phdhelper

Installation

1. Clone the repository and navigate to the root folder.
2. If using virtualenv make sure to workon the environment you wish to install in.
3. Run the following command to install an editable version of the module to your python installation using pip:

   pip install -e .

   The -e stands for 'editable' & means that any edits to the code are updated live across any/all installs without needing to pip install again.
4. To update the module to latest, simply git pull

Structure

. @ Wed  2 Jun 2021 16:30:59 BST
├── .gitignore
├── LICENSE
├── README.md
├── phdhelper
│   ├── __init__.py
│   ├── __main__.py
│   ├── exceptions
│   │   ├── __init__.py
│   │   └── phdException.py
│   ├── helpers
│   │   ├── COLOURS.py
│   │   ├── CONSTANTS.py
│   │   ├── __init__.py
│   │   ├── format_timestamps.py
│   │   ├── os_shortcuts.py
│   │   └── override_mpl.py
│   ├── math
│   │   ├── __init__.py
│   │   ├── signal_processing.py
│   │   └── transforms.py
│   ├── suMMSary
│   │   ├── __init__.py
│   │   └── suMMSary.py
│   └── tests
│       ├── __init__.py
│       ├── helpers
│       │   ├── __init__.py
│       │   └── array_summary_test.py
│       └── math
│           ├── __init__.py
│           ├── autocorrelate_beating.npy
│           ├── autocorrelate_bigarray.npy
│           └── signal_processing_testes.py
└── setup.py

8 directories, 26 files

helpers

Contains most of the helper code.

COLOURS

Constants file containing colours (hex string) consistent with theme.

from phdhelper.helpers.COLOURS import red, green, blue

print(red, green, blue)

Returns

#BF245A #4BB977 #107EA9

CONSTANTS

Contains various astrophysical constants as pure floats, similar to np.pi=3.14159265...

from phdhelper.helpers.CONSTANTS import *

print(f"Permittivity of free space: {epsilon_0}")
print(f"Speed of light: {c}")

Returns

Permittivity of free space: 8.85418782e-12
Speed of light: 299792458.0

os_shortcuts

Contains helpers for navigating os. Includes get_path & new_path

from phdhelper.helpers.os_shortcuts import get_path, new_path

data_src = get_path(__file__, "..")  #  Full path to directory above current file
save_path = new_path(get_path(__file__))


# Generate data...

print(f"Path of data: {data_src}")
print(f"Save to path: {save_path('filename.txt')}")

Returns

Path of data: /Users/jamesplank
Save to path: /Users/jamesplank/Desktop/filename.txt

override_mpl

Routines for customising the default behaviour of matplotlib.

Contains an override() method which when called in a script will override some matplotlib defaults, including setting default colours (using the ones in COLOURS), changing line width, adding a grid, etc...

from phdhelper.helpers import override_mpl
from phdhelper.helpers.os_shortcuts import *
import matplotlib.pyplot as plt
import numpy as np

override_mpl.override()
plots_path = new_path(get_path(__file__))

x = np.arange(10)
y = np.sin(x) ** 2

x2 = np.linspace(0, 9, 100)
y2 = np.sin(x2) ** 3

plt.plot(x, y)
plt.plot(x2, y2)
plt.savefig(plots_path("new_default.png"))
plt.close()

override_mpl.override("book_gs")
plt.plot(x, y)
plt.plot(x2, y2)
plt.savefig(plots_path("book_style.png"))

Returns

Also contains cmap(). Currently only "custom_diverging" implemented. Use to initialise custom colour maps.

import numpy as np
import matplotlib.pyplot as plt
from phdhelper.helpers import override_mpl, os_shortcuts

save_fig = os_shortcuts.new_path(os_shortcuts.get_path(__file__))

override_mpl.override()
override_mpl.cmaps("custom_diverging")

x, y = np.mgrid[0:12:1000j, 0:12:1000j]
z = np.sin(x) ** 3 + np.sin(y) ** 3

fig, ax = plt.subplots(2, 1, sharex=True, sharey=True)

im1 = ax[0].pcolormesh(x, y, z, shading="nearest")
fig.colorbar(im1, ax=ax[0])
im2 = ax[1].pcolormesh(
    x,
    y,
    z,
    cmap="custom_diverging",
    shading="nearest",
)
fig.colorbar(im2, ax=ax[1])
plt.tight_layout()
plt.savefig(save_fig("default_cmaps.png"))
plt.close()

override_mpl.override("book_gs")
plt.pcolormesh(x, y, z, shading="nearest")
plt.colorbar()
plt.tight_layout()
plt.savefig(save_fig("book_cmap.png"))

Returns