gsfpy - Generic Sensor Format for Python

Python wrapper for the C implementation of the Generic Sensor Format library.

• Free software: MIT license
• Notes on licensing: The bundled gsfpy3_0x/libgsf/libgsf03_0x.so binaries are covered by the LGPL v2.1 license. Copies of this license are included in the project at gsfpy3_0x/libgsf/libgsf_LICENSE.md. The top-level MIT licensing of the overall gsfpy project is not affected by this. However, as required by the libgsf license, the libgsf shared object libraries used by the gsfpy3_0x packages at runtime may be replaced with a different version by setting the GSFPY3_08_LIBGSF_PATH and/or GSFPY3_09_LIBGSF_PATH environment variables to the absolute file path of the new library.

Namespaces and supported GSF versions

The gsfpy package provides three namespaces: gsfpy, gsfpy3_08 and gsfpy3_09.

The default version of GSF supported is 3.08. Top level package functionality for 3.08 can be used either via import gsfpy (without setting the DEFAULT_GSF_VERSION environment variable - see below) or import gsfpy3_08. Note that import gsfpy will also work for versions 3.06 and 3.07 of GSF as well (older versions have not been tested).

If you are using GSF v3.09, there are two options:

• Set the DEFAULT_GSF_VERSION environment variable to "3.09", then import gsfpy
• Import the 3.09 package directly with import gsfpy3_09

Features

• The gsfpy(3_0x).bindings modules provide wrappers for all GSFlib functions, including I/O, utility and info functions. Minor exceptions are noted in the sections below.

• For added convenience the gsfpy top level package provides the following higher level abstractions:

  • open_gsf()
  • GsfFile (class)
  • GsfFile.read()
  • GsfFile.get_number_records()
  • GsfFile.seek()
  • GsfFile.write()
  • GsfFile.close()

Install using pip

From PyPI

pip install gsfpy

From GitHub (SSH)

pip install git+ssh://git@github.com/UKHO/gsfpy.git@master

From GitHub (HTTPS)

pip install git+https://github.com/UKHO/gsfpy.git@master

Examples of usage

Open/close/read from a GSF file (GSF v3.08)

from ctypes import string_at

from gsfpy3_08 import open_gsf
from gsfpy3_08.enums import RecordType

with open_gsf("path/to/file.gsf") as gsf_file:
    # Note - file is closed automatically upon exiting 'with' block
    _, record = gsf_file.read(RecordType.GSF_RECORD_COMMENT)

    # Note use of ctypes.string_at() to access POINTER(c_char) contents of
    # c_gsfComment.comment field.
    print(string_at(record.comment.comment))

Write to a GSF file (GSF v3.09)

from ctypes import c_int, create_string_buffer

from gsfpy3_09 import open_gsf
from gsfpy3_09.enums import FileMode, RecordType
from gsfpy3_09.gsfRecords import c_gsfRecords

comment = b"My comment"

# Initialize the contents of the record that will be written.
# Note use of ctypes.create_string_buffer() to set POINTER(c_char) contents.
record = c_gsfRecords()
record.comment.comment_time.tvsec = c_int(1000)
record.comment.comment_length = c_int(len(comment))
record.comment.comment = create_string_buffer(comment)

with open_gsf("path/to/file.gsf", mode=FileMode.GSF_CREATE) as gsf_file:
    gsf_file.write(record, RecordType.GSF_RECORD_COMMENT)

Copy GSF records (GSF v3.08 as default)

from ctypes import byref, c_int, pointer

from gsfpy import *


# This example uses the bindings module to illustrate use of the lower level functions
file_handle = c_int(0)
data_id = gsfDataID.c_gsfDataID()
source_records = gsfRecords.c_gsfRecords()
target_records = gsfRecords.c_gsfRecords()

ret_val_open = bindings.gsfOpen(
    b"path/to/file.gsf", enums.FileMode.GSF_READONLY, byref(file_handle)
)

# Note use of ctypes.byref() as a shorthand way of passing POINTER parameters to
# the underlying foreign function call. ctypes.pointer() may also be used.
bytes_read = gsfpy.bindings.gsfRead(
    file_handle,
    enums.RecordType.GSF_RECORD_COMMENT,
    byref(data_id),
    byref(source_records),
)

# Note use of pointer() rather than byref() when passing parameters to
# gsfCopyRecords(). Implementation of this function is in Python as calling
# the native underlying function causes memory ownership clashes. byref()
# is only suitable for passing parameters to foreign function calls (see
# ctypes docs).
ret_val_cpy = bindings.gsfCopyRecords(
    pointer(target_records), pointer(source_records)
)
ret_val_close = bindings.gsfClose(file_handle)

Troubleshoot

from gsfpy3_09.bindings import gsfIntError, gsfStringError

# The gsfIntError() and gsfStringError() functions are useful for
# diagnostics. They return an error code and corresponding error
# message, respectively.
retValIntError = gsfIntError()
retValStringError = gsfStringError()
print(retValIntError, retValStringError)

Notes on implementation

gsfPrintError()

The gsfPrintError() method of GSFlib is not implemented as there is no FILE* equivalent in Python. Use gsfStringError() instead - this will give the same error message, which can then be written to file as required.

gsfCopyRecords() and gsfFree()

gsfFree() the sibling method to gsfCopyRecord() in GSFlib, used to deallocate memory assigned by the library but managed by the calling application, is not required by gsfpy as memory allocation and deallocation is handled by ctypes. gsfFree() is therefore omitted from the package.

gsf_register_progress_callback()

Implementation of the GSFlib function gsf_register_progress_callback() is not applicable for gsfpy as the DISPLAY_SPINNER macro was not defined during compilation. It is therefore omitted from the package.

Generic Sensor Format Documentation

Generic Sensor Format specification: see e.g. https://github.com/schwehr/generic-sensor-format/blob/master/doc/GSF_lib_03-06.pdf

Generic Sensor Format C library v3.06 specification: see e.g. https://github.com/schwehr/generic-sensor-format/blob/master/doc/GSF_spec_03-06.pdf

More recent versions of these documents can be downloaded from the Leidos website.

Dev Setup

Ensure Poetry is installed before proceeding

Poetry (Recommended)

By default Poetry will create it's own virtual environment using your system's Python. This feature can be disabled.

git clone git@github.com:UKHO/gsfpy.git
cd gsfpy
poetry install

Pyenv

A good choice if you want to run a version of Python different than available through your system's package manager

git clone git@github.com:UKHO/gsfpy.git
cd gsfpy
pyenv install 3.8.3
pyenv virtualenv 3.8.3 gsfpy
pyenv local gsfpy
poetry install

Run Tests

make test

Run Checks

make lint

Notes on Security

Some known concerns relating to the underlying GSFlib C library are documented at dwcaress/MB-System#368 and https://github.com/schwehr/generic-sensor-format/issues. Note that gsfpy simply wraps GSFlib and does not purport to stop or mitigate these potential vulnerabilities. It is left to the authors of applications calling gsfpy to assess these risks and mitigate where deemed necessary.

GSF data processed using gsfpy should be sourced from reliable providers and checked for integrity where possible.

Please also refer to the LICENSE file for the terms of use of gsfpy.

Credits

libgsf03-08.so was built from the Leidos C code using the Makefile in UKHO/libgsf

This package was created with Cookiecutter and the UKHO/cookiecutter-pypackage project template.

Related Projects

Also see schwehr/generic-sensor-format