CSV 2 GeoJSON

Recently I had another challenge, which I believe has the characteristics to be a common problem. I have a table with attributes, in CSV format, one of which is geospatial.

CSV is a structured format for storing tabular data (text and numbers), where each row corresponds to a record, and each field is separated by a known character(generally a comma). It is probably one of the most common formats to distribute that, probably because it is a standard output from relational databases.

Since people hand me data often in this format, and for a number of reasons it is more convenient for me to to use JSON data, I thought it would be handy to have a method to translating CSV into JSON, and this was the first milestone of this challenge.

The second milestone of this challenge, is that there is some geospatial information within this data, serialized in a non standard format, and I would like to convert it into a standard JSON format for spatial data; e.g.: GeoJSON. So the second milestone has actually two parts:

  • parse a GeoJSON geometry from the CSV fields
  • pack the geometry and the properties into GeoJSON field

To convert CSV (or XML) to JSON, I found this really nice website. It lets you upload a file, and save the results into another file,so I could transform this:

TMC,ROADNUMBER,DIR,PROV,CCAA,StartLatitude,StartLongitude,
EndLatitude,EndLongitude
E17+02412,A-2,E-90/AP-2/BARCELONA-ZARAGOZA (SOSES),LLEIDA,
CATALUNYA,41.5368273,0.4387071,
41.5388396,0.4638462

into this:

{
"TMC": "E17+02412",
"ROADNUMBER": "A-2",
"DIR": "E-90/AP-2/BARCELONA-ZARAGOZA (SOSES)",
"PROV": "LLEIDA",
"CCAA": "CATALUNYA",
"StartLatitude": "41.5368273",
"StartLongitude": "0.4387071",
"EndLatitude": "41.5388396",
"EndLongitude": "0.4638462"
}

This gave me a nicely formatted JSON output (the first milestone!), but as you can notice the geometry is not conform with any OGC standards. It is actually a linestring, which is defined by a start point (StartLongitude, StartLatitude) and an end point (EndLongitude, EndLatitude).

According to the JSON spec, a linestring is defined by an array of coordinates:

So the goal would be to transform the geometry above into:

"LineString",
"coordinates": [
[0.4387071, 41.5368273], [0.4638462, 41.5388396]
]

Once more, jq comes really handy to this task.

The JSON can be transformed into a feature using this syntax:

cat tramos.json | jq -c '[.[] | { type: "Feature", "geometry": {"type": "LineString","coordinates": [ [.StartLongitude, .StartLatitude| tonumber], [ .EndLongitude, .EndLatitude | tonumber] ] }, properties: {tmc: .TMC, roadnumber: .ROADNUMBER, dir: .DIR, prov: .PROV, ccaa: .CCAA}}]' > tramos.geojson

Since the JSON converser parse all the variables into strings, it is important to pass a filter (tonumber) to make sure that the coordinate numbers are converted back into numbers.

{
"properties": {
"ccaa": "CATALUNYA",
"prov": "LLEIDA",
"dir": "N-IIA/SOSES/TORRES DE SEGRE/ALCARRàS",
"roadnumber": "A-2",
"tmc": "E17+02413"
},
"geometry": {
"coordinates": [
[
0.4714937,
41.5420936
],
[
0.4891472,
41.5497014
]
],
"type": "LineString"
},
"type": "Feature"
}

Since we are creating an array of features (or “Feature Collection”), to be conform with GeoJSON, it is important to declare the root element too, by adding this outer element:

{ "type": "FeatureCollection","features": [ ]}

The result should be a valid GeoJSON, that you can view and manipulate in your favourite GIS (for instance QGIS!) 🙂

csv2geojson

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Piping an API into R: a Data Science Workflow

Inspired by @jeroenhjanssens, author of the Data Science Toolbox, I decided to give a go to one of the most unfriendly data sources: An XML API.
Apart from its rich syntax with query capabilities, I tend think XML is highly verbose and human unfriendly, which is quite a discouraging if you don’t want to take advantage of all its capabilities. And in my case I didn’t: I just wanted to grab a data stream, in order to be able to build some analysis in R. APIs are generally a pain for data scientists, because they tend to want to have “a look at things” and get a general feeling of the dataset, before start building code. Normally, this is not possible with an API, unless you use these high-end drag-and-drop interfaces, that are generally costly. But following this approach I was able to setup a chain of tools that enable me to reproduce this AGILE workflow, where you can have a feel of the dataset in R, without having to write a Python client.

The first step was to pipe the xml output of the query into a file, and that is easy enough to do with curl

curl -s 'http://someurl.com/Data/Entity.ashx?Action=GetStuff&Par=59&Resolution=250&&token=OxWDsixG6n5sometoken' > out.xml

Now, if you are an XML wiz you can follow a different approach, but I personally feel more comfortable with JSON, so the next step for me was to convert the XML dump into some nice JSON, and fortunately there is another free tool for that too: xml2json

xml2json < out.xml > out.json

Having the JSON, it is possible to query it using jq, a command line JSON parser that I find really intuitive. With this command, I am able to narrow the dataset to the fields I am interested, and pipe the results into another text file. In this case I am skipping all the “headers”, and grabbing an array of elements, which is what I want to analyse.

cat out.json | jq '[.Root.ResultSet.Entity[] | {color: .color, width: .with, average: .average, reference: .reference, Time: .Time}]' > test.json

Now here I could add another step, to convert the JSON results into csv, but actually R has interfaces to JSON, so why not use those to import the data directly. There is actually more than one package that can do this, but I had some nice results with jsonlite.

library("jsonlite")
data1 <- fromJSON("test.json")

And with these two lines of code, I have a data frame that I can use for running ML algorithms.

df