ShortestPath.SHP.Edge.MinDist

Calculate minimum-distance Hamiltonian Shortest Paths and probabilities for starting nodes.

NOTE: We explicitly model starting nodes. For symmetrical distance matrices, this reports begin/end probabilities. For asymmetrical distance matrices, a second instances with Last instead of First boundary should be created to calculate begin/end probabilities separately.

Documentation

aMinDist :: Monad m => ScoreMatrix Double -> SigMinDist m Double Double (From :. To) (Int :. To)

Minimal distance algebra

TODO The two Ints are the indices of the nodes and could be replaced?

aMaxEdgeProb :: Monad m => ScoreMatrix (Log Double) -> SigMinDist m (Log Double) (Log Double) (From :. To) (Int :. To)

Maximum edge probability following the probabilities generated from the EdgeProb grammar.

data PathBT

Constructors

BTnode !(Int :. To)

BTedge !(From :. To)

Instances

Show PathBT

Methods

showsPrec :: Int -> PathBT -> ShowS

show :: PathBT -> String

showList :: [PathBT] -> ShowS

aPathBT :: Monad m => ScoreMatrix t -> SigMinDist m [PathBT] [[PathBT]] (From :. To) (Int :. To)

This should give the correct order of nodes independent of the underlying Set1 First or Set1 Last because the (From:.To) system is agnostic over these.

aPretty :: Monad m => ScoreMatrix t -> SigMinDist m Text [Text] (From :. To) (Int :. To)

This should give the correct order of nodes independent of the underlying Set1 First or Set1 Last because the (From:.To) system is agnostic over these.

aInside :: Monad m => ScoreMatrix (Log Double) -> SigMinDist m (Log Double) (Log Double) (From :. To) (Int :. To)

Before using aInside the ScoreMatrix needs to be scaled appropriately! Due to performance reasons we don't want to do this within aInside.

type TS1 x = TwITbl Id Unboxed EmptyOk (BS1 First I) x

type U x = TwITbl Id Unboxed EmptyOk (Unit I) x

type PF x = TwITbl Id Unboxed EmptyOk (Boundary First I) x

type TS1L x = TwITbl Id Unboxed EmptyOk (BS1 Last I) x

type UL x = TwITbl Id Unboxed EmptyOk (Unit I) x

type PFL x = TwITbl Id Unboxed EmptyOk (Boundary Last I) x

type BT1 x b = TwITblBt Unboxed EmptyOk (BS1 First I) x Id Id b

type BTU x b = TwITblBt Unboxed EmptyOk (Unit I) x Id Id b

type BT1L x b = TwITblBt Unboxed EmptyOk (BS1 Last I) x Id Id b

type BTUL x b = TwITblBt Unboxed EmptyOk (Unit I) x Id Id b

forwardMinDist1 :: ScoreMatrix Double -> (Z :. TS1 Double) :. U Double

Run the minimal distance algebra.

This produces one-boundary sets. Meaning that for each boundary we get the total distance within the set.

backtrackMinDist1 :: ScoreMatrix Double -> ((Z :. TS1 Double) :. U Double) -> [Text]

pathbtMinDist :: ScoreMatrix Double -> ((Z :. TS1 Double) :. U Double) -> [[PathBT]]

runCoOptDist :: ScoreMatrix Double -> (Double, [Text])

Given the Set1 produced in forwardMinDist1 we can now extract the co-optimal paths using the Set1 -> () index change.

TODO do we want this one explicitly or make life easy and just extract from all forwardMinDist1 paths?

runMinDist :: ScoreMatrix Double -> (Double, [[PathBT]])

Return the minimal distance and provide a list of co-optimal backtraces.

boundaryPartFun :: Double -> ScoreMatrix Double -> [(Boundary First I, Log Double)]

Extract the individual partition scores.

forwardMaxEdgeProbFirst :: ScoreMatrix (Log Double) -> (Z :. TS1 (Log Double)) :. U (Log Double)

Run the maximal edge probability grammar.

forwardMaxEdgeProbLast :: ScoreMatrix (Log Double) -> (Z :. TS1L (Log Double)) :. UL (Log Double)

pathbtMaxEdgeProbFirst :: ScoreMatrix (Log Double) -> ((Z :. TS1 (Log Double)) :. U (Log Double)) -> [[PathBT]]

pathbtMaxEdgeProbLast :: ScoreMatrix (Log Double) -> ((Z :. TS1L (Log Double)) :. UL (Log Double)) -> [[PathBT]]

runMaxEdgeProbFirst :: ScoreMatrix (Log Double) -> (Log Double, [[PathBT]])

Given the Set1 produced in forwardMinDist1 we can now extract the co-optimal paths using the Set1 -> () index change.

TODO do we want this one explicitly or make life easy and just extract from all forwardMinDist1 paths?

runMaxEdgeProbLast :: ScoreMatrix (Log Double) -> (Log Double, [(Boundary Last I, Log Double)], [[PathBT]])

test :: Double -> FilePath -> IO ()