Trans Scend Survival

Trans: Latin prefix implying "across" or "Beyond", often used in gender nonconforming situations – Scend: Archaic word describing a strong "surge" or "wave", originating with 15th century english sailors – Survival: 15th century english compound word describing an existence only worth transcending.

Category: Uncategorized (page 1 of 3)

ppe & whatnot

Yep, we too are busy cooking up protective medical devices.......

¯_(ツ)_/¯


& whatnot:

Prototyping bits, bobs for an ada motorsports startup-

ADA auto prototyping


Quick pass at a low friction filament spool holder for some very fragile materials:

Some GDAL shell macros from R instead of rgdal

also here on github

it's not R sacrilege if nobody knows

Even the little stuff benefits from some organizational scripting, even if it’s just to catalog one’s actions. Here are some examples for common tasks.

Get all the source data into a R-friendly format like csv. ogr2ogr has a nifty option -lco GEOMETRY=AS_WKT (Well-Known-Text) to keep track of spatial data throughout abstractions- we can add the WKT as a cell until it is time to write the data out again.

# define a shapefile conversion to csv from system's shell:
sys_SHP2CSV <- function(shp) {
  csvfile <- paste0(shp, '.csv')
  shpfile <-paste0(shp, '.shp')
  if (!file.exists(csvfile)) {
    # use -lco GEOMETRY to maintain location
    # for reference, shp --> geojson would look like:
    # system('ogr2ogr -f geojson output.geojson input.shp')
    # keeps geometry as WKT:
    cmd <- paste('ogr2ogr -f CSV', csvfile, shpfile, '-lco GEOMETRY=AS_WKT')
    system(cmd)  # executes command
  } else {
    print(paste('output file already exists, please delete', csvfile, 'before converting again'))
  }
  return(csvfile)
}

Read the new csv into R:

# for file 'foo.shp':
foo_raw <- read.csv(sys_SHP2CSV(shp='foo'), sep = ',')

One might do any number of things now, some here lets snag some columns and rename them:

# rename the subset of data "foo" we want in a data.frame:
foo <- data.frame(foo_raw[1:5])
colnames(foo) <- c('bar', 'eggs', 'ham', 'hello', 'world')

We could do some more careful parsing too, here a semicolon in cell strings can be converted to a comma:

# replace ` ; ` to ` , ` in col "bar":
foo$bar <- gsub(pattern=";", replacement=",", foo$bar)

Do whatever you do for an output directory:

# make a output file directory if you're into that
# my preference is to only keep one set of output files per run
# here, we'd reset the directory before adding any new output files
redir <- function(outdir) {
  if (dir.exists(outdir)) {
    system(paste('rm -rf', outdir))
  }
  dir.create(outdir)
}

Of course, once your data is in R there are countless "R things" one could do...

# iterate to fill empty cells with preceding values
for (i in 1:length(foo[,1])) {
  if (nchar(foo$bar[i]) < 1) {
    foo$bar[i] <- foo$bar[i-1]
  }
  # fill incomplete rows with NA values:
  if (nchar(foo$bar[i]) < 1) {
    foo[i,] <- NA  
  }
}

# remove NA rows if there is nothing better to do:
newfoo <- na.omit(foo)

Even though this is totally adding a level of complexity to what could be a single ogr2ogr command, I've decided it is still worth it- I'd definitely rather keep track of everything I do over forget what I did.... xD

# make some methods to write out various kinds of files via gdal:
to_GEO <- function(target) {
  print(paste('converting', target, 'to geojson .... '))
  system(paste('ogr2ogr -f', " geojson ",  paste0(target, '.geojson'), paste0(target, '.csv')))
}

to_SHP <- function(target) {
  print(paste('converting ', target, ' to ESRI Shapefile .... '))
  system(paste('ogr2ogr -f', " 'ESRI Shapefile' ",  paste0(target, '.shp'), paste0(target, '.csv')))
}

# name files:
foo_name <- 'output_foo'

# for table data 'foo', first:
write.csv(foo, paste0(foo_name, '.csv'))

# convert with the above csv:
to_SHP(foo_name)

Cheers!
-Jess

Mac OSX: Fixing GPT and PMBR Tables

My computer recently crashed very, very hard, while I was removing an small empty alternative OS partition I no longer needed.  This is a fairly mundane operation that I do now and again, and is a ongoing fight to keep at least a few gigs of space free for actual work on precious 250gb Mac SSD.  

The crash results?  Toasted GPT tables all around.   My 2015 computer’s next move was to reboot- only to find essentially no partitions of memory… at all.  What it did show was (wait for it) Clover bootloader of all things, with a single windows boot camp icon (nothing in there either).  That is so wrong…. On all levels!

I brought the machine to the local university repair.  They declared this machine bricked and offered to wipe it.  Back to me it came…

I scheduled an Apple support session with a phone rep, which after around 45 minutes of actually productive troubleshooting ideas (none helping though) was forwarded to a senior supervisor.  She was interested in this problem, and we scheduled a larger block of time. But, in the meantime, I still wanted to try again….

How to recover a garbled GPT table for Mac OSX:

Start with clean SMC and PRAM / NVRAM.

Clearing these actually made accessing internet recovery (how we get to a stand-in OS with a terminal) dozens of times faster.  2.5 hours to 7 minutes. I actually waited 2.5 hours twice on separate attempts before I cleared these.

Follow these Apple links to perform these operations:

https://support.apple.com/en-us/HT204063

https://support.apple.com/en-us/HT201295

Get the computer with a text editor open.

Restart the computer into internet recovery.  Command + R or Command + Shift + R.

Wait.

Open a Terminal.  The graphical disk utility is useless because the disk / partition we want is unreachable(so it will say everything is great).

Run:

diskutil list

For me, I see disk0s2 is 180.6 gb.  That’s my stuff!

I also found /dev/disk2 → /dev/disk14 to be tiny partitions- don’t worry about those.

The syntax you are looking for is:

Name: “untitled” Identifier: disk#

(NOT disk#s#)

Write down ALL of the above information for the disk you are after.  That is probably disk0.

Then:

gpt -r show disk0

Copy the following readout in your terminal for all entries bigger than “32”.  The critical fields here are Start, Size, Index, and Contents. Each field is supremely important.

Here is mine (formatted for web):

# Disk0, with contents > “32” :

# First Table:

Start: 40  

Size: 409600

Index:  1

Contents: C12A7328-F81F-11D2-BA4B-00A0C93EC93B

# Second table, the one with my data:

Start: 409640

Size: 352637568

Index: 2

Contents: FFFFFFFF-FFFF-FFFF-FFFF-FFFFFFFFFFFF

Note, this is the initial Contents.  I rewrote this once with the correct Apple Index 2 data but did not create a new table (leaving the rest of the broken bits broken).  We are replacing / destroying a table here, but not the data.     

Actions:

# unmount the disk.  From here we are doing tables, not disks / data.

diskutil unmountDisk disk0

# Get rid of the GPT on the disk we are recovering.  We are not touching the data.

gpt destroy disk0

# Make a new one to start with some fresh values.

gpt create -f disk0

# perform magic trick

# USE THE DATA YOU WROTE DOWN FROM “gpt -r show disk0”.  THIS IS IMPORTANT.

# we must add that first small partition at index 1.  Verbatim.

gpt add -i 1 -b 40 -s 409600 -t C12A7328-F81F-11D2-BA4B-00A0C93EC93B disk0

# index two (for me) is my data.  We are going to use the default OSX / Mac HD partition values.

# the Length of “372637568” is not as sure fire as the GPT Contents.  

# YMMV, but YOLO.

gpt add -i 2 -b 409640 -s 372637568 -t 7C3457EF-0000-11AA-AA11-00306543ECAC disk0

Again, that Contents value is 7C3457EF-0000-11AA-AA11-00306543ECAC.

- Jess

written in the recovered computer xD

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Evaluating Ubuntu Pop OS: Dual Boot Setup

Dual OS on a 2015 MacBook pro

As the costs of Apple computers continue to skyrocket and the price of useable amounts of storage zoom past a neighboring galaxy (for a college student at least), I am always on on the hunt for cost effective solutions to house and process big projects and large data.

Pop OS (a neatly wrapped Ubuntu) is the in-house OS from System76.  After looking through their catalog of incredible computers and servers, I thought it would be a good time to see how far I can go with an Ubuntu daily driver.  Of course, there are many major and do-not-pass-go downsides- see the below list:

  • Logic Pro X → There is no replacement 🙁   A killer DAW with fantastic AU libraries. I am versed with Reaper and Bitwig, but neither is as complete as Logic Pro.  I will be evaluating POP with an installation of Reaper, but with so few plugins (I own very few third party sets) this is not a fair replacement.
  • Adobe PS and LR:  I do not like Adobe, but these programs are... ...kind of crucial for most project of mine that involve 2d, raster graphics.  I continue to use Inkscape for many tasks, but it is irrelevant when it comes to pixel-based work and photo management / bulk operations.
  • AutoCAD / Fusion 360 / Sketchup:  I like FreeCAD a lot, but it is not at all like the other programs.  Not worse or better, but these are all very different animals for different uses.
  • Apple notes and other apple-y things:  OSX is extremely refined. Inter-device solutions are superb.  I have gotten myself used to Google Keep, but it is not quite at the in-house Apple level.
  • XCode and IOS Simulator environments:  I do use Expo, but frankly to make products for Apple you need a Mac.

Dual Boot (OSX and Pop Ubuntu) Installation on a 2015 MBP:

This process is quite simple, and only calls for a small handful of post-installation tweaks.  My intent is to create a small sandbox with minimal use of “extras” (no extra boot managers or anything like that)

Steps:

Partition separate “boot”, “home”, and other drives

  • I am using a 256gb micro sd partitioned in half for OSX and Pop_OS (Sandisk extreme, “v3” speed rating version card via a BaseQi slot adapter)

Use the partition tool in Mac disk utility.  Be sure to set these new partitions as FAT 32- we will be using ext4 and other more linux-y filesystems upon installation, so these need to be as generic as possible.

Get a copy of Pop_OS from System76.

Use Etcher (recommended) or any other image burning tool to create a boot key for Pop.  

The USB key only has one small job, in which Pop_os will be burned into a better location in your boot partition made in the previous step.  If you are coming from a hackintosh experience, fear not: everything will stay in the Macbook Pro, not extra USB safety dongles or Kexts, or Plist mods…!

BOOT INTO POP_OS:

Restart your computer and hold down the alt-option Key.  THIS IS HOW TO SWITCH from Pop_os, OSX, Bootcamp, and anything else you have in there.  You should see an “efi” option next to the default OSX. (note- at least in my case, the built-in bootloader defaults to the last used OS at each restart.)

Once you are in the Pop_OS installer, click through and select the appropriate partitions when prompted.  After this installation, you may remove the USB key and continue to select
“efi” in the bootloader.


ASSUMING ALL GOES WELL:

You are now in Pop_OS!  Using the alt/option key will become second nature… but some Pop key mappings may not.  Continue for a list of Macbook Pro - specific tweaks and notes.

First moves:

Go to the Pop Shop and get the “Tweaks” tool.  I made one or two small keymap changes, but this is likely personal preference.  

Default, important Key Mappings:

Command will act as a “control center-ish” thing.  It will not copy or paste anything for you.

Control does what Command did on OSX.  

Terminal uses Control+Shift for copy and paste, but only in Terminal:  if you pull a Control+Shift+C in Chrome, you will get the Dev tool GUI...  The Shift key thing is needed unless you are inclined to root around and change it.

Custom Boot Scripts and Services:

In an effort to make things simple, I made a shell script to house the processes I want running when I turn on the computer- this is to streamline the “.service” making process.  While it may only take marginally more time to make a new service, this way I can keep track of what is doing what from a file in my documents folder.

In terminal, go to where your services live if you want to look:

cd /etc/systemd/system

Or, cut to the chase:

sudo nano /etc/systemd/system/startsh.sh.service

Paste the following into this new file:

_____________Begin _After_This_Line____________________

[Unit]

Description=Start at Open plz

[Service]

ExecStart=/Documents/startsh.sh

[Install]

WantedBy=multi-user.target

_____________End _Above_This_Line____________________

Exit nano (saving as you go) and cd back to “/”.

cd

sudo nano /Documents/startsh.sh

Paste the following (and any scripts you may want, see the one I have commented out for odrive CLI) into this new file:

_____________Begin _After_This_Line____________________

#!/bin/bash

# Uncomment the following if you want 24/7 odrive in your system

# otherwise do whatever you want

#nohup "$HOME/.odrive-agent/bin/odriveagent" > /dev/null 2>&1 &

# end

_____________End _Above_This_Line____________________

After exiting the shell script, start it all up with the following:

sudo systemctl start startsh.sh

sudo systemctl enable startsh.sh

Cloud file management with Odrive CLI and Odrive Utilities:

Visit one of the two Odrive CLI pages- this one has linux in it:

https://forum.odrive.com/t/odrive-sync-agent-a-cli-scriptable-interface-for-odrives-progressive-sync-engine-for-linux-os-x-and-windows/499#linuxinst

Please visit this repo to get going with --recursive and other odrive utilities

https://github.com/amagliul/odrive-utilities


These are the two commands I ended up putting in a markdown file on my desktop for easy access.  Nope, not nearly as cool as it is on OSX. But it works…

Odrive sync: [-h] for help

```

python "$HOME/.odrive-agent/bin/odrive.py" sync

```

Odrive utilities:

```

python "$HOME/odrive-utilities/odrivecli.py" sync --recursive

```

Next, Get Some Apps:

Download Chrome.  Sign into Chrome to get your chrome OS apps loaded into the launcher- in my case, I needed Chrome remote desktop.  DO NOT DOWNLOAD ADDITIONAL PACKAGES for Chrome Remote Desktop, if that is your thing. They will halt all system tools (disk utils, Gnome terminal, graphical file viewer…   !!See this thread, it happened to me!! )

Stock up!  

Get Atom editor:  https://atom.io/

...Or my favorites: https://www.jetbrains.com/toolbox/app/

Rstudio:  https://www.rstudio.com/products/rstudio/download/#download

Mysql:  https://dev.mysql.com/downloads/mysql/

MySQL Workbench:  https://dev.mysql.com/downloads/workbench/

If you get stuck:  make sure you have tried installing as root ($ sudo su -) and verified passwords with ($ sudo mysql_secure_installation)  

See here to start “rooting around” MySQL issues:  https://stackoverflow.com/questions/50132282/problems-installing-mysql-in-ubuntu-18-04/50746032#50746032

Get some GIS tools:

QGIS!

sudo apt-get install qgis python-qgis qgis-plugin-grass

uGet for bulk USGS data download!

sudo add-apt-repository ppa:plushuang-tw/uget-stable

sudo apt install uget

That's all for now- Cheers!

-Jess

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