This article is part of the AfterMath Data Organizer User’s Guide
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AfterMath: Page Template
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AfterMath: Permissions Files
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This article is part of the AfterMath Data Organizer User’s GuideThe AfterMath software is typically used in conjunction with one or more instruments manufactured by Pine. Your license to use AfterMath with these designated instruments is activated by placing one or more permissions files in the AfterMath folder on your hard drive.
Permissions files have the filename extension ”.papx” at the end of the filename.
In most cases, the permission file(s) are automatically placed in the AfterMath folder during the installation procedure.
In some cases, the permissions file(s) may be sent to you by Pine in a different way (perhaps as an attachment to an e-mail message). In these cases, you must manually copy the files to the AfterMath folder.
AfterMath User’s Guide: Introduction
This article is part of the AfterMath Data Organizer User’s Guide
Scope of this Guide
This User's Guide describes the basic functions of the AfterMath software package, including basic data archiving, plotting scientific data, and instrument control using AfterMath.
This guide is written for the professional scientist or engineer (or student of science and engineering) and assumes a basic knowledge of scientific measurement and data presentation.
AfterMath: Archive Data Types
This article is part of the AfterMath Data Organizer User's Guide
Each archive that you have opened appears on the left side of the screen as a separate “root” in the “tree control”. The symbol shown to the left represents an open archive. The name of an archive is always the same as the filename used to save the archive on your hard drive. Aftermath archives are stored on your hard drive as individual files with the filename extension “paax” (which indicates that the file is a Pine AfterMath Archive XML file).
Within the tree-like structure of an archive, you are free to create folders in which to organize your data. You may also create folders within folders so that your archive has a multi-level internal structure. You can move or copy items from one folder to another using standard Cut, Copy, and Paste commands or by using simple Drag-n-Drop mouse actions.
Items Found in an Archive
Plot. A plot is a two-dimensional graph of the results of an experiment. A plot may have one or many different traces on it. It is very easy to create and edit plots using AfterMath. A plot may show the results from one particular experiment, or it may overlay the results from many different experiments.
Experiment. An experiment is a very special, read-only container that holds the uneditable record of the outcome of a particular experiment. AfterMath does not permit you to edit the original copy of the raw data from an experiment. You are permitted to make a copy of the original raw data which you can alter or edit, but the original copy remains unchanged.
Study. A study is a special type of folder that is automatically created when an instrument completes an experiment. Depending upon the type of experiment, the study will contain the original (uneditable) raw data from the experiment plus a few “default” plots of this data to help you visualize the results of the experiment. The plots can be edited, but the original raw data cannot be edited.
Specification. The set of parameters which instruct an instrument exactly how to perform an experiment is called an ”experiment specification”. You can use specifications to hold your “favorite” set of parameters for doing a particular kind of experiment. Just like any other item in an archive, specifications are easily edited, copied, duplicated, and modified. The only time you cannot edit or alter a specification is when it is part of the permanent, read-only record of a previously completed experiment. But, even in this case, you can make a duplicate copy of the specification which can be modified.
Tabular Data. Any scientist who has ever worked with a spreadsheet application has experience working with rows and columns of numeric data. Most instrumentation records how a response signal changes with respect to some applied stimulus signal. In general, this measurement consists of at least two columns of numbers (such as voltage versus time, current versus voltage, temperature vs time, etc.). AfterMath stores this type of data as a data table in an archive.
Note. A note is simply a scratch-pad on which you can write down just about anything you wish regarding an experiment or anything else. One or more notes can be attached to any item in the archive (including the folders themselves) so that you can document any special information associated with that item. The contents of notes are stored in Rich Text Format, meaning that your notes can contain all sorts of text formatting, including superscripts, subscripts, symbols, colors, and various fonts and font sizes.
Layout. A layout defines a particular arrangement that you would like various plots, notes, and other information to be arranged on a sheet of paper. Most common international paper sizes are supported, and you can put one, two, four, or nine different items on the same sheet of paper using a layout.
AfterMath: Software License
This article is part of the AfterMath Data Organizer User’s Guide
The AfterMath software package is usually sold to Pine's customers along with one or more instruments (such as an electrochemical potentiostat) manufactured by Pine. We understand that our instruments are used in laboratory environments where multiple computers are present and where data acquired using one computer might be analyzed using a different computer. So, we have done our best to craft a license agreement that meets your needs as a user of Pine's products. Without further ado, here is the legalese…
PINE RESEARCH INSTRUMENTATION
AFTERMATH DATA ORGANIZER SOFTWARE LICENSE
Pine Research Instrumentation, Inc. (hereafter “PINE”) licenses purchasers (hereafter “LICENSEES”) of Pine electrochemical potentiostats (hereafter “INSTRUMENTS”) to use the AfterMath Data Organizer software (hereafter “SOFTWARE”) in conjunction with these INSTRUMENTS. This License contains the terms and conditions of use of the SOFTWARE.
- Scope of License: This License covers the software, user documentation and any related computer programs provided by PINE for use with one or more specific INSTRUMENTS. This License does not grant any proprietary or ownership rights in the SOFTWARE or related technology. The scope of this License is limited to an exclusive group of one or more specific INSTRUMENTS, where the members of this exclusive group are specifically enumerated and identified by make, model, and serial number at the time this License is purchased. The one or more specific INSTRUMENTS belonging to this exclusive group are hereafter referred to as the “DESIGNATED INSTRUMENTS”.
- License: PINE grants to LICENSEE a nonexclusive, nontransferable license to use the SOFTWARE in object code form on any computer which is connected to the DESIGNATED INSTRUMENTS for purposes of controlling the operation of the DESIGNATED INSTRUMENTS. The LICENSEE is not authorized to use the SOFTWARE to control the operation of any instruments other than the DESIGNATED INSTRUMENTS. PINE further grants to LICENSEE a nonexclusive, nontransferable license to use the SOFTWARE in object code form on up to five (5) other computers which are not connected to the DESIGNATED INSTRUMENTS for the sole purpose of analyzing data previously generated by the DESIGNATED INSTRUMENTS. PINE further grants permission to LICENSEE to make one (1) archival copy of the SOFTWARE for back-up purposes if required. Except as expressly authorized above, LICENSEE shall not: copy, in whole or in part, any of the SOFTWARE or documentation, modify the SOFTWARE, reverse engineer, reverse compile (de-compile), or reverse assemble all or any portion of the SOFTWARE, or rent, lease, distribute, sell or create derivative works of the SOFTWARE.
- Term and Termination: The License hereby granted will continue in force until terminated, as set forth herein. If LICENSEE fails to pay any monies owed to PINE or its agents in connection with LICENSEE’s purchase of the DESIGNATED INSTRUMENTS or this SOFTWARE, or violates any term of condition of this License, PINE or its agents may terminate this License immediately by giving notice of termination to LICENSEE.
- Limited Warranty: PINE warrants the SOFTWARE to conform to the description of its function and performance. In the event that the SOFTWARE does not perform in accordance with this warranty, PINE agrees to repair or fix any non-conformity free of charge, or to refund any amount paid by LICENSEE for the SOFTWARE. Any modifications made to the SOFTWARE by LICENSEE shall void this warranty entirely.
- Ownership of SOFTWARE: PINE has and will retain all ownership rights in the SOFTWARE, including all patent rights, copyrights, trade secrets, trademarks, service marks, related goodwill and confidential and proprietary information. LICENSEE will have no rights in the SOFTWARE except as explicitly stated in this Agreement. Title to the SOFTWARE and documentation remains solely with PINE. LICENSEE may not assign this Agreement or any rights under it and may not delegate any duties under this Agreement without PINE’s prior written consent. Any attempt to assign or delegate without such consent will be void.
- Confidential Information: LICENSEE agrees that aspects of the SOFTWARE embody or constitute trade secrets and/or copyrighted material of Pine. LICENSEE agrees not to disclose, provide, or otherwise make available such trade secrets or copyrighted material in any form to any third party without the prior written consent of PINE. LICENSEE agrees to implement reasonable security measures to protect such trade secrets and copyrighted material.
- Applicable Law: This License shall be governed by and construed in accordance with the laws of the State of Pennsylvania, United States of America, as if performed wholly within the State and without giving effect to the principles of conflict of law. If any portion hereof is found to be void or unenforceable, the remaining provisions of this License shall remain in full force and effect. This License constitutes the entire understanding and agreement between the parties with respect to the licensed use of the SOFTWARE.
- Modifications, Taxes: Any modification of this Agreement must be in writing and signed by PINE and LICENSEE. Terms and conditions set forth in any purchase order which differ from, conflict with, or are not included in this Agreement, shall not become part of this License unless specifically accepted by PINE in writing. LICENSEE shall be responsible for and shall pay, and shall reimburse PINE on request if PINE is required to pay, any sales, use, value added (VAT), consumption or other tax (excluding any tax that is based on PINE’s net income), assessment, duty, tariff, or other fee or charge of any kind or nature that is levied or imposed by any governmental authority on the SOFTWARE.
DISCLAIMER OF WARRANTY FOR SOFTWARE. EXCEPT FOR THE EXPRESS WARRANTIES SET FORTH IN THIS AGREEMENT, PINE DISCLAIMS ALL IMPLIED WARRANTIES FOR THE SOFTWARE, INCLUDING WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. PINE MAKES NO REPRESENTATIONS CONCERNING THE QUALITY OF THE SOFTWARE AND DOES NOT PROMISE THAT THE SOFTWARE WILL BE ERROR FREE OR WILL OPERATE WITHOUT INTERRUPTION.
LIMITATION OF LIABILITY. IN NO EVENT WILL PINE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, CONSEQUENTIAL OR OTHER DAMAGES ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE BY ANY PERSON, REGARDLESS OF WHETHER PINE IS INFORMED OF THE POSSIBILITY OF DAMAGES IN ADVANCE. THESE LIMITATIONS APPLY TO ALL CAUSES OF ACTION, INCLUDING BREACH OF CONTRACT, BREACH OF WARRANTY, PINE’S NEGLIGENCE, STRICT LIABILITY, MISREPRESENTATION AND OTHER TORTS. In no event shall PINE’s liability or liability of PINE’s suppliers exceed the price paid by the LICENSEE for the SOFTWARE. The foregoing limitations shall apply even if the above-stated warranty fails of its essential purpose.
LICENSEE HAS READ THIS AGREEMENT AND UNDERSTANDS AND AGREES TO ALL OF ITS TERMS AND CONDITIONS.
AfterMath: Viewing Instrument Properties
This article is part of the AfterMath Data Organizer User’s Guide
Device Properties
When you want to view the detailed device properties of a given instrument, click on the particular instrument in question in the instrument list found in the lower-left corner of the window (see example below). After you click on the instrument, click on the “Device” tab (on the right side of the window).
Connection Properties
If you want to view the detailed connection properties of a given instrument, click on the particular instrument in question in the instrument list found in the lower-left corner of the window (see example below). After you click on the instrument, click on the “Connection” tab (on the right side of the window).
AfterMath: Viewing the Experiment Queue
This article is part of the AfterMath Data Organizer User’s Guide
The Experiment Queue
AfterMath permits you to submit multiple experiments to an instrument at the same time. The experiments are performed by the instrument in the order in which you submit them. To view the experiments that are in the queue waiting to be performed, go to the instrument status window and click on the “Queue” tab (see figure below).
The queue lists several of the most recently performed experiments, it indicates the experiment presently in progress, and it shows those experiments that are queued up for subsequent execution.
Locating Experiment Results
In some cases, it is possible to use the queue to find the results from an experiment that has already been completed. If you double-click on one of the completed experiments and if the archive in which the results are stored is still open, then the results from that experiment will be displayed.
Cancelling an Experiment
If you wish to cancel one or more experiments which are pending in the queue, then right-click on the experiment(s) and choose “Delete” from the popup menu.
Purging the Queue
If the queue has filled with information from a large number of previous experiments, you may wish to clear out the queue. You may click the “Purge History” button at the bottom of the screen. This will clear out all of the previously completed experiments. It will not clear out any experiment in progress or any experiments that are pending in the queue.
Note that the queue is always purged whenever you exit the AfterMath application.
AfterMath: Instrument Serial Numbers
In the event that you need to determine the serial number and/or hardware ID number for an instrument, this information can be found on the Device tab as shown below.
AfterMath: Detailed Instrument Status
This article is part of the AfterMath Data Organizer User’s Guide
When you want to view the detailed status of a given instrument, click on the particular instrument in question in the instrument list found in the lower-left corner of the window (see example below). After you click on the instrument, the display (on the right side of the window) shows you the status of the instrument.
The example (above) shows the status controls and indicators for an electrochemical potentiostat. These controls are quite specific to potentiostat instruments. The display would appear differently for other catagories of scientific instrumentation.
AfterMath: Installation Folder
This article is part of the AfterMath Data Organizer User’s Guide
Location of AfterMath Application
The AfterMath software application is normally installed in the “Program Files” folder on your hard drive (see below). The “aftermath.exe” file located in this folder is the main AfterMath application.
Other Files
The ”.papx” files appearing in this folder are the permissions files corresponding to your license to use AfterMath with designated instruments.