03 Jul 2018
SCT Part 2
Embracing Text
In the previous blog, we explored how we can load (explicitly) spatial data, initially in shapefile format, to a geopackage. In this post we explore the loading of relations a.k.a table to the geopackage. Again, data from the Open Data Portal is used.
Data Is Rarely Clean!
We will explore “Data showing City land that has been disposed of.” The data is spread over several spreadsheets covering various time periods. In some instance yearly quarters. The data custodian is given as “Manager: Property Development & Acquisitions city of capetown.”
In the data wrangling process using LibreOfficeCalc, the open source equivalent of MS Excel. Several attributes will be learnt about the data. Especially that which hinders a refined data structure. Issue will be varied, among them:
- Not all records being filled in.
- No consistency to period of registrations.
- Inconsistent formatting of currency.
- Sale price included or excluded VAT inconsistently.
- Typos in area names.
- A regions field which definition could not be got from the Open Data Portal.
To improve the data we may end up
- Adding some fields to improve schema
- Concluding area field = Suburb Name (per suburb_layer from previous blog post)
- Matching the area field names to match up with Suburb Name in the Base Suburbs reference data we adopted.This procedure inadvertently modifies data from it’s original structure. However, knowledge of local suburb boundaries and place locations means the impact will be minimised.
Casual inspection reveals
- A lot of sales to churches and trusts. Possible follow-up questions would be. Was this influenced by any legislation in a particular year? Which year saw the largest number of sales to churches?
Loading Tabular Data To Geopackage
With the Land Disposals data, covering several years, curated and consolidated into one spreadsheet. It is time to import this data into our geopackage. Here are the steps to do it:
1. From the Spreadsheet application (OpenOfficeCalc), Save file as and choose Text CSV (Comma Separated Values).
To load the Text File to the geopackage we use any one of the two approaches.
Method 1: Using QGIS
1. Start Q if not already running.
2. Select Add Delimited Text. This is a large comma icon with a (+)plus sign. When you load the file, it will likely look like the screenshot below. (Note that the image shown here is of a file that would have undergone considerable pre-processing. Especially on field names and data types in cells.)
Make the selections as shown above. In particular ‘No Geometry’.
Opening the table in Q we see the data we just imported.
Now let’s save this to the GeoPackage.
3. Rick Click the Layer name, –> Save As. Then specify the location of the geopackage. In the dialog box that comes up, under Geometry, choose No Geometry. (We are just importing a non-spatial table.).
That’s it!
Let’s explore an alternative way of getting the text file into the GeoPackage.
Method 2: Using SQLite Browser
1. Open the GeoPackage in the SQLite Database Browser.
2. Do File –> Import –> Table from CSV.
Check on; Column Names in first line and Trim fields?. Separator is comma.
Done!
3 Switch to the Browse Data tab to see what we have just loaded.
A Review: What To Choose
On inspecting the table loaded with QGIS and SQLite Browser. Somehow Q correctly and auto-magically distinguish text and numeric field data types. SQLite Browser made everything type “TEXT” in this particular case.
Let’s experiments some more with our data.
Close SQlite Browser and switch to QGIS. (It is good practice to close one application when accessing data from another. Particularly if you are to do editing.)
Launch DB Manager and Browse to the geopackage.
Let’s see how many distinct suburbs do we have in this table.
Start the SQL Windows and run…
SELECT DISTINCT area FROM land_disposals_2009_2018
ORDER by area ASC;
we get 102 records . We see there is NULL in first entry so we really have 101 records. On close inspection we notice there are a lot of typos in some names.
We will need to clean this data if we are to have meaningful analysis later on.
Let’s check the suburbs layer and see how the data compares
SELECT DISTINCT NAME FROM suburbs
ORDER by NAME ASC;
We get 773! This is gonna be interesting, especially getting exact matches.
Before cleaning the data further, lets see if we can ‘connect’ the suburbs and land_disposals datasets.
SELECT * FROM suburbs
JOIN land_disposals_2009_2018
ON suburbs.NAME = land_disposals_2009_2018.area;
Yep! We have some hits.
We are going to be basing our analysis on the suburbs layer so we use that layer for a base and format subsequent datasets after that it as much as possible. Cleaning can be done in QGIS user interface editing or better still in the sqlite database (geopackage) using SQL.
#PostScript
The take away is that GeoPackage can store tables, no sweat.
The join operation used above is simplistic. One would need to appropriately use LEFT, RIGHT, INNER JOIN.
I used:
- QGIS 2.18 (DB Manager)
- DB Browser for SQLite 3.10.1
- SublimeText 3.1.1
15 Jun 2018
When A Relate Won’t Do
While working on the next part of my series of blogs I ran into an interesting ‘discovery’ which warrants an interjection. Testing the data loads into a geopackage, I decided to join a spatial and attribute data AND retain the results as a new ‘layer’. Tools in the QGIS Processing didn’t help much. So I Googled for a solution. To my surprise I got a few first time hits. I learnt MapInfo can do it so can ArcMap. There we also suggestions of having a relate in QGIS. But, that’s not what I sought.
Buried in a Google Forum was the solution by Thomas McAdam. So here’s how I ended up doing it … so we have one more source for the solution on the web.
Love The Database
A pre-requisite to the procedure is to have the data stored in some database and that’s not scary at all. I explain one way to doing that here creating a Geopackage. You can also create a SQLite Database as explained here. You don’t even have to leave the comfort of Q while doing it.
A One To May (1-M) Join
With the objective of joining two datasets and keeping the results. The assumption is that your data is clean and you have common fields between your two datasets.
- Table 1: suburbs - Has polygons of suburbs I wish to join (One Record).
- Table 2: land_disposals_2009_2018 - which has sales records per suburb (Many Records).
Now, with the target datasets loaded in a ‘spatial database’ as suggested above.
- Within the window write SQL Statement to JOIN our suburbs with the land_disposals_2009_2018 table.
Which translates to
SELECT *
FROM suburbs
JOIN land_disposals_2009_2018
ON suburbs.alt_name = land_disposals_2009_2018.area;
Simply put this says, “Basing on the common valued fields alt_name and area of the suburbs and land_disposals_2009_2018 layers respectively, join these two.”
-
Click on Execute to see what results this gives. (An inspection will help verify the legitimacy of the operation we just ran.)
- Tick the Load as new layer Check Box near the bottom of the SQL Window.
-
Tick the Geometry column Check Box. (Selecting a value that looks/ read something like geom).
- Now click on Load now! to have the results display in Q.
Results, If You Please.
On clicking Load Now! The Q canvas will fill with spatial, familiar ground!
To Save the results, Right Click the layer name in Q, Save As and we can save to any format supported by Q to our heart’s content.
#PostScript
The JOIN used here is an overly simplified approach to tip-top SQL queries. I would recommend intensive reading up on the JOIN operation as things can really go wrong surreptitiously.
01 Jun 2018
SCT Part 1
Scrapping For Data
The City of Capetown has a great and searchable place where data on and about the city is shared openly. The data is currently being migrated to a Portal for ArcGIS site which will bring with it a wealth of features and functionality. For now (June 2018), I am happy with the ‘simple’ site. This post is about collating spatially formatted data on the City of CapeTown. (Well, as provided on the open-data portal.)
So to start out I got city-wide base data from the Open Data Portal site and any apparently interesting themes, storing it locally for easy reach. The data was in compressed zip files, excel spreadsheets, pdfs and ODS files. I just dumped these, after some processing, in one folder. Fortunately there was sanity to the file naming from source.
Creating a Geodatabase
I went with GeoPackage for data storage/file format. So I could learn more about it and also because I have been hearing about it more often. Recently from FOSS4GNA 2018. I used primarily Q, QGIS and other tools I will mention. Here’s the step by step:
1. From the Open Data Portal, search and download the suburbs spatial data. This is available in zipped shapefile format.
2. Load the official planning suburbs data (zipped) shapefile in Q. The CRS(Coordinate Reference System) in Q set to ESPG:4326,
3. Right click on the suburbs layer, then Save As…leads to a dialog box of format choice and other options. Choose GeoPackage for a format.
- Select FileName and browse to the appropriate location. Enter the Geopackage Name (cct_opendata.gpkg).
-
Edit Layer name (suburbs). (Taking out the original Planning and Official to reduce characters in the layer name). CRS Auto populates to EPSG:4326, WGS84.
-
(Encoding is Grayed out at UTF-8 which is okay. we chose this when we loaded the suburbs shapefile).
-
Expanding the “Select fields to export and their export options”. Tick off SHAPE_leng and SHAPE_area. (Area and Length are not really useful especially when using a Geographic Coordinate System. Additionally, these where values calculated in the original gis software the data was exported from so we drop them to avoid confusing ourselves when using this data in our new geodatabase we are building.)
-
Keep “Add saved file to map”. (So we will be able to see if our export went well).
- There is no Symbology to export so skip that part. (We have not done any styling to our data yet which we would want to keep.)
On “Geometry”, Q has it as Automatic. (Q will correctly interpret this as polygon which it truly is.)
On “Extent”, Choose layer. Which defines the bounds of City of Capetown .(Well, I have prior knowledge of this. Local context data)
Layer Options:
Q has a tooltip for these fields. So hovering a mouse gives a hint what a field is for.)
- DESCRIPTION: set to “Official Planning Suburbs”
- FID:fid (Kept as is. Means Feature IDentity we infer.)
- GEOMETRY NAME: geom (Shortened from geometry. A matter of preference from previous experience. Conveniently short when writing out SQL statements.)
- IDENTIFIER: Suburbs
- SPATIAL _INDEX: YES (This helps in speeding things up when doing queries and spatial stuff with this layer.)
Custom Options:
Conveniently, the data from the Open Data Portal comes with some metadata. So we use that to populate these fields. Better build a comprehensive database from the ground up for future usage’s sake.
On OK.Q loads the GeoPackage and subsequently the layer. Q has made the export MultiPolygon and not just Polygon. (We will investigate this later.)
Our Geodata, The GeoPackage
To see what we just did. In Q, Load Vector data. Point to the GeoPackage (cct_opendata.gpkg ) and Voila! Our Suburbs data ‘geopackaged’ and with only two fields “fid” and “NAME”.
(From previous database fiddle experience, something about the “NAME” field in CAPS bothers me. We’ll deal with it late if need be.)
To take a peek into our GeoPackage
Launch DB Manager from Q.
-
From Menu –> Database –>DB Manager –>DB Manager
-
Right Click on GeoPackage.–>New Connection. Point to the GeoPackage (cct_opendata). A connection is added and therein is the suburbs layer we just added.
From here there is a plethora (I could be exaggerating) of GeoPackage versions. So lets’s investigate which version we just created so we know in case of eventualities as we build our datastore. We get a tip from here on how we can check a geopackage version.
With the GeoPackage opened in DB Manager.
- Launch the SQL Window (Database – >SQL Window).
- Then type
then Run (F5) the query.
User_version ‘0’ is not very indicative.
- Run the following query in stead
then Run (F5) the query.
We get a better results. Let’s interpret ‘1196437808’. from this guide we learn “1196437808 (the 32-bit integer value of 0x47503130 or GP10 in ASCII) for GPKG 1.0 or 1.1”
So our geopackage version is atleast 1.0.
While we are still at the SQL Interface. Let’s interrogate our ‘suburbs’ data.
How many suburbs are in our table?
SELECT Count(fid) FROM suburbs,
792 suburbs!
Fiddle
“A GeoPackage is a platform-independent SQLite [5] database file that contains GeoPackage data and metadata tables.” Source.
From this we infer that we should be able to explore the GeoPackage somemore with DB Manager as a SpatiaLite database.
- Right Click SpatialLite icon —>New Connection, then point to cct_opendata.gpkg. Expanding it reveals the contents.
More about those fields is explained here. Not for the faint hearted. Gladly we can just point Q at the geopackage and get our layer(s) to display!
Stacking The Store
To add more data to the GeoPackage. Repeat the procedure described in Creating a GeoDatabase above.
So I went on to load several layers form the Open Data Portal. After several clicks, some typing and 1.5Gigs later, 22 spatial data layers! (These were pseudo-randomly selected. No particular preference just a hunch that the data may help answer a question yet unknown.)
So while scrolling through the data (in Q via DB Manager),I noticed a triangle warning one of the layers did not have a spatial index. I opted to create one as prompted by Q. Q did it behind the scenes I simply had to click a hyperlink.
Using the SQLite Database Browser, we can get more insight into the GeoPackage.
#PostScript
While browsing to the geopackage location. I couldn’t help noticing two extra files
I found out these are temprary files used by SQLite. For a moment I thought the multi-file legacy of the Shapefile was back.
- wal - Write-ahead Log File –*“the purpose of the WAL file is to implement atomic commit and rollback”**
- shm - Shared memory file – *“The only purpose of the shared-memory file is to provide a block of shared memory for use by multiple processes all accessing the same database in WAL mode.”**
I used:
- QGIS 2.18 (DB Manager)
- DB Browser for SQLite 3.10.1
- SublimeText 3.1.1
Refs:
1. FOSS4GNA 2018 Geopackage Presentation
2. Geopackage Website
3. Fulcrum’s Working With GeoData
4. More On GeoPackage
5. SQLite Browser Site
24 May 2018
SCT Part 0
Driven To It
At one geo-software hands-on training I attended. A colleague alluded to the instructor, during feedback time, that it would be great if the training providers used data with a local context. In defence the instructor indicated the concept(s) being taught remained the same. I couldn’t help thinking though how I struggled remembering place names of the data we wrangled. Yes, it had a location but it would have been even better if it were from a place I knew. That somehow takes away a layer of learning hindrance.
I also recently (May 2018) bumped into a job advert for a GIS/Location Intelligence Market Analyst.It was (is) a fascinating job, requiring an intriguing skill set. I struck on the idea of evaluating how well I would fare if I was hired for such a post.[Personal box ticking]. Additionally, constantly in my tweeter feeds. There is much chatter on Data Science, Data Analyst, R, TidyVerse, SQL, JavaScript, Visualisations …[well, must be who I chose to follow, but the fact that I hadn’t unfollowed them was an indication of interest in the topic(s) . ]
So, I will start on a Blog Series - Spatial CapeTown (SCT) with the objective of, well, having a more focused approach to my blogging:
- Improve my writing skills. (Writing tutorials/ reports that are easy to follow).
- Develop and improve work flows while using exclusively FOSS. (So that the workflows are reproducible, software availabiity angle)
- Data massage and honing. (Local context data - the City of Cape Town in particular).
- Improve data analysis and Interpretation skills (Draw insights about the City from the data).
As a spin-off I hope to have fun and quench my insatiable desire for cool visualisations and code in software packages.
The City of Cape Town has a magnificent spatial data viewer from where one can find a ton of information about the city. If you are a tinkeror though, you also want access to the raw data. Frame your own questions and answer them yourself or answer unasked questions while playing with the data . So this series of blog posts is an alternative window to the wealth of spatio-temporal information about the City of Capetown. It will border on data manipulation to statistical inference about matters and phenomena.
On twitter ~ #spatialcct
#PostScript - Disclaimer
The proceeding work is no way authoritative and is purely my work in my personal capacity and not representative of City of Cape Town authority. It is neither official communication nor authoritative data dissemination. Consider it a weekend hack by a fanatic in some garage with data gotten off the internet.
26 Mar 2018
Arc who?
I am a fan of the file geodatabase. Somehow I feel I own the thing and can fire up Q and ogle in there with Open FileGeodatabase. But, enterprise geodatabase, I’m not too sure. While I edited some point data, well, point SDE Feature Class in an *ArcSDE Geodatabase. The machine froze and the software struggled to show selected features. By some stroke of luck I managed to save my edit and exit the program. Relaunch and errr….Where are my points?
Instead of
I get
I commenced in no strategic order troubleshooting why the data was showing all the way up there. The projection, extend and orientation all looked correct. Recalculate extend, Check geometry - No change.
I exported the data to shapefile (yes, back to basics right?). Delete .prj, redefine the projection, still ‘wrong place’. I was still curious to know where on earth, literally, the points fell, if not outer-space.
EPSG_Polygons_Ver_9.2.1.shp from epsg.org was my destination for a projection galore.
The IOGP’s EPSG Geodetic Parameter Dataset is a collection of definitions of coordinate reference systems and coordinate transformations which may be global, regional, national or local in application.
Congo? Jumping all the way up to the Equator, past the Tropic of Capricorn.
I added/ calculated the X,Y fields on the shapefile. The coordinates were as expected but still the points displayed at the ‘wrong place’. Exported the tabular data to the magical csv. Add to the gis software, ‘Display X,Y’. Tada!! Back home.
I imported the data back to the multiuser environment for a trouble free feature class for my team members.
How, why the data behaved this way I am still to know. But, a chase by the hands of time didn’t permit a thorough investigation nor Googling for the right way to fix such an anomaly.
#Postscript
Oftimes QGIS is my go to app for alternative behaviour. This time around nothing was auto-fixed. Imports, exports and tens of arctools in my preferred filegeodatabase sandbox didn’t get this anomaly resolved. It was good remembering that first principles get things done - the x,y coordinate pair is at the heart of geo.
