Q: What is BatScope and what can I do with it?
A: BatScope is free software built upon FileMaker Pro 11 Advanced for Mac OS X that accompanies the BATLOGGER device for recording bat calls. It offers its users a way of transferring the BATLOGGER sound recordings from their SD cards into a well-structured database on a computer, and managing it with a comfortable graphical user interface. BatScope 2 also offers automated species recognition. Imported BATLOGGER recordings can be automatically cut into single bat calls and classified using well-established automated classification algorithms that have been trained with a large database containing calls from 27 Swiss bat species. BatScope is also suited for exchanging recorded data with other BatScope users, who can integrate it into their own databases.
Q: Do I need BatScope in order for my BATLOGGER device to unfold its full functionality?
A: No, but we nevertheless recommend it for organizing the large amounts of data BATLOGGER will write to your SD cards. Eventually, you will need a convenient way of handling that data, which is what BatScope offers you. But you may also use other tools instead to extract the information you wish to obtain from the recordings, such as the BatExplorer software offered by ELEKON AG. However, you wouldn't want to miss the powerful automated species recognition feature of BatScope, which will significantly enhance the usefulness of your BATLOGGER device.
Q: Why should I register BatScope? Do any limitations apply to unregistered versions?
A: Registrations help us getting an idea of who is using BatScope. They allow us to inform you about essential progress in new versions. You can use BatScope without registering if you wish. The only limitation in unregistered versions is the splash screen at startup.
Q: Where is my data stored?
A: On one hand, all your audio files, spectrogram images etc. are stored within the project folders on disk. As of version 3 of BatScope, these folder structures also contain SQLite databases. You can find out where your project folders are located in the project panels in the overview layout in BatScope. The BatScope FileMaker database file BatScope.dbd, on the other hand, is stored within BatScope itself. The database file holds the logic structure of your data and contains the classification statistics. As it is contained within the BatScope application, all necessary files are kept consistent if you copy or move BatScope. The project folders therefore are separated, and you can reimport ("integrate") them directly into new BatScope databases.
Q: I'm confused by the way BatScope is structured. Why can't I just have a folder with subfolders of my BATLOGGER recordings?
A: BatScope is a FileMaker database which we chose to divide in four hierarchy levels: Projects, SD cards, sequences, and calls. The top level consists of projects. Each project can hold an unlimited number of SD cards, each of which may contain up to 10’000 audio sequences (BATLOGGER recordings). Each sequence may again contain a theoretically unlimited number of bat calls. The structure you're asking for is exactly what BatScope offers you. You can create as many projects in BatScope as you like. Each of them is assigned to a project folder on disk, which may be anywhere in your file system. These project folders are then populated by folders belonging to SD cards you import into BatScope. Within these, BatScope creates another level of subfolders during import: the *.batseq bundles, one for each audio sequence. Once these sequences are cut into calls from within BatScope, each *.batseq bundle is be accompanied by a folder containing its calls, which are again stored in bundle folders (*.batcall).
You may further organize your data in different copies of BatScope, which you may rename freely, e.g. BatScope_MyData etc.
Q: I need to import and analyze many large SD cards, which takes a long time. Is there a way to speed things up?
A: We hope we have cured this problem with version 3 of BatScope. During import, a lot of work needs to be done aside from copying the raw data, like generating a spectrogram image, recognizing bat calls and feeding the databases. Cutting many sequences into even more bat calls can be quite time-consuming as well. As of version 3, BatScope can handle these processes in parallel on as many processing units (CPU's) as your computer offers. Typically in BatScope 3 these processes thus take only a fraction of the time it took in earlier versions.
One of BatScope's strength is that all data is always consistently written to disk, allowing you to access it with your own tools at any time. Unfortunately, this also means that many tasks require substantial disk I/O when it comes to processing recordings weighing gigabytes in total. If your computer is equipped with a solid-state disk (SSD), reading and writing data will speed up substantially.
Q: Can I import multiple SD cards at once?
A: Yes, this is possible in BatScope. Just select multiple folders containing SD card data at once when specifying the location of the SD card. To this end, it may become useful to copy the contents of your SD cards to a folder on your disk beforehand. Do this with multiple SD cards and you will be able to select them all at once at import, even if you have only one SD card slot. Also, reimporting ("integrating") multiple SD card folders or projects folders is possible in the same way. Just select multiple source folders when prompted to. BatScope will then process them sequentially, but multi-threaded on all CPUs your computer contains.
Q: I would like to update to a newer version of BatScope. Can I just continue using my old database with the newer version? How do I go about transferring my data?
A: Due to technical limitations in FileMaker, you cannot simply continue using your database file with a newer version of BatScope. Instead, a new empty database is contained with each release of BatScope. But don't worry, your data collection is not lost. Follow one of the two procedures described in the manual to transfer your data between old and new BatScope databases (Chapter: Updating to a Newer Version of BatScope). When migrating from BatScope 2 to version 3, reintegrating of your projects is necessary, but future versions of BatScope 3 do allow direct transfer of the database content between versions.
ATTENTION: As of BatScope 3, new SQLite database files are generated in the data folders. Therefore, you can not use the data with BatScope 2 anymore! If you still do want to use these with an old version, make a copy of your project data to be integrated into BatScope 3.!
Q: How can I share parts of my database with other BatScope users?
A: BatScope offers a convenient way of sharing imported data with others. Simply pass them a copy of a whole project folder or SD card subfolder you wish to share. They will be able to integrate them into their databases by clicking the corresponding buttons on the Overview layout, provided the file's owner attributes are set correctly. This can even be done with multiple project folders or SD card folders at once!
Furthermore, BatScope 3 also allows to export selected sequences and calls to a destination of your choice. For convenience and to avoid overwriting duplicate filenames, this will rebuild the folder structure that your original project had at the chosen destination.
Q: I have classified a sequence with BatScope, but the result is wrong. Why doesn't BatScope always recognize bat calls correctly?
A: Just like in any machine learning situation, automated bat classification is a statistical prediction that is subject to inevitable errors. BatScope uses state-of-the-art classification algorithms that have been trained with a large database of bat calls. As with any such training sets, it is finite and cannot capture the full range of reality. The implemented classifiers are optimized for correctness, but misclassifications, particularly within very similar species, are unavoidable.
Q: How can I exclude a selection of calls from the classification statistics of a whole audio sequence?
In BatScope, all calls that are found in a sequence automatically enter the sequence statistics. To exclude some, instead of deleting them, just 'deactivate' them in BatScope 3, and recalculate the statistics.
Q: How can I move an audio sequence or call to a different SD card or project?
A: You can't. Only SD cards in whole can be moved to different projects, and whole projects can be moved to different places on disk. However, you can export single sequences, calls or just wav-files of the sequences. These can then be imported again. See above.
Q: How can I rename a single sequence or call?
A: You can't. Only SD cards and projects can be renamed. Don't rename on the file system level as BatScope will not recognize the path anymore!
Q: What is the "author" of a project good for?
A: Some users manage recordings from different people. It can thus be useful to have the name of a person as an additional attribute of a project. You may then, for instance, sort your projects according to the people they belong to.
Q: How can I change the color/size/style of fonts?
A: The visual elements of BatScope are not modifiable.
Q: I'm getting an error message saying that data is being accessed by another user, script or transaction. How do I get rid of it?
A: This can happen occasionally and is nothing to be seriously worried about. It simply means that some communication between single program components of BatScope was blocked due to unexpected user interaction during the execution of a script or similar. Normally you should be able to restart the process that brought the error message up and it should work that time. Be advised to suspend further interaction with BatScope while a certain action is running (import/export, classification, deletion etc.) unless prompted. This should help preventing the problem.
Q: Can I run multiple tasks, such as classification and importing, simultaneously in BatScope?
A: Even though it might be theoretically possible to do so in some cases, it is strongly discouraged, as it may produce script errors. Always wait until a running process has finished before interacting with BatScope again. However, in BatScope 3 many processes run in parallel on as many CPUs as are available, thus speeding up processing considerably. You can work with other programs normally, while BatScope is processing data in the background.
Q: After killing BatScope while it was processing data, I can't open my database anymore. How can I recover my data?
A: Never ever kill BatScope while the database is being modified! It many cases, this will corrupt the database file. Unless the automated database recovery reports full success, your database file is lost and you will have to reintegrate your project folders into a new empty database. See the next question for how to create a new database. To generally minimize the harm done in case of a data loss, we recommend to profit from Apple's excellent backup solution Time Machine!
Q: I how can I create a new, empty database?
A: Reinstall BatScope. You don't need to uninstall it first, the previous installation will be renamed -.old. A new BatScope with an empty database file will be created. If you expect to need more databases in future, create a backup copy of BatScope, so it can just be restored whenever needed, without having to reinstall BatScope every time.
Q: Will there be a version of BatScope for Microsoft Windows or Linux?
A: No, BatScope is limited to Mac OS X. A port to other platforms is not planned. If you're bound to Windows, use the BatExplorer software from ELEKON AG to manage and view your data.
Q: When will new versions be released? When will feature X be implemented?
A: BatScope is used and developed in a research environment and comes as is, without warranty of fitness for any particular purpose. Improved or enhanced versions are being released whenever we can provide them, which is usually unknown in advance.
Q: Can I share a copy of BatScope with my family/colleagues/friends?
A: Yes, we encourage you to pass BatScope along.
Q: What do I need Batit for? Can't I just install BatScope without it?
A: No, Batit is absolutely required for BatScope. It provides essential functionality like cutting/filtering/measuring bat calls, generating spectrogram images and much more.
Q: How do I uninstall BatScope?
A: BatScope does not need any uninstalling. Because the BatScope application file contains all program and database data you can just remove this BatScope application file.
The BatScope installer also installs Batit into the applications folder and an accompagnying framework /Library/Frameworks/BatitSnd.framework that you may want to remove if completely uninstalling. Python 2.7, and wxPython for Cocoa are additionally installed. Due to varying dependencies please refer to the documentation of these packages for instruction on how to uninstall them.
Q: Whom should I contact if I have other questions or suggestions? Where can I hand in problem reports?
A: Our contact address can be found on www.batscope.ch. You will also find updates and an online help there. Feedback to batscope@wsl.ch is welcome.
