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ncio.f90
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ncio.f90
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! The MIT License (MIT)
!
! Copyright (c) 2014 Alexander Robinson and Mahé Perrette
!
! Permission is hereby granted, free of charge, to any person obtaining a copy
! of this software and associated documentation files (the "Software"), to deal
! in the Software without restriction, including without limitation the rights
! to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
! copies of the Software, and to permit persons to whom the Software is
! furnished to do so, subject to the following conditions:
!
! The above copyright notice and this permission notice shall be included in all
! copies or substantial portions of the Software.
!
! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
! AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
! OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
! SOFTWARE.
module ncio
use netcdf
implicit none
double precision, parameter :: NCIO_VERSION = 0.2d0
integer, parameter :: NC_STRLEN = 256
integer, parameter :: NC_STRLEN_MAX = 10000
character(len=2) :: NC_STR_SEP = "; "
double precision, parameter :: NC_TOL = 1d-7
double precision, parameter :: NC_LIM = 1d25
character(len=NC_STRLEN), parameter :: NC_CHARDIM = "strlen"
type ncvar
character (len=NC_STRLEN) :: name, long_name, standard_name, units
character (len=NC_STRLEN) :: axis, calendar, grid_mapping
character (len=NC_STRLEN) :: xtype, dims_in(4)
character (len=NC_STRLEN), allocatable :: dims(:)
integer, allocatable :: dlen(:), start(:), count(:)
integer :: n, dimid, varid, ndims_in
double precision :: add_offset, scale_factor, missing_value, FillValue
double precision :: actual_range(2)
logical :: missing_set, FillValue_set
double precision, allocatable :: dim(:)
logical :: coord
end type
interface nc_write
module procedure nc_write_int_pt, &
nc_write_int_1D, nc_write_int_2D, &
nc_write_int_3D, nc_write_int_4D
module procedure nc_write_double_pt, &
nc_write_double_1D, nc_write_double_2D, &
nc_write_double_3D, nc_write_double_4D, &
nc_write_double_5D, nc_write_double_6D
module procedure nc_write_float_pt, &
nc_write_float_1D, nc_write_float_2D, &
nc_write_float_3D, nc_write_float_4D
module procedure nc_write_logical_pt, &
nc_write_logical_1D, nc_write_logical_2D, &
nc_write_logical_3D, nc_write_logical_4D
! Note: character writing and reading do not
! follow the conventions of the other data types
module procedure nc_write_internal_char, &
nc_write_char_1D, nc_write_char_2D, &
nc_write_char_3D, nc_write_char_4D ! Dummy procedures
end interface
interface nc_read
module procedure nc_read_int_pt, &
nc_read_int_1D, nc_read_int_2D, &
nc_read_int_3D, nc_read_int_4D, &
nc_read_int_5D, nc_read_int_6D
module procedure nc_read_double_pt, &
nc_read_double_1D, nc_read_double_2D, &
nc_read_double_3D, nc_read_double_4D, &
nc_read_double_5D, nc_read_double_6D
module procedure nc_read_float_pt, &
nc_read_float_1D, nc_read_float_2D, &
nc_read_float_3D, nc_read_float_4D, &
nc_read_float_5D, nc_read_float_6D
module procedure nc_read_logical_pt, &
nc_read_logical_1D, nc_read_logical_2D, &
nc_read_logical_3D, nc_read_logical_4D, &
nc_read_logical_5D, nc_read_logical_6D
! Note: character writing and reading do not
! follow the conventions of the other data types
module procedure nc_read_internal_char, &
nc_read_char_1D
end interface
interface nc_write_dim
module procedure nc_write_dim_int_pt, nc_write_dim_int_1D
module procedure nc_write_dim_double_pt, nc_write_dim_double_1D
module procedure nc_write_dim_float_pt, nc_write_dim_float_1D
end interface
interface nc_read_attr
module procedure nc_read_attr_variable_char, nc_read_attr_variable_int
module procedure nc_read_attr_variable_sp, nc_read_attr_variable_dp
module procedure nc_read_attr_global_char, nc_read_attr_global_int
module procedure nc_read_attr_global_sp, nc_read_attr_global_dp
end interface
interface nc_write_attr
module procedure nc_write_attr_variable_char, nc_write_attr_variable_int
module procedure nc_write_attr_variable_sp, nc_write_attr_variable_dp
module procedure nc_write_attr_global_char, nc_write_attr_global_int
module procedure nc_write_attr_global_sp, nc_write_attr_global_dp
end interface
interface nc_exists_attr
module procedure nc_exists_attr_global, nc_exists_attr_variable
end interface
private
public :: nc_read, nc_read_attr
public :: nc_create, nc_write_map, nc_write_dim
public :: nc_open, nc_close
public :: nc_write, nc_write_attr, nc_size
public :: nc_dims, nc_ndims
public :: nc_write_attr_std_dim
public :: nc_exists_var, nc_exists_attr
contains
! =================================
!
! INTERNAL WRITE/READ FUNCTIONS
!
! =================================
subroutine nc4_write_internal(filename,name,dat,xtype,size_in,&
ncid,dims,dim1,dim2,dim3,dim4,dim5,dim6, &
start,count,long_name,standard_name,grid_mapping,units, &
missing_value_int,missing_value_float,missing_value_double)
implicit none
type(ncvar) :: v
double precision :: dat(:)
character (len=*), optional :: dims(:), dim1, dim2, dim3, dim4, dim5, dim6
integer, optional :: start(:), count(:)
character (len=*) :: filename, name, xtype
character (len=*), optional :: long_name, standard_name, grid_mapping, units
integer, optional :: missing_value_int
real(4), optional :: missing_value_float
double precision, optional :: missing_value_double
integer :: size_in(:)
integer, allocatable :: size_var(:)
integer, optional :: ncid
integer :: nc_id
! netCDF needed counters, array, and names of dims
integer :: stat, ncount, nvar, RecordDimID
! Additional helper variables
integer :: i, j, k, m, ndims, dimid
double precision :: actual_range(2)
! Initialize ncvar type
call nc_v_init(v,trim(name),xtype=trim(xtype))
! Add extra var info if available from arguments
if ( present(long_name) ) v%long_name = trim(long_name)
if ( present(standard_name) ) v%standard_name = trim(standard_name)
if ( present(grid_mapping) ) v%grid_mapping = trim(grid_mapping)
if ( present(units) ) v%units = trim(units)
if (present(missing_value_int)) then
v%missing_set = .TRUE.
v%missing_value = dble(missing_value_int)
else if (present(missing_value_float)) then
v%missing_set = .TRUE.
v%missing_value = dble(missing_value_float)
else if (present(missing_value_double)) then
v%missing_set = .TRUE.
v%missing_value = missing_value_double
end if
! Open the file in write mode from filename or ncid
call nc_check_open(filename, ncid, nf90_write, nc_id)
! and get attributes if variable already exist
call nc_get_att(nc_id,v)
call nc_check( nf90_inquire(nc_id, unlimitedDimID=RecordDimID) ) ! Get Unlimited dimension ID if any
! Determine number of dims in file from arguments
if (present(dims)) then
ndims = size(dims)
! Consistency check
if (present(dim1)) then
write(*,*) "nc_write:: Warning, either `dims` or `dim1,dim2,...` arguments "
write(*,*) " should be specified - not both. Using `dims`."
end if
else
ndims = 1
if (present(dim2)) ndims = 2
if (present(dim3)) ndims = 3
if (present(dim4)) ndims = 4
if (present(dim5)) ndims = 5
if (present(dim6)) ndims = 6
end if
! Allocate dimensions of variable on file
if (allocated(v%dims)) deallocate(v%dims)
allocate( v%dims(ndims) )
if (present(dims)) then
do i = 1, ndims
v%dims(i) = trim(dims(i))
end do
else
do i = 1, ndims
select case(i)
case(1)
v%dims(i) = trim(dim1)
case(2)
v%dims(i) = trim(dim2)
case(3)
v%dims(i) = trim(dim3)
case(4)
v%dims(i) = trim(dim4)
case(5)
v%dims(i) = trim(dim5)
case(6)
v%dims(i) = trim(dim6)
end select
end do
end if
! Initialize the start and count arrays
allocate(v%start(ndims),v%count(ndims),size_var(ndims))
v%start = 1
if (present(start)) v%start = start
nvar = 1
do i = 1, ndims
size_var(i) = nc_size(filename,v%dims(i),ncid=nc_id)
nvar = nvar*size_var(i)
end do
! Initialize count such that the entire input array will be stored in file
! unless count argument is given
v%count = 1
if (present(count)) then
! Assign argument as count
v%count = count
else if (size(dat) .eq. nvar) then
! Assign count from size of variable on file
v%count = size_var
else
! Assign count from input dimension size
v%count(1:size(size_in)) = size_in
end if
! Reset or initialize the actual range of the variable
if (v%missing_set) then
actual_range = [minval(dat,mask=dabs(dat-v%missing_value) .gt. NC_TOL), &
maxval(dat,mask=dabs(dat-v%missing_value) .gt. NC_TOL)]
else
actual_range = [minval(dat),maxval(dat)]
end if
if (v%start(ndims) .ne. 1) then
v%actual_range(1) = min(v%actual_range(1),actual_range(1))
v%actual_range(2) = max(v%actual_range(2),actual_range(2))
else
v%actual_range = actual_range
end if
! Check if the variable gave us reasonable values
if (maxval(dabs(v%actual_range)) .gt. 1d98) then
write(*,*) "ncio:: nc_write:: warning: actual range too high,&
& variable may not be defined: "//trim(v%name)
v%actual_range = [0.d0,0.d0]
end if
! Modify the variable according to scale and offset (if working with real or double data)
if (trim(v%xtype) .eq. "NF90_FLOAT" .or. trim(v%xtype) .eq. "NF90_DOUBLE") then
if (v%missing_set) then
where( dabs(dat-v%missing_value) .gt. NC_TOL ) dat = (dat-v%add_offset)/v%scale_factor
else
! Apply the scalar and offset if available
dat = (dat-v%add_offset)/v%scale_factor
end if
end if
! Make sure count size makes sense
ncount = 1
do i = 1, ndims
ncount = ncount*v%count(i)
end do
if (size(dat) .ne. ncount) then
write(0,*) "ncio:: error: "// &
"The input variable size does not match the count of values to write to file."
write(0,*) trim(filename)//": "//trim(v%name)
write(0,*) "Size of variable, count: ",size(dat), ncount
write(0,*) " start: ",start
write(0,*) " count: ",count
write(0,*) "v%count: ",v%count
stop
end if
do i = 1, ndims
call nc_check( nf90_inq_dimid(nc_id, v%dims(i), dimid) )
! If unlimited dimension, the size does not matter
if (dimid .eq. RecordDimID) cycle
call nc_check( nf90_inquire_dimension(nc_id, dimid, len=size_var(i)) )
if (v%count(i) .gt. size_var(i)) then
write(0,*) "ncio:: error: "// &
"count exceeds this dimension length."
write(0,*) trim(filename)//": "//trim(v%name)
write(0,*) "Dimension exceeded: ",trim(v%dims(i)), size_var(i)," < ",v%count(i)
write(0,*) "Are the data values a different shape than the file dimensions?"
write(0,*) " In that case, specify start+count as arguments."
stop
end if
end do
! Define / update the netCDF variable for the data.
call nc_check( nf90_redef(nc_id) )
call nc_put_att(nc_id, v)
call nc_check( nf90_enddef(nc_id) )
! Write the data to the netcdf file
! Note: NF90 converts dat to proper type (int, real, dble) and shape
call nc_check( nf90_put_var(nc_id, v%varid, dat,v%start,v%count) )
! Close the file. This causes netCDF to flush all buffers and make
! sure your data are really written to disk.
if (.not. present(ncid)) call nc_check( nf90_close(nc_id) )
! write(*,"(a,a,a14)") "ncio:: nc_write:: ",trim(filename)//" : ",trim(v%name)
return
end subroutine nc4_write_internal
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Subroutine : n c _ r e a d
! Author : Alex Robinson
! Purpose : Read a variable from a netcdf file
! (only one time step 'ndat' at a time)
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc4_read_internal_numeric(filename,name,dat,size_in,start,count,xtype, &
missing_value_int,missing_value_float,missing_value_double, ncid, iostat)
implicit none
integer :: nc_id, v_id, stat, ndims, ndat, dim_in, n1
integer, optional :: start(:), count(:), ncid
character (len=*) :: filename, name, xtype
type(ncvar) :: v
double precision, dimension(:) :: dat
integer :: size_in(:)
integer, optional :: missing_value_int
real(4), optional :: missing_value_float
double precision, optional :: missing_value_double
double precision :: tmp
character (len=NC_STRLEN) :: tmpstr
integer, optional :: iostat
integer :: i, status
! Open the file.
call nc_check_open(filename, ncid, nf90_nowrite, nc_id)
! Check to make sure variable exists !!!!
status = nf90_inq_varid(nc_id, trim(name), v_id)
if (status /= nf90_noerr) then
if (present(iostat)) then
iostat = status
return
else
write(0,*) "ncio :: error when reading file: ",trim(filename)
write(0,*) "ncio :: error when reading variable: ",trim(name)
write(0,*) "ncio :: error: "//trim(nf90_strerror(status))
stop "stopped by ncio."
endif
endif
! Initialize the netcdf variable info and load attributes
call nc_v_init(v,name)
call nc_get_att(nc_id,v,readmeta=.TRUE.)
v%xtype = trim(xtype)
! Get variable dimension
ndims = size(v%dims)
if (present(start)) then
allocate(v%start(size(start)))
v%start = start
else
allocate(v%start(ndims))
v%start(:) = 1
end if
if (present(count)) then
allocate(v%count(size(count)))
v%count = count
else
if (.not. ndims .eq. size(size_in)) then
write(*,"(a)") "nc_read:: ","Warning: "// &
"Variable dimensions in the file do not match those being read in."
write(*,"(' ndim = ', i2, ', size(size_in) = ', i2)") ndims, size(size_in)
write(*,*) trim(filename)//": ",trim(name)
end if
allocate(v%count(ndims))
v%count = 1
do i = 1, size(size_in)
v%count(i) = size_in(i)
end do
end if
! Read the variable data from the file
! (NF90 converts dat to proper type (int, real, dble)
call nc_check( nf90_get_var(nc_id, v%varid, dat, v%start, v%count) )
! Close the file. This frees up any internal netCDF resources
! associated with the file.
if (.not. present(ncid)) call nc_check( nf90_close(nc_id) )
if (v%missing_set) then
where( dabs(dat-v%missing_value) .gt. NC_TOL ) dat = dat*v%scale_factor + v%add_offset
! Fill with user-desired missing value
if (present(missing_value_int)) &
where( dabs(dat-v%missing_value) .le. NC_TOL ) dat = dble(missing_value_int)
if (present(missing_value_float)) &
where( dabs(dat-v%missing_value) .le. NC_TOL ) dat = dble(missing_value_float)
if (present(missing_value_double)) &
where( dabs(dat-v%missing_value) .le. NC_TOL ) dat = dble(missing_value_double)
else
! Apply the scalar and offset if available
if (v%scale_factor .ne. 1.d0 .and. v%add_offset .ne. 0.d0) &
dat = dat*v%scale_factor + v%add_offset
end if
! Also eliminate crazy values (in case they are not handled by missing_value for some reason)
! Fill with user-desired missing value
if (present(missing_value_int)) &
where( dabs(dat) .ge. NC_LIM ) dat = dble(missing_value_int)
if (present(missing_value_float)) &
where( dabs(dat) .ge. NC_LIM ) dat = dble(missing_value_float)
if (present(missing_value_double)) &
where( dabs(dat) .ge. NC_LIM ) dat = dble(missing_value_double)
! write(*,"(a,a,a)") "ncio:: nc_read:: ",trim(filename)//" : ",trim(v%name)
if (present(iostat)) iostat = nf90_noerr
return
end subroutine nc4_read_internal_numeric
! Open a netcdf file and return a valid ncid
subroutine nc_open(filename,ncid,writable)
implicit none
character(len=*) filename
logical, optional :: writable
logical :: is_writable
integer :: ncid
is_writable = .TRUE.
if (present(writable)) is_writable = writable
if (is_writable) then
call nc_check( nf90_open(filename, nf90_write, ncid) )
else
call nc_check( nf90_open(filename, nf90_nowrite, ncid) )
end if
return
end subroutine nc_open
! Close a netcdf file returning the ncid=0
subroutine nc_close(ncid)
implicit none
integer :: ncid
call nc_check( nf90_close(ncid) )
ncid = 0
return
end subroutine nc_close
!! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!! Subroutine : nc_v_init
!! Author : Alex Robinson
!! Purpose : Make some default initializations of netcdf dim vars
!! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc_v_init(v,name,xtype,ndims_in,long_name,standard_name, &
grid_mapping,units,axis,calendar,coord)
implicit none
type(ncvar) :: v
character(len=*) :: name
character(len=*), optional :: xtype
integer, optional :: ndims_in
character(len=*), optional :: long_name, standard_name
character(len=*), optional :: grid_mapping, units, axis, calendar
logical, optional :: coord
integer :: i
! Intialize all variable information with default values
v%name = trim(name)
v%long_name = ""
v%standard_name = ""
v%units = ""
v%axis = ""
v%calendar = ""
v%add_offset = 0.d0
v%scale_factor = 1.d0
v%actual_range = (/ 0.d0, 0.d0 /)
v%missing_set = .TRUE.
v%missing_value = -9999d0
v%FillValue = v%missing_value
v%FillValue_set = .FALSE.
v%xtype = "NF90_DOUBLE"
v%coord = .FALSE.
v%grid_mapping = ""
! If args are present, reassign these variables
if ( present(long_name) ) v%long_name = trim(long_name)
if ( present(grid_mapping) ) v%grid_mapping = trim(grid_mapping)
if ( present(units) ) v%units = trim(units)
if ( present(axis) ) v%axis = trim(axis)
if ( present(calendar) .and. trim(name) == "time" ) &
v%calendar = trim(calendar)
if ( present(coord)) v%coord = coord
if ( present(xtype)) v%xtype = trim(xtype)
! Deallocate all arrays
if (allocated(v%dim)) deallocate(v%dim)
if (allocated(v%dims)) deallocate(v%dims)
if (allocated(v%dlen)) deallocate(v%dlen)
do i = 1, 4
v%dims_in(i) = ""
end do
v%ndims_in = 0
if (present(ndims_in)) v%ndims_in = ndims_in
return
end subroutine nc_v_init
!
! Write attributes for standard dimensions found in a netCDF file
! (if attribute not already defined)
!
subroutine nc_write_attr_std_dim(filename, ncid)
integer :: nc_id, ndims, varid, stat, i
integer, allocatable :: dimids(:)
integer, optional, intent(in) :: ncid
character (len=*), intent(in) :: filename
character (len=NC_STRLEN) :: name
! Open netCDF file and get file ID
call nc_check_open(filename, ncid, nf90_write, nc_id)
! Make netCDF file ready for writing attributes
call nc_check( nf90_redef(nc_id) )
! Loop over dimensions and update attributes
do i = 1, 99
! Check whether a dimension corresponds to this ID
! exit loop if not
stat = nf90_inquire_dimension(nc_id,i,name=name)
if ( stat .ne. NF90_NOERR) then
exit
endif
! Check whether a variable is associated with this dimension
stat = nf90_inq_varid(nc_id, trim(name), varid)
if ( varid .ne. NF90_NOERR) cycle ! if dimension is not defined as variable, skip it
! Update some variable info based on further default cases
select case(trim(name))
case("x","xc")
!call nc_check( nf90_put_att(nc_id, varid, "long", v%scale_factor) )
call put_att_check(nc_id, varid, "long_name" , "x-coordinate in Cartesian system")
call put_att_check(nc_id, varid, "standard_name" , "projection_x_coordinate")
call put_att_check(nc_id, varid, "units" , "kilometers")
call put_att_check(nc_id, varid, "axis" , "X")
case("y","yc")
call put_att_check(nc_id, varid, "long_name" , "y-coordinate in Cartesian system")
call put_att_check(nc_id, varid, "standard_name" , "projection_y_coordinate")
call put_att_check(nc_id, varid, "units" , "kilometers")
call put_att_check(nc_id, varid, "axis" , "Y")
case("z","lev")
call put_att_check(nc_id, varid, "units" , "meters")
call put_att_check(nc_id, varid, "axis" , "Z")
case("kc","kt","kr")
call put_att_check(nc_id, varid, "axis" , "Z")
case("time")
call put_att_check(nc_id, varid, "units" , "years since 0-0-0")
call put_att_check(nc_id, varid, "axis" , "T")
case("lon","longitude")
call put_att_check(nc_id, varid, "long_name" , "longitude")
call put_att_check(nc_id, varid, "standard_name" , "longitude")
call put_att_check(nc_id, varid, "units" , "degrees_east")
case("lat","latitude")
call put_att_check(nc_id, varid, "long_name" , "latitude")
call put_att_check(nc_id, varid, "standard_name" , "latitude")
call put_att_check(nc_id, varid, "units" , "degrees_north")
case default
! Do nothing
end select
end do
! End definition mode and close file
call nc_check( nf90_enddef(nc_id) )
if (.not.present(ncid)) call nc_check( nf90_close(nc_id) )
end subroutine
! write a variable attribute if not already defined
subroutine put_att_check(ncid, varid, name, value)
integer, intent(in) :: ncid, varid
character (len=*), intent(in) :: name, value
! internal variables
integer :: stat
character (len=NC_STRLEN) :: tmpstr
! Try to retrieve attribute
stat = nf90_get_att(ncid, varid, name, tmpstr)
! Write new attribute only if not already defined
if ( stat .ne. NF90_NOERR) then
call nc_check( nf90_put_att(ncid, varid, name, value) )
endif
end subroutine
!! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!! Subroutine : c h e c k
!! Author : Alex Robinson
!! Purpose : Wrap a netcdf function to perform error checking
!! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc_check(status,stat)
implicit none
integer, intent ( in) :: status
integer, intent (out), optional :: stat
if(status /= nf90_noerr .and. (.not. present(stat)) ) then
write(0,*) "ncio:: error: "//trim(nf90_strerror(status))
stop "stopped by ncio."
end if
if (present(stat)) then
stat = 0
if(status /= nf90_noerr) stat = -1
end if
return
end subroutine nc_check
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Subroutine : c h e c k _ a t t
! Author : Alex Robinson
! Purpose : Wrap an attribute function to perform error checking
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
function nc_check_att(status)
implicit none
integer, intent (in) :: status
integer :: nc_check_att
integer, parameter :: noerr = NF90_NOERR
nc_check_att = noerr
if(status /= nf90_noerr) then
if (trim(nf90_strerror(status)) .eq. "NetCDF: Attribute not found") then
nc_check_att = -1
else
write(0,*) trim(nf90_strerror(status))
stop "Stopped"
end if
end if
return
end function nc_check_att
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Purpose : Open file when necessary, informative error message
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc_check_open(filename, ncid, mode, nc_id)
implicit none
character(len=*), optional, intent ( in) :: filename
integer, optional, intent ( in) :: ncid
integer, intent (in) :: mode
integer, intent (out) :: nc_id
integer stat
! Open the file.
if (present(ncid)) then
nc_id = ncid
else
if (.not. present(filename)) then
write(0,*) "ncio :: neither filename nor ncid provided, stop"
stop
endif
stat = nf90_open(filename, mode, nc_id)
if (stat .ne. NF90_NOERR) then
write(0,*) "ncio :: error when opening file, no such file or directory? :: ",trim(filename)
stop
endif
end if
return
end subroutine nc_check_open
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Subroutine : a t t r _ p r i n t
! Author : Alex Robinson
! Purpose : Print all major netcdf attributes
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc_print_attr(v)
implicit none
type(ncvar) :: v
integer :: i
character(len=512) :: dims_char
write(dims_char,*) (trim(v%dims(i))//" ", i=1,size(v%dims))
write(*,*)
write(*,*) "nc_print_attr::"
write(*,"(10x,a20,a1,2x,a)") "name", ":",trim(v%name)
write(*,"(10x,a20,a1,2x,a)") "xtype",":",trim(v%xtype)
write(*,"(10x,a20,a1,2x,a)") "dims", ":",trim(dims_char)
if (.not. trim(v%long_name) .eq. "") &
write(*,"(10x,a20,a1,2x,a)") "long_name",":", trim(v%long_name)
if (.not. trim(v%standard_name) .eq. "") &
write(*,"(10x,a20,a1,2x,a)") "standard_name",":", trim(v%standard_name)
if (.not. trim(v%units) .eq. "") &
write(*,"(10x,a20,a1,2x,a)") "units", ":", trim(v%units)
if (.not. trim(v%axis) .eq. "") &
write(*,"(10x,a20,a1,2x,a)") "axis",":", trim(v%axis)
write(*,"(10x,a20,a1,2x,2e12.4)") "actual_range",":", v%actual_range
write(*,"(10x,a20,a1,2x,e12.4)") "add_offset",":", v%add_offset
write(*,"(10x,a20,a1,2x,e12.4)") "scale_factor",":", v%scale_factor
write(*,"(10x,a20,a1,2x,e12.4)") "missing_value",":", v%missing_value
write(*,"(10x,a20,a1,2x,L2)") "missing_set",":", v%missing_set
if (.not. trim(v%grid_mapping) .eq. "") &
write(*,"(10x,a20,a1,2x,a)") "grid_mapping",":", trim(v%grid_mapping)
write(*,*)
return
end subroutine nc_print_attr
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Subroutine : p u t _ a t t
! Author : Alex Robinson
! Purpose : Put a set of attribute into netcdf file for a given variable
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc_put_att(ncid, v)
implicit none
integer :: i, ncid, stat, ndims
integer, allocatable :: dimids(:)
type(ncvar) :: v
integer, parameter :: noerr = NF90_NOERR
ndims = size(v%dims)
! Check if variable already exists - if so, gets the varid
stat = nf90_inq_varid(ncid, trim(v%name), v%varid)
! Define the variable if it doesn't exist
if ( stat .ne. noerr ) then
! Check if it's a dimension (coordinate) variable or a data variable
! Get the dimension ids for the variable to be defined
if ( v%coord ) then
! This is a coordinate variable (ie, a dimension defintion)
! Only one dimid needed (that of current variable)
allocate(dimids(1))
dimids(1) = v%dimid
else
! This is a data variable
! Determine ids of dimensions
allocate(dimids(ndims))
do i = 1, ndims
call nc_check ( nf90_inq_dimid(ncid, v%dims(i), dimids(i)) )
end do
end if
! Define the variable
select case(trim(v%xtype))
case("NF90_INT")
call nc_check( nf90_def_var(ncid,name=trim(v%name),xtype=NF90_INT,dimids=dimids,varid=v%varid) )
case("NF90_FLOAT")
call nc_check( nf90_def_var(ncid,name=trim(v%name),xtype=NF90_FLOAT,dimids=dimids,varid=v%varid) )
case("NF90_DOUBLE")
call nc_check( nf90_def_var(ncid,name=trim(v%name),xtype=NF90_DOUBLE,dimids=dimids,varid=v%varid) )
case("NF90_CHAR")
call nc_check( nf90_def_var(ncid,name=trim(v%name),xtype=NF90_CHAR,dimids=dimids,varid=v%varid) )
case DEFAULT
write(*,*) "nc_put_att:: Error, wrong xtype defined:"//trim(v%xtype)
stop
end select
if (trim(v%xtype) .ne. "NF90_CHAR") then
if (v%scale_factor .ne. 1.d0 .and. v%add_offset .ne. 0.d0) then
call nc_check( nf90_put_att(ncid, v%varid, "scale_factor", v%scale_factor) )
call nc_check( nf90_put_att(ncid, v%varid, "add_offset", v%add_offset) )
end if
if (v%missing_set) then
select case(trim(v%xtype))
case("NF90_INT")
call nc_check( nf90_put_att(ncid, v%varid, "missing_value", int(v%missing_value)) )
case("NF90_FLOAT")
call nc_check( nf90_put_att(ncid, v%varid, "missing_value", real(v%missing_value)) )
case("NF90_DOUBLE")
call nc_check( nf90_put_att(ncid, v%varid, "missing_value", v%missing_value) )
end select
end if
if (v%FillValue_set) then
select case(trim(v%xtype))
case("NF90_INT")
call nc_check( nf90_put_att(ncid, v%varid, "FillValue", int(v%FillValue)) )
case("NF90_FLOAT")
call nc_check( nf90_put_att(ncid, v%varid, "FillValue", real(v%FillValue)) )
case("NF90_DOUBLE")
call nc_check( nf90_put_att(ncid, v%varid, "FillValue", v%FillValue) )
end select
end if
end if
! Add additional variable attributes
if (trim(v%long_name) .ne. "") &
call nc_check( nf90_put_att(ncid, v%varid, "long_name", trim(v%long_name)) )
if (trim(v%standard_name) .ne. "") &
call nc_check( nf90_put_att(ncid, v%varid, "standard_name", trim(v%standard_name)) )
if (trim(v%units) .ne. "") &
call nc_check( nf90_put_att(ncid, v%varid, "units", trim(v%units) ) )
if (trim(v%axis) .ne. "") &
call nc_check( nf90_put_att(ncid, v%varid, "axis", trim(v%axis) ) )
if (trim(v%calendar) .ne. "") &
call nc_check( nf90_put_att(ncid, v%varid, "calendar", trim(v%calendar) ) )
if (trim(v%grid_mapping) .ne. "") &
call nc_check( nf90_put_att(ncid, v%varid, "grid_mapping", trim(v%grid_mapping) ) )
end if
! ! Always update the actual range (whether new or not) if it exists
if (v%actual_range(1) .ne. 0.d0 .and. v%actual_range(2) .ne. 0.d0) then
select case(trim(v%xtype))
case("NF90_INT")
call nc_check( nf90_put_att(ncid, v%varid, "actual_range", int(v%actual_range)) )
case("NF90_FLOAT")
call nc_check( nf90_put_att(ncid, v%varid, "actual_range", real(v%actual_range)) )
case("NF90_DOUBLE")
call nc_check( nf90_put_att(ncid, v%varid, "actual_range", v%actual_range) )
case("NF90_CHAR")
v%actual_range = (/ 0.d0, 0.d0 /)
case DEFAULT
write(*,*) "nc_put_att:: Error, wrong xtype defined:"//trim(v%xtype)
stop
end select
end if
return
end subroutine nc_put_att
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
! Subroutine : g e t _ a t t
! Author : Alex Robinson
! Purpose : Get attributes from a netcdf file for a given variable
! ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
subroutine nc_get_att(ncid, v, readmeta)
implicit none
integer :: ncid, stat, i
double precision :: tmp, tmp2(2)
integer :: tmpi, tmpi2(2)
character(len=NC_STRLEN) :: tmpstr
type(ncvar) :: v
integer :: ndims
integer, allocatable :: dimids(:)
integer, parameter :: noerr = NF90_NOERR
logical, optional :: readmeta
logical :: read_meta
read_meta = .TRUE.
if (present(readmeta)) read_meta = readmeta
! Get the current variable's id, if it exists
stat = nf90_inq_varid(ncid, trim(v%name), v%varid)
! If variable exists, get attributes from file
if ( stat .eq. noerr ) then
! Get number of dimensions and dimids
call nc_check ( nf90_inquire_variable(ncid, v%varid, ndims=ndims) )
if (allocated(dimids)) deallocate(dimids); allocate(dimids(ndims))
call nc_check ( nf90_inquire_variable(ncid, v%varid, dimids=dimids) )
! Re-allocate dimnames for current variable
if (allocated(v%dims)) deallocate(v%dims); allocate(v%dims(ndims))
if (allocated(v%dlen)) deallocate(v%dlen); allocate(v%dlen(ndims))
! Loop over dimensions and get the dimension names
do i = 1, ndims
call nc_check ( nf90_inquire_dimension(ncid,dimids(i),name=v%dims(i),len=v%dlen(i)) )
end do
if ( read_meta ) then
stat = nc_check_att( nf90_get_att(ncid, v%varid, "units", tmpstr) )
if (stat .eq. noerr) v%units = trim(tmpstr)
stat = nc_check_att( nf90_get_att(ncid, v%varid, "long_name", tmpstr) )
if (stat .eq. noerr) v%long_name = trim(tmpstr)
stat = nc_check_att( nf90_get_att(ncid, v%varid, "standard_name", tmpstr) )
if (stat .eq. noerr) v%standard_name = trim(tmpstr)
stat = nc_check_att( nf90_get_att(ncid, v%varid, "axis", tmpstr) )
if (stat .eq. noerr) v%axis = trim(tmpstr)
stat = nc_check_att( nf90_get_att(ncid, v%varid, "calendar", tmpstr) )
if (stat .eq. noerr) v%calendar = trim(tmpstr)
stat = nc_check_att( nf90_get_att(ncid, v%varid, "grid_mapping", tmpstr) )
if (stat .eq. noerr) v%grid_mapping = trim(tmpstr)
select case(trim(v%xtype))
case("NF90_INT")
stat = nc_check_att( nf90_get_att(ncid, v%varid, "actual_range", tmpi2) )