Added new sample transmission calculation

Refs #11015

Code/Mantid/Framework/PythonInterface/plugins/algorithms/CalculateSampleTransmission.py

@@ -0,0 +1,94 @@
+from mantid.simpleapi import *
+from mantid.api import *
+from mantid.kernel import *
+import math
+import numpy as np
+
+
+class CalculateSampleTransmission(PythonAlgorithm):
+
+    def category(self):
+        return 'Sample'
+
+
+    def summary(self):
+        return 'Calculates the scattering & transmission for a given sample material and size over a given wavelength range.'
+
+
+    def PyInit(self):
+        self.declareProperty(name='WavelengthRange', defaultValue='', validator=StringMandatoryValidator(),
+                             doc='Wavelength range to calculate transmission for.')
+
+        self.declareProperty(name='ChemicalFormula', defaultValue='', validator=StringMandatoryValidator(),
+                             doc='Sample chemical formula')
+
+        self.declareProperty(name='NumberDensity', defaultValue=0.1,
+                             doc='Number denisty (atoms/Angstrom^3). Default=0.1')
+
+        self.declareProperty(name='Thickness', defaultValue=0.1,
+                             doc='Sample thickness (cm). Default=0.1')
+
+        self.declareProperty(MatrixWorkspaceProperty('OutputWorkspace', '', Direction.Output),
+                             doc='Outputs the sample transmission over the wavelength range as a function of wavelength.')
+
+
+    def PyExec(self):
+        self._setup()
+
+        # Create the workspace and set the sample material
+        CreateWorkspace(OutputWorkspace=self._output_ws, NSpec=2, DataX=[0, 0], DataY=[0, 0])
+        Rebin(InputWorkspace=self._output_ws, OutputWorkspace=self._output_ws, Params=self._bin_params)
+        SetSampleMaterial(InputWorkspace=self._output_ws, ChemicalFormula=self._chamical_formula)
+        ConvertToPointData(InputWorkspace=self._output_ws, OutputWorkspace=self._output_ws)
+
+        ws = mtd[self._output_ws]
+        wavelengths = ws.readX(0)
+        transmission_data = np.zeros(len(wavelengths))
+        scattering_data = np.zeros(len(wavelengths))
+
+        # Calculate transmission and scattering for each wavelength point
+        for idx in range(0, len(wavelengths)):
+            transmission, scattering = self._calculate_at_wavelength(wavelengths[idx])
+            transmission_data[idx] = transmission
+            scattering_data[idx] = scattering
+
+        ws.setY(0, transmission_data)
+        ws.setY(1, scattering_data)
+
+        self.setProperty('OutputWorkspace', self._output_ws)
+
+
+    def _setup(self):
+        """
+        Gets algorithm properties.
+        """
+
+        self._bin_params = self.getPropertyValue('WavelengthRange')
+        self._chamical_formula = self.getPropertyValue('ChemicalFormula')
+        self._density = self.getProperty('NumberDensity').value
+        self._thickness = self.getProperty('Thickness').value
+        self._output_ws = self.getPropertyValue('OutputWorkspace')
+
+
+    def _calculate_at_wavelength(self, wavelength):
+        """
+        Calculates transmission and scattering at a given wavelength.
+
+        @param wavelength Wavelength at which to calculate (in Angstrom)
+        @return Tuple of transmission and scattering
+        """
+
+        material = mtd[self._output_ws].mutableSample().getMaterial()
+
+        absorption_x_section = material.absorbXSection() * wavelength
+        total_x_section = absorption_x_section + material.totalScatterXSection()
+
+        transmission = math.exp(-self._density * total_x_section * self._thickness)
+        scattering = 1.0 - math.exp(-self._density * material.totalScatterXSection() * self._thickness)
+
+        return transmission, scattering
+
+
+
+# Register algorithm with Mantid
+AlgorithmFactory.subscribe(CalculateSampleTransmission)