Using F2PY bindings in Python¶
All wrappers for Fortran/C routines, common blocks, or for Fortran
90 module data generated by F2PY are exposed to Python as fortran
type objects. Routine wrappers are callable fortran type objects
while wrappers to Fortran data have attributes referring to data
objects.
All fortran type objects have an attribute _cpointer that contains a
CObject referring to the C pointer of the corresponding Fortran/C function
or variable at the C level. Such CObjects can be used as a callback argument
for F2PY generated functions to bypass the Python C/API layer for calling Python
functions from Fortran or C when the computational aspects of such functions are
implemented in C or Fortran and wrapped with F2PY (or any other tool capable of
providing the CObject of a function).
Consider a Fortran 77 file `ftype.f:
C FILE: FTYPE.F SUBROUTINE FOO(N) INTEGER N Cf2py integer optional,intent(in) :: n = 13 REAL A,X COMMON /DATA/ A,X(3) PRINT*, "IN FOO: N=",N," A=",A," X=[",X(1),X(2),X(3),"]" END C END OF FTYPE.F
and a wrapper built using f2py -c ftype.f -m ftype.
In Python:
>>> import ftype >>> print(ftype.__doc__) This module 'ftype' is auto-generated with f2py (version:2). Functions: foo(n=13) COMMON blocks: /data/ a,x(3) . >>> type(ftype.foo), type(ftype.data) (<class 'fortran'>, <class 'fortran'>) >>> ftype.foo() IN FOO: N= 13 A= 0. X=[ 0. 0. 0.] >>> ftype.data.a = 3 >>> ftype.data.x = [1,2,3] >>> ftype.foo() IN FOO: N= 13 A= 3. X=[ 1. 2. 3.] >>> ftype.data.x[1] = 45 >>> ftype.foo(24) IN FOO: N= 24 A= 3. X=[ 1. 45. 3.] >>> ftype.data.x array([ 1., 45., 3.], dtype=float32)
Scalar arguments¶
In general, a scalar argument for a F2PY generated wrapper function can be an ordinary Python scalar (integer, float, complex number) as well as an arbitrary sequence object (list, tuple, array, string) of scalars. In the latter case, the first element of the sequence object is passed to Fortran routine as a scalar argument.
Note
When type-casting is required and there is possible loss of information via narrowing e.g. when type-casting float to integer or complex to float, F2PY does not raise an exception.
For complex to real type-casting only the real part of a complex number is used.
intent(inout)scalar arguments are assumed to be array objects in order to have in situ changes be effective. It is recommended to use arrays with proper type but also other types work.
Consider the following Fortran 77 code:
C FILE: SCALAR.F SUBROUTINE FOO(A,B) REAL*8 A, B Cf2py intent(in) a Cf2py intent(inout) b PRINT*, " A=",A," B=",B PRINT*, "INCREMENT A AND B" A = A + 1D0 B = B + 1D0 PRINT*, "NEW A=",A," B=",B END C END OF FILE SCALAR.F
and wrap it using f2py -c -m scalar scalar.f.
In Python:
>>> import scalar >>> print(scalar.foo.__doc__) foo(a,b) Wrapper for ``foo``. Parameters ---------- a : input float b : in/output rank-0 array(float,'d') >>> scalar.foo(2, 3) A= 2. B= 3. INCREMENT A AND B NEW A= 3. B= 4. >>> import numpy >>> a = numpy.array(2) # these are integer rank-0 arrays >>> b = numpy.array(3) >>> scalar.foo(a, b) A= 2. B= 3. INCREMENT A AND B NEW A= 3. B= 4. >>> print(a, b) # note that only b is changed in situ 2 4
String arguments¶
F2PY generated wrapper functions accept almost any Python object as
a string argument, since str is applied for non-string objects.
Exceptions are NumPy arrays that must have type code 'c' or
'1' when used as string arguments.
A string can have an arbitrary length when used as a string argument
for an F2PY generated wrapper function. If the length is greater than
expected, the string is truncated silently. If the length is smaller than
expected, additional memory is allocated and filled with \0.
Because Python strings are immutable, an intent(inout) argument
expects an array version of a string in order to have in situ changes be effective.
Consider the following Fortran 77 code:
C FILE: STRING.F SUBROUTINE FOO(A,B,C,D) CHARACTER*5 A, B CHARACTER*(*) C,D Cf2py intent(in) a,c Cf2py intent(inout) b,d PRINT*, "A=",A PRINT*, "B=",B PRINT*, "C=",C PRINT*, "D=",D PRINT*, "CHANGE A,B,C,D" A(1:1) = 'A' B(1:1) = 'B' C(1:1) = 'C' D(1:1) = 'D' PRINT*, "A=",A PRINT*, "B=",B PRINT*, "C=",C PRINT*, "D=",D END C END OF FILE STRING.F
and wrap it using f2py -c -m mystring string.f.
Python session:
>>> import mystring >>> print(mystring.foo.__doc__) foo(a,b,c,d) Wrapper for ``foo``. Parameters ---------- a : input string(len=5) b : in/output rank-0 array(string(len=5),'c') c : input string(len=-1) d : in/output rank-0 array(string(len=-1),'c') >>> from numpy import array >>> a = array(b'123\0\0') >>> b = array(b'123\0\0') >>> c = array(b'123') >>> d = array(b'123') >>> mystring.foo(a, b, c, d) A=123 B=123 C=123 D=123 CHANGE A,B,C,D A=A23 B=B23 C=C23 D=D23 >>> a[()], b[()], c[()], d[()] (b'123', b'B23', b'123', b'D2')
Array arguments¶
In general, array arguments for F2PY generated wrapper functions accept arbitrary sequences that can be transformed to NumPy array objects. There are two notable exceptions:
intent(inout)array arguments must always be proper-contiguous (defined below) and have a compatibledtype, otherwise an exception is raised.intent(inplace)array arguments will be changed in situ if the argument has a different type than expected (see theintent(inplace)attribute for more information).
In general, if a NumPy array is proper-contiguous and has a proper type then it is directly passed to the wrapped Fortran/C function. Otherwise, an element-wise copy of the input array is made and the copy, being proper-contiguous and with proper type, is used as the array argument.
There are two types of proper-contiguous NumPy arrays:
Fortran-contiguous arrays refer to data that is stored columnwise, i.e. the indexing of data as stored in memory starts from the lowest dimension;
C-contiguous, or simply contiguous arrays, refer to data that is stored rowwise, i.e. the indexing of data as stored in memory starts from the highest dimension.
For one-dimensional arrays these notions coincide.
For example, a 2x2 array A is Fortran-contiguous if its elements
are stored in memory in the following order:
A[0,0] A[1,0] A[0,1] A[1,1]
and C-contiguous if the order is as follows:
A[0,0] A[0,1] A[1,0] A[1,1]
To test whether an array is C-contiguous, use the .flags.c_contiguous
attribute of NumPy arrays. To test for Fortran contiguity, use the
.flags.f_contiguous attribute.
Usually there is no need to worry about how the arrays are stored in memory and whether the wrapped functions, being either Fortran or C functions, assume one or another storage order. F2PY automatically ensures that wrapped functions get arguments with the proper storage order; the underlying algorithm is designed to make copies of arrays only when absolutely necessary. However, when dealing with very large multidimensional input arrays with sizes close to the size of the physical memory in your computer, then care must be taken to ensure the usage of proper-contiguous and proper type arguments.
To transform input arrays to column major storage order before passing
them to Fortran routines, use the function numpy.asfortranarray(<array>).
Consider the following Fortran 77 code:
C FILE: ARRAY.F SUBROUTINE FOO(A,N,M) C C INCREMENT THE FIRST ROW AND DECREMENT THE FIRST COLUMN OF A C INTEGER N,M,I,J REAL*8 A(N,M) Cf2py intent(in,out,copy) a Cf2py integer intent(hide),depend(a) :: n=shape(a,0), m=shape(a,1) DO J=1,M A(1,J) = A(1,J) + 1D0 ENDDO DO I=1,N A(I,1) = A(I,1) - 1D0 ENDDO END C END OF FILE ARRAY.F
and wrap it using f2py -c -m arr array.f -DF2PY_REPORT_ON_ARRAY_COPY=1.
In Python:
>>> import arr >>> from numpy import asfortranarray >>> print(arr.foo.__doc__) a = foo(a,[overwrite_a]) Wrapper for ``foo``. Parameters ---------- a : input rank-2 array('d') with bounds (n,m) Other Parameters ---------------- overwrite_a : input int, optional Default: 0 Returns ------- a : rank-2 array('d') with bounds (n,m) >>> a = arr.foo([[1, 2, 3], ... [4, 5, 6]]) created an array from object >>> print(a) [[ 1. 3. 4.] [ 3. 5. 6.]] >>> a.flags.c_contiguous False >>> a.flags.f_contiguous True # even if a is proper-contiguous and has proper type, # a copy is made forced by intent(copy) attribute # to preserve its original contents >>> b = arr.foo(a) copied an array: size=6, elsize=8 >>> print(a) [[ 1. 3. 4.] [ 3. 5. 6.]] >>> print(b) [[ 1. 4. 5.] [ 2. 5. 6.]] >>> b = arr.foo(a, overwrite_a = 1) # a is passed directly to Fortran ... # routine and its contents is discarded ... >>> print(a) [[ 1. 4. 5.] [ 2. 5. 6.]] >>> print(b) [[ 1. 4. 5.] [ 2. 5. 6.]] >>> a is b # a and b are actually the same objects True >>> print(arr.foo([1, 2, 3])) # different rank arrays are allowed created an array from object [ 1. 1. 2.] >>> print(arr.foo([[[1], [2], [3]]])) created an array from object [[[ 1.] [ 1.] [ 2.]]] >>> >>> # Creating arrays with column major data storage order: ... >>> s = asfortranarray([[1, 2, 3], [4, 5, 6]]) >>> s.flags.f_contiguous True >>> print(s) [[1 2 3] [4 5 6]] >>> print(arr.foo(s)) >>> s2 = asfortranarray(s) >>> s2 is s # an array with column major storage order # is returned immediately True >>> # Note that arr.foo returns a column major data storage order array: ... >>> s3 = ascontiguousarray(s) >>> s3.flags.f_contiguous False >>> s3.flags.c_contiguous True >>> s3 = arr.foo(s3) copied an array: size=6, elsize=8 >>> s3.flags.f_contiguous True >>> s3.flags.c_contiguous False
Call-back arguments¶
F2PY supports calling Python functions from Fortran or C codes.
Consider the following Fortran 77 code:
C FILE: CALLBACK.F SUBROUTINE FOO(FUN,R) EXTERNAL FUN INTEGER I REAL*8 R, FUN Cf2py intent(out) r R = 0D0 DO I=-5,5 R = R + FUN(I) ENDDO END C END OF FILE CALLBACK.F
and wrap it using f2py -c -m callback callback.f.
In Python:
>>> import callback >>> print(callback.foo.__doc__) r = foo(fun,[fun_extra_args]) Wrapper for ``foo``. Parameters ---------- fun : call-back function Other Parameters ---------------- fun_extra_args : input tuple, optional Default: () Returns ------- r : float Notes ----- Call-back functions:: def fun(i): return r Required arguments: i : input int Return objects: r : float >>> def f(i): return i*i ... >>> print(callback.foo(f)) 110.0 >>> print(callback.foo(lambda i:1)) 11.0
In the above example F2PY was able to guess accurately the signature of the call-back function. However, sometimes F2PY cannot establish the appropriate signature; in these cases the signature of the call-back function must be explicitly defined in the signature file.
To facilitate this, signature files may contain special modules (the names of
these modules contain the special __user__ sub-string) that defines the
various signatures for call-back functions. Callback arguments in routine
signatures have the external attribute (see also the intent(callback)
attribute). To relate a callback argument with its signature in a __user__
module block, a use statement can be utilized as illustrated below. The same
signature for a callback argument can be referred to in different routine
signatures.
We use the same Fortran 77 code as in the previous example but now
we will pretend that F2PY was not able to guess the signatures of
call-back arguments correctly. First, we create an initial signature
file callback2.pyf using F2PY:
f2py -m callback2 -h callback2.pyf callback.f
Then modify it as follows
! -*- f90 -*- python module __user__routines interface function fun(i) result (r) integer :: i real*8 :: r end function fun end interface end python module __user__routines python module callback2 interface subroutine foo(f,r) use __user__routines, f=>fun external f real*8 intent(out) :: r end subroutine foo end interface end python module callback2
Finally, we build the extension module using f2py -c callback2.pyf callback.f.
An example Python session for this snippet would be identical to the previous example except that the argument names would differ.
Sometimes a Fortran package may require that users provide routines that the package will use. F2PY can construct an interface to such routines so that Python functions can be called from Fortran.
Consider the following Fortran 77 subroutine that takes an array as its input
and applies a function func to its elements.
subroutine calculate(x,n) cf2py intent(callback) func external func c The following lines define the signature of func for F2PY: cf2py real*8 y cf2py y = func(y) c cf2py intent(in,out,copy) x integer n,i real*8 x(n), func do i=1,n x(i) = func(x(i)) end do end
The Fortran code expects that the function func has been defined externally.
In order to use a Python function for func, it must have an attribute
intent(callback) and, it must be specified before the external statement.
Finally, build an extension module using f2py -c -m foo calculate.f
In Python:
>>> import foo >>> foo.calculate(range(5), lambda x: x*x) array([ 0., 1., 4., 9., 16.]) >>> import math >>> foo.calculate(range(5), math.exp) array([ 1. , 2.71828183, 7.3890561, 20.08553692, 54.59815003])
The function is included as an argument to the python function call to the Fortran subroutine even though it was not in the Fortran subroutine argument list. The “external” keyword refers to the C function generated by f2py, not the python function itself. The python function is essentially being supplied to the C function.
The callback function may also be explicitly set in the module. Then it is not necessary to pass the function in the argument list to the Fortran function. This may be desired if the Fortran function calling the python callback function is itself called by another Fortran function.
Consider the following Fortran 77 subroutine:
subroutine f1() print *, "in f1, calling f2 twice.." call f2() call f2() return end subroutine f2() cf2py intent(callback, hide) fpy external fpy print *, "in f2, calling f2py.." call fpy() return end
and wrap it using f2py -c -m pfromf extcallback.f.
In Python:
>>> import pfromf >>> pfromf.f2() Traceback (most recent call last): File "<stdin>", line 1, in <module> pfromf.error: Callback fpy not defined (as an argument or module pfromf attribute). >>> def f(): print("python f") ... >>> pfromf.fpy = f >>> pfromf.f2() in f2, calling f2py.. python f >>> pfromf.f1() in f1, calling f2 twice.. in f2, calling f2py.. python f in f2, calling f2py.. python f >>>
Resolving arguments to call-back functions¶
F2PY generated interfaces are very flexible with respect to call-back
arguments. For each call-back argument an additional optional
argument <name>_extra_args is introduced by F2PY. This argument
can be used to pass extra arguments to user provided call-back
functions.
If a F2PY generated wrapper function expects the following call-back argument:
def fun(a_1,...,a_n):
...
return x_1,...,x_k
but the following Python function
def gun(b_1,...,b_m):
...
return y_1,...,y_l
is provided by a user, and in addition,
fun_extra_args = (e_1,...,e_p)
is used, then the following rules are applied when a Fortran or C
function evaluates the call-back argument gun:
If
p == 0thengun(a_1, ..., a_q)is called, hereq = min(m, n).If
n + p <= mthengun(a_1, ..., a_n, e_1, ..., e_p)is called.If
p <= m < n + pthengun(a_1, ..., a_q, e_1, ..., e_p)is called, hereq=m-p.If
p > mthengun(e_1, ..., e_m)is called.If
n + pis less than the number of required arguments togunthen an exception is raised.
If the function gun may return any number of objects as a tuple; then
the following rules are applied:
If
k < l, theny_{k + 1}, ..., y_lare ignored.If
k > l, then onlyx_1, ..., x_lare set.
Common blocks¶
F2PY generates wrappers to common blocks defined in a routine
signature block. Common blocks are visible to all Fortran codes linked
to the current extension module, but not to other extension modules
(this restriction is due to the way Python imports shared libraries). In
Python, the F2PY wrappers to common blocks are fortran type
objects that have (dynamic) attributes related to the data members of
the common blocks. When accessed, these attributes return as NumPy array
objects (multidimensional arrays are Fortran-contiguous) which
directly link to data members in common blocks. Data members can be
changed by direct assignment or by in-place changes to the
corresponding array objects.
Consider the following Fortran 77 code:
C FILE: COMMON.F SUBROUTINE FOO INTEGER I,X REAL A COMMON /DATA/ I,X(4),A(2,3) PRINT*, "I=",I PRINT*, "X=[",X,"]" PRINT*, "A=[" PRINT*, "[",A(1,1),",",A(1,2),",",A(1,3),"]" PRINT*, "[",A(2,1),",",A(2,2),",",A(2,3),"]" PRINT*, "]" END C END OF COMMON.F
and wrap it using f2py -c -m common common.f.
In Python:
>>> import common >>> print(common.data.__doc__) i : 'i'-scalar x : 'i'-array(4) a : 'f'-array(2,3) >>> common.data.i = 5 >>> common.data.x[1] = 2 >>> common.data.a = [[1,2,3],[4,5,6]] >>> common.foo() >>> common.foo() I= 5 X=[ 0 2 0 0 ] A=[ [ 1.00000000 , 2.00000000 , 3.00000000 ] [ 4.00000000 , 5.00000000 , 6.00000000 ] ] >>> common.data.a[1] = 45 >>> common.foo() I= 5 X=[ 0 2 0 0 ] A=[ [ 1.00000000 , 2.00000000 , 3.00000000 ] [ 45.0000000 , 45.0000000 , 45.0000000 ] ] >>> common.data.a # a is Fortran-contiguous array([[ 1., 2., 3.], [ 45., 45., 45.]], dtype=float32) >>> common.data.a.flags.f_contiguous True
Fortran 90 module data¶
The F2PY interface to Fortran 90 module data is similar to the handling of Fortran 77 common blocks.
Consider the following Fortran 90 code:
module mod integer i integer :: x(4) real, dimension(2,3) :: a real, allocatable, dimension(:,:) :: b contains subroutine foo integer k print*, "i=",i print*, "x=[",x,"]" print*, "a=[" print*, "[",a(1,1),",",a(1,2),",",a(1,3),"]" print*, "[",a(2,1),",",a(2,2),",",a(2,3),"]" print*, "]" print*, "Setting a(1,2)=a(1,2)+3" a(1,2) = a(1,2)+3 end subroutine foo end module mod
and wrap it using f2py -c -m moddata moddata.f90.
In Python:
>>> import moddata >>> print(moddata.mod.__doc__) i : 'i'-scalar x : 'i'-array(4) a : 'f'-array(2,3) b : 'f'-array(-1,-1), not allocated foo() Wrapper for ``foo``. >>> moddata.mod.i = 5 >>> moddata.mod.x[:2] = [1,2] >>> moddata.mod.a = [[1,2,3],[4,5,6]] >>> moddata.mod.foo() i= 5 x=[ 1 2 0 0 ] a=[ [ 1.000000 , 2.000000 , 3.000000 ] [ 4.000000 , 5.000000 , 6.000000 ] ] Setting a(1,2)=a(1,2)+3 >>> moddata.mod.a # a is Fortran-contiguous array([[ 1., 5., 3.], [ 4., 5., 6.]], dtype=float32) >>> moddata.mod.a.flags.f_contiguous True
Allocatable arrays¶
F2PY has basic support for Fortran 90 module allocatable arrays.
Consider the following Fortran 90 code:
module mod real, allocatable, dimension(:,:) :: b contains subroutine foo integer k if (allocated(b)) then print*, "b=[" do k = 1,size(b,1) print*, b(k,1:size(b,2)) enddo print*, "]" else print*, "b is not allocated" endif end subroutine foo end module mod
and wrap it using f2py -c -m allocarr allocarr.f90.
In Python:
>>> import allocarr >>> print(allocarr.mod.__doc__) b : 'f'-array(-1,-1), not allocated foo() Wrapper for ``foo``. >>> allocarr.mod.foo() b is not allocated >>> allocarr.mod.b = [[1, 2, 3], [4, 5, 6]] # allocate/initialize b >>> allocarr.mod.foo() b=[ 1.000000 2.000000 3.000000 4.000000 5.000000 6.000000 ] >>> allocarr.mod.b # b is Fortran-contiguous array([[ 1., 2., 3.], [ 4., 5., 6.]], dtype=float32) >>> allocarr.mod.b.flags.f_contiguous True >>> allocarr.mod.b = [[1, 2, 3], [4, 5, 6], [7, 8, 9]] # reallocate/initialize b >>> allocarr.mod.foo() b=[ 1.000000 2.000000 3.000000 4.000000 5.000000 6.000000 7.000000 8.000000 9.000000 ] >>> allocarr.mod.b = None # deallocate array >>> allocarr.mod.foo() b is not allocated