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Merged
alexhroom merged 3 commits into from
Jan 29, 2025
Merged

Updates to RATapi v0.0.0dev4 #28

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a687dee
updated backgrounds/resolutions
alexhroom Jan 22, 2025
0c848dc
moved ratapi to requirements
alexhroom Jan 29, 2025
17d7a2a
changed all non-polarised to normal
alexhroom Jan 29, 2025
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1 change: 0 additions & 1 deletion .github/workflows/build_docs.yml
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Expand Up @@ -26,7 +26,6 @@ jobs:
python -m pip install --upgrade pip
pip install matlabengine==24.1.*
pip install -r requirements.txt
pip install RATapi
python build_docs.py
- name: Checkout gh-pages
if: github.ref == 'refs/heads/main'
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1 change: 1 addition & 0 deletions requirements.txt
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Expand Up @@ -3,3 +3,4 @@ sphinxcontrib-matlabdomain==0.18
pydata-sphinx-theme==0.15.2
sphinx_design==0.6.0
sphinx-copybutton==0.5.2
RATapi==0.0.0.dev4
8 changes: 4 additions & 4 deletions source/examples/DSPC_custom_XY.rst
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Expand Up @@ -50,27 +50,27 @@ This example can be run as a script or interactively using the instructions belo
.. tab-item:: Python
:sync: Python

.. note:: The custom model used is a Python model - **RATapi.examples.non_polarised.custom_XY_DSPC.py**.
.. note:: The custom model used is a Python model - **RATapi.examples.normal_reflectivity.custom_XY_DSPC.py**.


**Run Script**:

.. code-block:: console

python RATapi.examples.non_polarised.DSPC_custom_XY.py
python RATapi.examples.normal_reflectivity.DSPC_custom_XY.py

**Run as Function**:

.. code-block:: Python

import RATapi as RAT
problem, results = RAT.examples.non_polarised.DSPC_custom_XY()
problem, results = RAT.examples.normal_reflectivity.DSPC_custom_XY()

**Run Interactively**:

.. code-block:: console

jupyter notebook RATapi.examples.non_polarised.DSPC_custom_XY.ipynb
jupyter notebook RATapi.examples.normal_reflectivity.DSPC_custom_XY.ipynb


.. _ref_1:
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8 changes: 4 additions & 4 deletions source/examples/DSPC_custom_layers.rst
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Expand Up @@ -45,23 +45,23 @@ This example can be run as a script or interactively using the instructions belo
.. tab-item:: Python
:sync: Python

.. note:: The custom model used is a Python model - **RATapi.examples.non_polarised.custom_bilayer_DSPC.py**.
.. note:: The custom model used is a Python model - **RATapi.examples.normal_reflectivity.custom_bilayer_DSPC.py**.

**Run Script**:

.. code-block:: console

python RATapi.examples.non_polarised.DSPC_custom_layers.py
python RATapi.examples.normal_reflectivity.DSPC_custom_layers.py

**Run as Function**:

.. code-block:: Python

import RATapi as RAT
problem, results = RAT.examples.non_polarised.DSPC_custom_layers()
problem, results = RAT.examples.normal_reflectivity.DSPC_custom_layers()

**Run Interactively**:

.. code-block:: console

jupyter notebook RATapi.examples.non_polarised.DSPC_custom_layers.ipynb
jupyter notebook RATapi.examples.normal_reflectivity.DSPC_custom_layers.ipynb
6 changes: 3 additions & 3 deletions source/examples/DSPC_standard_layers.rst
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Expand Up @@ -39,17 +39,17 @@ This example can be run as a script or interactively using the instructions belo

.. code-block:: console

python RATapi.examples.non_polarised.DSPC_standard_layers.py
python RATapi.examples.normal_reflectivity.DSPC_standard_layers.py

**Run as Function**:

.. code-block:: Python

import RATapi as RAT
problem, results = RAT.examples.non_polarised.DSPC_standard_layers()
problem, results = RAT.examples.normal_reflectivity.DSPC_standard_layers()

**Run Interactively**:

.. code-block:: console

jupyter notebook RATapi.examples.non_polarised.DSPC_standard_layers.ipynb
jupyter notebook RATapi.examples.normal_reflectivity.DSPC_standard_layers.ipynb
2 changes: 1 addition & 1 deletion source/reference/matlab/projectClass.rst
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Expand Up @@ -54,7 +54,7 @@ Although, Project class provides one level higher interface so that one can use
*************
Domains Class
*************
RAT currently supports two calculation types (nonPolarised and Domains). The Domains Class is a project class with extra parameters (domainRatio, domainContrasts) for the Domains calculation.
RAT currently supports two calculation types (normal and Domains). The Domains Class is a project class with extra parameters (domainRatio, domainContrasts) for the Domains calculation.

.. note::
It is recommended to use `API.createProject` instead of creating a Project or Domains object directly.
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2 changes: 1 addition & 1 deletion source/reference/matlab/targetFunctions.rst
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Expand Up @@ -18,7 +18,7 @@ Common Functions
.. automodule:: targetFunctions.common.groupLayers
:members:

.. _nonPolarisedTF:
.. _normalTF:

Normal Target Functions (normalTF)

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16 changes: 8 additions & 8 deletions source/tutorial/chapter2.rst
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Expand Up @@ -700,7 +700,7 @@ The backgrounds can be one of three types: 'constant', 'function' or 'data'. The
.. code-block:: Python

problem.background_parameters.append(name='My New BackPar', min=1e-8, value=1e-7, max=1e-6, fit=True)
problem.backgrounds.append(name='My New Background', type='constant', value_1='My New BackPar')
problem.backgrounds.append(name='My New Background', type='constant', source='My New BackPar')


With this code snippet we've made a new background, with the value taken from the (fittable) parameter called 'My New BackPar':
Expand All @@ -724,7 +724,7 @@ With this code snippet we've made a new background, with the value taken from th
.. output:: Python

problem.background_parameters.append(name='My New BackPar', min=1e-8, value=1e-7, max=1e-6, fit=True)
problem.backgrounds.append(name='My New Background', type='constant', value_1='My New BackPar')
problem.backgrounds.append(name='My New Background', type='constant', source='My New BackPar')
print(problem.background_parameters)
print(problem.backgrounds)

Expand All @@ -740,7 +740,7 @@ This is then available to be used by any of our contrasts (see later).

.. code-block:: Python

problem.backgrounds.append(name='Data Background 1', type='data', value_1='My Background Data')
problem.backgrounds.append(name='Data Background 1', type='data', source='My Background Data')

.. .. tab-set::
.. :class: tab-label-hidden
Expand All @@ -759,7 +759,7 @@ This is then available to be used by any of our contrasts (see later).

.. .. output:: Python

.. problem.backgrounds.append(name='Data Background 1', type='data', value_1='My Background Data')
.. problem.backgrounds.append(name='Data Background 1', type='data', source='My Background Data')
.. print(problem.backgrounds)

This is then used in the reflectivity calculation for any contrast in which it is specified.
Expand Down Expand Up @@ -822,7 +822,7 @@ Then, we make the actual resolution referring to whichever one of the resolution

.. code-block:: Python

problem.resolutions.append(name='My new resolution', type='constant', value_1='My Resolution Param')
problem.resolutions.append(name='My new resolution', type='constant', source='My Resolution Param')
problem.resolutions.append(name='My Data Resolution', type='data')

.. tab-set::
Expand All @@ -845,7 +845,7 @@ Then, we make the actual resolution referring to whichever one of the resolution
.. output:: Python

problem.resolution_parameters.append(name='My Resolution Param', min=0.02, value=0.05, max=0.08, fit=True)
problem.resolutions.append(name='My new resolution', type='constant', value_1='My Resolution Param')
problem.resolutions.append(name='My new resolution', type='constant', source='My Resolution Param')
problem.resolutions.append(name='My Data Resolution', type='data')
print(problem.resolutions)

Expand Down Expand Up @@ -1102,8 +1102,8 @@ Use these parameters to define two constant backgrounds, again using the existin

.. code-block:: Python

problem.backgrounds.append(name='Background D2O', type='constant', value_1='Backs Value D2O')
problem.backgrounds.set_fields(0, name='Background ACMW', value_1='Backs Value ACMW')
problem.backgrounds.append(name='Background D2O', type='constant', source='Backs Value D2O')
problem.backgrounds.set_fields(0, name='Background ACMW', source='Backs Value ACMW')

We need two sub-phases for our project. D2O is already in the project as a default, so we only need to add the bulk out for ACMW

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6 changes: 3 additions & 3 deletions source/tutorial/customModels.rst
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Expand Up @@ -605,11 +605,11 @@ The rest of the custom model is defined similar to the standard layers model sho
problem.background_parameters.append(name='Background parameter H2O', min=1.0e-10, value=1.0e-7, max=1.0e-5, fit=True)

# And add the two new constant backgrounds
problem.backgrounds.append(name='Background SMW', type='constant', value_1='Background parameter SMW')
problem.backgrounds.append(name='Background H2O', type='constant', value_1='Background parameter H2O')
problem.backgrounds.append(name='Background SMW', type='constant', source='Background parameter SMW')
problem.backgrounds.append(name='Background H2O', type='constant', source='Background parameter H2O')

# And edit the other one....
problem.backgrounds.set_fields(0, name='Background D2O', value_1='Background parameter D2O')
problem.backgrounds.set_fields(0, name='Background D2O', source='Background parameter D2O')

# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment
problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)
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4 changes: 2 additions & 2 deletions source/tutorial/data/two_contrast_example.py
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Expand Up @@ -34,8 +34,8 @@
problem.background_parameters.set_fields(0, value=5.5e-6)
problem.background_parameters.append(name='Backs Value D2O', min=1e-8, value=2.8e-6, max=1e-5)

problem.backgrounds.append(name='Background D2O', type='constant', value_1='Backs Value D2O')
problem.backgrounds.set_fields(0, name='Background ACMW', value_1='Backs Value ACMW')
problem.backgrounds.append(name='Background D2O', type='constant', source='Backs Value D2O')
problem.backgrounds.set_fields(0, name='Background ACMW', source='Backs Value ACMW')

problem.bulk_out.append(name='SLD ACMW', min=-0.6e-6, value=-0.56e-6, max=-0.3e-6, fit=True)

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6 changes: 3 additions & 3 deletions source/tutorial/savingAndClasses.rst
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Expand Up @@ -205,15 +205,15 @@ Then, RAT will create a file containing all the statements needed to re-create y
from numpy import array, inf

problem = RAT.Project(
name='', calculation='non polarised', model='standard layers', geometry='air/substrate', absorption=False,
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', value_1='Background Param 1', value_2='', value_3='', value_4='', value_5='')]),
resolutions=RAT.ClassList([Resolution(name='Resolution 1', type='constant', value_1='Resolution Param 1', value_2='', value_3='', value_4='', value_5='')]),
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')]),
)

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