Consider the case where I have a set of nodes, and I want to declare some ordering over them. The easiest way to do this is to declare both the set of nodes and their ranking as constants:
CONSTANTS Node, NodeRank
ASSUME NodeRank \in [Node -> Nat]
ASSUME \A n, m \in Node : NodeRank[n] = NodeRank[m] <=> n = m
Now it comes time to assign model values to these constants. Node is easy enough, I just define it as a set of model values in the toolbox:
Node <- [ model value ] {n1, n2}
I try to do something similar with NodeRank with ordinary assignment:
NodeRank <- [n1 |-> 1, n2 |-> 2]
However, when I run TLC the ASSUME statements are violated. Further examination reveals this is because in the ordinary assignment of NodeRank, n1 and n2 are treated as strings instead of model values. This makes sense, because that is the usual method of defining records (which use strings as their domain). How do I define NodeRank such that it uses the n1 and n2 model values as its domain?
If you extend TLC, you can write this as n1 :> 1 ## n2 :> 2.
Related
What is the difference between a A terra SpatRaster generated from terra and a Formal class raster layer generated by raster, if both are derived from the same raster file, let's say a tif?
They are instances of different classes defined in different R packages. They are not directly related in any way. And it does not matter whether they were constructed by reading the same file or not.
Likewise, you can represent the number 10 in many different ways (by different classes).
x <- 10
y <- list(10)
z <- data.frame(d=10)
a <- matrix(10)
You can use class to find out what class an object belongs to
class(x)
#[1] "numeric"
class(y)
#[1] "list"
class(z)
#[1] "data.frame"
class(a)
#[1] "matrix" "array"
And you can often coerce an object from one class to another.
b <- as.data.frame(a)
class(a)
#[1] "matrix" "array"
class(b)
#[1] "data.frame"
But there are things you can do with a matrix that you cannot do with a data.frame and vice versa.
Note that we also have generic functions. That is, functions that are implemented for objects of different classes. So you can do
nrow(a)
#[1] 1
nrow(z)
#[1] 1
And even
nrow(x)
#NULL
You can also use nrow with a SpatRaster and RasterLayer.
The meaning of the value returned by a generic function may depend on the object type that you are using. For example, compare the use of length for two objects of different classes holding the same numbers.
length(1:3)
#[1] 3
length(data.frame(v=1:3))
#[1] 1
Finally, with these generic functions, the actual implementation of the function that is used depends on the class of the object. Therefore, with SpatRaster x the below function calls are identical (the both call the nrow method implemented in "terra".
library(terra)
x <- rast(nrow=1, ncol=1, vals=10)
terra::nrow(x)
#[1] 1
raster::nrow(x)
#[1] 1
You do not provide a motivation for your question. In your previous question you are using the "raster" and "terra" packages at the same time. That is possible but it can easily lead to confusion because they are so similar (as illustrated by that question). See the top and the bottom of the page returned by ?terra::terra for some of the major differences.
Once you start using "terra" it is best stick with that, but if you need Raster* objects, for use with a package that only supports that class, you can coerce a SpatRaster to a RasterLayer or RasterStack like this
library(raster)
r <- raster(x)
s <- stack(x)
b <- brick(r)
# or let the software determine whether you get a Layer, Stack or Brick
y <- as(x, "Raster")
Inspect what classes they belong to
class(x)
#[1] "SpatRaster"
#attr(,"package")
#[1] "terra"
class(y)
#[1] "RasterLayer"
#attr(,"package")
#[1] "raster"
And you can take a Raster object to terra like this
rr <- rast(s)
rr
#class : SpatRaster
#dimensions : 1, 1, 1 (nrow, ncol, nlyr)
#resolution : 360, 180 (x, y)
#extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
#coord. ref. : +proj=longlat +datum=WGS84 +no_defs
#source(s) : memory
#name : lyr.1
#min value : 10
#max value : 10
I am trying to specify a collection of memory cells in TLA+, each holding 256 32-bit integers. I would like to specify that at initialization time all the memory is zeroed out. I intuit that the correct approach is something like nested forall statements, but I don't know how to express that in TLA+.
---------------------------- MODULE combinators ----------------------------
EXTENDS Integers, FiniteSets, Sequences
CONSTANTS Keys, Values
VARIABLES Cells
TypeOK ==
/\ Channels = 0 .. 255
/\ Values = -2147483648 .. 2147483647
/\ Cells \in Seq([Keys -> Values])
Init == ???
A few things.
If Values are constants, specify their domain in an ASSUME, not in an invariant. CONSTANT means some arbitray input; if you meant actual constants, then just define Values == -2147483648 .. 2147483647.
Keys could even be infinite; you must always specify an ASSUME for each constant (even IsFiniteSet).
You didn't declare Channels, but, like Values it seems like it should be a simple definition, not an invariant.
You didn't say how many Cells you're starting out with. The TypeOK is defined, the number of Cells can change at each step, and even be empty.
But suppose you want N cells for some N, so:
Cells = [c ∈ 1..N ↦ [k ∈ Keys ↦ 0]]
But you wrote "domain" and here 0 is in the range, so I'm not sure I understand your question. You also mention channels so perhaps you meant:
Cells = [c ∈ 1..N ↦ [k ∈ Channels ↦ 0]]
I'm developing an optimization problem that is a variant on Traveling Salesman. In this case, you don't have to visit all the cities, there's a required start and end point, there's a min and max bound on the tour length, you can traverse each arc multiple times if you want, and you have a nonlinear objective function that is associated with the arcs traversed (and number of times you traverse each arc). Decision variables are integers, how many times you traverse each arc.
I've developed a nonlinear integer program in Pyomo and am getting results from the NEOS server. However I didn't put in subtour constraints and my results are two disconnected subtours.
I can find integer programming formulations of TSP that say how to formulate subtour constraints, but this is a little different from the standard TSP and I'm trying to figure out how to start. Any help that can be provided would be greatly appreciated.
EDIT: problem formulation
50 arcs , not exhaustive pairs between nodes. 50 Decision variables N_ab are integer >=0, corresponds to how many times you traverse from a to b. There is a length and profit associated with each N_ab . There are two constraints that the sum of length_ab * N_ab for all ab are between a min and max distance. I have a constraint that the sum of N_ab into each node is equal to the sum N_ab out of the node you can either not visit a node at all, or visit it multiple times. Objective function is nonlinear and related to the interaction between pairs of arcs (not relevant for subtour).
Subtours: looking at math.uwaterloo.ca/tsp/methods/opt/subtour.htm , the formulation isn't applicable since I am not required to visit all cities, and may not be able to. So for example, let's say I have 20 nodes and 50 arcs (all arcs length 10). Distance constraints are for a tour of exactly length 30, which means I can visit at most three nodes (start at A -> B -> C ->A = length 30). So I will not visit the other nodes at all. TSP subtour elimination would require that I have edges from node subgroup ABC to subgroup of nonvisited nodes - which isn't needed for my problem
Here is an approach that is adapted from the prize-collecting TSP (e.g., this paper). Let V be the set of all nodes. I am assuming V includes a depot node, call it node 1, that must be on the tour. (If not, you can probably add a dummy node that serves this role.)
Let x[i] be a decision variable that equals 1 if we visit node i at least once, and 0 otherwise. (You might already have such a decision variable in your model.)
Add these constraints, which define x[i]:
x[i] <= sum {j in V} N[i,j] for all i in V
M * x[i] >= N[i,j] for all i, j in V
In other words: x[i] cannot equal 1 if there are no edges coming out of node i, and x[i] must equal 1 if there are any edges coming out of node i.
(Here, N[i,j] is 1 if we go from i to j, and M is a sufficiently large number, perhaps equal to the maximum number of times you can traverse one edge.)
Here is the subtour-elimination constraint, defined for all subsets S of V such that S includes node 1, and for all nodes i in V \ S:
sum {j in S} (N[i,j] + N[j,i]) >= 2 * x[i]
In other words, if we visit node i, which is not in S, then there must be at least two edges into or out of S. (A subtour would violate this constraint for S equal to the nodes that are on the subtour that contains 1.)
We also need a constraint requiring node 1 to be on the tour:
x[1] = 1
I might be playing a little fast and loose with the directional indices, i.e., I'm not sure if your model sets N[i,j] = N[j,i] or something like that, but hopefully the idea is clear enough and you can modify my approach as necessary.
The following model produces instances with exactly 2 address relations when the number of Books is limited to 1, however, if more Books are allowed it will create instances with 0-3 address relations. My misunderstanding of how Alloy works?
sig Name{}
sig Addr{}
sig Book { addr: Name -> lone Addr }
pred show(b:Book) { #b.addr = 2 }
// nr. of address relations in every Book should be 2
run show for 3 but 2 Book
// works as expected with 1 Book
Each instance of show should include one Book, labeled as being the b of show, which has two address pairs. But show does not say that every book must have two address pairs, only that at least one must have two address pairs.
[Postscript]
When you ask Alloy to show you an instance of a predicate, for example by the command run show, then Alloy should show you an instance: that is (quoting section 5.2.1 of Software abstractions, which you already have open) "an assignment of values to the variables of the constraint for which the constraint evaluates to true." In any given universe, there may be many other possible assignments of values to the variables for which the constraint evaluates to false; the existence of such possible non-suitable assignments is unavoidable in any universe with more than one atom.
Informally, we can think of a run command for a predicate P with arguments X, Y, Z as requesting that Alloy show us universes which satisfy the expression
some X, Y, Z : univ | P[X, Y, Z]
The run command does not amount to the expression
all X, Y, Z : univ | P[X, Y, Z]
If you want to see only universes in which every book has two pairs in its addr relation, then say so:
pred all_books_have_2 { all b : Book | #b.addr = 2 }
I think it's better that run have implicit existential quantification, rather than implicit universal quantification. One way to see why is to imagine a model that defines trees, such as:
sig Node { parent : lone Node }
fact parent_acyclic { no n : Node | n in n.^parent }
Suppose we get tired of seeing universes in which every tree is trivial and contains a single node. I'd like to be able to define a predicate that guarantees at least one tree with depth greater than 1, by writing
pred nontrivial[n : Node]{ some n.parent }
Given the constraint that trees be acyclic, there can never be a non-empty universe in which the predicate nontrivial holds for all nodes. So if run and pred had the semantics you have been supposing, we could not use nontrivial to find universes containing non-trivial trees.
I hope this helps.
My program (Hartree-Fock/iterative SCF) has two matrices F and F' which are really the same matrix expressed in two different bases. I just lost three hours of debugging time because I accidentally used F' instead of F. In C++, the type-checker doesn't catch this kind of error because both variables are Eigen::Matrix<double, 2, 2> objects.
I was wondering, for the Haskell/ML/etc. people, whether if you were writing this program you would have constructed a type system where F and F' had different types? What would that look like? I'm basically trying to get an idea how I can outsource some logic errors onto the type checker.
Edit: The basis of a matrix is like the unit. You can say 1L or however many gallons, they both mean the same thing. Or, to give a vector example, you can say (0,1) in Cartesian coordinates or (1,pi/2) in polar. But even though the meaning is the same, the numerical values are different.
Edit: Maybe units was the wrong analogy. I'm not looking for some kind of record type where I can specify that the first field will be litres and the second gallons, but rather a way to say that this matrix as a whole, is defined in terms of some other matrix (the basis), where the basis could be any matrix of the same dimensions. E.g., the constructor would look something like mkMatrix [[1, 2], [3, 4]] [[5, 6], [7, 8]] and then adding that object to another matrix would type-check only if both objects had the same matrix as their second parameters. Does that make sense?
Edit: definition on Wikipedia, worked examples
This is entirely possible in Haskell.
Statically checked dimensions
Haskell has arrays with statically checked dimensions, where the dimensions can be manipulated and checked statically, preventing indexing into the wrong dimension. Some examples:
This will only work on 2-D arrays:
multiplyMM :: Array DIM2 Double -> Array DIM2 Double -> Array DIM2 Double
An example from repa should give you a sense. Here, taking a diagonal requires a 2D array, returns a 1D array of the same type.
diagonal :: Array DIM2 e -> Array DIM1 e
or, from Matt sottile's repa tutorial, statically checked dimensions on a 3D matrix transform:
f :: Array DIM3 Double -> Array DIM2 Double
f u =
let slabX = (Z:.All:.All:.(0::Int))
slabY = (Z:.All:.All:.(1::Int))
u' = (slice u slabX) * (slice u slabX) +
(slice u slabY) * (slice u slabY)
in
R.map sqrt u'
Statically checked units
Another example from outside of matrix programming: statically checked units of dimension, making it a type error to confuse e.g. feet and meters, without doing the conversion.
Prelude> 3 *~ foot + 1 *~ metre
1.9144 m
or for a whole suite of SI units and quanities.
E.g. can't add things of different dimension, such as volumes and lengths:
> 1 *~ centi litre + 2 *~ inch
Error:
Expected type: Unit DVolume a1
Actual type: Unit DLength a0
So, following the repa-style array dimension types, I'd suggest adding a Base phantom type parameter to your array type, and using that to distinguish between bases. In Haskell, the index Dim
type argument gives the rank of the array (i.e. its shape), and you could do similarly.
Or, if by base you mean some dimension on the units, using dimensional types.
So, yep, this is almost a commodity technique in Haskell now, and there's some examples of designing with types like this to help you get started.
This is a very good question. I don't think you can encode the notion of a basis in most type systems, because essentially anything that the type checker does needs to be able to terminate, and making judgments about whether two real-valued vectors are equal is too difficult. You could have (2 v_1) + (2 v_2) or 2 (v_1 + v_2), for example. There are some languages which use dependent types [ wikipedia ], but these are relatively academic.
I think most of your debugging pain would be alleviated if you simply encoded the bases in which you matrix works along with the matrix. For example,
newtype Matrix = Matrix { transform :: [[Double]],
srcbasis :: [Double], dstbasis :: [Double] }
and then, when you M from basis a to b with N, check that N is from b to c, and return a matrix with basis a to c.
NOTE -- it seems most people here have programming instead of math background, so I'll provide short explanation here. Matrices are encodings of linear transformations between vector spaces. For example, if you're encoding a rotation by 45 degrees in R^2 (2-dimensional reals), then the standard way of encoding this in a matrix is saying that the standard basis vector e_1, written "[1, 0]", is sent to a combination of e_1 and e_2, namely [1/sqrt(2), 1/sqrt(2)]. The point is that you can encode the same rotation by saying where different vectors go, for example, you could say where you're sending [1,1] and [1,-1] instead of e_1=[1,0] and e_2=[0,1], and this would have a different matrix representation.
Edit 1
If you have a finite set of bases you are working with, you can do it...
{-# LANGUAGE EmptyDataDecls #-}
data BasisA
data BasisB
data BasisC
newtype Matrix a b = Matrix { coefficients :: [[Double]] }
multiply :: Matrix a b -> Matrix b c -> Matrix a c
multiply (Matrix a_coeff) (Matrix b_coeff) = (Matrix multiplied) :: Matrix a c
where multiplied = undefined -- your algorithm here
Then, in ghci (the interactive Haskell interpreter),
*Matrix> let m = Matrix [[1, 2], [3, 4]] :: Matrix BasisA BasisB
*Matrix> m `multiply` m
<interactive>:1:13:
Couldn't match expected type `BasisB'
against inferred type `BasisA'
*Matrix> let m2 = Matrix [[1, 2], [3, 4]] :: Matrix BasisB BasisC
*Matrix> m `multiply` m2
-- works after you finish defining show and the multiplication algorithm
While I realize this does not strictly address the (clarified) question – my apologies – it seems relevant at least in relation to Don Stewart's popular answer...
I am the author of the Haskell dimensional library that Don referenced and provided examples from. I have also been writing – somewhat under the radar – an experimental rudimentary linear algebra library based on dimensional. This linear algebra library statically tracks the sizes of vectors and matrices as well as the physical dimensions ("units") of their elements on a per element basis.
This last point – tracking physical dimensions on a per element basis – is rather challenging and perhaps overkill for most uses, and one could even argue that it makes little mathematical sense to have quantities of different physical dimensions as elements in any given vector/matrix. However, some linear algebra applications of interest to me such as kalman filtering and weighted least squares estimation typically use heterogeneous state vectors and covariance matrices.
Using a Kalman filter as an example, consider a state vector x = [d, v] which has physical dimensions [L, LT^-1]. The next (future) state vector is predicted by multiplication by the state transition matrix F, i.e.: x' = F x_. Clearly for this equation to make sense F cannot be arbitrary but must have size and physical dimensions [[1, T], [T^-1, 1]]. The predict_x' function below statically ensures that this relationship holds:
predict_x' :: (Num a, MatrixVector f x x) => Mat f a -> Vec x a -> Vec x a
predict_x' f x_ = f |*< x_
(The unsightly operator |*< denotes multiplication of a matrix on the left with a vector on the right.)
More generally, for an a priori state vector x_ of arbitrary size and with elements of arbitrary physical dimensions, passing a state transition matrix f with "incompatible" size and/or physical dimensions to predict_x' will cause a compile time error.
In F# (which originally evolved from OCaml), you can use units of measure. Andrew Kenned, who designed the feature (and also created a very interesting theory behind it) has a great series of articles that demonstrate it.
This can quite likely be used in your scenario - although I don't fully understand the question. For example, you can declare two unit types like this:
[<Measure>] type litre
[<Measure>] type gallon
Adding litres and gallons gives you a compile time error:
1.0<litre> + 1.0<gallon> // Error!
F# doesn't automatically insert conversion between different units, but you can write a conversion function:
let toLitres gal = gal * 3.78541178<litre/gallon>
1.0<litre> + (toLitres 1.0<gallon>)
The beautiful thing about units of measure in F# is that they are automatically inferred and functions are generic. If you multiply 1.0<gallon> * 1.0<gallon>, the result is 1.0<gallon^2>.
People have used this feature for various things - ranging from conversion of virtual meters to screen pixels (in solar system simulations) to converting currencies (dollars in financial systems). Although I'm not expert, it is quite likely that you could use it in some way for your problem domain too.
If it's expressed in a different base, you can just add a template parameter to act as the base. That will differentiate those types. A float is a float is a float- if you don't want two float values to be the same if they actually have the same value, then you need to tell the type system about it.