Simple Inversion (Code Examples)

Refer to the Simple Inversion format specification while reading these examples and writing your own code.

Write a Simple Inversion

MATLAB

% write_simple_inversion.m: A template for writing your own Simple Inversion

%% Construct object
siv = SimpleInversion;

%% Set datasets and attributes
M = 800; % image first dimension
N = 600; % image second dimension

siv.phi = zeros(M, N); % optional* | Deflection potential in the object plane, the gradient of which gives the deflection angles. Omit only if the solution is not representable by a potential -- in which case specifying the deflection angles is required. | meters
% siv.defl_ax1 = zeros(M,N); % optional* | Deflection angle along axis-1 (= grad phi, axis 1 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad
% siv.defl_ax2 = zeros(M,N); % optional* | Deflection angle along axis-2 (= grad phi, axis 2 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad

% disp(siv.object_type) % already-set | Specification of the HDF5 object type | "inversion" (always this value)
% disp(siv.inversion_type) % already-set | Specification of the inversion sub-type | "simple" (always this value)
% disp(siv.pradformat_version) % already-set | HDF5 pradformat file format version followed | e.g. "0.1.0"

siv.dr = 2.5e-6; % required | Bin spacing along axis-1, in the object plane | meters
[siv.defl_ax2, siv.defl_ax1] = gradient(siv.phi, siv.dr); % sic (MATLAB returns first the gradient with respect to the second axis, then the gradient with respect to the first axis)

siv.source_object_dist = 0.11; % required | Approximate distance from the particle source to the object plane (the E & M structures). Used to estimate image magnification. | meters
siv.object_image_dist = 1.45; % required | Approximate distance from the object plane (the E & M structures) to the image plane (the radiograph). Used to estimate image magnification. | meters

siv.spec_name = "p+"; % required | Shortname for the particle species**
siv.spec_mass = 1.67262e-27; % required | Particle mass | kg
siv.spec_charge = 1.6021766208e-19; % required | Particle charge | Coulombs
siv.spec_energy = 14.7e6; % required | Particle energy | eV

% siv.dr_ax2 = 5.0e-6; % optional | Bin spacing along axis-2, in the object plane | meters
siv.source_radius = 80.0e-6; % optional | Approximate characteristic radius of the particle source (set as zero for a point source). Helpful in estimating image resolution. | meters
siv.label = "PROBLEM_inversion_shot3"; % optional | Short, identifying label for this file (with no spaces or crazy characters). This can be stamped onto plots, etc.
siv.description = "Inversion using PROBLEM of a CR39 radiograph from shot 3 on the February 2021 NIF DISC run."; % optional | Longer description of this file. This can be read by people trying to figure out where this file came from.
% disp(siv.file_date); % automatically-set | Date the (future) file will be created, in the format "YYYY-MM-DD" | You don't need to set this, it will be set automatically
% siv.radiograph_filename = "/home/scott/prad/myradiograph.h5"; % optional | If this is an inversion, the *SimpleRadiograph* pradformat file from which this data was inverted
% siv.fields_filename = "/home/scott/synth/myfields.h5"; % optional | If this is an exact solution, the *SimpleFields* pradformat file from which this data was projected

%% Pretty print your newly-minted radiograph object
disp(siv)

%% Save to file
[status, msg, msgID] = mkdir('outs');
h5filename = fullfile('outs', 'myinversion.h5');
prad_save(siv, h5filename);

%%  Asterixed footnotes referenced above:
%
%  *  Either deflection potential or deflection angles must be specified (or both if you'd like).
%
%  ** For best compatibility, consider using the PlasmaPy particle symbol conventions. https://docs.plasmapy.org/en/stable/api/plasmapy.particles.particle_symbol.html
%     For example, protons can be specified as just "p+", and electrons by "e-". Any arbitrary isotope of Hydrogen can be specified "H-I q+"? where I is the mass number and q is the charge.
%

Python

# write_simple_inversion.py: A template for writing your own Simple Inversion

import os
import numpy as np
import pradformat as prf

## Construct object
siv = prf.SimpleInversion()

## Set datasets and attributes
M = 800 # image first dimension
N = 600 # image second dimension

siv.phi = np.zeros((M, N)) # optional* | Deflection potential in the object plane, the gradient of which gives the deflection angles. Omit only if the solution is not representable by a potential -- in which case specifying the deflection angles is required. | meters
# siv.defl_ax1 = np.zeros((M,N)) # optional* | Deflection angle along axis-1 (= grad phi, axis 1 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad
# siv.defl_ax2 = np.zeros((M,N)) # optional* | Deflection angle along axis-2 (= grad phi, axis 2 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad

# print(siv.object_type) # already-set | Specification of the HDF5 object type | "inversion" (always this value)
# print(siv.inversion_type) # already-set | Specification of the inversion sub-type | "simple" (always this value)
# print(siv.pradformat_version) # already-set | HDF5 pradformat file format version followed | e.g. "0.1.0"

siv.dr = 2.5e-6 # required | Bin spacing along axis-1, in the object plane | meters
siv.defl_ax1 = np.gradient(siv.phi, siv.dr, axis=0)
siv.defl_ax2 = np.gradient(siv.phi, siv.dr, axis=1)

siv.source_object_dist = 0.11 # required | Approximate distance from the particle source to the object plane (the E & M structures). Used to estimate image magnification. | meters
siv.object_image_dist = 1.45 # required | Approximate distance from the object plane (the E & M structures) to the image plane (the radiograph). Used to estimate image magnification. | meters

siv.spec_name = "p+" # required | Shortname for the particle species**
siv.spec_mass = 1.67262e-27 # required | Particle mass | kg
siv.spec_charge = 1.6021766208e-19 # required | Particle charge | Coulombs
siv.spec_energy = 14.7e6 # required | Particle energy | eV

# siv.dr_ax2 = 5.0e-6 # optional | Bin spacing along axis-2, in the object plane | meters
siv.source_radius = 80.0e-6 # optional | Approximate characteristic radius of the particle source (set as zero for a point source). Helpful in estimating image resolution. | meters
siv.label = "PROBLEM_inversion_shot3" # optional | Short, identifying label for this file (with no spaces or crazy characters). This can be stamped onto plots, etc.
siv.description = "Inversion using PROBLEM of a CR39 radiograph from shot 3 on the February 2021 NIF DISC run." # optional | Longer description of this file. This can be read by people trying to figure out where this file came from.
# print(siv.file_date) # automatically-set | Date the (future) file will be created, in the format "YYYY-MM-DD" | You don't need to set this, it will be set automatically
# siv.radiograph_filename = "/home/scott/prad/myradiograph.h5" # optional | If this is an inversion, the *SimpleRadiograph* pradformat file from which this data was inverted
# siv.fields_filename = "/home/scott/synth/myfields.h5" # optional | If this is an exact solution, the *SimpleFields* pradformat file from which this data was projected

## Pretty print your newly-minted radiograph object
print(siv)

## Save to file
if not os.path.isdir("outs"):
    os.mkdir("outs")
h5filename = os.path.join('outs', 'myinversion.h5')
siv.save(h5filename)

##  Asterixed footnotes referenced above:
#
#  *  Either deflection potential or deflection angles must be specified (or both if you'd like).
#
#  ** For best compatibility, consider using the PlasmaPy particle symbol conventions. https://docs.plasmapy.org/en/stable/api/plasmapy.particles.particle_symbol.html
#     For example, protons can be specified as just "p+", and electrons by "e-". Any arbitrary isotope of Hydrogen can be specified "H-I q+"? where I is the mass number and q is the charge.
#

Read a Simple Inversion

MATLAB

% read_simple_inversion.m: Template for reading a Simple Inversion file

%% Load object from pradformat file
h5filename = fullfile('outs', 'myinversion.h5');
siv = prad_load(h5filename);

%% Examine your newly loaded object
disp(siv)

%% Utilize object's datasets and attributes in your own scripts
assert(isa(siv, 'SimpleInversion'));

% siv.phi; % optional* | Deflection potential in the object plane, the gradient of which gives the deflection angles. Omit only if the solution is not representable by a potential -- in which case specifying the deflection angles is required. | meters
% siv.defl_ax1; % optional* | Deflection angle along axis-1 (= grad phi, axis 1 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad
% siv.defl_ax2; % optional* | Deflection angle along axis-2 (= grad phi, axis 2 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad
%
% siv.object_type % required | Specification of the HDF5 object type | "inversion" (always this value)
% siv.inversion_type % required | Specification of the inversion sub-type | "simple" (always this value)
% siv.pradformat_version % required | HDF5 pradformat file format version followed | e.g. "0.1.0"
% 
% siv.dr; % required | Bin spacing along axis-1, in the object plane | meters
% 
% siv.source_object_dist; % required | Approximate distance from the particle source to the object plane (the E & M structures). Used to estimate image magnification. | meters
% siv.object_image_dist; % required | Approximate distance from the object plane (the E & M structures) to the image plane (the radiograph). Used to estimate image magnification. | meters
% 
% siv.spec_name; % required | Shortname for the particle species**
% siv.spec_mass; % required | Particle mass | kg
% siv.spec_charge; % required | Particle charge | Coulombs
% siv.spec_energy; % required | Particle energy | eV
% 
% siv.dr_ax2; % optional | Bin spacing along axis-2, in the object plane | meters
% siv.source_radius; % optional | Approximate characteristic radius of the particle source (set as zero for a point source). Helpful in estimating image resolution. | meters
% siv.label; % optional | Short, identifying label for this file (with no spaces or crazy characters). This can be stamped onto plots, etc.
% siv.description; % optional | Longer description of this file. This can be read by people trying to figure out where this file came from.
% siv.file_date; % optional | Date the (future) file will be created, in the format "YYYY-MM-DD" | You don't need to set this, it will be set automatically
% siv.radiograph_filename; % optional | If this is an inversion, the *SimpleRadiograph* pradformat file from which this data was inverted
% siv.fields_filename; % optional | If this is an exact solution, the *SimpleFields* pradformat file from which this data was projected


% Dealing with required attributes/datasets
disp(siv.pradformat_version)
disp(siv.dr)

% Dealing with optional attributes/datasets
if ~isempty(siv.label)
    disp(siv.label)
else
    disp("Well, I'd like to show you the label attribute, but I guess it wasn't set. Oh well.")
end

if isempty(siv.defl_ax1) || isempty(siv.defl_ax2)
    [defl_ax2, defl_ax1] = gradient(siv.phi, siv.dr); % sic (MATLAB gives the first axis derivative second)
end

%%  Asterixed footnotes referenced above:
%
%  *  Either deflection potential or deflection angles must be specified (or both if you'd like).
%
%  ** For best compatibility, consider using the PlasmaPy particle symbol conventions. https://docs.plasmapy.org/en/stable/api/plasmapy.particles.particle_symbol.html
%     For example, protons can be specified as just "p+", and electrons by "e-". Any arbitrary isotope of Hydrogen can be specified "H-I q+"? where I is the mass number and q is the charge.
%

Python

# read_simple_inversion.py: Template for reading a Simple Inversion file

import os
import numpy as np
import pradformat as prf

## Load object from pradformat file
h5filename = os.path.join('outs', 'myinversion.h5')
siv = prf.prad_load(h5filename)

## Examine your newly loaded object
print(siv)

## Utilize object's datasets and attributes in your own scripts
assert isinstance(siv, prf.SimpleInversion)

# siv.phi # optional* | Deflection potential in the object plane, the gradient of which gives the deflection angles. Omit only if the solution is not representable by a potential -- in which case specifying the deflection angles is required. | meters
# siv.defl_ax1 # optional* | Deflection angle along axis-1 (= grad phi, axis 1 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad
# siv.defl_ax2 # optional* | Deflection angle along axis-2 (= grad phi, axis 2 component). Values can be positive (for deflection in +ax1 direction) or negative (for deflection in -ax1 direction). | rad
#
# siv.object_type # required | Specification of the HDF5 object type | "inversion" (always this value)
# siv.inversion_type # required | Specification of the inversion sub-type | "simple" (always this value)
# siv.pradformat_version # required | HDF5 pradformat file format version followed | e.g. "0.1.0"
# 
# siv.dr # required | Bin spacing along axis-1, in the object plane | meters
# 
# siv.source_object_dist # required | Approximate distance from the particle source to the object plane (the E & M structures). Used to estimate image magnification. | meters
# siv.object_image_dist # required | Approximate distance from the object plane (the E & M structures) to the image plane (the radiograph). Used to estimate image magnification. | meters
# 
# siv.spec_name # required | Shortname for the particle species**
# siv.spec_mass # required | Particle mass | kg
# siv.spec_charge # required | Particle charge | Coulombs
# siv.spec_energy # required | Particle energy | eV
# 
# siv.dr_ax2 # optional | Bin spacing along axis-2, in the object plane | meters
# siv.source_radius # optional | Approximate characteristic radius of the particle source (set as zero for a point source). Helpful in estimating image resolution. | meters
# siv.label # optional | Short, identifying label for this file (with no spaces or crazy characters). This can be stamped onto plots, etc.
# siv.description # optional | Longer description of this file. This can be read by people trying to figure out where this file came from.
# siv.file_date # optional | Date the (future) file will be created, in the format "YYYY-MM-DD" | You don't need to set this, it will be set automatically
# siv.radiograph_filename # optional | If this is an inversion, the *SimpleRadiograph* pradformat file from which this data was inverted
# siv.fields_filename # optional | If this is an exact solution, the *SimpleFields* pradformat file from which this data was projected


# Dealing with required attributes/datasets
print(siv.pradformat_version)
print(siv.dr)

# Dealing with optional attributes/datasets
if  not isinstance(siv.label, type(None)):
    print(siv.label)
else:
    print("Well, I'd like to show you the label attribute, but I guess it wasn't set. Oh well.")

if isinstance(siv.defl_ax1, type(None)) or  isinstance(siv.defl_ax2, type(None)):
    defl_ax1 = np.gradient(siv.phi, siv.dr, axis=0)
    defl_ax2 = np.gradient(siv.phi, siv.dr, axis=1)

##  Asterixed footnotes referenced above:
#
#  *  Either deflection potential or deflection angles must be specified (or both if you'd like).
#
#  ** For best compatibility, consider using the PlasmaPy particle symbol conventions. https://docs.plasmapy.org/en/stable/api/plasmapy.particles.particle_symbol.html
#     For example, protons can be specified as just "p+", and electrons by "e-". Any arbitrary isotope of Hydrogen can be specified "H-I q+"? where I is the mass number and q is the charge.
#