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Tests

Check if the module has been installed

After installing the module with pip (as described here), you can check that the module has been actually installed in your environment by opening a Python terminal and trying to import the module:

import omegapy
import omegapy.omega_data as od
import omegapy.omega_plots as op
import omegapy.useful_functions as uf

If these commands do not raise any error, the OMEGA-Py module is installed in your Python environment.

Failure

If the module is not available, here are a few things that you can try:

  • Restart your terminal or application to reload the environment.
  • Check that you are in the expected Python environment.
  • Re-install the module: 
     pip3 install omegapy

If it is still not working, does it work if you try to install an other module? Search for how to install a Python module with your local setup.

Check the module version

You can also check that you have the latest version of the module installed:

omegapy-version

From a Python console 

omegapy.__version__

From a terminal with pip 

pip freeze | grep omegapy

Failure

If you don't have the last version, update it with 

pip3 install omegapy --upgrade

Check the paths configuration

Please refer to this page for how to configure the default paths for the OMEGA binary and the omegapy-made files.

You can check the values stored in them by displaying the output of od.get_omega_bin_path() (OMEGA .QUB & .NAV binary files) and od.get_omega_py_path() (omegapy-made files).

Failure

If these functions do not return the expected path, please refer to this paragraph and use the od.set_omega_bin_path() and od.set_omega_py_path() functions.

Test to process and display an OMEGA observation

The final test would be to actually download and process an OMEGA observation.

For instance, download the data from cube 2 of orbit 0979:

Then download the example_test_script.py Python file and run it to load, process, and display this OMEGA observation.

Source code for example_test_script.py
example_test_script.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-

## example_test_script.py
## Created by Aurélien STCHERBININE
## Last modified by Aurélien STCHERBININE : 29/05/2024

##----------------------------------------------------------------------------------------
"""Example test for OMEGA-Py: import, apply corrections, compute band depth and display
figures for OMEGA observation 0979_2.
"""
##----------------------------------------------------------------------------------------
##----------------------------------------------------------------------------------------
## Package importation
import omegapy.omega_data as od
import omegapy.omega_plots as op
import omegapy.useful_functions as uf

import numpy as np
import matplotlib.pyplot as plt
plt.ion()   # Activation of Matplotlib interactive mode

##----------------------------------------------------------------------------------------
## Parameters to adjust
# Number of simultaneous processes uses to perform the thermal correction
npool = 10

# Colormap for reflectance maps
cmap_refl = 'Greys_r'

# Colormap for BD maps
cmap_bd = 'Blues'

########
## Alternative with cmocean (if installed)
# import cmocean.cm as cmo
# cmap_bd = cmo.ice
########

## If needed, set the paths with the functions below
## (see https://astcherbinine.github.io/omegapy/configuration/#windows-or-if-you-have-troubles-using-the-environment-variables)
# od.set_omega_bin_path("/path/to/binary/files/folder/")
# od.set_omega_py_path("/path/to/omegapy-made/files/folder/")
##

##----------------------------------------------------------------------------------------
## Data importation & correction
# Load the data cube
omega0 = od.OMEGAdata('0979_2')

# Apply thermal and atmospheric corrections
omega = od.corr_therm_atm(
    omega0, 
    npool = npool,    # Adjust npool according to your system
    )

##----------------------------------------------------------------------------------------
## OMEGA mask to hide bad pixels / calibration lines
mask = od.omega_mask(
    omega,
    hide_128 = True,
    emer_lim = 10,
    inci_lim = 70,
    tempc_lim = -194,
    limsat_c = 500
    )

##----------------------------------------------------------------------------------------
## Compute band depth at 1.5μm
bd_15 = od.BD_omega(
    omega, 
    [1.5, 1.51], 
    1.30, 
    1.71, 
    norm = True
    )

# Mask on band depth values for overplotting
mask_bd15 = np.ones(bd_15.shape)    # Initialisation with array of 1
mask_bd15[bd_15 < 0.1] = np.nan     # NaN for the pixels with no ice that we want to hide

##----------------------------------------------------------------------------------------
## Display figures
# Surface reflectance
op.show_omega_v2(
    omega, 
    lam = 1.085, 
    polar = True, 
    vmin = 0, 
    vmax = 0.6,
    Nfig = "reflectance",
    cmap = cmap_refl,
    )

# 1.5μm Band Depth
op.show_data_v2(
    omega, 
    data = bd_15, 
    cb_title = "1.5μm BD", 
    polar = True, 
    cmap = cmap_bd, 
    vmin = 0, 
    vmax = 0.75,
    Nfig = "BD15",
    )

# Overplotting 1.5μm BD over surface reflectance
op.show_omega_v2(
    omega,
    lam = 1.085,
    polar = True,
    vmin = 0,
    vmax = 0.5,
    cbar = False,
    Nfig = "overplot",
    cmap = cmap_refl,
    )

op.show_data_v2(
    omega,
    data = bd_15,
    mask = mask_bd15,
    polar = True,
    cmap = cmap_bd,
    cb_title = "1.5 μm BD",
    vmin = 0,
    vmax = 0.75,
    Nfig = "overplot",
    title = 'Overplot map for ORB0979_2',
    )

plt.figure('reflectance').savefig('omegapy_ORB0979_2_reflectance.png')
plt.figure('BD15').savefig('omegapy_ORB0979_2_BD15.png')
plt.figure('overplot').savefig('omegapy_ORB0979_2_overplot_reflectance_BD15.png')

# Interactive display of the observation (@ λ = 1.085 µm)
op.show_omega_interactif_v2(
    omega, 
    lam = 1.085, 
    cmap = cmap_refl, 
    vmin = 0, 
    vmax = 0.5, 
    polar = True,
    mask = mask,
    title = 'Interactive map',
    autoyscale = False,
    ylim_sp = (0, 0.6),
    )

plt.show()

##----------------------------------------------------------------------------------------
# Search for the index of λ = 1.085 µm in the wavelength array
i_lam = uf.where_closer(1.085, omega.lam)

##----------------------------------------------------------------------------------------
## Print completed
print("\n\033[32;1m[OMEGA-Py test example completed]\033[0m")

##----------------------------------------------------------------------------------------
## End of code
##----------------------------------------------------------------------------------------

This example script will:

  • load the binary files;
  • apply the atmospheric and thermal corrections to the OMEGA observation;
  • compute the 1.5μm band depth criteria (see the band depth example);
  • display and save the reflectance, 1.5μm BD, and overplotted maps (see the overplotting example);
  • display the interactive visualization tool (if running the code in an IPython shell).

You can then check that you have reproduced the figures shown in the examples.

Notes

If running the code directly from a bash terminal (with python3 example_test_script.py), the data will be processed, and the figures saved in your current directory. But you will not have access to the interactive visualization of the cube.

To use the interactive aspect of OMEGA-Py, open an IPython terminal to run the code with run example_test_script.py (or execute it from your favorite IDE with a IPython console).

Failure

  • If encountering an error in the data loading/processing, check your installation with the above steps.
  • If encountering an error with displaying the interactive map, check that you have an appropriate matplotlib backend installed and activated (e.g., PyQt5) and refer to this paragraph.