forbit 1.0.5

Fortran based direct access binary reader/writer for Python

FORtran-based Binary-io Interface Toolkit (FORBIT)

Programmer : Kosei Ohara

FORBIT is a Python package for reading and writing Fortran direct-access unformatted binary files as NumPy arrays. It is designed for no-header binary files whose records are written by Fortran with ACCESS='DIRECT' and FORM='UNFORMATTED'. The Python interface keeps track of the current Fortran record number, reads or writes one fixed-size record at a time, and returns ordinary numpy.ndarray objects.

Features

• Read and write Fortran direct-access unformatted binary files
• Handle no-header fixed-record binary files
• Return data as numpy.ndarray
• Support 1D to 6D arrays
• Support single precision and double precision floating-point data
• Support explicit endian selection through Fortran's CONVERT specifier
• Keep the current record number internally and update it after each read or write

Requirements

FORBIT is implemented with Python, NumPy, Cython, and Fortran. The package metadata declares support for CPython on POSIX/Linux with Python 3.7 to 3.13.

Runtime dependency:

• NumPy

Build dependencies:

• setuptools
• wheel
• Cython
• NumPy
• A Fortran compiler, such as gfortran
• A C compiler, such as gcc

Compile and Path

Install from PyPI

$ pip install forbit

Build from Source

$ git clone https://github.com/koseiohara/forbit.git
$ cd forbit/src/
$ make
$ make install

When building manually, make install copies the generated shared libraries to the directory specified by LIB_INSTALL in src/Makefile. Add that directory to both PYTHONPATH and LD_LIBRARY_PATH before importing the module.

$ export PYTHONPATH="${YOUR_PATH}:${PYTHONPATH}" 
$ export LD_LIBRARY_PATH="${YOUR_PATH}:${LD_LIBRARY_PATH}"

Usages

### Read sample.grd ###
import numpy as np
import forbit

raw_binary_file = "sample.grd"
nx = 3
ny = 4
nz = 2
shape   = [nz,ny,nx]
kind    = 4                 ## Kind Parameter
endian  = "little_endian"   ## Endian of the Target File
record  = 1                 ## Initial Record
recstep = 1                 ## Record Increment

if (kind == 4):
    arr_type = np.float32
elif (kind == 8):
    arr_type = np.float64

arr = np.empty(shape, dtype=arr_type)

file = forbit.open(raw_binary_file,
                   action ="read" ,
                   shape  =shape  ,
                   kind   =kind   ,
                   record =record ,
                   recstep=recstep,
                   endian =endian )

nt = 10     ## Number of TImesteps
# record 1 -> 10
for t in range(nt):
    print(f"Record: {file.get_record()}")

    arr[:,:,:] = file.fread()
    ## Write any processes here

    print(f"{arr[:,:,:]}\n")

record = 16
nt = 5      ## Number of TImesteps
file.reset_record(newRecord=record)
# record 16 -> 20
for t in range(nt):
    print(f"Record: {file.get_record()}")

    arr[:,:,:] = file.fread()
    ## Write any processes here

    print(f"{arr[:,:,:]}\n")

file.close()

### Write to sample.grd ###
import numpy as np
import forbit

raw_binary_file = "sample.grd"
nx = 3
ny = 4
nz = 2
shape   = [nz,ny,nx]
kind    = 4                 ## Kind Parameter
endian  = "little_endian"   ## Endian of the Target File
record  = 1                 ## Initial Record
recstep = 1                 ## Record Increment

if (kind == 4):
    arr_type = np.float32
elif (kind == 8):
    arr_type = np.float64

arr = np.empty(shape, dtype=arr_type)

file = forbit.open(raw_binary_file,
                   action ="write",
                   shape  =shape  ,
                   kind   =kind   ,
                   record =record ,
                   recstep=recstep,
                   endian =endian )

rng = np.random.default_rng()       ## Random Generator
nt = 20     ## Number of TImesteps
# record 1 -> 20
for t in range(nt):
    print(f"Record: {file.get_record()}")

    arr[:,:,:] = rng.random(shape)
    file.fwrite(arr[:,:,:])

    print(f"{arr[:,:,:]}\n")

file.close()

API

forbit.open()

file = forbit.open(filename, action, shape, kind, record, recstep, endian)

Open a Fortran direct-access unformatted binary file.

Parameters

• filename
  type=str
  File name of a no-header binary file.

• action
  type=str
  File access mode. Accepted values are case-insensitive:

  • "read"
  • "write"
  • "readwrite"

  The value is passed to the Fortran OPEN statement as the ACTION specifier.

• shape
  type=ndarray
  Other types of array such as list and tuple may be allowed.
  Shape of one Fortran direct-access record as it should appear on the Python side.
  Examples:

  • For a 1D record: [nx]
  • For a 2D record returned as (ny, nx): [ny, nx]
  • For a 3D record returned as (nz, ny, nx): [nz, ny, nx]

  The shape is given in normal NumPy order. Internally, FORBIT reverses the dimensions when calling the Fortran routines so that a Python array shaped like [nz, ny, nx] corresponds to a Fortran array shaped like (nx, ny, nz) in the low-level read/write routine.
  All dimensions must be positive integers. The number of dimensions must be between 1 and 6.

• kind
  type=int
  Floating-point precision of the binary file.
  Accepted values:

  • 4: single precision, returned/written as numpy.float32
  • 8: double precision, returned/written as numpy.float64

  This parameter describes the precision stored in the binary file. When writing, input arrays are converted to the selected precision before being passed to the Fortran write routine.

• record
  type=int
  Initial Fortran direct-access record number. Record numbers are 1-based, as in Fortran.

• recstep
  type=int
  Increment added to the internal record number after each fread() or fwrite() call. The value to increment record after every access.
  Examples:

  • recstep=1: read/write consecutive records
  • recstep=0: keep using the same record number
  • recstep=12: jump by 12 records after each access

• endian
  type=str
  Endian conversion mode passed to Fortran's CONVERT specifier.
  Accepted values are case-insensitive:

  • "little_endian"
  • "big_endian"

close()

file.close()

The file is also closed by the object's destructor, but explicit close() is recommended.

fread()

arr = file.fread()

Read the current record and return a NumPy array. The returned array has the shape specified by shape and dtype determined by kind. After reading, the internal record number is updated by recstep.

fwrite()

file.fwrite(arr)

The input array must have the same shape as the shape specified when opening the file. Before writing, FORBIT converts the array to a C-contiguous NumPy array with dtype determined by kind. After writing, the internal record number is updated by recstep.

get_record()

record = file.get_record()

Return the current internal record number.

reset_record(newRecord=None, increment=None)

file.reset_record(newRecord=10)
file.reset_record(increment=3)

Change the internal record number.
If newRecord is provided, the internal record number is set to that value. If newRecord is not provided and increment is provided, the internal record number is increased by increment. If both arguments are provided, newRecord takes priority.

File Format

FORBIT assumes that the file is a Fortran direct-access unformatted file with fixed-size records.
For one record, the record length used internally is computed from shape and kind:

recl = kind * product(shape)

This value is passed to the Fortran OPEN statement as RECL.
The file is opened in Fortran with settings equivalent to:

open(newunit=unit, file=..., action=..., form='unformatted', access='direct', recl=..., convert=...)

Dimension Ordering

FORBIT's public Python API uses NumPy-style shapes.
For example, if a Fortran program writes a 3D array as (nx, ny, nz), the corresponding Python shape should normally be written as:

shape = [nz, ny, nx]

This convention makes the returned NumPy array natural to index as:

arr[0:nz,0:ny,0:nx]

Precision and Dtype

kind	File Precision	Returned dtype
4	single precision (real32)	numpy.float32
8	double precision (real64)	numpy.float64

Only floating-point data are supported by the public API. Integer, complex, logical, character, and quadruple-precision records are not supported by the current implementation.

Record Handling

The current record number is stored inside the forbit object. Each call to fread() or fwrite() uses the current record number and then updates it as follows:

record = record + recstep

Fortran direct-access record numbers are positive and 1-based. The low-level Fortran routines stop with an error if a non-positive record number is used.