I have a global IGBP land use dataset in which the land cover exists out of forest cover (depicted with a '1') and non-forest cover (depicted with a '0'), hence, each land grid cell has either the value 1 or 0.
This dataset has a spatial resolution of approximately 1 km at the equator, however, I am going to regrid the dataset to a spatial resolution of approx 100 km at the equator. For this new grid resolution I want to calculate the fraction of forest cover (so the fraction of 1's) for each grid cell, but I am not sure how this can be done without GIS. Is there a way to do this with cdo remapping or perhaps with python?
Thank you in advance!
if you want to translate to a new grid that is an integer multiple of the original then you can do
cdo gridboxmean,n,m in.nc out.nc
where n and m are the numbers of points to average over in the lon and lat directions.
Otherwise you can interpolate using the conversative remapping which means that you don't need to worry if the new grid is not a multiple of the old
cdo remapcon,new_grid_specification in.nc out.nc
Note that in the latter case, however, the result is only first order accurate. There is also a slightly slower second order conservative remapping available using the command remapcon2. The paper describing the two implemented conservative remapping methods is Jones (1999). For further info on remapping you can also see my video guide.
Thanks to Robert for reminding also that you may need to convert to float, which would mean using the option
cdo -b f32
This is more a design question so please bear with me.
I have a system that stores locations consisting of the ID, Longitude and Latitude.
I need to compare the distance between my current location and the locations in the database a only choose ones that are within a certain distance.
I have the formula that calculates the distance between 2 locations based on the long/lat and that works great.
My issue is I may have 10 of thousands of locations in the database and don't want to loop through them all every time I need a list of locations close by.
Not sure what other datapoint I can store with the location to make it so I only have to compare a smaller subset.
Thanks.
As was mentioned in the comments, SQL Server has had support for geospatial since (iirc) SQL 2008. And I know that there is support within .NET for that as well so you should be able to define the data and query it from within your application.
Since the datatype is index-able, k nearest neighbor queries are pretty efficient. There's even a topic in the documentation for that use case. Doing a lift and shift from that page:
DECLARE #g geography = 'POINT(-121.626 47.8315)';
SELECT TOP(7) SpatialLocation.ToString(), City
FROM Person.Address
WHERE SpatialLocation.STDistance(#g) IS NOT NULL
ORDER BY SpatialLocation.STDistance(#g);
If you need all the points within that radius, omit the top clause and change the predicate on STDistance() to something like SpatialLocation.STDistance(#g) < 1000 (the SRID I typically use has meters as the unit of measure, so this would say 'within 1 km').
https://gis.stackexchange.com/ is a good place for in-depth advice on this topic.
A classic approach to quickly locating "nearby" values, is to "grid" the area of interest:
Associate each location with a "grid cell", where each cell is a convenient size. Pick a cell-edge-length such that most cells will hold a small number of values and/or that is similar to the distance range you typically query.
If cell edge is 1 km, and you need locations within 2 km, then get data from 5x5 cells centered at the "target" location.
This is guaranteed to include all data +- 2 km from any location within the central cell.
Apply distance formula to each returned location; some will be beyond 2 km.
I've only done this in memory, not from a DB. I think you add two columns, one for X cell number, other for Y cell number.
With indexes on both of those. So can efficiently get a range of Xs by a range of Ys.
Not sure if a combined "X,Y" index helps or not.
I'm trying to find locations within some distance from given coordinates. On a table with about 32k records query takes about 2 seconds - which is way too slow, imo.
It is doing a clustered index scan, which is logical - it has to calculate distance for every location.. However, I still think this should be faster over a data set this small. I do have spatial index defined, however it's not used, and query fails if I'm forcing it.
Most of the time (~86%) is spent on Filter that calculates the distance - so I'm looking for a ways to optimize that, and I need some help here..
The query I'm using is this:
SELECT Name
FROM Venue
WHERE (Coordinates.STDistance(geography::STPointFromText('POINT(-113.512245 51.498212)', 4326)) / 1000) <= 100
One old approach is to use a BOX firxt.
From your point, make two points on opposite ends of the box. +R/+R and -R/-R from the center.
Then you can filter - a point has to be in this box AND in the circle you describe.
The box check can run on the index and kills most elements.
Simple school geometry. You draw a rectangular box around the circle you describe.
Your current approach can not use the index because the index does not contain the fields.
ALTERNATIVELY: DRAW A CIRCLE - do not use a distance calculation. Draw a circle. With points.
Or read https://stackoverflow.com/questions/11311363/my-application-is-about-asp-net-using-linq-and-remote-mssql-my-connection-is-be which is the same issue you ask.
This is more of a challenge question than something I urgently need, so don't spend all day on it guys.
I built a dating site (long gone) back in 2000 or so, and one of the challenges was calculating the distance between users so we could present your "matches" within an X mile radius. To just state the problem, given the following database schema (roughly):
USER TABLE
UserId
UserName
ZipCode
ZIPCODE TABLE
ZipCode
Latitude
Longitude
With USER and ZIPCODE being joined on USER.ZipCode = ZIPCODE.ZipCode.
What approach would you take to answer the following question: What other users live in Zip Codes that are within X miles of a given user's Zip Code.
We used the 2000 census data, which has tables for zip codes and their approximate lattitude and longitude.
We also used the Haversine Formula to calculate distances between any two points on a sphere... pretty simple math really.
The question, at least for us, being the 19 year old college students we were, really became how to efficiently calculate and/store distances from all members to all other members. One approach (the one we used) would be to import all the data and calculate the distance FROM every zip code TO every other zip code. Then you'd store and index the results. Something like:
SELECT User.UserId
FROM ZipCode AS MyZipCode
INNER JOIN ZipDistance ON MyZipCode.ZipCode = ZipDistance.MyZipCode
INNER JOIN ZipCode AS TheirZipCode ON ZipDistance.OtherZipCode = TheirZipCode.ZipCode
INNER JOIN User AS User ON TheirZipCode.ZipCode = User.ZipCode
WHERE ( MyZipCode.ZipCode = 75044 )
AND ( ZipDistance.Distance < 50 )
The problem, of course, is that the ZipDistance table is going to have a LOT of rows in it. It isn't completely unworkable, but it is really big. Also it requires complete pre-work on the whole data set, which is also not unmanageable, but not necessarily desireable.
Anyway, I was wondering what approach some of you gurus might take on something like this. Also, I think this is a common issue programmers have to tackle from time to time, especially if you consider problems that are just algorithmically similar. I'm interested in a thorough solution that includes at least HINTS on all the pieces to do this really quickly end efficiently. Thanks!
Ok, for starters, you don't really need to use the Haversine formula here. For large distances where a less accurate formula produces a larger error, your users don't care if the match is plus or minus a few miles, and for closer distances, the error is very small. There are easier (to calculate) formulas listed on the Geographical Distance Wikipedia article.
Since zip codes are nothing like evenly spaced, any process that partitions them evenly is going to suffer mightily in areas where they are clustered tightly (east coast near DC being a good example). If you want a visual comparison, check out http://benfry.com/zipdecode and compare the zipcode prefix 89 with 07.
A far better way to deal with indexing this space is to use a data structure like a Quadtree or an R-tree. This structure allows you to do spatial and distance searches over data which is not evenly spaced.
Here's what an Quadtree looks like:
To search over it, you drill down through each larger cell using the index of smaller cells that are within it. Wikipedia explains it more thoroughly.
Of course, since this is a fairly common thing to do, someone else has already done the hard part for you. Since you haven't specified what database you're using, the PostgreSQL extension PostGIS will serve as an example. PostGIS includes the ability to do R-tree spatial indexes which allow you to do efficient spatial querying.
Once you've imported your data and built the spatial index, querying for distance is a query like:
SELECT zip
FROM zipcode
WHERE
geom && expand(transform(PointFromText('POINT(-116.768347 33.911404)', 4269),32661), 16093)
AND
distance(
transform(PointFromText('POINT(-116.768347 33.911404)', 4269),32661),
geom) < 16093
I'll let you work through the rest of the tutorial yourself.
http://unserializableone.blogspot.com/2007/02/using-postgis-to-find-points-of.html
Here are some other references to get you started.
http://www.bostongis.com/PrinterFriendly.aspx?content_name=postgis_tut02
http://www.manning.com/obe/PostGIS_MEAPCH01.pdf
http://postgis.refractions.net/docs/ch04.html
I'd simply just create a zip_code_distances table and pre-compute the distances between all 42K zipcodes in the US which are within a 20-25 mile radius of each other.
create table zip_code_distances
(
from_zip_code mediumint not null,
to_zip_code mediumint not null,
distance decimal(6,2) default 0.0,
primary key (from_zip_code, to_zip_code),
key (to_zip_code)
)
engine=innodb;
Only including zipcodes within a 20-25 miles radius of each other reduces the number of rows you need to store in the distance table from it's maximum of 1.7 billion (42K ^ 2) - 42K to a much more manageable 4 million or so.
I downloaded a zipcode datafile from the web which contained the longitudes and latitudes of all the official US zipcodes in csv format:
"00601","Adjuntas","Adjuntas","Puerto Rico","PR","787","Atlantic", 18.166, -66.7236
"00602","Aguada","Aguada","Puerto Rico","PR","787","Atlantic", 18.383, -67.1866
...
"91210","Glendale","Los Angeles","California","CA","818","Pacific", 34.1419, -118.261
"91214","La Crescenta","Los Angeles","California","CA","818","Pacific", 34.2325, -118.246
"91221","Glendale","Los Angeles","California","CA","818","Pacific", 34.1653, -118.289
...
I wrote a quick and dirty C# program to read the file and compute the distances between every zipcode but only output zipcodes that fall within a 25 mile radius:
sw = new StreamWriter(path);
foreach (ZipCode fromZip in zips){
foreach (ZipCode toZip in zips)
{
if (toZip.ZipArea == fromZip.ZipArea) continue;
double dist = ZipCode.GetDistance(fromZip, toZip);
if (dist > 25) continue;
string s = string.Format("{0}|{1}|{2}", fromZip.ZipArea, toZip.ZipArea, dist);
sw.WriteLine(s);
}
}
The resultant output file looks as follows:
from_zip_code|to_zip_code|distance
...
00601|00606|16.7042215574185
00601|00611|9.70353520976393
00601|00612|21.0815707704904
00601|00613|21.1780461311929
00601|00614|20.101431539283
...
91210|90001|11.6815708119899
91210|90002|13.3915723402714
91210|90003|12.371251171873
91210|90004|5.26634939906721
91210|90005|6.56649623829871
...
I would then just load this distance data into my zip_code_distances table using load data infile and then use it to limit the search space of my application.
For example if you have a user whose zipcode is 91210 and they want to find people who are within a 10 mile radius of them then you can now simply do the following:
select
p.*
from
people p
inner join
(
select
to_zip_code
from
zip_code_distances
where
from_zip_code = 91210 and distance <= 10
) search
on p.zip_code = search.to_zip_code
where
p.gender = 'F'....
Hope this helps
EDIT: extended radius to 100 miles which increased the number of zipcode distances to 32.5 million rows.
quick performance check for zipcode 91210 runtime 0.009 seconds.
select count(*) from zip_code_distances
count(*)
========
32589820
select
to_zip_code
from
zip_code_distances
where
from_zip_code = 91210 and distance <= 10;
0:00:00.009: Query OK
You could shortcut the calculation by just assuming a box instead of a circular radius. Then when searching you simply calculate the lower/upper bound of lat/lon for a given point+"radius", and as long as you have an index on the lat/lon columns you could pull back all records that fall within the box pretty easily.
I know that this post is TOO old, but making some research for a client I've found some useful functionality of Google Maps API and is so simple to implement, you just need to pass to the url the origin and destination ZIP codes, and it calculates the distance even with the traffic, you can use it with any language:
origins = 90210
destinations = 93030
mode = driving
http://maps.googleapis.com/maps/api/distancematrix/json?origins=90210&destinations=93030&mode=driving&language=en-EN&sensor=false%22
following the link you can see that it returns a json. Remember that you need an API key to use this on your own hosting.
source:
http://stanhub.com/find-distance-between-two-postcodes-zipcodes-driving-time-in-current-traffic-using-google-maps-api/
You could divide your space into regions of roughly equal size -- for instance, approximate the earth as a buckyball or icosahedron. The regions could even overlap a bit, if that's easier (e.g. make them circular). Record which region(s) each ZIP code is in. Then you can precalculate the maximum distance possible between every region pair, which has the same O(n^2) problem as calculating all the ZIP code pairs, but for smaller n.
Now, for any given ZIP code, you can get a list of regions that are definitely within your given range, and a list of regions that cross the border. For the former, just grab all the ZIP codes. For the latter, drill down into each border region and calculate against individual ZIP codes.
It's certainly more complex mathematically, and in particular the number of regions would have to be chosen for a good balance between the size of the table vs. the time spent calculating on the fly, but it reduces the size of the precalculated table by a good margin.
I would use latitude and longitude. For example, if you have a latitude of 45 and a longitude of 45 and were asked to find matches within 50 miles, then you could do it by moving 50/69 ths up in latitude and 50/69 ths down in latitude (1 deg latitude ~ 69 miles). Select zip codes with latitudes in this range. Longitudes are a little different, because they get smaller as you move closer to the poles.
But at 45 deg, 1 longitude ~ 49 miles, so you could move 50/49ths left in latitude and 50/49ths right in latitude, and select all zip codes from the latitude set with this longitude. This gives you all zip codes within a square with lengths of a hundred miles. If you wanted to be really precise, you could then use the Haversine formula witch you mentioned to weed out zips in the corners of the box, to give you a sphere.
Not every possible pair of zip codes are going to be used. I would build zipdistance as a 'cache' table. For each request calculate the distance for that pair and save it in the cache. When a request for a distance pair comes, first look in the cache, then compute if it's not available.
I do not know the intricacies of distance calculations, so I would also check whether computing on the fly is cheaper than looking up (also taking into consideration how often you have to compute).
I have the problem running great, and pretty much everyone's answer got used. I was thinking about this in terms of the old solution instead of just "starting over." Babtek gets the nod for stating in in simplest terms.
I'll skip the code because I'll provide references to derive the needed formulas, and there is too much to cleanly post here.
Consider Point A on a sphere, represented by latitude and longitude. Figure out North, South, East, and West edges of a box 2X miles across with Point A at the center.
Select all point within the box from the ZipCode table. This includes a simple WHERE clause with two Between statements limiting by Lat and Long.
Use the haversine formula to determine the spherical distance between Point A and every point B returned in step 2.
Discard all points B where distance A -> B > X.
Select users where ZipCode is in the remaining set of points B.
This is pretty fast for > 100 miles. Longest result was ~ 0.014 seconds to calculate the match, and trivial to run the select statement.
Also, as a side note, it was necessary to implement the math in a couple of functions and call them in SQL. Once I got past a certain distance the matching number of ZipCodes was too large to pass back to SQL and use as an IN statement, so I had to use a temp table and join the resulting ZipCodes to User on the ZipCode column.
I suspect that using a ZipDistance table will not provide a long-term performance gain. The number of rows just gets really big. If you calculate the distance from every zip to to every other zip code (eventually) then the resultant row count from 40,000 zip codes would be ~ 1.6B. Whoah!
Alternately, I am interested in using SQL's built in geography type to see if that will make this easier, but good old int/float types served fine for this sample.
So... final list of online resources I used, for your easy reference:
Maximum Difference, Latitude and Longitude.
The Haversine Formula.
Lengthy but complete discussion of the whole process, which I found from Googling stuff in your answers.
I am working in a chemistry/biology project. We are building a web-application for fast matching of the user's experimental data with predicted data in a reference database. The reference database will contain up to a million entries. The data for one entry is a list (vector) of tuples containing a float value between 0.0 and 20.0 and an integer value between 1 and 18. For instance (7.2394 , 2) , (7.4011, 1) , (9.9367, 3) , ... etc.
The user will enter a similar list of tuples and the web-app must then return the - let's say - top 50 best matching database entries.
One thing is crucial: the search algorithm must allow for discrepancies between the query data and the reference data because both can contain small errors in the float values (NOT in the integer values). (The query data can contain errors because it is derived from a real-life experiment and the reference data because it is the result of a prediction.)
Edit - Moved text to answer -
How can we get an efficient ranking of 1 query on 1 million records?
You should add a physicist to the project :-) This is a very common problem to compare functions e.g. look here:
http://en.wikipedia.org/wiki/Autocorrelation
http://en.wikipedia.org/wiki/Correlation_function
In the first link you can read: "The SEQUEST algorithm for analyzing mass spectra makes use of autocorrelation in conjunction with cross-correlation to score the similarity of an observed spectrum to an idealized spectrum representing a peptide."
An efficient linear scan of 1 million records of that type should take a fraction of a second on a modern machine; a compiled loop should be able to do it at about memory bandwidth, which would transfer that in a two or three milliseconds.
But, if you really need to optimise this, you could construct a hash table of the integer values, which would divide the job by the number of integer bins. And, if the data is stored sorted by the floats, that improves the locality of matching by those; you know you can stop once you're out of tolerance. Storing the offsets of each of a number of bins would give you a position to start.
I guess I don't see the need for a fancy algorithm yet... describe the problem a bit more, perhaps (you can assume a fairly high level of chemistry and physics knowledge if you like; I'm a physicist by training)?
Ok, given the extra info, I still see no need for anything better than a direct linear search, if there's only 1 million reference vectors and the algorithm is that simple. I just tried it, and even a pure Python implementation of linear scan took only around three seconds. It took several times longer to make up some random data to test with. This does somewhat depend on the rather lunatic level of optimisation in Python's sorting library, but that's the advantage of high level languages.
from cmath import *
import random
r = [(random.uniform(0,20), random.randint(1,18)) for i in range(1000000)]
# this is a decorate-sort-undecorate pattern
# look for matches to (7,9)
# obviously, you can use whatever distance expression you want
zz=[(abs((7-x)+(9-y)),x,y) for x,y in r]
zz.sort()
# return the 50 best matches
[(x,y) for a,x,y in zz[:50]]
Can't you sort the tuples and perform binary search on the sorted array ?
I assume your database is done once for all, and the positions of the entries is not important. You can sort this array so that the tuples are in a given order. When a tuple is entered by the user, you just look in the middle of the sorted array. If the query value is larger of the center value, you repeat the work on the upper half, otherwise on the lower one.
Worst case is log(n)
If you can "map" your reference data to x-y coordinates on a plane there is a nifty technique which allows you to select all points under a given distance/tolerance (using Hilbert curves).
Here is a detailed example.
One approach we are trying ourselves which allows for the discrepancies between query and reference is by binning the float values. We are testing and want to offer the user the choice of different bin sizes. Bin sizes will be 0.1 , 0.2 , 0.3 or 0.4. So binning leaves us with between 50 and 200 bins, each with a corresponding integer value between 0 and 18, where 0 means there was no value within that bin. The reference data can be pre-binned and stored in the database. We can then take the binned query data and compare it with the reference data. One approach could be for all bins, subtract the query integer value from the reference integer value. By summing up all differences we get the similarity score, with the the most similar reference entries resulting in the lowest scores.
Another (simpler) search option we want to offer is where the user only enters the float values. The integer values in both query as reference list can then be set to 1. We then use Hamming distance to compute the difference between the query and the reference binned values. I have previously asked about an efficient algorithm for that search.
This binning is only one way of achieving our goal. I am open to other suggestions. Perhaps we can use Principal Component Analysis (PCA), as described here