Note on using webdav idisk for experiment data

One of the problems I had before with setting up a script to manage the experimental scenario and data on a webdav idisk was that I hadn't stumbled across how to automatically mount & unmount the filesystem. It turns out that this is very easy.

First, create a directory to use as the mountpoint. For example, assuming you are in a writable directory, use something like this:

mkdir mnt

Next, use a command of this form:

/sbin/mount_webdav -s http://idisk.mac.com/groups.labname mnt

("groups.labname" should be replaced with the actual name of your idisk)

If the login info us not in your keychain, it will ask you for it. You might consider putting in the keychain for convenience. Note that any user (i.e., any RA who will access the database) must have access to the idisk.

Note that it is possible for a subdirectory to mounted directly with a command like this:

/sbin/mount_webdav -s http://idisk.mac.com/groups.labname/Databases/Thisdatabase mnt

However, in this case, a separate keychain entry will be needed to log in. It would normally be simpler to mount the root of the idisk and navigate its hierarchy programatically.

When complete, a simple "umount mnt" will be required.

Note that this method will work even if the idisk had already been mounted in the standard location or somewhere else.

Combining image and rsync backups

This is from a note on the Apple server list.

The procedure is to start out with an asr image of the root volume using the -erase flag. This is now a bootable volume.

Then, each night, perform an rsync on this volume, using -delete and other flags so that all changes are written to the volume. This is now an updated, but still fully bootable volume.

This is almost equivalent to doing a nightly clone. It is food for thought. Here are some related issues:

• Unless you want to bring the system down to single user mode every night, you are still going to have to deal with open database files during the rsync.
  
• Assuming that those files have been dealth with, would it be faster just to do the image dump every night?
• Is the target system more likely to be bootable in the even of a catastrophe mid-copy if rsync is used?
• One of the biggest advantages of using rsync is the ability to do snapshots. Clearly, the original image could be used as the starting point for nightly snapshots, but then the image itself would never be updated. Is there some way for the root hierarchy to be the most recent snapshot, with previous versions stored elsewhere? (See below)

It seems to me that what might be needed here is for there to be two rsyncs each night. The first one is to update the bootable image from the working image, as in the original hint. The second one, to be done when the first one is finished, is to make a snapshot of the bootable image.

In other words, the backup would go like this:

1. Before any backup, go through the process of dumping all system databases.
   
2. For the first (labor intensive) backup, use asr to make a complete copy of the base system. The system should be as quiesent as possible for this, and the system database dumps should contain the current database contents. The backup volume should be considerably larger than the working volume.
3. Dump the databases and use rsync to update the smaller backup volume. Be careful to exclude the /snapshots directory on the backup volume; this should be untouched by this run of rsync.
4. Then use rsync again to create a new snapshot of the non-snapshot regions of the backup volume (there is no need for an additional database dump). This will be stored in /snapshots on that volume (and so /snapshots will again be excluded).

Both runs of rsync could be run at fairly low priorities.

Note that if this were to be done over the network via an rsync server, the second (snapshot) rsync run could be done locally on the server. Not sure if that would be worth it, though. For now, I'm assuming an attached drive.

Also, it would be possible for /snapshots to be a different drive. For example, with two internal drives, the second drive could be the mirror of the first, with a larger external firewire drive for the snapshots. In a fairly non-intensive application like in our lab, this use of the second internal drive would probably be better than mirroring RAID, which is how it is being used now.

In any case, we would want to avoid spotlight on the backup drives, and also we would want them to be mounted read-only except when actually being written during backups.

A variation of the above would be to split drive 1 between the backup-able part and a large non-backupable part, so that less space would be needed on drive 2.

OS/X single-user-mode backups

I've been trying to take advantage of the script /etc/rc.server to do full backups of the boot drive. This file is present in OS/X server, and it can be added to non-server systems. Basically, the script is run via /bin/sh early in the boot process, at a time similar to single-user mode. Only kernel drivers are present, which means that the internal harddrive and firewire drives are available, but not (at least not yet) USB drives. The boot drive is semi-mounted, in read-only mode. Semi-mounted means that its device is listed as "root_device", not as an actual drive.

The advantage of bringing a server down on a regular schedule for backups is that there are no open files, and the entire system drive is unwritable. This maximized the thoroughness of the backup. Furthermore, there are some cases where backup programs such as asr(1) can use more efficient techniques for read-only drives than for read-write drives.

The are huge disadvantages, though. First and foremost is that while the server is down for backups, it can't provide whatever services it is responsible for. In the case of our servers, that's at least DHCP, DNS, OD, and file and web services. However, in a situation such as in our lab, where the amount of data is relatively small (probably less than 20-25 GB), the down-time will not be excessive, probably an hour or less.

The second class of disadvantages is almost a deal-breaker. OS/X has chosen to implement so much of its device and file-system interface code in terms of user-mode "frameworks" rather than kernel-mode drivers, hardly any even of the command-line utilities are available for use in single-user mode! For example, diskutil, the main filesystem tool, is unavailable. Disktool doesn't work any better. Hdiutil will do some things, but cannot attach images or use the -srcfolder mode. It turns out that the best tool of the ones that will actually work in single-user mode is asr.

Asr works far faster when it is in "device" mode. In order to enter device mode, the target drive must be greater than or equal to the size of the source drive, the "-erase" flag must be used, the source drive must be mounted in read-only mode. Asr is only for hfs-format drives. There is also "copy" mode, which is also fairly fast; it is used when device mode's criteria are not met.

The biggest problem with asr is that it copies everything, including the volume label, and there is no way to avoid this. Therefore, the copy ends up as a filesystem named the same as the boot drive. This can cause confusion. One would think that the solution would be to simply change the volume name after the clone operation. However, due to the impoverished runtime environment of single-user mode, there is no tool available to do it. The pdisk(1) program has a partition-labeling option that does work in single-user mode, but it turns out that this is not the same thing as the hfs volume label. When the system comes up, the clone will be mounted under the same name as the main drive with a " 1" suffix, like "Macintosh HD 1". If there are several backup partitions and nothing is done, they will all end up with the same name, like "... 1", "... 2", etc. (See update below.)

This can cause considerable confusion. The only "solution" I've been able to come up with is to write some information into the /tmp directory regarding the backup itself, and then once the system comes back up, use diskutil to rename the volume accordingly. A good way to do this is in crontab, with the "@reboot" time indicator.

As for a general strategy, it is important to have at least 2 backup partitions (2 drives would be better), so in case something bad happens, the previous backup would be available. Also, the backup partitions should be larger than the system disk.

At present, my servers both have 250GB Raid mirrors, and I have a 300GB firewire drive for each of them. As an initial test, I will simply do a single asr backup of the main drive onto the firewire drive--this is nearly as safe as having two partition on the firewire drive. Later, I'll get another firewire drive for each one, and swap the drives.

UPDATE

Here's a kind of strange way to get around the problem of the volume name. Instead of trying to change, ex post facto, the name of the clone, why not change the volume name of the system disk? This can be run very early in the launchd process, and all it takes is "[sudo] diskutil rename / newname". Obviously, the name will have the boot time in it, or, more difficult, a sequence number related to the backup system. I think a timestamp of the form: 200901171402 would be good. As for the rest of the string, why not simply look for the current name (you can get this from the "list -plist" diskutil command). If the last 12 digits of the current name (which will be identical to that of the most recent backup) are digits, then they will be replaced, otherwise nothing will happen. If there is a reasonably short system name, like "Lab 13", then why not name the root drive something like "Lab 13 System Disk " ? Each time the system is rebooted, the timestamp will be updated. The volume names of the clones will contain the timestamp of the previous boot. Since the root volume, unlike other mounted volumes, doesn't get mounted as /Volumes/VolName, the change of name will have no effect on paths, etc.

Plan 2: A slightly more satisfactory but more risky way to do a similar thing would be to change the name of the root volume (e.g., to "Lab 13 Clone 200901171402") before restarting the system for an automated backup. The name would be changed always to a constant (e.g., "Lab 13" or to the part before " Clone...") during the early the boot process.

In either case, there would need to be three scripts:

1. The setup-and-reboot script, which would search for the target volumes, decide which one to write to next, and if there is one, to store that information in /tmp/rc.autoclone or whatever. This script will change the name of the root volume just before rebooting under plan 2.
   
2. The clone script, which would expect information in /tmp/autoclone that if it checked out will control the clone operation.
3. The cleanup script, to be run very early in the boot process, to change the name of the root volume back to its normal name. In plan 1, the name will contain a time stamp, in plan 2, it will be an ordinary name like "Lab 13".

The first script can be run either from the command line or from a launchd/crontab entry. The second script must be run at the end of/etc/rc.server, and it must contain safety checks to prevent writing into the wrong medium. The third script would ordinarily be run very early in the boot sequence from launchd/crontab.

As always, the most dangerous possibility is that the clone will be written into the wrong place. Since diskutil doesn't work right in single-user mode, probably the safest way to handle this is to write a check string into the destination volume, for example, a file in its root directory called rc.autoclone identical to the one in /tmp. Also, there must be a directory created in /tmp called "mnt" as a place to mount the destination volume, so that /tmp/mnt/rc.autoclone can be compared to /tmp/rc.autoclone.

So in rc.server,

1. Check for /tmp/rc.autoclone
2. Check that the timeout interval has not passed (e.g., 5 minutes)
3. Check for /tmp/mnt
4. Get info on all current drives
5. Search for the drive indicated in /tmp/rc.autoclone
6. Mount the drive on /tmp/mnt and compare its version of rc.autoclone
7. Unmount the target drive
8. Perform the clone operation
9. Done

In the after-boot crontab (plan 2),

1. Get the current / volume name
2. If it needs to be changed, change it

The setup script does:

1. Do general checking to prevent being called at the wrong time (e.g., too soon)
2. Make sure that at least one target volume is available
3. Look through all possible target volumes to find the one with the oldest timestamp.
4. Compute its ID string
5. Create an rc.autoboot containing the ID string
6. Write the rc.autoboot into the root directory of the target volume
7. Reboot

An example experimental project

This project, which we call "picolf6" consists of six experiments, four of which use Sensonics odor labels as stimuli. In addition, the counterbalancing and randomization is within each of the two sets of three experiments. Therefore, this was done by scripts rather than within Superlab.

One discovery we made about Superlab in the course of setting up picolf6 was that any time that a file system path is stored within Superlab, all symbolic links within the path are expanded and the path converted to an absolute path. This complicated several aspects of the process.

There are three types of stimuli used: pictures (stored as .jpg files), words (stored as .png files) and ticket numbers (stored as .png files). If you will refer to my recent blog entry on the sl4am hierarchy, you will see the layout we used here. Under the project directory, there is a Shared directory containing all of the .sl4 Superlab scenarios, and folders for all stimuli. The general idea is that the folder for each experiment (with subjects and groups) will have a link back to the scenario for that experiment in Shared, plus a "stim" folder containing links back to specific stimulus files within Shared.

The odor labels we used were mounted on standard 1"x2" event tickets and torn off one at a time to be "scratched and sniffed" and given to the subject. So, one of the things required is for there to be an inobtrusive ticket number displayed on the screen at the beginning of each trial. In superlab, the only way to do that is to make a graphic with the numbers in the corners and then specify that superlab scale it to fill the screen. We used the least significant digits of the tickets for this, so experiment 1 used tickets 1-30, exp 4 31-42, exp 5 43-54, and exp 6 55-66. Since this was always the same for all subjects, we set up folders in Shared named ticket[1456] and stored the .png files with the images there, named, e.g., 23.png.

One thing we learned the hard way was that it is best to set Superlab up so that the scenario is in a file hierarchy identical to where the experiment will be run. So for example, we simply specified /Users/.../Shared/ticket1 and Superlab could use the same relative path at runtime and find the stimulus folders.

The other stimuli were more complicated, because they had to be different for each subject. Superlab always accesses stimulus list folder contents in alphabetical order, so while setting up the experiment, we set up dummy folders containing files with names like w/img34.png (for word image event #34). Later, when setting up the hierarchy, we put links with those names to image files in Shared. So if for example on trial #34, a certain subject needs to see the word "alligator", stim/w/img34.png would be a link to ../../../../../Shared/words/alligator.png (for example).

Now, Superlab doesn't print the name of the file in a stimulus list folder, only its sequence number. So in order to figure out which stimuli were presented to a give subject without going back to the setup data, we inserted a dummy text event into each trial. These events were simply numbered like "@=1-34=@" for experiment 1, trial 34. As part of the setup sequence, we created a sed script that we placed into each experiment folder that translates that dummy code into a condition code for that trial, for example "alligator:old". This allows the actual stimuli that were used to be determined.

We also placed a link to a superlab scenario file in Shared into each experiment subfolder. However, we were not able to use symbolic links for this, since superlab then assumes that the scenario file is actually in the Shared folder and all of the subject-specific links fail to work. As a work-around, we just used hard links for it, since it is a file rather than a directory (file system rules disallow hard-linking to directories).

Here is a tar archive (tgz) of the Korn shell scripts I used to set this experiment up. Note that you also will need to install some packages to generate the graphics versions of the textual stimuli. I also didn't include the picture stimuli we used.

Multiple superlab stimulus folders

Apparently when you set up an experiment in Superlab that uses external stimulus files or folders, it saves two pointers to the files: the absolute path at the time the file or folder was specified, and the file or folder relative to the scenario file when it was saved. In fact, it appears that sometimeis if you use "save as" within superlab to save a scenario, it recomputes the relative address(es) using the new scenario location. Therefore, as long as the relative path points to folders and/or files that exist, and that the absolute path does NOT exist, things will work. However, this latter approach will not always work

However, if the absolute path is valid, then those files will be used instead of the local relative path, and the wrong stimuli will be presented. What is needed is some way to relocate the scenario file, relative to a certain version of the stimulus files.

Say for example you have 25 subject folders named 01-25, and they are all "sister" folders, that is, subfolders of the same superordinate folder. You might think that if you set up the scenario and stored the scenario in subject 01's folder, you could then copy the scenario into each of the others and use their stimulus set-up. But since the absolute address of subject 01's stimuli would still exist, I strongly suspect that they would be used instead of the relative address. What is needed is some way to relocate the paths in the scenario file so that they point to the new location.

If superlab can't find the stimuli, it asks the experimenter where they are. This could cause some fairly minor problems, but the larger issue is when it does find them, in the wrong place.

It turns out that it is possible simply to overlay the absolute paths (or as many of them as you want to relativize) with a sequence of X's of the same length, using some method such as a binary editor like bbe(1). Superlab is quite content to use the relative address. Note that if you should happen to save the scenario, new absolute addresses will be written in there.

It would be better if there were some way to identify the absolute addresses automatically, but since they can be located almost anywhere, that's a bit tricky. There are some other paths in there, such as the default logfile location. Maybe the best way is simply to specify them as part of the setup, since they will be known then, and do the overlay as part of building the project.

UPDATE

One very important lesson: take the time to do all development of superlab scenarios in a directory hierarchy that matches how it will eventually be installed. This is a little less convenient in the beginning, but pays off hugely later on.

Converting text to graphic files for Superlab

Since graphics files usually exist outside of the immediate Superlab scenario folder, and are not loaded until the experiment runs (and if the appropriate option is selected, not until just before a trial runs), it is possible to use an external script to re-randomize graphics files before running a particular subject.

The way it works is, you set up Superlab to use generic names for files, for example, "trial001.png", "trial002.png", and so on. You have your real stimuli in a different folder, with names like "elephant.png" and "COW.png". Then, when you are setting up for a particular experiment, you get rid of the dummy files and put in links in to the real stimuli, in the appropriate order, for example, trial001.png --> elephant.png ; trial002.png --> COW.png. Obviously, you have to keep the mapping around so that the logfile can be patched up after the run, by replacing instances of "trial001.png" with "elephant.png" and so on.

Obviously, you can't do this with text stimuli because text stimuli are internal to Superlab. I have written a utility to patch an existing scenario file to contain a different order of stimuli, but this method is very risky and isn't flexible enough. So the correct solution is to convert the text stimuli you want to use into graphics files.

There are many ways to do this, but one of the easiest to use from a scripting standpoint is called "a2png". This is a utility that can be downloaded from sourceforge. It needs either the cairo or the gdlib graphics libraries; one or the other also has to be installed for a2png to build. Once it has been installed, you can use .ttf font files to create .png files from text strings. By default, the image is cropped to the font's cell size, and has a black background. There are a number of options to change the background, foreground, size, font, spacing, and so on. The .png files can be used directly by Superlab on both Windows and Mac systems, or they can be converted to jpeg or some other supported graphics format.

By default, if you give a2png the name of a .txt file containing a stimulus, it will create a .png file in the same folder with the same basename. So for example, "a2png ... elephant.txt" should result in an output file "elephant.png". If you don't want all those *.txt files, a2png will also accept standard input if the file is "-", and will write to X in "--output=X". So, an alternative way to create elephant.png is "print elephant | a2png ... --output=elephant.png -".

How to specify the right font

Now, at least on my system, a2png doesn't want to find the ttf fonts. The built-in font folder list is a poor match for the fonts I have installed on my system. So, what I do is to give the whole path to the .ttf file I want to use. You can find all the appropriate fonts on your system with "locate .ttf | grep ttf$". Also, there are thousands of truetype fonts (ttf) out there on the internet. It's probably better to give the whole path anyway. I like a sans-serif font for displaying stimuli, such as free-sans, which can be readily downloaded.

You can also mix text and pictures, and randomly switch, for example, which kind is on the left or the right of the display, just by setting the link appropriately before running.

UPDATE

There appears to be some kind of glitch in a2png such that the cropping that it does removes the bottom of each character on the last (i.e., only) line. There is a workaround of suffixing a '\n', but this adds too much space.

There is a completely different approach available with the classic netpbm package. This command line:

print JjKg_Xq \

| pbmtext -font ~/Downloads/bdffont/100dpi/helvR24.bdf \

| pnmcrop | ppmchange white black black white \

| pnmtopng > foo.png

isn't too bad. An alternative is:

pbmtextps -font=Helvetica JJKG_XQ \

| pnmcrop | ppmchange white black black white \

| pnmtopng > foo.png

So, one way or another, there will be a way to do this. Frankly, a2png produces prettier output. The pbmtextps output is quite fuzzy, while the pbmtext output depends on having the bdf fonts available, and in turn, they have limitations on size. Since a2png uses the Cairo graphics library, it can use ttf fonts and scale them, etc., very prettily. Hopefully I will find a fix for a2png.

UPDATE2

It is true that a2png produces more attractive lettering, but as it turns out, there is a very real application for the netpbm package here: setting up the experiment template. The scheme I am trying to use involves setting up a single experiment with all of the trials indexing external event files, usually images or images of text. By changing the names of these external files, you can change the stimuli presented to subjects with none of the limitations imposed by superlab. So, what I've been doing is to generate dummy stimuli to be used while testing. These are graphics containing text strings that make it easy to identify the order and type of the stimuli for debugging purposes.

In one of the experiments I'm setting up now, there are 30 640x480 pictures. Here is the shell function I'm using to create jpeg dummy files for them:

jpg640x480(){
ppmmake lightblue 640 480 \
    | ppmlabel -x $((320-(5*${#1}))) -y 240 -size 10 -background lightblue -color black -text "$1" \
    | pnmtojpeg > $2 2>/dev/null
}

I chose black over lightblue so they would be very contrastive with the white over black text stimuli.

UPDATE3

Well, there is a fairly easy way to get images cropped correctly with a2png that will work until the program is fixed somehow: use the --no-crop option in a2png, and crop the result using netpbm. For example:

print Somejunque \

| a2png --no-crop -s --overwrite --font-size-0.1 --output=uncropped.png \

; pngtopnm < uncropped.png

| pnmcrop \

| pnmtopng > cropped.png

This yields the best of both worlds: flexible, high-quality text rendering plus correct cropping of the result.

How to set up an sl4am project

Once the basic SuperLab experiments are running, the next step is to set up the hierarchy of files and folders. This can be done with a fairly simple script, given the names of the population and condition groups and the initial number of subjects in each cell. Options include setting up an empty Shared folder and links to it in each experiment folder. Empty rc files and flag.free files are created everywhere. Another option is to clone a new population group from an existing one; another is to look for empty rc files (this would be the sign that an external setup script didn't do its job completely).

However, once the hierarchy is all set up -- and it probably is a good idea to set up only the Try population group first, and clone the other groups from it -- the next step is to populate all of the experiment folders and to put actual code into the rc files. The best way to do this is to write a custom script. This script could use find(1) and be driven by the existing factors as an organizational approach.

Update:

Just stumbled across the automator(1) command. This should be very useful for running experiments, since it is a way to invoke Automator workflows from the command line. There are options to set variables and to pass input, including standard input, to the workflow. It is less clear to to take output from the workflow, probably temporary files will be needed.