace” in this example.

    Moving a Trace

    To drag and move a trace from one plot to another plot, the following three-step sequence is performed directly on the traces and plots in the archive tree.

    Step One

    Expand Tree and View the Destination Plot
    aftermath_orange_plot.jpg

    Step Two

    Left-Click on Trace and Drag to Destination Plot
    aftermath_trace_drag.jpg

    Final Step

    Trace Has Moved to Destination Plot
    aftermath_orange_moved.jpg

    Note that the source plot no longer has the “blue trace” on it. This trace was moved to the destination plot. The source plot no longer has any traces on it (it is empty).

    Copying a Trace

    If you wish to copy (rather than move) a trace from one plot to another, then perform the same sequence described above, but hold down the Control Key while dragging the trace from one plot to another. This will leave the original trace on the source plot and put a copy of the trace on the destination plot.

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  • AfterMath: System Requirements

    AfterMath_NEW
        These requirements were last updated on 03-FEB-2014

    Minimum System Requirements

    • Processor Class: Intel Pentium IV or equivalent/compatible
    • Processor Speed: 1 GHz minimum
    • Physical Memory: 1 GB minimum for 32-bit operating systems; 2 GB minimum for 64-bit operating systems
    • Screen Resolution: 1024 x 768 pixels or greater required
    • Operating System: see instrument specific notes below
    • Prerequisite Software: Microsoft .NET 2.0 (what’s this?) and Microsoft Visual C++ 8.0 runtime library (free downloads from Microsoft)

    Suggested System Requirements

    • Processor Class: Intel multi-core (dual or quad) or equivalent/compatible
    • Processor Speed: 2.4+ GHz
    • Physical Memory: 4 GB for 32-bit operating systems, 6+ GB for 64-bit operating systems
    • Screen Resolution: see “Minimum System Requirements” above
    • Operating System: Windows 8 or Windows 7 or Windows XP (see instrument specific notes below)
    • Prerequisite Software: see “Minimum System Requirements” above

    Instrument-Specific Requirements

    The following specifications are the minimum requirements needed if AfterMath is being used in conjunction with scientific instrumentation offered by Pine.

    Pine WaveNow and WaveDriver USB Potentiostats

    • Operating System: Windows 8 (32 or 64 bit), Windows 7 (32 or 64 bit), Windows Vista (32 or 64 bit), Windows XP (32-bit only)
    • USB Port: one USB 2.0 compatible port must be available

    Pine AFCBP1 Bipotentiostat

    • PCI Port: one PCI slot must be available for the interface board
    • Interface Board: A variety of interface boards are available (click here for details)
    • Operating System: Windows 8 (32 or 64 bit), Windows 7 (32 or 64 bit), Windows Vista (32 or 64 bit), Windows XP (32-bit only)
    • Device Driver: Device driver version must match the interface board and operating system (click here for details)
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  • AfterMath: Adding Traces to a Plot

    AfterMath_NEW
          This article is part of the AfterMath Data Organizer User’s Guide

    Trace Plotting Methods

    There are a variety of ways to put a trace on a plot, and you should take the time to learn about all of them. Here is a list of some of the ways to do this:

    "Add Trace" Menu Option

    One way to add a new trace to an existing plot is to right-click on the plot area an choose “Add Trace” from the popup menu. This causes the AfterMath “Quick Browser” to appear. The Quick Browser lists all possible data sources for the new trace from all presently open archives. Choose the data source of interest and click on the “OK” button. This process is illustrated in the example below.

    Step 1

    Right-Click on Plot and Choose “Add Trace” Option
    aftermath_add_trace_action_1.jpg

    Step 2

    Choose a Data Source for the New Trace
    aftermath_data_quick_browser.jpg

    Final Result

    An Overlay Plot
    aftermath_dual_axis_overlay.jpg

      The axis coloring (red and blue) was added subsequently for clarity.

    Automatic Axis Creation

    In the example provided, the original plot had one trace showing a distance versus time relationship. But, the trace added to the plot was a voltage versus time relationship. AfterMath recognized that a second vertical axis was needed, and automatically added the voltage axis on the right side of the plot. In the resulting overlay plot, the original trace is plotted against the left axis (distance), and the added trace is plotted against the right axis (voltage). Both traces were able to share the same horizontal axis because both traces are plotted against time, so there was no need to create a second horizontal axis.

    Sometimes when you try to add a trace to a plot, there is no room to add an new axis against which to plot the trace. In this case, AfterMath will add the trace to the plot, and you will be able to see it in the archive tree. However, the trace will not actually be drawn on the plot because an appropriate axis is not available. If you delete one of the other conflicting traces from the plot, then the added trace may be drawn.

    Using the Quick Browser

    In the example above, the Quick Browser shows all possible data sources from all open archives. There are three open archives containing a variety of plots and data tables. The Quick Browser allows you to select any of the available signals from a data table or any of the traces from an existing plot.

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  • AfterMath: Copying Traces

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    Multiple Methods to Put a Trace on a Plot

    There are a variety of ways to put a trace on a plot, and you should take the time to learn about all of them. Here is a list of some of the ways to do this:

    Copy a Trace from an Existing Plot

    AfterMath makes it very easy for you to copy traces from one plot to another plot. This portion of the User's Guide describes how to do this using traditional copy and paste operations. Traces may also be moved or copied between plots using drag-and-drop mouse actions.

    As an example for illustrating how to copy a trace from one plot to another, consider the archive shown below. This archive contains two plots. One plot is called “Activation Barrier” and the other plot is called “Potential Well”. Note that the figure below shows two views of the same archive so that you can see how each plot appears initially.

    aftermath_well_and_barrier.jpg


    Note that by fully expanding the archive tree (on the left side of the screen) to reveal all levels of the archive hierarchy, it is possible to see the individual traces in the tree. The traces on both plots are named “trace” in this example.

    To copy the trace from one plot to another plot, the following three-step, copy-and-paste sequence is performed directly on the traces and plots in the archive tree.

    Step One

    Right-Click on Trace and Choose Copy
    aftermath_copy_trace.jpg

    Step Two

    Right-Click on Destination Plot and Choose Paste
    aftermath_plot_trace_paste.jpg

    Final Result

    Trace Now Appears on Destination Plot
    aftermath_plot_traces_overlaid.jpg

      Note that the trace was automatically renamed “Copy of trace” to prevent both traces on the second plot from having the same name.

    Using Cut and Paste with Plot Traces

    If you wish to move (rather than copy) traces from one plot to another, then use the “Cut” option rather than the “Copy” option when performing the sequence of operations described above. If you use “Cut”, then the trace is removed from the original plot when you “Paste” it on to the destination plot.

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  • AfterMath: Plot Terminology

    AfterMath_NEW
        This article is part of the AfterMath Data Organizer User’s Guide

    AfterMath has the capability to plot data as an experiment is progressing and to view data in plots thereafter. The article herein serves to explain important plot features by defining the following terms:

    • sheet
    • plot area
    • axis area
    • data point
    • trace
    • point marker
    • point connector
    • plot axis
    • major tick mark
    • minor tick mark
    • axis title
    • axis unit
    • trace segment

    Sheet, Plot Area, Axis Area

    aftermath_plot_page_area.jpgPlots are viewed on computer display screens as well as printed as hard copy records of experimental data. Because plots are frequently printed, it is useful to think of some aspects of plotting in terms of where the plot is located on a printed page.

    The entire page on which the plot appears is called the sheet (yellow shading in the plot). The sheet often has the same aspect ratio as a standard paper size, but for purposes of viewing on a computer display, the aspect ratio may sometimes be stretched to make better use of the available area on the display.

    The region on the plot where data points are actually drawn (shaded green in the example to the right) is called the plot area. The plot area may be resized and moved to any location on the sheet that you wish. In general, it is a good idea to make the plot area as large as possible so that the data points are easy to see.

    Any region just outside of the plot area where axis labels and an axis title are displayed is called the axis area (shaded pink in the example to the right). Most plots have two axis areas (left and bottom), but some plots may have an additional vertical axis (right) or horizontal axis (top), and in these cases there may be three or four axis areas.

    Data Points, Traces, and Point Markers

    aftermath_plot_marker_example.jpgThe smallest entity found on a plot is a single data point, representing the location of an ordered pair within the plot area. When a series of related data points are drawn on the plot in a manner intended to show that they are related, this series of points is collectively referred to as a trace.

    The example plot herein shows a portion of a larger trace. The four visible points on this trace are represented using a point marker. AfterMath allows you to choose the point marker for each trace (circle, square, diamond, etc.), and you may choose the fill color and border color for most markers. You may choose to mark each individual point on a trace with a different point marker, or you may choose not to mark any of the points at all.

    The four points are connected together using short blue line segments called point connectors. AfterMath allows you to choose the color and line width for point connectors, or you may choose not to use point connectors. In general, if a trace contains a large number of data points, it is better not to use point markers, but rather to draw only the point connectors.

    Plot Axes, Axis Title, and Tick Marks

    aftermath_axis_example.jpgMost plots have at least one visible plot axis. A plot axis is typically divided into regular intervals using tick marks. The tick marks which have a numeric tick mark label next to them are called major tick marks, and the those which fall between the labels are called minor tick marks.

    It is good practice for a plot axis to have an axis title to indicate what quantity is being measured along the axis, and this title should also include the scientific unit associated with the measurement, such as “Current (mA)” or “Pressure (kPa)”. The scientific unit used to scale the axis is called the axis unit. The axis unit should be chosen so that the numeric tick mark labels have a reasonable magnitude (i.e., avoid units which cause excessing leading or trailing zeros).

    Trace Segments

    The AfterMath software supports the idea that a single trace may be logically broken up into smaller pieces called trace segments. This concept is best illustrated using an example. The trace shown in the plot below represents several successive scans acquired during an electrochemical experiment. One of these scans has been colored red to distinguish it from the rest of the trace. This red portion of the trace represents one of several trace segments which, taken together, comprise the entire trace.

    As a result of the voltage being scanned back and forth during the experiment, the trace consists of several overlapping scans. Because of the way the data from this experiment was recorded, AfterMath can distinguish between one scan and the next scan, treating each scan as a separate trace segment. AfterMath provides a special “Segment Selector” tool which permits you to select data points from a single trace segment or from several specific trace segments.

    aftermath_trace_segment_example.jpg
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