Graphing Annual Tidal Cycles

I made a graph many years ago of one year of tide predictions for Saipan, plotted with height as a function of time of day, month by month.  Each month is represented in a distinct color.  This exercise was inspired by Roy Tsuda, my Marine Botany professor at U of Guam.  Roy made a big deal of the times of the spring low tides, in for example the life cycle of a shallow water benthic alga on coral reefs, Hydroclathrus clathratus.   .  Roy was a student of annual cycles.   I was inspired, and observed Hydroclathrus sp.  in Chuuk, and sure enough, when the tides started to expose the algae in the “spring” (there is, technically, no spring in Micronesia), this species floated away to deeper water.

I made a new graph today, which I will post.  However, WordPress doesn’t seem to allow me to upload it as a photo.  It is an svg file.  Too bad.  Back to blogger?

The point being: this graph, visualiziing the distinct tidal differences, month to month.  Particularly the spring lows.

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My aperiodic report about usage of GNU/Linux

Well, here’s my aperiodic update on GNU/Linux distros.  (I haven’t installed BSD, maybe someday.)

I am now cleaning up an install of FUNTOO.  It’s a bit unnerving.  Works ok so far.  I have stumbled across a few Gordian knots of entangling dependencies and version incompatibility, enough to remind me why I bailed on Gentoo, not enough to stop.  Good way to install Gentoo, easy install, but there is damned little instruction on the finer points, and the slight incompatibilities with Gentoo.  Daniel Robbins was the originator of Gentoo, and Funtoo also uses Gentoo’s repos, and Gentoo bugzilla is good, and helps with most of this too.   Feels ok.    I installed Funtoo from a running Arch.  The instructions were good, except there are two sets that are not fully compatible.

I am starting to like KDE more, but there are some issues that are show stoppers, that will scare me away eventually.  For now, it’s not the clunking hulk of a molasses pit that it was in the past, and things just work, and are nice to work with (pretty).  STOPPERS: why does KDE have to reinvent every application with one of their own?  The UNIX philosophy was supposed to be everything works together, you bring in pieces from there and here.  KDE seems like WINDOZE, or APP-L, anything that’s nice is good enough to emulate in some sloppy way.  Also, KDE uses a different set of libraries that probably affects the compatibility of some programs (see emacs, below).

I have been using Ubuntu for a long while, as it just works, and everything fits together.  The new install failed on my two HP laptops, with zero KB or Mouse.  Will try again later.

Mint is not right in some way that I cannot quite get at.   Doesn’t feel right.

I futz around with desktops: I am using KDE, but started out with XFCE4 on Funtoo, and have tried installing the various flavors of Ubuntu, including Xbuntu.  Not nice, not as facile as the full on Unity Ubuntu, even as much as I DESPISE unity.  A pal says he is using Ubuntu/Unity, even though it is difficult for him, because he wants to learn it; he wants to get a Ubuntu phone eventually, or tablet.  List of desktops I’ve monkeyed around with, in no particular orderd:

  1. Gnome3
  2. Cinnamon
  3. Unity (stock Ubuntu)
  4. KDE4
  5. enlightenment 17 (recently better, always some incompatibility.  Love it though.)
  6. enlightenment 16 (derrier garde)
  7. lxde
  8. xfce4
  9. fluxbox

One important point has been that KDE4 and some other desktops on Ubuntu 13.04 beta didn’t play nicely with emacs.  I didn’t figure that one out.  Maybe a library issue?  XFCE4 seems pretty standardly vanilla in this way, and just works.   It ran fine on Unity.   If I thought about it, I could track down some particulars.   Seems ok today on Funtoo KDE4.  That’s nice.  Important to me.

I am stuck in the tarpit of Sansung Galaxy S, on T-Mobile.  The costs are killers.  T-Mobile finally replaced my handset, with four months left on contract.  I need a keyboard.   I want a better camera.  The phone is  impossible to hold without touching some button, randomly.  SLOW.  But the replacement is faster.  Small footprint.  Need an Sansung Galaxy S4, I fear, with a bluetooth keyboard.  Or, NOT.  Probably a flip phone, or just get used to this one.  Does T-Mobile charge extra to use this oldphone when it’s paid for, if I sign up for a new no-contract account?  (I will eventually move to Ting, requiring to purchase a phone at full price that is Sprint compatible.)

I have been using Arch off and on for the couple of months just prior to installing Funtoo.  Pretty cool, up to date catch-ups, and has alot of software.  I don’t quite get how it relates to Gentoo, it’s ancestor, so to speak.   There are some issues I had not gotten around; I don’t keep track: when I hit the wall of frustration, I just install some other OS.  Arch is good, it’s likeable, but not quite what I want.   Hard to install up until the most recent install disk, due to WIFI issues.

All these distros do something different with connecting to networks, esp. wifi.  Have been bogged down in this all for a while.

Probably leaving out something or another.

One thing: I have found it more than useful to have a /home partition, separate from the root (/) partition.  Thus, with these updates, I don’t fear trampling on my work.  Sometimes I keep a separate /usr/local partition for stuff I’ve compiled myself, like up to date gimp, or emacs, or a bunch of stuff for tide calendars, etc.   Then when I update, I have the source available on the new setup.  The probably with using the same /home partition, is that if I use the same username, the new install will try to use that directory again, so if my name is “user”, the home partition will be /home/user, in both linux setups.  For Ubuntu, in the dim past, that didn’t work, and Ubuntu even deleted the  old /home/user.  I don’t think it does any more, but I haven’t checked.

To counteract this, and have a handle on all my important data, I started keeping a back up of a subdir on /home/user, /home/user/Workbench.  So when I start a new distro, I just restore the Workbench partition to the new user directory.   I have gotten into the habit of using new usernames with each linux distro I install.

I have used git to keep the ~/Workbench partition up to date.  Well, anymore, I am less careful.  I just back it up.   I’ll get back to the git work flow.  I use the same User ID Number and Group ID Number (uid and gid) for my personal work-related user account in each distro, by assigning them manually.  Thus, the files are readable and writable by me in any configuration.   And git requires this.

For completeness, I’ve also installed Manjaro somewhat recently, and Bodhi.  And others.  And SystemRescueCD was useful at some point.

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FSF Certifies USB Wifi Device—little people change the world.

From Slashdot:

the FSF announced certification of the ThinkPenguin TPE-N150USB, Wireless N USB Adapter, which uses the Atheros ARAR9271 chip.

This little note makes all the difference:

There’s also a cool story that is within this story… which is that the firmware for the Atheros AR9271 chipset was released as a result of a small device seller (ThinkPenguin) striking a deal with a large electronic device manufacturer (Qualcomm Atheros) to build a WLAN USB adapter that shipped with 100% free software firmware. This deal was possible largely because two motivated Qualcomm Atheros employees, Adrian Chadd and Luis Rodriguez, made the internal-push to get the firmware released as free software.”

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Lilacs are blooming

Blooming_Lilacs---02_April_2013---IMG_5280Lilacs are a phenologically interesting species.  My plant in Oakland is flush with flowers today, 2 April 2013.

Lilac--beginning_burst----10Mar2013---IMG_5058This photo was taken March 10th in Oakland, California. Leaves had just started to break out from buds of this plant outside our door.

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San Francisco has the oldest working tide gauge in North America

From the following link:

San Francisco has the oldest continually operating tidal gauge in the Americas, which has recorded the varying sea levels since 1854. Over the past 100 years, it has tracked an 8-inch rise in water level. It will continue rising, scientists say, and could rise by 1.5 feet by 2050.

Hmmm…  A new magical mystery bucketlist item!

Google is my friend:  From this page

The nation’s oldest tide gauge, housed in a wooden shack on a pier at Fort Point in San Francisco, recorded something unusual over the past 30 years.

And here at SF Gate, is found a photo.  As well as a clarification:

A tiny, wooden white building with a red roof at the end of a pier near Crissy Field in the Presidio of San Francisco is … the oldest continually operating tidal gauge in the Western Hemisphere. (emphasis my own.)



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GNU/Linux Distro Roulette: back to Ubuntu (Sort of)

For some months, now, I’ve had my fun with Arch Linux, and I’ve been happy with it.   It’s solid; the updates are uncannily smooth and go without error, all the time; software is up to date; emacs is handled sanely (one of my highest priorities).   What’s not to like?

Well, one thing I haven’t mastered has been networking: I have followed instructions to set up a wifi connection at home, using my wireless router, and it’s never failed.   However, when I carry my laptop elsewhere, I cannot seem to be able to log into even an open wifi network.   Finally, at a Berkeley Linux Users’ Group meeting, this became a sufficient impediment to say, “Enough with Arch Linux, for now.”  But I have had other issues.

One glaring problem is the handling (or, more precisely, lack of handling) of documentation.  For example, TeXlive was installable without a problem, and it was up to date.  It didn’t take long, as often is the case, to discover that documentation had not been  installed by default, so I sought a means to do so.  Gentoo, which (IIUC) is claimed as an inspiration or a progenitor of Arch Linux, allows one to raise a documentation flag in order to control the inclusion, or NOT, of documentation either by default, or for a particular “package” (a word which is more reasonable in my humble opinion than APP, and which does not leave one grovelling to go to a “STORE” to “purchase” it).   It took some of my precious time to discover that no means is available whatsover to optionally install documentaiton with the Arch TeXlive package.

Another reason to just move on.

The system documentation is lousy.

I’m thinking Gentoo, but I don’t have time this month for that installation.  My Arch installation was not particularly careful.  I did install unofficial packages via the Packer and Yaourt utilities.  I don’t recall ever being painted into a corner by an update, as has happened to me with Gentoo.  This may have been my fault.   I must note that the most recent Gentoo installation survived a pretty long time before presenting me with an un-capsizable Gordian knot.  That aspect of Gentoo had improved alot.  The system documentation—once the very best of all the documentation I had ever seen—has fallen along the wayside; but the documentation is installed with packages when it is wanted.

Linux Mint 14:

I decided to try Mint, so I downloaded a DVD image, burned a disk, and installed.  Within two days (less) I had dumped it.  Mint is, for me, off the wall.  I’m not even going to get into it.   The last straw was the unease, the difficulty of using google as my default search engine in Firefox.   That hasn’t improved from early days.   That and various other aspects of Mint 14 led me to install Ubuntu.   But I wanted a lightweight desktop.

I maintain a separate /home partition, and have recommended that to others.  My /home partition has been “shrinking” so I’d made a larger partition available and copied all my files over.  That new partition was used in the Mint setup, but the Mint installer has inherited one of Ubuntu’s most horrible bad habits: it doesn’t respect the /home partition.   Ubuntu had wiped /home partitions of mine several times, in the deep past; I think it’s solved that issue, as it hasn’t happened in years.  I lost 90GB of personal, irretrievable data once.   I somehow managed to encourage Mint to erase the data on and I suppose reformat the new copy of my /home files.  THought I ought to mention it, as it harkens of certain shortcomings in the process for installing Mint, that echo those of Ubuntu’s distant past.


I have installed Xubuntu from a CD.  As a long time Debian and Ubuntu user, it’s somewhat second nature.  (I haven’t been able to get my head around Fedora or YUM, even though I liked the live cd experience a few releases ago.  It never made sense.  I guess you are either a dpkg/apt person or a <whatever redhat is using> person.  Neither is perfect, but I learned to use dpkg, apt-get, and synaptic at some point, and they seem to work pretty solidly.   [Gentoo’s system is still the best, IMHO—a “ports-based” system, that grabs the upstream source for installation on the current system.]

Xubuntu is not as nice as having a full Ubuntu install, then installing xfce4 from the repos.   I had more than 1/2 dozen of desktops installed on Arch.  I liked KDE4, because it’s now more lean than in the recent past; on my machine it lagged very little, while GNOME desktops all lagged a good bit, including Cinnamon.   I used XFCE4, as it is fast and has most of the bells and whistles of Gnome or KDE.   Enlightenment 17 is nice: beautiful and very fast; it does tend, however, to tie itself into a knot, especially with my help.   I may install Ubuntu or Kubuntu soon, in another partition.

One final note: it’s probably going to be Gentoo, but not this month, or next.   Then if I get knotted up, what then?

I started installing LFS (Linux From Scratch).  After a couple of days, I realized I’d just started, and I saw how gargantuan an undertaking would be the full install.





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Mini Macro Setup: Canon PowerShot SD1100 IS

Using an eyepiece from a broken microscope as a macro attachment for a point and shoot digital camera.

Canon Macro Setup

A microscope eyepiece is reversed, fitted onto the open lens of the camera, using carboard from a starbucks coffee insulator to form a collar.

By coincidence, the diameter of the extended part of the lens of this camera is almost identical to that of a microscope eyepiece. I made a collar from thin corrugated cardboard, wrapped tightly around the eyepiece extension that normally fits into the eyetube of the microscope, leaving about a quarter of an inch or less of overhang. (Make sure the collar is tighly wrapped; use transparent tape efifcaciously, to wrap the collar *tightly*.

If you are lucky, a takeout coffee insulator jacket will be corrugated. If not, keep looking (in my opinion): the corrugated nature of this card stock helps to hold the “macro adaptor” tightly onto the lens extension.

The next photo shows the system ready to be assembled.

Prior to fitting the “adaptor” to the lens.

Be sure the eyepiece is square to the lens, and that all lens surfaces are clean.

Using the Canon Hacker’s Development Kit (CHDK), one can do some additional gymnastics with this system: digital macro, with the stock firmware, does not permit the use of a flash; however, with CHDK, this is possible, and one of three flash intensities may be selected.

The flash is not properly aligned with the lens axis; however, if the flash is intense enough, illumination can be sufficient even for objects very close to the lens.

CHDK permits setting several parameters separately:

  1. override the subject distance
  2. flash on or off, or flash intensity (#2 is brighter than the normal intensity as canon has set it)
  3. set a “neutral density filter”.   This camera does not have an iris.
  4. set a custom ISO, such as 12 or 16, if the light is too intense.
  5. Zoom in, to minimize vignetting.
  6. I have had good results using macro mode, or even digital macro mode.

I find it useful to set the camera on continuous shooting mode.  When using this unit for handheld macro, the flash can freeze action, and the recovery time is fast enough to make multiple shots a useful feature.  Even without a flash, continuous shooting often helps: after pushing the button down, hold the camera as steady as possible, and one of the shots might be less affected by camera shake.

One may even make videos through this setup.

Here are a couple of photos taken with this unit:

Head end of an inchworm.

The next shot is a spittlebug on a redwood tip.

An unknown, small flower.

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