Various small tricks I’ve found helpful. Most of these only work on OSX or Linux.

Speed up a time machine backup

This removes the CPU use throttling, so only use it when you aren’t actively using the computer

sudo sysctl debug.lowpri_throttle_enabled=0

Once the backup is complete

sudo sysctl debug.lowpri_throttle_enabled=1

Remove columns from a space delimited txt file

Keep only the first four columns from the file lol.txt

> awk '{print $1" "$2" "$3" "$4}' lol.txt > lol2.txt

Run this as a script for all of the files in a directory

for file in *.txt
    awk '{print $1" "$2" "$3" "$4}' $file > $file\_edited.txt
    echo $file

Note that we had to use the system-specific escape character “_” in order to clear the underscore, this could be different on different platforms

To rename files with sequential numbers, run a similar script:

for file in *.txt
    awk '{print $1" "$2" "$3" "$4}' $file > $velocity$a.txt
    let a=a+1
    echo $file


Sublime Text customization of settings

Open preferences from the menus and put your preferences in a single pair of curly braces (XML formatting)

	"color_scheme": "Packages/User/Tomorrow-Night.tmTheme",
	"font_size": 11,
	"open_files_in_new_window": false,

Weird LaTeX error with natbib

When compiling a document, I kept running into an error ending in the following string


Trashing aux files did not fix the issue. The problem ended up being a citation missing a reference / year. However, in order to fix the bibliography, I needed to manually delete the .log and .bbl files and re-compile with BibTeX. See additional info here

Put parentheses around all citations in LaTeX

This is useful for switching a document over to NatBib

\renewcommand{\cite}[1]{(\citenum{#1})} % parentheses around citations

This can go anywhere in the preamble

Run multiple Mathematica notebooks at once

The goal here is to have two notebooks open that don’t interact with eachother—separate kernels and namespaces

Evaluation > Kernel Configuration

Add a new kernel with a cool name, set “Launch on” to “Local Machine”

Open new notebook, go to Evaluation > Notebook's Kernel > Select the cool kernel name you just made

See this article

Shrink PDF files with minimal loss of quality

Install ghostscript if you don’t have it

brew install ghostscript

Compress the PDF file using the command

gs -sDEVICE=pdfwrite -dNOPAUSE -dQUIET -dBATCH -dPDFSETTINGS=/default -dCompatibilityLevel=1.4 -sOutputFile=output.pdf input.pdf

For different quality, try these flags:

Use the following ghostscript command:

-dPDFSETTINGS=/screen lower quality, smaller size.
-dPDFSETTINGS=/ebook for better quality, but slightly larger pdfs.
-dPDFSETTINGS=/prepress output similar to Acrobat Distiller "Prepress Optimized" setting
-dPDFSETTINGS=/printer selects output similar to the Acrobat Distiller "Print Optimized" setting
-dPDFSETTINGS=/default selects output intended to be useful across a wide variety of uses, possibly at the expense of a larger output file

More information on StackExchange

Finer grain control of the embedding image resolution:

gs -sDEVICE=pdfwrite -dNOPAUSE -dQUIET -dBATCH -dPDFSETTINGS=/default -dCompatibilityLevel=1.4 -sOutputFile=output.pdf -dDownsampleColorImages=true -dColorImageResolution=600 input.pdf

Open tar gz file

Convert a directory of FLAC to ALAC for iTunes

Using ffmpeg

for i in *.flac ; do
    ffmpeg -i "$i" -acodec alac "$(basename "${i/.flac}").m4a"
    sleep 2
    # may need to adjust sleep time for processor speed                               

I saved this as a bash script, so just cd into the directory containing the FLAC files and then run

bash ~/codebits/utility_scripts/

Make spectrograms to check quality of audio files

Using sox

sox audiofile.flac -n spectrogram

A good FLAC file should have features at 22 kHz. A transcode low quality will have a plateau around 19 kHz (with some spikes). Great info here

Update packages in MacTeX

There is an actual package manager called tlmgr installed by default on TeX Live and MacTeX

First, update it

tlmgr update --self

Can install a package like this

tlmgr install revtex

Can view all installed packages like this

tlmgr update --list

Can update everything with this

tlmgr update --all

Note: I had to sudo all of these, since I installed MacTeX like a standard application on macOS

Fix focusing issue on Sublime text OSX

Add the following plugin “Tools > Developer > New Plugin” and save with a descriptive name. Copied from this GitHub thread

import sublime
import sublime_plugin
import os

cmd = '''
tell application \\"System Events\\"
    tell application process \\"Sublime Text\\"
        set frontmost to true
    end tell
end tell

class FocusOnLoad (sublime_plugin.EventListener):
    def on_load(self, view):
        os.system('osascript -e "{0}"'.format(cmd))

Extract data from tables in a PDF file

Use this software here

  • Install the software and run it in order to start the server
  • Then, navigate to the server in your browser in order to use the software (instructions are in the README)

Fix bad Dropbox (Enterprise) folder names

When using both Dropbox business and personal accounts, your Dropbox folde will be renamed to “Dropbox (Personal)” and your business folder will become “Dropbox (Business Name)”. This scheme is not Unix-friendly, and it cannot currently be resolved by renaming the folder.

To resolve this, navigate to the home directory, and then create an alias and symlink through the terminal

ln -s ~/"Dropbox (Harvard University)"/ "./dbx_harvard"
ln -s ~/"Dropbox (Personal)"/ "./dbx_personal"

Synchronize two backup drives

To copy and update all files from destination to source:

rsync -avPi --dry-run /Volumes/source/allfiles/ /Volumes/destination/

Note the unintuitive syntax. If destination already contains an earlier version of allfiles, the path to that folder should not be included in the path to destination—otherwise this command will create a new folder /Volumes/destination/destination/

The flag --dry-run shows a preview of what files will be changed, and how. The other flags facilitate visualization. By default, this command appends and updates. To delete files from the destination, use the flag --delete

See info here and here

Vector Trace in Adobe Illustrator

In Adobe Illustrator, perform vector tracing using the included macro

File > Scripts > ImageTracing

This does all of the line tracing and canvas cropping for a collection of photos

I also wrote an Illustrator action that saves as multiple file types and changes the ARtboards to the size of the iamge, which can be found in the Actions > User Actions menu

Restart our lab’s remote servers

Our servers are PCs running Windows 8 Server Edition. They are located in the smaller room adjacent to the main SOE server room, in the rack closest to the far wall. Boa and Mamba are on the bottom rack, and boa is the computer closer to the wall.

After a power outage: restart the PC, connect a monitor and keyboard and enter the password

Putting ticks on a log log plot in Mathematical

See answer here

Basically any valid function for Ticks will also work with FrameTicks