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Removing security features from a pdf

Whoops, I totally made my own pdf and accidentally included a bunch of security features, so now I can’t use my highlighter or type notes on the document. It sure would be handy to take off those security features that I put there myself when I made the pdf, myself.

With a full copy of Adobe Acrobat and the associated Acrobat Distiller software, the process is as follows:

1. Open the secured pdf in Acrobat.

2. Go to File>Export>Postscript>Postscript and save a .ps version of the pdf file.

3. Open the .ps postscript file in a text editor (WordPad on Windows works fine).

4. Use … Continue Reading

ImageJ StartupMacros

Before I lose this file again: StartupMacros.txt This is a text file, based on the original StartupMacros.txt file that came with ImageJ, that can be dropped in the ImageJ/macros folder that is created when you install ImageJ. Start up ImageJ, and if this macro doesn’t automatically run, go to Plugins>Macros>Startup Macros to load it. It installs a few more drawing tools on the ImageJ toolbar and creates some keyboard shortcuts for the following tools:

  • Line tool – press ‘l’
  • Brush tool – press ‘b’
  • Eraser tool – press ‘e’
  • Wand tool – press ‘w’

I either found or created some code … Continue Reading

Adventures in kludgy software – Diving PAM edition

As a general rule, expensive pieces of lab equipment must come with software of questionable quality. In this case, I just want the raw data off a $20,000 submersible DIVING-PAM fluorometer, which can be used for measuring the photosynthetic yield of algae and plants out in the field, away from a computer. But downloading the data requires a mini-odyssey through some needlessly confusing software that comes with the unit.

To start with, the packaged instruction manual for our DIVING-PAM still references a DOS-era utility for downloading the data, because the (brand new, delivered in 2012) instruction manual was printed in 1998. … Continue Reading

Waterproofing iButtons, and reading waterproofed iButtons

iButton temperature dataloggers are tiny, long-lived temperature sensors that are great for all kinds of environmental and biological monitoring, but they’re a long ways from waterproof. Old farts will regale you with tales of a bygone era when you could leave a bare iButton submerged in seawater for months at a time without problems, but those days are long gone, due to a re-design in the early 2000’s. Nowadays you can’t even get away with leaving them in moist soil without eventual water intrusion, component failure, and data loss. But given their tiny size and relatively low price … Continue Reading

Have some squid

You might be forgiven for thinking that the ocean is an endless bounty of edible goodies when you walk outside and find squid just strewn everywhere on the beach, waiting for you to pick them up and eat them. This happened the other day at work, when a group of juvenile Humboldt squid (Dosidicus gigas) decided to sun themselves on the beach. And then they died. And some seabirds got a good meal out of it. Enjoy some pictures and video.

Squid galore.

Continue Reading

ATtiny84 LED display and heater project

Here’s a little project that uses an ATtiny84 microcontroller, programmed with the Arduino software, to build a thermostatically-controlled heater. It allows the user to choose a temperature setpoint, and then displays the current temperature using an Adafruit 4-digit 7-segment LED display over I2C. The youtube video below demonstrates part of the project, where an ATtiny84 processor is used to drive the Adafruit display.

To get the project rolling, I installed the ATtiny core files available from High-Low Tech. The instructions there helped get the ATtiny84 running on a breadboard. I use … Continue Reading

USB extension cables

Here’s a standard USB webcam sitting on top of 30 meters of USB extension cables (three 10 meter cables). Three cables daisy chained together with the webcam attached to the end seems to be the functional limit. Adding a 4th 10-meter cable results in the camera not being recognized.

30 meters of cable powering a USB webcam, which is taking its self-portrait in the mirror.

These 10 meter extension cables, also called “repeater” cables, are available for around $10 apiece. We’ve been using them to run a … Continue Reading

ncdf4 R package binaries for Windows

David Pierce has made available a pre-packaged Windows binary version of his ncdf4 package for R. Go to his ncdf page to download the zip file you need. The current file at the time of this writing is ncdf_1.8.1.zip.

http://cirrus.ucsd.edu/~pierce/ncdf/

After downloading the zip file to your Windows computer, you can install this R package most quickly by opening a Rgui.exe window, then going to the menus and choosing Packages>Install package(s) from local zip files…, select the zip file you downloaded, and hit Open to have R install the package.

To use the package in R, you must run a 32-bit … Continue Reading

Digitizing data from old figures with ImageJ

Following on this earlier post concerning the retrieval of data from figures in published papers with R, here is a method for doing the same with ImageJ. This is a freely available program that should run on Windows/Mac/Linux, just like R. To extract data points from a figure, you’ll need the Figure_Calibration plugin developed by Frederic V. Hessman, available here. Download the Figure_Calibration.class file from that page and save it to your ImageJ/plugins/ directory. Then load up ImageJ.

[caption id=”attachment_1051″ align=”aligncenter” width=”400″ caption=”The example figure that we wish to retrieve data from. We can use … Continue Reading

ImageJ paint brush tool keyboard shortcut

ImageJ is easy to modify if you know a bit of Java. I don’t know any Java. But here’s what I did to add keyboard shortcuts for the paint brush tool and the line selection tool. The code is based off this help file from the ImageJ website: http://rsbweb.nih.gov/ij/docs/guide/userguide-32.html

The first step was to figure out to refer to the line tool and paint brush tools. I did this by going to Plugins>Macros>Record and clicking on the line tool and the paint brush tool in succession. The numeric codes for those tools were revealed in the macro recording window … Continue Reading

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