this post was submitted on 02 Aug 2024
349 points (97.5% liked)
Science Memes
10940 readers
1706 users here now
Welcome to c/science_memes @ Mander.xyz!
A place for majestic STEMLORD peacocking, as well as memes about the realities of working in a lab.
Rules
- Don't throw mud. Behave like an intellectual and remember the human.
- Keep it rooted (on topic).
- No spam.
- Infographics welcome, get schooled.
This is a science community. We use the Dawkins definition of meme.
Research Committee
Other Mander Communities
Science and Research
Biology and Life Sciences
- !abiogenesis@mander.xyz
- !animal-behavior@mander.xyz
- !anthropology@mander.xyz
- !arachnology@mander.xyz
- !balconygardening@slrpnk.net
- !biodiversity@mander.xyz
- !biology@mander.xyz
- !biophysics@mander.xyz
- !botany@mander.xyz
- !ecology@mander.xyz
- !entomology@mander.xyz
- !fermentation@mander.xyz
- !herpetology@mander.xyz
- !houseplants@mander.xyz
- !medicine@mander.xyz
- !microscopy@mander.xyz
- !mycology@mander.xyz
- !nudibranchs@mander.xyz
- !nutrition@mander.xyz
- !palaeoecology@mander.xyz
- !palaeontology@mander.xyz
- !photosynthesis@mander.xyz
- !plantid@mander.xyz
- !plants@mander.xyz
- !reptiles and amphibians@mander.xyz
Physical Sciences
- !astronomy@mander.xyz
- !chemistry@mander.xyz
- !earthscience@mander.xyz
- !geography@mander.xyz
- !geospatial@mander.xyz
- !nuclear@mander.xyz
- !physics@mander.xyz
- !quantum-computing@mander.xyz
- !spectroscopy@mander.xyz
Humanities and Social Sciences
Practical and Applied Sciences
- !exercise-and sports-science@mander.xyz
- !gardening@mander.xyz
- !self sufficiency@mander.xyz
- !soilscience@slrpnk.net
- !terrariums@mander.xyz
- !timelapse@mander.xyz
Memes
Miscellaneous
founded 2 years ago
MODERATORS
you are viewing a single comment's thread
view the rest of the comments
view the rest of the comments
Is 600 MB a lot for pandas? Of course, CSV isn't really optimal but I would've sworn pandas happily works with gigabytes of data.
What do you mean not optimal? This is quite literally the most popular format for any serious data handling and exchange. One byte per separator and newline is all you need. It is not compressed so allows you to stream as well. If you don't need tree structure it is massively better than others
I think portability and easy parsing is the only advantage od CSV. It's definitely good enough (maybe even the best) for small datasets but if you have a lot of data you need a compressed binary format, something like parquet.
But which separator is it, and which line ending? ASCII, UTF-8, UTF-16 or something else? What about quoting separators and line endings? Yes, there is an RFC, but a million programs were made before the RFC and won't change their ways now.
Also you can gzip CSV and still stream them.
Have you heard that there are great serialised file formats like .parquet from appache arrow, that can easily be used in typical data science packages like duckdb or polars. Perhaps it even works with pandas (although do not know it that well. I avoid pandas as much as possible as someone who comes from the R tidyverse and try to use polars more when I work in python, because it often feels more intuitive to work with for me.)
I used to export my pandas DataFrames as pickles, but decided to test parquet and it was great. It was like 10x smaller and allowed me to had the the databases on a server directory instead of having to copy everything to the local machine.
If you have a csv bigger than like 500mb you need more than 8gb of ram to open it
Wait till you hear about WSV
It really depends on the machine that is running the code. Pandas will always have the entire thing loaded in memory, and while 600Mb is not a concern for our modern laptops running a single analysis at a time, it can get really messy if the person is not thinking about hardware limitations
Pandas supports lazy loading and can read files in chunks. Hell, even regular ole Python doesn't need to read the whole file at once with
csvI didn't know about lazy loading, that's cool!
Then I guess that the meme doesn't apply anymore. Though I will state that (from my anedoctal experience) people that can use Panda's most advanced features* are also comfortable with other data processing frameworks (usually more suitable to large datasets**)
*Anything beyond the standard
groupby-applycan be considered advanced, from the placrs I've been**I feel the urge to note that 60Mb isn' lt a large dataset by any means, but I believe that's beyond the point
No, but it's easy to make a program in Python that doesn't like it.
Oh, I know, believe me. I have some painful first-hand experience with such code.
I guess it's more of a critique of how bad CSV is for storing large data than pandas being inefficient
CSV is not optimal, but then someone shows up and gives you 60GB of JSON instead of 600MB of CSV.
Why do you have to personally attack me like that?
Or they dump their entire 6gb SQL database, customer info and all, into a SQL file that you have to load into a mariadb docker container when you just needed a subset that you were going to turn into csv anyway ☺️
Fine! .csv.gz ftw!
It's more likely you'll eat up storage when you read a 600mb parquet and try to write it as CSV.
I mean, yeah, that's the point of compression. I don't quite get what you mean by that comment.
Ah I was trying to point out that CSV is the inefficient format. Reading a large amount of data from a more efficient format like parquet is more likely to cause trouble because the memory required can be more than the file size. CSV is the opposite where it will almost always use more disk space than is required to represent the data in memory.
Right, true!