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up vote 3 down vote favorite

My app will be running on an iPad with A7. I pass in 3 JSON arrays and right now do some simple filtering, in the future the operation will be much more complicated. I realize the if statement is slowing down the process, but how can I avoid it? Is there a way to have this loop on one CPU and run the GUI on the other CPU (assign affinity)?

class func filterPhenotypeByPvalues(
    phenotypeJSON:[String],
    SNPJSON:[String],
    dataJSON:[Float],
    limit:Float) -> ([Float],[String],[String])
  {
    let dbg:Bool = true
    var PvalueFiltered:[Float] = []
    var PhenotypeFiltered:[String] = []
    var SNPFiltered:[String] = []
    //initialize arrays with value
    //[Float](count: data.count, repeatedValue: 0.0)

    var i:Int = 0

    let startTime = CFAbsoluteTimeGetCurrent()

    for (i = 0; i < dataJSON.count; i++) {
      if dataJSON[i] <= limit {
        PvalueFiltered.append(-log10(dataJSON[i]))
        PhenotypeFiltered.append(phenotypeJSON[i])
        SNPFiltered.append(SNPJSON[i])
      }
    }

    let timeElapsed = CFAbsoluteTimeGetCurrent() - startTime
    if(dbg){println("Time elapsed filterPhenotypeByPvalues: \(timeElapsed) s")}

    return (PvalueFiltered,PhenotypeFiltered,SNPFiltered)
  }

A very small sample of the JSON data file:

{
    "data": [
        ["rs6855911","Negative control - flare length",0.0000000002],
        ["rs6855911","BMD of intertrochanter region - gm/cm sq",0.0000000007],
        ["rs1501908","BMD of intertrochanter region - gm/cm sq",0.000000001]
    ]
}

Screenshot of timing profile:

enter image description here

share|improve this question
1  
Have you run this through Instruments to actually assess which part is slow? –  nhgrif yesterday
    
Yes and I didn't find the results useful as there are lots of things going on besides this and so put timing code in specifically for this function. –  G Alexander yesterday
    
Sharing the information that Instruments gave you can be helpful to some of us with more experience looking at it (or it may be useless). Also, some sample inputs would be helpful (so we can plug this into Playground or run it in Instruments ourselves). –  nhgrif yesterday

1 Answer 1

up vote 3 down vote accepted

There may exist a way to make this particular loop run faster. In fact, I'm sure there probably is... however, it's kind of a futile effort.

There's a lot of time also being wasted elsewhere where we're creating these original three arrays we're passing in here. We need to take a far more OOP approach to this problem.

I don't know what this code actually represents, but for now, I'm going to use "Phenotype" and assume that's an accurate noun to give to the object that the JSON data is trying to describe.

The way the JSON data is structured suggests that the these three data points are obviously tied to each other. We don't need to create three separate arrays and somehow rely on a common index among them to remember what goes with what. Let's make a container to hold all of this information:

struct Phenotype {
    var phenotype: String
    var SNP: String
    var data: String
}

(The struct name and its variable names are probably far from optimal.)

Now, when we parse out the JSON data, we create a single array of instances of our Phenotype struct rather than three arrays of the different types.

Now we don't even need to write the method in your question, because we can do it with the built-in filter method:

let limit = someValue
let dataFromJSON = someFuncCreatingArrayOfPhenotypesFromJSONData(data)

let filteredData = dataFromJSON.filter { $0.data <= limit }

And filteredData represents exactly the data your method was trying to extract.

share|improve this answer
    
Thanks, I'll have a go at implementation and see what timing results are. Well, I use 3 different arrays as the data can be filtered by each variable, which would leave large sparse matrix. With separate arrays, I can independently vectorize operations. –  G Alexander 23 hours ago
    
It's easy to filter by any of the variables when they're in the struct too. –  nhgrif 23 hours ago
    
let filteredPhenotype = dataFromJSON.filter { $0.phenotype = "rs6855911" } –  nhgrif 23 hours ago

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