Move jump fit from Python script to algoriithm

Refs #9345

Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/JumpFit.py

@@ -0,0 +1,153 @@
+from mantid.kernel import *
+from mantid.api import *
+from mantid.simpleapi import *
+from mantid import logger, mtd
+from IndirectCommon import *
+from IndirectImport import import_mantidplot
+
+import os.path
+
+
+class JumpFit(PythonAlgorithm):
+
+
+    def category(self):
+        return 'Workflow\\Inelastic;PythonAlgorithms;Inelastic'
+
+
+    def summary(self):
+        return ''  ##TODO
+
+
+    def PyInit(self):
+        self.declareProperty(WorkspaceProperty('InputWorkspace', '', direction=Direction.Input),
+                doc='Input workspace')
+
+        valid_functions = ['ChudleyElliot', 'HallRoss', 'FickDiffusion', 'TeixeiraWater']
+        self.declareProperty(name='JumpFunction', defaultValue=valid_functions[0],
+                             validator=StringListValidator(valid_functions),
+                             doc='')  ##TODO
+
+        self.declareProperty(name='Width', defaultValue=0, validator=IntMandatoryValidator(), doc='')  ##TODO
+        self.declareProperty(name='QMin', defaultValue=0.0, validator=FloatMandatoryValidator(), doc='')  ##TODO
+        self.declareProperty(name='QMax', defaultValue=0.0, validator=FloatMandatoryValidator(), doc='')  ##TODO
+
+        self.declareProperty(name='Output', defaultValue='', direction=Direction.InOut,
+                doc='Output name')
+
+        self.declareProperty(name='Verbose', defaultValue=False, doc='Output more verbose message to log')
+        self.declareProperty(name='Plot', defaultValue=False, doc='Plot result workspace')
+        self.declareProperty(name='Save', defaultValue=False, doc='Save result workspace to nexus file in the default save directory')
+
+
+    def PyExec(self):
+        in_ws = self.getPropertyValue('InputWorkspace')
+        out_name = self.getPropertyValue('Output')
+
+        jump_function = self.getProperty('JumpFunction').value
+        width = self.getProperty('Width').value
+        q_min = self.getProperty('QMin').value
+        q_max = self.getProperty('QMax').value
+
+        verbose = self.getProperty('Verbose').value
+        plot = self.getProperty('Plot').value
+        save = self.getProperty('Save').value
+
+        workdir = getDefaultWorkingDirectory()
+
+        StartTime('Jump fit : ' + jump_function + ' ; ')
+
+        # Select the width we wish to fit
+        spectrum_ws = "__" + in_ws
+        ExtractSingleSpectrum(InputWorkspace=in_ws, OutputWorkspace=spectrum_ws, WorkspaceIndex=width)
+
+        # Convert to HWHM
+        Scale(InputWorkspace=spectrum_ws, Factor=0.5, OutputWorkspace=spectrum_ws)
+
+        # Crop the workspace between the given ranges
+        if verbose:
+            logger.notice('Cropping from Q= ' + str(q_min) + ' to ' + str(q_max))
+
+        # Give the user some extra infromation if required
+        if verbose:
+            in_run = mtd[in_ws].getRun()
+            try:
+                log = in_run.getLogData('fit_program')
+                if log:
+                    val = log.value
+                    logger.notice('Fit program was : ' + val)
+            except RuntimeError:
+                # If we couldn't find the fit program, just pass
+                pass
+
+            logger.notice('Parameters in ' + in_ws)
+
+        x_data = mtd[in_ws].readX(0)
+        xmax = x_data[-1]
+
+        # Select fit function to use
+        if jump_function == 'ChudleyElliot':
+            # Chudley-Elliott: HWHM=(1-sin*(Q*L)/(Q*L))/Tau
+            # for Q->0 W=Q^2*L^2/(6*Tau)
+
+            tval = 1.0 / xmax
+            lval = 1.5
+            func = 'name=ChudleyElliot, Tau=' + str(tval) + ', L=' + str(lval)
+
+        elif jump_function == 'HallRoss':
+            # Hall-Ross: HWHM=(1-exp(-L*Q^2))/Tau
+            # for Q->0 W=A*Q^2*r
+
+            tval = 1.0 / xmax
+            lval = 1.5
+            func = 'name=HallRoss, Tau=' + str(tval) + ', L=' + str(lval)
+
+        elif jump_function == 'FickDiffusion':
+            # Fick: HWHM=D*Q^2
+
+            y_data = mtd[in_ws].readY(0)
+            diff = (y_data[2] - y_data[0]) / ((x_data[2] - x_data[0]) * (x_data[2] - x_data[0]))
+            func = 'name=FickDiffusion, D=' + str(diff)
+
+        elif jump_function == 'TeixeiraWater':
+            # Teixeira: HWHM=Q^2*L/((1+Q^2*L)*tau)
+            # for Q->0 W=
+
+            tval = 1.0 / xmax
+            lval = 1.5
+            func = 'name=TeixeiraWater, Tau=' + str(tval) + ', L=' + str(lval)
+
+        # Run fit function
+        if out_name is "":
+            out_name = in_ws[:-10] + '_' + jump_function + 'fit'
+
+        Fit(Function=func, InputWorkspace=spectrum_ws, CreateOutput=True, Output=out_name, StartX=q_min, EndX=q_max)
+        fit_workspace = out_name + '_Workspace'
+
+        # Populate sample logs
+        CopyLogs(InputWorkspace=in_ws, OutputWorkspace=fit_workspace)
+        AddSampleLog(Workspace=fit_workspace, LogName="jump_function", LogType="String", LogText=jump_function)
+        AddSampleLog(Workspace=fit_workspace, LogName="q_min", LogType="Number", LogText=str(q_min))
+        AddSampleLog(Workspace=fit_workspace, LogName="q_max", LogType="Number", LogText=str(q_max))
+
+        # Process output options
+        if save:
+            fit_path = os.path.join(workdir, fit_workspace + '.nxs')
+            SaveNexusProcessed(InputWorkspace=fit_workspace, Filename=fit_path)
+
+            if verbose:
+                logger.notice('Fit file is ' + fit_path)
+
+        if plot:
+            mtd_plot = import_mantidplot()
+            mtd_plot.plotSpectrum(fit_workspace, [0, 1, 2], True)
+
+        self.setProperty('Output', out_name)
+
+        DeleteWorkspace(Workspace=spectrum_ws)
+
+        EndTime('Jump fit : ' + jump_function + ' ; ')
+
+
+# Register algorithm with Mantid
+AlgorithmFactory.subscribe(JumpFit)