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Copying and Saving Outputs#

When you have completed your analysis, usually you will want to save a copy of your work for subsequent analysis. The problem definition can either be cloned so analysis is attempted with different parameters without risk of losing the best fits, or it can be saved to a file or as a script as detailed in the sections below

Saving to a file#

After a RAT calculation run, problem is the problem definition with updated fit parameters, controls is the settings used for the calculation and results is the computed reflectivities, SLD’s and so on.

RAT input model

Saving these objects to the current file directory can be done as shown below.

myResults = struct('problem', problem, 'results', results, 'controls', controls);
save('myResultsFile.mat', 'myResults');

import pickle

problem.save('problem.json')
controls.save('controls.json')
# Result file is saved using the builtin "pickle" library
with open('results.pickle', 'wb') as result_file:
    # dump result into that file
    pickle.dump(results, result_file)

Later on, the objects can be loaded from the save directory as shown below:

myWork = load('myResultsFile.mat');
problem = myWork.myResults.problem;
controls = myWork.myResults.controls;
results = myWork.myResults.results;

problem = RAT.Project.load('problem.json')
controls = RAT.Controls.load('controls.json')
with open('results.pickle', 'rb') as result_file:
    # load result from file
    results = pickle.load(result_file)

Copying a project class#

During an analysis, it may be necessary to make a copy of your project, so that you can modify one of them in order to carry out some kind of comparison between them for example. In the example below, problem1 and problem2 are references to the same instance of project class so modifying problem2 will also modify original object problem1 which is not ideal.

>> problem1 = projectClass();
>> problem2 = problem1;
>> problem1.geometry

ans =

    'air/substrate'

>> problem2.setGeometry('substrate/liquid');
>> problem1.geometry

ans =

    'substrate/liquid'

>>> problem1 = RAT.Project()
>>> problem2 = problem1
>>> print(problem1.geometry)

air/substrate

>>> problem2.geometry = "substrate/liquid"
>>> print(problem1.geometry)

substrate/liquid

The proper way to make a copy/clone of the project class is shown in the example below,

>> problem1 = projectClass();
>> problem2 = problem1.clone(); % Copy with clone method
>> problem1.geometry

ans =

    'air/substrate'

>> problem2.setGeometry('substrate/liquid');
>> problem1.geometry

ans =

    'air/substrate'

>>> import copy
>>> problem1 = RAT.Project()
>>> problem2 = copy.deepcopy(problem1) # Copy using deepcopy function in the copy module
>>> print(problem1.geometry)

air/substrate

>>> problem2.geometry = "substrate/liquid"
>>> print(pproblem1.geometry)

air/substrate

Now problem1 and problem2 are seperate instances of project class and changing problem2 no longer changes problem1.

Exporting as a script#

Although saving a binary version of the class is useful, sometimes it would be better to have a script version which will reproduce the class. This can be done as shown below:

problem = projectClass();
problem.writeScript(script="myProjectScript");

problem = RAT.Project()
problem.write_script(script='myProjectScript')

Then, RAT will create a file containing all the statements needed to re-create your project:

% THIS FILE IS GENERATED FROM RAT VIA THE "WRITESCRIPT" ROUTINE. IT IS NOT PART OF THE RAT CODE.

project = createProject(name='', calcType='normal', model='standard layers', geometry='air/substrate', absorption=false);

project.setParameterValue(1, 20);
project.setParameterLimits(1, 1, 5);
project.setParameterFit(1, true);
project.setParameterPrior(1, 'uniform', 0, Inf);


project.removeBulkIn(1);
project.addBulkIn('SLD Air', 0, 0, 0, false, 'uniform', 0, Inf);

project.removeBulkOut(1);
project.addBulkOut('SLD D2O', 6.2e-06, 6.35e-06, 6.35e-06, false, 'uniform', 0, Inf);

project.removeScalefactor(1);
project.addScalefactor('Scalefactor 1', 0.02, 0.23, 0.25, false, 'uniform', 0, Inf);

project.removeQzshift(1);
project.addQzshift('Qz shift 1', -0.0001, 0, 0.0001, false, 'uniform', 0, Inf);

project.removeBackgroundParam(1);
project.addBackgroundParam('Background Param 1', 1e-07, 1e-06, 1e-05, false, 'uniform', 0, Inf);

project.removeResolutionParam(1);
project.addResolutionParam('Resolution par 1', 0.01, 0.03, 0.05, false, 'uniform', 0, Inf);

project.removeBackground(1);
project.removeResolution(1);

project.addBackground('Background 1', 'constant', 'Background Param 1', '', '', '', '');

project.addResolution('Resolution 1', 'constant', 'Resolution par 1', '', '', '', '');

project.removeData(1);
project.addData('Simulation');
project.setData(1, 'simRange', [0.005 0.7]);

# THIS FILE IS GENERATED FROM RAT VIA THE "WRITE_SCRIPT" ROUTINE. IT IS NOT PART OF THE RAT CODE.

import RAT
from RAT.models import *
from numpy import array, inf

problem = RAT.Project(
    name='', calculation='normal', model='standard layers', geometry='air/substrate', absorption=False,
    parameters=RAT.ClassList([ProtectedRAT.models.Parameter(name='Substrate Roughness', min=1.0, value=3.0, max=5.0, fit=True, prior_type='uniform', mu=0.0, sigma=inf)]),
    background_parameters=RAT.ClassList([RAT.models.Parameter(name='Background Param 1', min=1e-07, value=1e-06, max=1e-05, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),
    scalefactors=RAT.ClassList([RAT.models.Parameter(name='Scalefactor 1', min=0.02, value=0.23, max=0.25, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),
    bulk_in=RAT.ClassList([RAT.models.Parameter(name='SLD Air', min=0.0, value=0.0, max=0.0, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),
    bulk_out=RAT.ClassList([RAT.models.Parameter(name='SLD D2O', min=6.2e-06, value=6.35e-06, max=6.35e-06, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),
    resolution_parameters=RAT.ClassList([RAT.models.Parameter(name='Resolution Param 1', min=0.01, value=0.03, max=0.05, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),
    backgrounds=RAT.ClassList([Background(name='Background 1', type='constant', source='Background Param 1', value_2='', value_3='', value_4='', value_5='')]),
    resolutions=RAT.ClassList([Resolution(name='Resolution 1', type='constant', source='Resolution Param 1', value_2='', value_3='', value_4='', value_5='')]),
    data=RAT.ClassList([Data(name='Simulation')]),
    )

This is useful because you can then edit this file as you wish, to re-use it as a template for further projects.

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