Welcome to Planarradpy’s documentation!

Warning

Pre-Alpha Not ready for any one to use except for testers!

Planarradpy

Planarradpy is a tool written in python that can execute Planarrad

Example Use [command line]

python planarradpy.py -i <input_parameter_file>

Example input parameters file

#----------------------------------------#
# Name of the batch run
#----------------------------------------#
batch_name = P_VARY_HOPE_2

#----------------------------------------#
# Bio-optical parameters list
#----------------------------------------#
saa_list = 0.0
sza_list = 130.0
p_list = 0.01,0.05,0.1,0.2
x_list = 0.01
y_list = 1.0
g_list = 0.1
s_list = 0.015
z_list = 30.0

#----------------------------------------#
# Wavelengths
# All IOPs are interpolated to these
# Wavelengths
#----------------------------------------#
wavelengths = 410.0,430.0,450.0,470.0,490.0,510.0,530.0,550.0,570.0,590.0,610.0,630.0,650.0,670.0,690.0,710.0,730.0

#----------------------------------------#
# Number of CPUs
# -1 means query the number of CPUs
#----------------------------------------#
num_cpus = 1

#----------------------------------------#
# Path of Planarrad
#----------------------------------------#
exec_path = /home/marrabld/Apps/jude2_install/bin

#----------------------------------------#
# Logging level
#----------------------------------------#
verbose = 6

#----------------------------------------#
# File paths
# Using absolute paths
#----------------------------------------#
phytoplankton_absorption_file =/home/marrabld/Projects/planarradpy/inputs/iop_files/a_phi.csv
bottom_reflectance_file = /home/marrabld/Projects/hope_test/RodFiles/Refl_BenthicMixture_1_17Bands.txt

#----------------------------------------#
# Set the parameter to report
#----------------------------------------#
report_parameter = Rrs@6.0:135.0

Source code

Planarradpy

Contents:

class libplanarradpy.planrad.BatchRun(object, batch_name='batch')

This class is used for batch running PlanarRad for many different IOPs.

It will also distribute the work over many CPUs. It will run an single instance for PlanarRad on each available cores or the number of cores defined in the batchrun file.

Available ‘batchable’ parameters are:

Sun Azimuth Angle (deg) [saa]

Sun Zenith Angle (deg) [sza]

Phytoplankton scaling parameter [p]

particulate scattering parameters [x, y] see BioOpticalParameters

CDOM absorption parameters [g, s]

depth (m) [z]

batch_parameters(saa, sza, p, x, y, g, s, z)

Takes lists for parameters and saves them as class properties

Parameters:

• saa – <list> Sun Azimuth Angle (deg)
• sza – <list> Sun Zenith Angle (deg)
• p – <list> Phytoplankton linear scalling factor
• x – <list> Scattering scaling factor
• y – <list> Scattering slope factor
• g – <list> CDOM absorption scaling factor
• s – <list> CDOM absorption slope factor
• z – <list> depth (m)

generate_directories(overwrite=False)

For all possible combinations of ‘batchable’ parameters. create a unique directory to story outputs

Each directory name is unique and contains the run parameters in the directory name

Parameters:overwrite – If set to True will over write all files default = False

run()

Distributes the work across the CPUs. It actually uses _run()

class libplanarradpy.planrad.BioOpticalParameters(wavelengths)

Contains useful parameters and methods for modelling IOPs using bio-optical models

Constructor takes wavelengths. This is a common wavelength that all IOPs will be interpolated to

build_a()

Calculates the total absorption from water, phytoplankton and CDOM

a = awater + acdom + aphi

build_a_cdom(g, s, wave_const=400)

Builds the CDOM absorption function :: \(G \exp (-S(\lambda - 400))\)

Parameters:

• g – function coefficient
• s – slope factor
• wave_const – wave constant default = 400 (nm)

Returns null:

build_all_iop()

Meta method that calls all of the build methods in the correct order

self.build_a() self.build_bb() self.build_b() self.build_c()

build_b(scattering_fraction=0.01833)

Calculates the total scattering from back-scattering

Parameters:scattering_fraction – the fraction of back-scattering to total scattering default = 0.01833

b = ( bb[sea water] + bb[p] ) /0.01833

build_bb()

Calculates the total backscattering

build_bbp(x, y, wave_const=550)

Builds the particle backscattering function \(X(\frac{550}{\lambda})^Y\)

Parameters:

• x – function coefficient
• y – order of the power function
• wave_const – wave constant default 550 (nm)

Returns null:

build_c()

Calculates the total attenuation from the total absorption and total scattering

c = a + b

read_aphi_from_file(file_name)

Read the phytoplankton absorption file from a csv formatted file

Parameters:file_name – filename and path of the csv file

read_pure_water_absorption_from_file(file_name)

Read the pure water absorption from a csv formatted file

Parameters:file_name – filename and path of the csv file

read_pure_water_scattering_from_file(file_name)

Read the pure water scattering from a csv formatted file

Parameters:file_name – filename and path of the csv file

scale_aphi(scale_parameter)

Scale the spectra by multiplying by linear scaling factor

Parameters:scale_parameter – Linear scaling factor

write_b_to_file(file_name)

Write the total scattering to csv file

Parameters:file_name – filename and path of the csv file

write_c_to_file(file_name)

Write the total attentuation to file

Parameters:file_name – filename and path of the csv file

class libplanarradpy.planrad.FileTools

Useful static methods for file mangling

static dict_to_object(data_object, data_dict)

Maps a dictionary to an object. Variable names become the key in the dict

Parameters:

• data_object – Is an instantiated class
• data_dict – is the python dictionary

Returns data_object:  

static read_param_file_to_dict(file_name)

Loads a text file to a python dictionary using ‘=’ as the delimiter

Parameters:file_name – the name and path of the text file

class libplanarradpy.planrad.HelperMethods

Useful static methods

static string_to_float_list(string_var)

Pull comma separated string values out of a text file and converts them to float list

class libplanarradpy.planrad.ReportTools

Load the report in to a dictionary

calc_directional_aop(report, parameter, parameter_dir)

Will calcuate the directional AOP (only sub-surface rrs for now) if the direction is defined using @ e.g. rrs@32.0:45 where <zenith-theta>:<azimuth-phi>

Parameters:

• report – The planarrad report dictionary. should include the quadtables and the directional info
• parameter – parameter to calc. Currently only sub-surface reflectance rrs.

Returns:

read_pr_report(filename)

Reads in a PlanarRad generated report

Saves the single line reported parameters as a python dictionary

Parameters:filename – The name and path of the PlanarRad generated file Returns self.data_dictionary:  python dictionary with the key and values from the report

write_batch_report(input_directory, parameter)

Collect all of the batch reports and concatenate the results. The report should be :

Parameters:

• input_directory –
• parameter – This is the parameter in which to report.

class libplanarradpy.planrad.RunParameters(wavelengths)

Run parameters required by PlanarRad

All parameters are properties of this class

update_filenames()

Does nothing currently. May not need this method

write_phase_params_to_file()

Write the params to file that surftool_Free needs to generate the surface facets

write_run_parameters_to_file()

All of the class properties are written to a text file

Each property is on a new line with the key and value seperated with an equals sign ‘=’ This is the mane planarrad properties file used by slabtool

write_sky_params_to_file()

Writes the params to file that skytool_Free needs to generate the sky radiance distribution.

write_surf_params_to_file()

Write the params to file that surftool_Free needs to generate the surface facets

Indices and tables

• Index
• Module Index
• Search Page