Scientific Computing

To allow a for loop to make an arbitrary number of overlaid plots in a single axes, we may wish to endlessly cycle colors using itertools. This technique only makes sense up to a few dozen cycles depending on the Matplotlib color palette but it can be better than just ending a loop after the palette is exhausted.

import itertools

import matplotlib.pyplot as plt
import matplotlib.colors as mplcolors

color_cycle = itertools.cycle(mplcolors.TABLEAU_COLORS)

xy = [(x, x**1.2) for x in range(20)]
# toy data

ax = plt.figure().gca()

for (x, y), color in zip(xy, color_cycle):
    ax.scatter(x, y, color=color)

print(xy)

plt.show()

If an external program needs a subdirectory to create and load multiple files, Python tempfile.TemporaryDirectory() creates a temporary working directory. shutil.copytree is used to recursively copy all files if the call to the external program succeeds.

from pathlib import Path
import tempfile
import subprocess
import shutil
import uuid

file = Path(f"~/{uuid.uuid4().hex}.txt").expanduser()
# toy file
file.write_text("Hello World!")

with tempfile.TemporaryDirectory(ignore_cleanup_errors=True) as f:
    shutil.copy(file, f)
    subprocess.check_call(["cat", Path(f) / file.name])

    new_dir = file.parent / f"{file.stem}"
    print(f"\n{file}  Solved, copy to {new_dir}")
    shutil.copytree(f, new_dir)

Public Git repo clone via HTTPS and push via SSH is fast and generally effective for security. For private Git repos do Git clone over SSH. Optionally, SSH Agent avoids the need to constantly type the SSH password.

Git clone with Git over SSH by simply replacing “https://” in the Git repo URL with “ssh://”. Be sure to remove the trailing “.git” from the URL if present. For example:

git clone ssh://github.invalid/username/private-repo-name

Related: GitHub Oauth access private repo

On Unix-like platforms, CMake variable CMAKE_DL_LIBS is populated to link with target_link_libraries(), providing functions like “dlopen” and “dladdr”. For some libdl functions it’s necessary to also define “_GNU_SOURCE” like:

add_library(mylib SHARED mylib.c)
target_link_libraries(mylib PRIVATE ${CMAKE_DL_LIBS})
target_compile_definitions(mylib PRIVATE _GNU_SOURCE)

On Windows different mechanisms can be used to access dynamic libraries. With MSYS2 libdl is available.

Run path (Rpath)

On Unix-like systems, the concept of run path is the search path for libraries used by a binary at runtime. For Windows there is no separate Rpath, just PATH is used–necessary .dll files must be on PATH environment variable at the time of running a binary. For Unix-like systems life can be easier since the Rpath is compiled into a binary. Optionally, using $ORIGIN in Rpath allows relocating binary packages.

For CMake, set all the time – no need for “if()” statements.

include(GNUInstallDirs)

set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS true)
# must be before all targets

Note that we use CMake defaults (we do NOT set values for these) for the following to avoid problems on HPC where library modules may be loaded dynamically. Instead we allow the end user to set these variables in the top level executable.

CMAKE_INSTALL_NAME_DIR
CMAKE_INSTALL_RPATH
CMAKE_INSTALL_RPATH_USE_LINK_PATH

Exporting symbols for MSVC-based compilers is necessary to generate a “example.lib” corresponding to the “example.dll”.

To have the installed CMake binaries work correctly, it’s necessary to set CMAKE_PREFIX_PATH at configure time. That is, the configure-build-install sequence for shared library project in CMake is like:

cmake -Bbuild -DBUILD_SHARED_LIBS=on --install-prefix=/opt/my_program

cmake --build build

cmake --install build

In general the rpath in a binary can be checked like:

• Linux: readelf -d /path/to/binary | head -n 25
• macOS: otool -l /path/to/binary | tail

References:

• Linux standard base core

The POSIX C type ssize_t is available on Unix-like systems in <sys/types.h>. Windows Visual Studio BaseTsd.h has SSIZE_T.

However, ssize_t is POSIX, but not C standard. It’s possible to define a signed size type “ssize_t” using “ptrdiff_t” for “ssize_t” in C and C++. Using ptrdiff_t instead of ssize_t is the practice of major projects like Emacs.

size_t bit width is guaranteed by C and C++ standards to have bit width not less than 16.

ptrdiff_t bit width is guaranteed by C standard to have bit width not less than 16, and C++ standard to have bit width not less than 17.

This example shows how to use ssize_t across computing platforms.

Related: C++ size_type property vs size_t

As with HDF5 and h5py, using xarray to_netcdf() to write netCDF files can losslessly compress Datasets and DataArrays, but file compression is off by default. Each data variable must have the compression option set to take effect. We typically only compress variables of 2-D or higher rank.

Notes:

• Specify format="NETCDF4", engine="netcdf4" to allow a broader range of data types.
• if “chunksizes” is not set, the data variable will not compress. We arbitrarily made the chunk sizes half of each dimension, but this can be optimized for particular data.
• “fletcher32” is a checksum that can be used to detect data corruption.
• Setting “.attr” of a data variable will be written to the netCDF file as well. This is useful to note physical units, for example.

from pathlib import Path
import xarray


def write_netcdf(ds: xarray.Dataset, out_file: Path) -> None:
    enc = {}

    for k in ds.data_vars:
        if ds[k].ndim < 2:
            continue

        enc[k] = {
            "zlib": True,
            "complevel": 3,
            "fletcher32": True,
            "chunksizes": tuple(map(lambda x: x//2, ds[k].shape))
        }

    ds.to_netcdf(out_file, format="NETCDF4", engine="netcdf4", encoding=enc)

The Python imageio package reads and writes numerous image formats and their metadata. The time and location of citizen science images are often critical to their interpretation. Not all cameras have GPS modules. Not all cameras have sufficiently accurately set clocks (including time zone).

A typical metadata item of interest is “DateTimeOriginal”. How this is defined and its accuracy is up to the camera implementation.

We show the reading of image metadata in a few distinct ways.

ImageIO read metadata

Get the image time using imageio.immeta:

import imageio.v3 as iio

from sys import argv
from pathlib import Path

fn = Path(argv[1]).expanduser()

meta = iio.immeta(fn)

for k in ("DateTimeOriginal", "DateTimeDigitized", "DateTime"):
    print(k, meta.get(k))

Consider that the timezone may need to be corrected.

ExifRead metadata

ExifRead Python module is powerful for reading EXIF image metadata.

If the camera had a GPS module, the location may be available. An ExifRead example of reading the EXIF GPS location:

import exifread

from sys import argv
from pathlib import Path

fn = Path(argv[1]).expanduser()

with open(fn, "rb") as f:
    tags = exifread.process_file(f)

latitude = tags["GPS GPSLatitude"]
longitude = tags["GPS GPSLongitude"]

print(f"{fn}  latitude, longitude: {latitude}, {longitude}")

Exif metadata

import exif

from sys import argv
from pathlib import Path

fn = Path(argv[1]).expanduser()

with open(fn, "rb") as f:
    tags = exif.Image(f)

latitude = tags.gps_latitude
longitude = tags.gps_longitude

print(f"{fn}  latitude, longitude: {latitude}, {longitude}")

These environment variables are common across build systems as a de facto standard, and assume a compiler like GCC or Clang environment variables.

Dynamic library path:

• Linux: LD_LIBRARY_PATH
• macOS: LIBRARY_PATH
• Windows: must be on environment variable PATH

Include path (where .h C header files are located):

Linux / macOS: CPATH

An example GNU Make Unix-like shell command would be like:

LD_LIBRARY_PATH=/path/to/lib CPATH=/path/to/include make

GCC Toolset enables modern compiler selection for RHEL users. G++ / Gfortran example:

dnf install gcc-toolset-13-gcc-gfortran gcc-toolset-13-gcc-c++

Thereafter, users without sudo use the new Gfortran version by:

source scl_source enable gcc-toolset-13

Previously this was known as Developer Toolset devtoolset.

By default, the typical directory listing command “ls” does not show paths that start with a dot. That is, paths that start with a dot are hidden like “.ssh” or “.git” etc. Most shells will list all paths including those with a leading dot by:

ls -a

For PowerShell to list paths with a leading dot:

ls -Fo

“-Fo” is short for “-Force”.