Organise your data¶
Step by step
Go through the installation guide first before jumping into this guide.
When you first run
scdata, it will create a
scdata folder in your
~/.cache directory containing the following structure:
export: we will export processed data or images here
interim: we will place files used internally for the framework, such as sensor calibration data
processed: the most important folder of our data directory. This will contain a hierarchy with the different tests after loading into our database. The tests in this folder will have an unified format to easily navigate them. It's the folder we will load our data from, once we have created a test.
raw: raw sdcard data can be placed here. It will feed our pre-processing script below
reports: reports will be generated here. Have a look at the guide
tasks: tasks will be loaded from here (WIP)
uploads: directory to put information when uploading data to zenodo
scdata folder with a
config.yaml file is created in your
Visit the readme in the github repository for more information about configuring this.
Two main ways to access and organise the data:
- device: single device holding information from different sources. Learn how to use it in the examples
- test: intended for experimentation with the data and posterior reproducibility. See below.
The concept is very simple. A test is a collection of devices (SCKs or not), that have a common purpose. They can be located in the same spot (co-location) or not, and the main idea is that we centralise the data in a common instance for easy analysis.
Tests have dates, authors, can have comments (for us to remember what we did), a report attached and can be in different conditions (outdoor, indoor)... We will put all this metadata in a
yaml file to help use look for the tests later on.
Tests can also have different sources. They could be csv files, xls files or data from the Smart Citizen API. For the local files, we will first pre-process them with the scripts in the
data/scripts folder and then place them in the
data/raw folder, in csv format. We use this format because it's a common usable format and, although it is not the most efficient way of archiving the data, it can be easily explored by other common applications.
Pre-process the sd card data¶
Direct upload also available
You can directly upload SD card data following the example here
In order to make our files usable, we will need to have them in a format like
YY-MM-DD.CSV. However, if the kit has been reset, we can find some files like:
YY-MM-DD.02 and they should be something like
We can rename them manually, but if we have many of them, we can use this one-liner (works in oh-my-zsh):
autoload -Uz zmv
zmv '(*).(0*)' '$1_$2.CSV'
We can now concatenate all the sd card data from a device with the
concat_script.py in the scripts folder.
We can access the script's help by typing in the terminal:
python concat_script.py -h
usage: concat_script.py [-h] [--output OUTPUT] [--index INDEX] [--keep]
[--ignore IGNORE] [--directory DIRECTORY]
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
Output file name, including extension
--index INDEX, -i INDEX
Final name of time index
--keep, -k Keep full CSV header
--ignore IGNORE, -ig IGNORE
Ignore files in concatenation
--directory DIRECTORY, -d DIRECTORY
Directory for csv files to concatenate
Create a directory (
FILES) and put the sd card data of one device in it. Then, run the script with:
python concat_script.py -k -d FILES
Using files in /Users/macoscar/Documents/04_Projects/02_FabLab/01_SmartCitizen/01_Repositories/DataAnalysis/smartcitizen-iscape-data/data/scripts/FILES
Files to concat:
Saving file to: Log_Concat.csv
And if we now navigate to the
18-11-08.CSV 18-11-13.CSV 18-11-15.CSV 18-11-17.CSV Log_Concat.csv
18-11-09.CSV 18-11-14.CSV 18-11-16.CSV 18-11-18.CSV
We can find our concatenated file!
Create a test¶
Once we have all our concatenated files, we can proceed to create our test. For this, you can launch
jupyter lab and open the examples notebooks. In it, we can follow the instructions in the notebook by filling up the input data.
A note about the timestamps
To synchronise our tests, we will always need to specify the location. This means that all our tests will be in 'UTC'.
There's a lot more to it
Check the examples in the repository to:
- Plot data
- Calibrate sensors
- Upload it to zenodo