Release 1.4.0

CHANGELOG.md

@@ -15,6 +15,8 @@ New:
 * Add Thomson Scattering model. (#97)
 * Add Generomak core plasma profiles. (#360)
 * Add toroidal_mesh_from_polygon for making mesh for not fully-360 degrees axisymmetric elements. (#365)
+* Add common spectroscopic instruments: Polychromator, SurveySpectrometer, CzernyTurnerSpectrometer. (#299)
+
 
 Bug Fixes:
 ----------

cherab/tools/spectroscopy/__init__.py

@@ -0,0 +1,22 @@
+
+# Copyright 2016-2021 Euratom
+# Copyright 2016-2021 United Kingdom Atomic Energy Authority
+# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+#
+# Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the
+# European Commission - subsequent versions of the EUPL (the "Licence");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+from .instrument import SpectroscopicInstrument
+from .polychromator import PolychromatorFilter, TrapezoidalFilter, Polychromator
+from .spectrometer import Spectrometer, CzernyTurnerSpectrometer

cherab/tools/spectroscopy/instrument.py

@@ -0,0 +1,118 @@
+
+# Copyright 2016-2021 Euratom
+# Copyright 2016-2021 United Kingdom Atomic Energy Authority
+# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+#
+# Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the
+# European Commission - subsequent versions of the EUPL (the "Licence");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+class SpectroscopicInstrument:
+ """
+ Base class for spectroscopic instruments (spectrometers, polychromators, etc.).
+ This is an abstract class.
+
+ :param str name: Instrument name.
+
+ :ivar list pipeline_classes: The list of pipeline classes used with this instrument.
+ :ivar list pipeline_kwargs: The list of dicts with keywords passed to init methods of
+ pipeline classes used with this instrument.
+ :ivar float min_wavelength: Lower wavelength bound for spectral range.
+ :ivar float max_wavelength: Upper wavelength bound for spectral range.
+ :ivar int spectral_bins: The number of spectral samples over the wavelength range.
+ """
+
+ def __init__(self, name=''):
+ self._pipeline_classes = None
+ self.name = name
+ self._clear_spectral_settings()
+
+ @property
+ def name(self):
+ # Instrument name.
+ return self._name
+
+ @name.setter
+ def name(self, value):
+ self._name = str(value)
+ self._pipeline_kwargs = None
+
+ @property
+ def pipeline_classes(self):
+ # The list of pipeline classes used with this instrument.
+ if self._pipeline_classes is None:
+ self._update_pipeline_classes()
+
+ return self._pipeline_classes
+
+ @property
+ def pipeline_kwargs(self):
+ # The list of dicts with keywords passed to init methods of
+ # pipeline classes used with this instrument.
+ if self._pipeline_kwargs is None:
+ self._update_pipeline_kwargs()
+
+ return self._pipeline_kwargs
+
+ def create_pipelines(self):
+ """ Returns a list of new pipelines created according to `pipeline_classes`
+ and keyword arguments."""
+ if self._pipeline_classes is None:
+ self._update_pipeline_classes()
+ if self._pipeline_kwargs is None:
+ self._update_pipeline_kwargs()
+
+ pipelines = []
+ for PipelineClass, kwargs in zip(self._pipeline_classes, self._pipeline_kwargs):
+ pipeline = PipelineClass(**kwargs)
+ pipelines.append(pipeline)
+
+ return pipelines
+
+ @property
+ def min_wavelength(self):
+ # Lower wavelength bound for spectral range.
+ if self._min_wavelength is None:
+ self._update_spectral_settings()
+
+ return self._min_wavelength
+
+ @property
+ def max_wavelength(self):
+ # Upper wavelength bound for spectral range.
+ if self._max_wavelength is None:
+ self._update_spectral_settings()
+
+ return self._max_wavelength
+
+ @property
+ def spectral_bins(self):
+ # The number of spectral samples over the wavelength range.
+ if self._spectral_bins is None:
+ self._update_spectral_settings()
+
+ return self._spectral_bins
+
+ def _clear_spectral_settings(self):
+ self._min_wavelength = None
+ self._max_wavelength = None
+ self._spectral_bins = None
+
+ def _update_spectral_settings(self):
+ raise NotImplementedError("To be defined in subclass.")
+
+ def _update_pipeline_classes(self):
+ raise NotImplementedError("To be defined in subclass.")
+
+ def _update_pipeline_kwargs(self):
+ raise NotImplementedError("To be defined in subclass.")

cherab/tools/spectroscopy/polychromator.py

@@ -0,0 +1,221 @@
+
+# Copyright 2016-2021 Euratom
+# Copyright 2016-2021 United Kingdom Atomic Energy Authority
+# Copyright 2016-2021 Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas
+#
+# Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the
+# European Commission - subsequent versions of the EUPL (the "Licence");
+# You may not use this work except in compliance with the Licence.
+# You may obtain a copy of the Licence at:
+#
+# https://joinup.ec.europa.eu/software/page/eupl5
+#
+# Unless required by applicable law or agreed to in writing, software distributed
+# under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR
+# CONDITIONS OF ANY KIND, either express or implied.
+#
+# See the Licence for the specific language governing permissions and limitations
+# under the Licence.
+
+import numpy as np
+from raysect.optical import InterpolatedSF
+from raysect.optical.observer import RadiancePipeline0D
+
+from .instrument import SpectroscopicInstrument
+
+
+class PolychromatorFilter(InterpolatedSF):
+ """
+ Defines a polychromator filter as a Raysect's InterpolatedSF.
+
+ :param object wavelengths: 1D array of wavelengths in nanometers.
+ :param object samples: 1D array of spectral samples.
+ :param bool normalise: True/false toggle for whether to normalise the
+ spectral function so its integral equals 1.
+ :param str name: Filter name (e.g. "H-alpha filter"). Default is ''.
+
+ :ivar float min_wavelength: Lower wavelength bound of the filter's spectral range in nm.
+ :ivar float max_wavelength: Upper wavelength bound of the filter's spectral range in nm.
+ """
+
+ def __init__(self, wavelengths, samples, normalise=False, name=''):
+
+ wavelengths = np.array(wavelengths, dtype=np.float64)
+ samples = np.array(samples, dtype=np.float64)
+
+ if wavelengths.ndim != 1:
+ raise ValueError("Wavelength array must be 1D.")
+
+ if samples.shape[0] != wavelengths.shape[0]:
+ raise ValueError("Wavelength and sample arrays must be the same length.")
+
+ indices = np.argsort(wavelengths)
+ wavelengths = wavelengths[indices]
+ samples = samples[indices]
+
+ self._min_wavelength = wavelengths[0]
+ self._max_wavelength = wavelengths[-1]
+ self._window = self._max_wavelength - self._min_wavelength
+ self._central_wavelength = 0.5 * (self._max_wavelength + self._min_wavelength)
+
+ # setting the ends of the filter to zero, if they are not
+ if samples[0] != 0:
+ wavelengths = np.insert(wavelengths, 0, wavelengths[0] * (1. - 1.e-15))
+ samples = np.insert(samples, 0, 0)
+ if samples[-1] != 0:
+ wavelengths = np.append(wavelengths, wavelengths[-1] * (1. + 1.e-15))
+ samples = np.append(samples, 0)
+
+ super().__init__(wavelengths, samples, normalise)
+ self._name = str(name)
+
+ @property
+ def name(self):
+ # Filter name.
+ return self._name
+
+ @property
+ def min_wavelength(self):
+ # Lower wavelength bound of the filter's spectral range in nm.
+ return self._min_wavelength
+
+ @property
+ def max_wavelength(self):
+ # Upper wavelength bound of the filter's spectral range in nm.
+ return self._max_wavelength
+
+ @property
+ def window(self):
+ # Size of the filtering window in nm.
+ return self._window
+
+ @property
+ def central_wavelength(self):
+ # Central wavelength of the filter in nm.
+ return self._central_wavelength
+
+
+class TrapezoidalFilter(PolychromatorFilter):
+ """
+ Symmetrical trapezoidal polychromator filter.
+
+ :param float wavelength: Central wavelength of the filter in nm.
+ :param float window: Size of the filtering window in nm. Default is 3.
+ :param float flat_top: Size of the flat top part of the filter in nm.
+ Default is None (equal to window).
+ :param str name: Filter name (e.g. "H-alpha filter"). Default is ''.
+ """
+
+ def __init__(self, central_wavelength, window=3., flat_top=None, name=''):
+
+ if central_wavelength <= 0:
+ raise ValueError("Argument 'central_wavelength' must be positive.")
+
+ if window <= 0:
+ raise ValueError("Argument 'window' must be positive.")
+
+ flat_top = flat_top or window
+
+ if flat_top <= 0:
+ raise ValueError("Argument 'flat_top' must be positive.")
+ if flat_top > window:
+ raise ValueError("Argument 'flat_top' must be less or equal than 'window'.")
+
+ self._flat_top = flat_top
+
+ if flat_top == window:
+ flat_top -= flat_top * 1.e-15
+
+ wavelengths = [central_wavelength - 0.5 * window,
+ central_wavelength - 0.5 * flat_top,
+ central_wavelength + 0.5 * flat_top,
+ central_wavelength + 0.5 * window]
+ samples = [0, 1, 1, 0]
+ super().__init__(wavelengths, samples, normalise=False, name=name)
+
+ @property
+ def flat_top(self):
+ # Size of the flat top part of the filter in nm.
+ return self._flat_top
+
+
+class Polychromator(SpectroscopicInstrument):
+ """
+ A polychromator assembly with a set of different filters.
+
+ :param list filters: List of the `PolychromatorFilter` instances.
+ :param int min_bins_per_window: Minimal number of spectral bins
+ per filtering window. Default is 10.
+ :param str name: Polychromator name.
+
+ .. code-block:: pycon
+
+ >>> from raysect.optical import World
+ >>> from raysect.optical.observer import FibreOptic
+ >>> from cherab.tools.spectroscopy import Polychromator, TrapezoidalFilter
+ >>>
+ >>> world = World()
+ >>> h_alpha_filter = TrapezoidalFilter(656.1, name='H-alpha filter')
+ >>> ciii_465nm_filter = TrapezoidalFilter(464.8, name='CIII 465 nm filter')
+ >>> polychromator = Polychromator([h_alpha_filter, ciii_465nm_filter], name='MyPolychromator')
+ >>> fibreoptic = FibreOptic(name="MyFibreOptic", parent=world)
+ >>> fibreoptic.min_wavelength = polychromator.min_wavelength
+ >>> fibreoptic.max_wavelength = polychromator.max_wavelength
+ >>> fibreoptic.spectral_bins = polychromator.spectral_bins
+ >>> fibreoptic.pipelines = polychromator.create_pipelines()
+ """
+
+ def __init__(self, filters, min_bins_per_window=10, name=''):
+ super().__init__(name)
+ self.min_bins_per_window = min_bins_per_window
+ self.filters = filters
+
+ @property
+ def min_bins_per_window(self):
+ # Minimal number of spectral bins per filtering window.
+ return self._min_bins_per_window
+
+ @min_bins_per_window.setter
+ def min_bins_per_window(self, value):
+ value = int(value)
+ if value <= 0:
+ raise ValueError("Attribute 'min_bins_per_window' must be positive.")
+
+ self._min_bins_per_window = value
+ self._clear_spectral_settings()
+
+ @property
+ def filters(self):
+ # List of the PolychromatorFilter instances.
+ return self._filters
+
+ @filters.setter
+ def filters(self, value):
+ for poly_filter in value:
+ if not isinstance(poly_filter, PolychromatorFilter):
+ raise TypeError('Property filters must contain only PolychromatorFilter instances.')
+
+ self._filters = value
+ self._clear_spectral_settings()
+ self._pipeline_classes = None
+ self._pipeline_kwargs = None
+
+ def _update_pipeline_classes(self):
+ self._pipeline_classes = [RadiancePipeline0D for poly_filter in self._filters]
+
+ def _update_pipeline_kwargs(self):
+ self._pipeline_kwargs = [{'name': self._name + ': ' + poly_filter.name, 'filter': poly_filter} for poly_filter in self._filters]
+
+ def _update_spectral_settings(self):
+
+ min_wavelength = np.inf
+ max_wavelength = 0
+ step = np.inf
+ for poly_filter in self._filters:
+ step = min(step, poly_filter.window / self._min_bins_per_window)
+ min_wavelength = min(min_wavelength, poly_filter.min_wavelength)
+ max_wavelength = max(max_wavelength, poly_filter.max_wavelength)
+
+ self._min_wavelength = min_wavelength
+ self._max_wavelength = max_wavelength
+ self._spectral_bins = int(np.ceil((max_wavelength - min_wavelength) / step))