-                      r4026380
+                      rd23528ee
     @author: Gervaise B. Alina/UTK
 """
+import math
+import numpy
+from DataLoader.data_info import Data1D as LoaderData1D
+from sans.fit.Fitting import Fit
+INFINITY = 10
+MIN = 0
+STEP= 1000
-import math
-from DataLoader.data_info import Data1D as LoaderData1D
 class InvariantCalculator(object):
     """
 …
             Initialize variables
             @param data: data must be of type DataLoader.Data1D
+            @param contrast: contrast value of type float
+            @param pConst: Porod Constant of type float
+        """
+        ## Invariant
+        self.q_star = self._get_q_star(data= data)
+    def _get_q_star(self, data):
+        """
+            @param data: data of type Data1D
+            @return invariant value
+        """
+        #Initialization of variables containing data's info
+        self.data = data
+        #Initialization  of the model to use to extrapolate a low q
+        self.model_min = None
+        #Initialization  of the model to use to extrapolate a high q
+        self.model_max = None
+        #Initialization of variable that contains invariant extrapolate to low q
+        self.q_star_min = 0
+        #Initialization of variable that contains invariant extrapolate to low q
+        self.q_star_max = 0
+        #Initialization of variables containing invariant's info
+        self.q_star = self._get_qstar(data= data)
+        # Initialization of the invariant total
+        self.q_star_total = self.q_star_min + self.q_star + self.q_star_max
+    def get_qstar_error(self, data):
+        """
+            @param data: data of type Data1D
+            @return invariant error
         """
         if not issubclass(data.__class__, LoaderData1D):
 …
             raise ValueError,"Data must be of type DataLoader.Data1D"
-        # Check whether we have slit smearing information
         if data.is_slit_smeared():
+            return self._get_qstar_unsmeared(data= data)
+        else:
+            return self._get_qstar_smeared(data= data)
+            return self._getQStarUnsmearError(data= data)
+        else:
+            return self._getQStarSmearError(data= data)
+    def get_qstar_min(self, data, model, npts):
+        """
+            Set parameters of the model send by the user to value return by the fit
+            engine. Store that model in self.model_min for further use such as plotting.
+            Extrapolate data to low q with npts number of point.
+            This function find the parameters that fit a data  with a given model.
+            Then create a new data with its q vector between 0 and the previous data
+            first q value.
+            where  the step between the points is the distance data.x[1] - data.x[0]
+            The new data has a y defines by model.evalDistrution(new data.x)
+            Finally compute the invariant for this new created data.
+            @param data: data of type Data1D
+            @param model: the model uses to extrapolate the data
+            @param npts: the number of points used to extrapolate. npts number
+            of points will be selected from the last of points of q data to the
+            npts th points of q data.
+            @return invariant value extrapolated to low q
+        """
+        if model == None or npts== 0:
+            return 0
+        npts = int(npts)
+        x = data.x[0: npts]
+        qmin = 0
+        qmax = x[len(x)-1]
+        dx = None
+        dy = None
+        dxl = None
+        dxw = None
+        if data.dx !=None:
+            dx = data.dx[0:int(npts)]
+        if data.dy !=None:
+            dxl = data.dy[0:int(npts)]
+        if data.dxl !=None:
+            dx = data.dxl[0:int(npts)]
+        if data.dxw !=None:
+            dxw = data.dxw[0:int(npts)]
+        # fit the data with a model to get the appropriate parameters
+        self.model_min = self._fit( data, model, qmin=qmin, qmax= qmax)
+        #Get x between 0 and data.x[0] with step define such as
+        step = math.fabs(x[1]- x[0])
+        #create new Data1D to compute the invariant
+        new_x = numpy.linspace(start= MIN,
+                           stop= x[0],
+                           num= npts,
+                           endpoint=True
+                           )
+        new_y = model.evalDistribution(new_x)
+        min_data = LoaderData1D(x= new_x,y= new_y)
+        min_data.dxl = dxl
+        min_data.dxw = dxw
+        data.clone_without_data( clone= min_data)
+        return self._get_qstar(data= min_data)
+    def get_qstar_max(self, data, model, npts):
+        """
+            Set parameters of the model send by the user to value return by the fit
+            engine. Store that model in self.model_max for further use such as plotting.
+            Extrapolate data to low q with npts number of point
+            @param data: data of type Data1D
+            @param model: the model uses to extrapolate the data
+            @param npts: the number of points used to extrapolate
+            @return invariant value extrapolated to low q
+        """
+        if model == None or npts== 0:
+            return 0
+        index_max = len(data.x) -1
+        index_min = index_max -int(npts)
+        x = data.x[index_min:index_max]
+        qmin = x[0]
+        qmax = x[len(x)-1]
+        dx = None
+        dy = None
+        dxl = None
+        dxw = None
+        if data.dx !=None:
+            dx = data.dx[qmin:qmax]
+        if data.dy !=None:
+            dxl = data.dy[qmin:qmax]
+        if data.dxl !=None:
+            dx = data.dxl[qmin:qmax]
+        if data.dxw !=None:
+            dxw = data.dxw[0:int(npts)]
+        # fit the data with a model to get the appropriate parameters
+        self.model_max = self._fit( data, model, qmin= qmin, qmax= qmax)
+        #Create new Data1D
+        new_x = numpy.linspace(start= data.x[qmax],
+                           stop= INFINITY,
+                           num= npts,
+                           endpoint=True
+                           )
+        new_y = model.evalDistribution(new_x)
+        #create a Data1D to compute the invariant
+        max_data = LoaderData1D(x= new_x,y= new_y)
+        max_data.dxl = dxl
+        max_data.dxw = dxw
+        data.clone_without_data( clone= max_data)
+        return self._get_qstar(data= max_data)
+    def get_volume_fraction(self, contrast):
+        """
+            Compute volume fraction is given by:
+                q_star= 2*(pi*contrast)**2* volume( 1- volume)
+                for k = 10^(8)*q_star/(2*(pi*|contrast|)**2)
+                we get 2 values of volume:
+                     volume1 = (1- sqrt(1- 4*k))/2
+                     volume2 = (1+ sqrt(1- 4*k))/2
+                contrast unit is 1/A^(2)= 10^(16)cm^(2)
+                q_star unit  1/A^(3)*1/cm
+            the result returned will be 0<= volume <= 1
+            @param contrast: contrast value provides by the user of type float
+            @return: volume fraction
+            @note: volume fraction must have no unit
+        """
+        if contrast < 0:
+            raise ValueError, "contrast must be greater than zero"
+        if self.q_star ==None:
+            raise RuntimeError, "Q_star is not defined"
+        #Get the total invariant with our without extrapolation
+        self.q_star_total = self.q_star + self.q_star_min + self.q_star_max
+        if self.q_star_total < 0:
+            raise ValueError, "invariant must be greater than zero"
+        #compute intermediate constant
+        k =  1.e-8*self.q_star_total /(2*(math.pi* math.fabs(float(contrast)))**2)
+        #check discriminant value
+        discrim= 1 - 4*k
+        if discrim < 0:
+            raise RuntimeError, "could not compute the volume fraction: negative discriminant"
+        elif discrim ==0:
+            volume = 1/2
+            return volume
+        else:
+            # compute the volume
+            volume1 = 0.5 *(1 - math.sqrt(discrim))
+            volume2 = 0.5 *(1 + math.sqrt(discrim))
+            if 0<= volume1 and volume1 <= 1:
+                return volume1
+            elif 0<= volume2 and volume2<= 1:
+                return volume2
+            raise RuntimeError, "could not compute the volume fraction: inconsistent results"
+    def get_surface(self, contrast, porod_const):
+        """
+            Compute the surface given by:
+                surface = (2*pi *volume(1- volume)*pConst)/ q_star
+            @param contrast: contrast value provides by the user of type float
+            @param porod_const: Porod constant
+            @return: specific surface
+        """
+        # Compute the volume
+        volume = self.get_volume_fraction(contrast)
+        #Check whether we have Q star
+        if self.q_star ==None:
+            raise RuntimeError, "Q_star is not defined"
+        #Get the total invariant with our without extrapolation
+        self.q_star_total = self.q_star + self.q_star_min + self.q_star_max
+        if self.q_star_total == 0:
+            raise ValueError, "invariant must be greater than zero. Q_star=%g" % self.q_star
+        return 2*math.pi* volume*(1- volume)*float(porod_const)/self.q_star_total
     def _get_qstar_unsmeared(self, data):
         """
 …
             where n= infinity
             dxi = 1/2*(xi+1 - xi) + (xi - xi-1)
             dx0 = x1 - x0
+            dx0 = x0+ (x1 - x0)/2
             dxn = xn - xn-1
+        """
+        if len(data.x)<=1 or len(data.y)<=1 or len(data.x)!=len(data.y):
+            msg=  "Length x and y must be equal"
+            msg +=" and greater than 1; got x=%s, y=%s"%(len(data.x), len(data.y))
+            raise ValueError, msg
+        elif len(data.x)==1 and len(data.y)==1:
+            return 0
+        else:
+            n = len(data.x)-1
+            #compute the first delta
+            dx0 = data.x[0] + (data.x[1]- data.x[0])/2
+            #compute the last delta
+            dxn= data.x[n]- data.x[n-1]
+            sum = 0
+            sum += data.x[0]* data.x[0]* data.y[0]*dx0
+            sum += data.x[n]* data.x[n]* data.y[n]*dxn
+            if len(data.x)==2:
+                return sum
+            else:
+                #iterate between for element different from the first and the last
+                for i in xrange(1, n-1):
+                    dxi = (data.x[i+1] - data.x[i-1])/2
+                    sum += data.x[i]*data.x[i]* data.y[i]* dxi
+                return sum
+    def _get_qstar(self, data):
+        """
+            @param data: data of type Data1D
+            @return invariant value
+        """
+        if not issubclass(data.__class__, LoaderData1D):
+            #Process only data that inherited from DataLoader.Data_info.Data1D
+            raise ValueError,"Data must be of type DataLoader.Data1D"
+        # Check whether we have slit smearing information
+        if data.is_slit_smeared():
+            return self._get_qstar_smeared(data= data)
+        else:
+            return self._get_qstar_unsmeared(data= data)
+    def _getQStarUnsmearError(self, data):
+        """
+            @param data: data of type Data1D
+            Compute invariant uncertainty on y given by
+            q_star = math.sqrt[(x0**2*(dy0)*dx0)**2 +
+                    (x1**2 *(dy1)*dx1)**2 + ..+ (xn**2 *(dyn)*dxn)**2 ]
+            where n = infinity
+            dxi = 1/2*(xi+1 - xi) + (xi - xi-1)
+            dx0 = x0+ (x1 - x0)/2
+            dxn = xn - xn-1
+            dyn: error on dy
+            note: if data doesn't contains dy assume dy= math.sqrt(data.y)
         """
         if len(data.x)<=1 or len(data.y)<=1 or len(data.x)!=len(data.y):
 …
         else:
+            n= len(data.x)-1
+            #Create error for data without dy error
+            if data.dy ==None or data.dy==[]:
+                dy=[math.sqrt(y) for y in data.y]
+            else:
+                dy= data.dy
+            n = len(data.x)-1
             #compute the first delta
             dx0= data.x[1]- data.x[0]
+            dx0 = data.x[0] + (data.x[1]- data.x[0])/2
             #compute the last delta
             dxn= data.x[n]- data.x[n-1]
             sum = 0
             sum += data.x[0]* data.x[0]* data.y[0]*dx0
             sum += data.x[n]* data.x[n]* data.y[n]*dxn
+            sum += (data.x[0]* data.x[0]* dy[0]*dx0)**2
+            sum += (data.x[n]* data.x[n]* dy[n]*dxn)**2
             if len(data.x)==2:
                 return sum
+                return math.sqrt(sum)
             else:
                 #iterate between for element different from the first and the last
                 for i in xrange(1, n-1):
                     dxi = (data.x[i+1] - data.x[i-1])/2
                     sum += data.x[i]*data.x[i]* data.y[i]* dxi
                 return sum
+                    sum += (data.x[i]*data.x[i]* dy[i]* dxi)**2
+                return math.sqrt(sum)
 …
         """
             @param data: data of type Data1D
             Compute invariant with slit smearing info
+            Compute invariant with slit-smearing info
             q_star= x0*dxl *y0 *dx0 + x1*dxl *y1 *dx1 + ..+ xn*dxl *yn *dxn
             where n= infinity
             dxi = 1/2*(xi+1 - xi) + (xi - xi-1)
             dx0 = x1 - x0
+            dx0 = x0+ (x1 - x0)/2
             dxn = xn - xn-1
             dxl: slit smearing value
+        """
+        if data.dxl ==None:
+            msg = "Cannot compute slit Smear invariant dxl "
+            msg +="must be a list, got dxl= %s , dxw= %s"%(str(data.dxl), str(data.dxw))
+            raise ValueError,msg
+        if len(data.x)<=1 or len(data.y)<=1 or len(data.x)!=len(data.y)\
+                or len(data.x)!= len(data.dxl):
+            msg = "x, dxl, and y must be have the same length and greater than 1"
+            raise ValueError,msg
+        else:
+            n= len(data.x)-1
+            #compute the first delta
+            dx0= data.x[0] +(data.x[1]- data.x[0])/2
+            #compute the last delta
+            dxn= data.x[n]- data.x[n-1]
+            sum = 0
+            sum += data.x[0]* data.dxl[0]* data.y[0]*dx0
+            sum += data.x[n]* data.dxl[n]* data.y[n]*dxn
+            if len(data.x)==2:
+                return sum
+            else:
+                #iterate between for element different from the first and the last
+                for i in xrange(1, n-1):
+                    dxi = (data.x[i+1] - data.x[i-1])/2
+                    sum += data.x[i]* data.dxl[i]* data.y[i]* dxi
+                return sum
+    def _getQStarSmearError(self, data):
+        """
+            @param data: data of type Data1D
+            Compute invariant with slit smearing info
+            q_star= x0*dxl *dy0 *dx0 + x1*dxl *dy1 *dx1 + ..+ xn*dxl *dyn *dxn
+            where n= infinity
+            dxi = 1/2*(xi+1 - xi) + (xi - xi-1)
+            dx0 = x0+ (x1 - x0)/2
+            dxn = xn - xn-1
+            dxl: slit smearing value
+            dyn : error on dy
+            note: if data doesn't contains dy assume dy= math.sqrt(data.y)
         """
         if data.dxl ==None:
 …
             raise ValueError,msg
         else:
+            #Create error for data without dy error
+            if data.dy ==None or data.dy==[]:
+                dy= [math.sqrt(y) for y in data.y]
+            else:
+                dy= data.dy
             n= len(data.x)-1
             #compute the first delta
             dx0= data.x[1]- data.x[0]
+            dx0= data.x[0] +(data.x[1]- data.x[0])/2
             #compute the last delta
             dxn= data.x[n]- data.x[n-1]
             sum = 0
             sum += data.x[0]* data.dxl[0]* data.y[0]*dx0
             sum += data.x[n]* data.dxl[n]* data.y[n]*dxn
+            sum += (data.x[0]* data.dxl[0]* dy[0]*dx0)**2
+            sum += (data.x[n]* data.dxl[n]* dy[n]*dxn)**2
             if len(data.x)==2:
                 return sum
+                return math.sqrt(sum)
             else:
                 #iterate between for element different from the first and the last
                 for i in xrange(1, n-1):
                     dxi = (data.x[i+1] - data.x[i-1])/2
+                    sum += data.x[i]* data.dxl[i]* data.y[i]* dxi
+                return sum
+    def get_volume_fraction(self, contrast):
+        """
+            Compute volume fraction is given by:
+                q_star= 2*(pi*contrast)**2* volume( 1- volume)
+                for k = 10^(8)*q_star/(2*(pi*|contrast|)**2)
+                we get 2 values of volume:
+                     volume1 = (1- sqrt(1- 4*k))/2
+                     volume2 = (1+ sqrt(1- 4*k))/2
+                contrast unit is 1/A^(2)= 10^(16)cm^(2)
+                q_star unit  1/A^(3)*1/cm
+            the result returned will be 0<= volume <= 1
+                    sum += (data.x[i]* data.dxl[i]* dy[i]* dxi)**2
+                return math.sqrt(sum)
+    def _getVolFracError(self, contrast):
+        """
+            Compute the error on volume fraction uncertainty where
+            uncertainty is delta volume = 1/2 * (4*k* uncertainty on q_star)
+                                 /(2* math.sqrt(1-k* q_star))
+            for k = 10^(8)*q_star/(2*(pi*|contrast|)**2)
             @param contrast: contrast value provides by the user of type float
+            @return: volume fraction
+            @note: volume fraction must have no unit
+        """
+        if contrast < 0:
+            raise ValueError, "contrast must be greater than zero"
+        if self.q_star ==None:
+            raise RuntimeError, "Q_star is not defined"
+        if self.q_star < 0:
+            raise ValueError, "invariant must be greater than zero. Q_star=%g" % self.q_star
+        #compute intermediate constant
+        k =  1.e-8*self.q_star /(2*(math.pi* math.fabs(float(contrast)))**2)
+        """
+        if self.q_star_total == None or self.q_star_err == None:
+            return
+        if self.q_star_total < 0:
+            raise ValueError, "invariant must be greater than zero"
+        k =  1.e-8*self.q_star_total /(2*(math.pi* math.fabs(float(contrast)))**2)
         #check discriminant value
+        discrim= 1 - 4*k
+        if discrim < 0:
+            raise RuntimeError, "could not compute the volume fraction: negative discriminant"
+        elif discrim ==0:
+            volume = 1/2
+            return volume
+        else:
+            # compute the volume
+            volume1 = 0.5 *(1 - math.sqrt(discrim))
+            volume2 = 0.5 *(1 + math.sqrt(discrim))
+            if 0<= volume1 and volume1 <= 1:
+                return volume1
+            elif 0<= volume2 and volume2<= 1:
+                return volume2
+            raise RuntimeError, "could not compute the volume fraction: inconsistent results"
+    def get_surface(self, contrast, porod_const):
+        """
+            Compute the surface given by:
+                surface = (2*pi *volume(1- volume)*pConst)/ q_star
+            @param contrast: contrast value provides by the user of type float
+            @param porod_const: Porod constant
+            @return: specific surface
+        """
+        # Compute the volume
+        volume = self.get_volume_fraction(contrast)
+        # Check whether we have Q star
+        if self.q_star ==None:
+            raise RuntimeError, "Q_star is not defined"
+        if self.q_star ==0:
+            raise ValueError, "invariant must be greater than zero. Q_star=%g" % self.q_star
+        return 2*math.pi*volume*(1-volume)*float(porod_const)/self.q_star
+        discrim = 1 - 4*k
+        if  1- k*self.q_star <=0:
+            raise ValueError, "Cannot compute incertainty on volume"
+        uncertainty = (0.5 *4*k* self.q_star_err)/(2*math.sqrt(1- k*self.q_star))
+        return math.fabs(uncertainty)
+    def _fit(self, data, model, qmin=None, qmax=None):
+        """
+            perform fit
+            @param data: data to fit
+            @param model: model to fit
+            @return: model with the parameters computed by the fitting engine
+        """
+        id = 1
+        fitter = Fit('scipy')
+        fitter.set_data(data,id)
+        pars=[]
+        for param  in model.getParamList() :
+            # TODO: Remove the background from computation before fitting?
+            if param not in model.getDispParamList():
+                pars.append(param)
+        fitter.set_model(model,id,pars)
+        fitter.select_problem_for_fit(Uid=id,value=1)
+        result =  fitter.fit()
+        out = result.pvec
+        # Set the new parameter back to the model
+        if out== None:
+            #The fit engine didn't find parameters , the model is returned in
+            # the same state
+            return model
+        # Assigned new parameters values to the model
+        if out.__class__== numpy.float64:
+            #Only one parameter was fitted
+            model.setParam(pars[0], out)
+        else:
+            for index in xrange(len(pars)):
+                model.setParam(pars[index], out[index])
+        return model

DataLoader/test/utest_invariant.py

-                      r4026380
+                      rd23528ee
     @author Gervaise Alina: unittest imcoplete so far
 """
 import unittest
 import numpy, math
 …
+class InvariantTest(unittest.TestCase):
+class TestInvPolySphere(unittest.TestCase):
+    """
+        Test unsmeared data for invariant computation
+    """
+    def setUp(self):
+        #Data with no slit smear information
+        data= Loader().load("PolySpheres.txt")
+        self.I = InvariantCalculator( data= data)
+    def testWrongData(self):
+        """ test receiving Data1D not of type loader"""
+        #compute invariant with smear information
+        from danse.common.plottools.plottables import Data1D
+        data= Data1D(x=[1,2],y=[2,3] )
+        try:
+            self.assertRaises(ValueError,InvariantCalculator(data))
+        except ValueError, msg:
+            print "test pass "+ str(msg)
+        else: raise ValueError, "fail to raise exception when expected"
+    def testInvariant(self):
+        """ test the invariant value for data without smearing"""
+        self.assertAlmostEquals(self.I.q_star, 7.48959e-5,2)
+    def testVolume(self):
+        """ test volume fraction for polysphere"""
+        volume = self.I.get_volume_fraction(contrast=2.6e-6)
+        self.assert_(volume >= 0 and volume <=1)
+        self.assertAlmostEqual(volume ,0.01)
+    def testSurface(self):
+        """ test surface for polysphere """
+        surface = self.I.get_surface(contrast=2.6e-6, porod_const=20)
+        self.assertAlmostEqual(surface,0.01)
+class TestInvariantSmear(unittest.TestCase):
+    """
+        Test smeared data for invariant computation
+    """
+    def setUp(self):
+        # data with smear info
+        list = Loader().load("latex_smeared.xml")
+        self.data_q_smear = list[0]
+        self.I_q_smear = InvariantCalculator( data= self.data_q_smear)
+        self.data_slit_smear = list[1]
+        self.I_slit_smear = InvariantCalculator( data= self.data_slit_smear)
+        from sans.models.PowerLawModel import PowerLawModel
+        self.power_law = PowerLawModel()
+        from sans.models.GuinierModel import GuinierModel
+        self.guinier = GuinierModel()
+    def test_invariant_slit(self):
+        """ test the invariant value for data with slit smear"""
+        self.assertTrue(self.I_slit_smear.q_star>0)
+        self.assertAlmostEquals(self.I_slit_smear.q_star, 4.1539e-4)
+    def test_volume_slit_smear(self):
+        """ test volume fraction for data with slit smear"""
+        volume = self.I_slit_smear.get_volume_fraction(contrast=2.6e-6)
+        self.assert_(volume >= 0 and volume <=1)
+        self.assertAlmostEqual(volume ,0.01)
+    def test_invariant_slit_low_guinier(self):
+        """ test the invariant with slit smear for data extrapolated low q range using guinier"""
+        q_star_min = self.I_slit_smear.get_qstar_min( data= self.data_slit_smear,
+                                                       model= self.guinier, npts=10)
+        self.assertAlmostEquals(q_star_min, 4.89783e-8)
+        self.assertAlmostEquals(self.I.q_star_min, q_star_min)
+    def test_invariant_slit_low_power(self):
+        """ test the invariant with slit smear for data extrapolated low q range using pow_law"""
+        q_star_min = self.I_slit_smear.get_qstar_min( data=self.data_slit_smear,
+                                                       model= self.power_law, npts=10)
+        self.assertFalse(numpy.isfinite(q_star_min))
+        self.assertEquals(self.I.q_star_min, q_star_min)
+    def test_invariant_slit_high_power(self):
+        """ test the invariant with slit smear for data extrapolated high q range using pow_law"""
+        q_star_max = self.I_slit_smear.get_qstar_max( data= self.data_slit_smear,
+                                                       model= self.power_law, npts=10)
+        self.assertFalse(numpy.isfinite(q_star_max))
+        self.assertEquals(self.I.q_star_max, q_star_max)
+    def testSurface(self):
+        """ test volume fraction for data with slit smear"""
+        surface = self.I_q_smear.get_surface(contrast=2.6e-6, porod_const=20)
+        self.assertAlmostEqual(surface,0.01)
+    def test_invariant_q(self):
+        """ test the invariant value for data with q smear"""
+        self.assertTrue(self.I_q_smear.q_star>0)
+        self.assertAlmostEquals(self.I_q_smear.q_star, 1.361677e-3)
+    def test_invariant_q_low_guinier(self):
+        """ test the invariant with q smear for data extrapolated low q range using guinier"""
+        q_star_min = self.I_slit_smear.get_qstar_min( data= self.data_q_smear,
+                                                       model= self.guinier, npts=10)
+        self.assertAlmostEquals(q_star_min,6.76e-4)
+        self.assertAlmostEquals(self.I.q_star_min, q_star_min)
+    def test_invariant_q_low_power(self):
+        """ test the invariant with q smear for data extrapolated low q range using pow_law"""
+        q_star_min = self.I_slit_smear.get_qstar_min( data= self.data_q_smear,
+                                                       model= self.power_law, npts=10)
+        self.assertFalse(numpy.isfinite(q_star_min))
+        self.assertEquals(self.I.q_star_min, q_star_min)
+    def test_invariant_q_high_power(self):
+        """ test the invariant with q smear for data extrapolated high q range using pow_law"""
+        q_star_max = self.I_slit_smear.get_qstar_max( data= self.data_q_smear,
+                                                       model= self.power_law, npts=10)
+        self.assertAlmostEquals(q_star_max,1.2e-4)
+        self.assertEquals(self.I.q_star_max, q_star_max)
+    def test_volume_q_smear(self):
+        """ test volume fraction for data with q smear"""
+        volume = self.I_slit_smear.get_volume_fraction(contrast=2.6e-6)
+        self.assert_(volume > 0 and volume <=1)
+        self.assertAlmostEqual(volume ,0.01)
+    def testSurface_q_smear(self):
+        """ test surface for data with q smear"""
+        surface = self.I_q_smear.get_surface(contrast=2.6e-6, porod_const=20)
+        self.assertAlmostEqual(surface,0.01)
+class ExtrapolationTest(unittest.TestCase):
     def setUp(self):
         #Data with no slit smear information
+        data0 = Loader().load("PolySpheres.txt")
+        self.I0 = InvariantCalculator( data=data0)
+        self.data= Loader().load("PolySpheres.txt")
+        from sans.models.PowerLawModel import PowerLawModel
+        self.power_law = PowerLawModel()
+        from sans.models.GuinierModel import GuinierModel
+        self.guinier = GuinierModel()
+        self.I = InvariantCalculator( data= self.data)
+        # data with smear info
+        list = Loader().load("latex_smeared.xml")
+        data1= list[0]
+        self.I1= InvariantCalculator( data= data1)
+    def testInvariant(self):
+        """ test the invariant value for data extrapolated"""
+        self.assertAlmostEquals(self.I.q_star, 7.48959e-5)
+        data2= list[1]
+        self.I2= InvariantCalculator( data= data2)
+    def test_invariant(self):
+        """ test the invariant value for data with no slit smear"""
+        self.assertAlmostEquals(self.I0.q_star, 7.48959e-5)
+        self.assertTrue(self.I1.q_star>0)
+        self.assertTrue(self.I2.q_star>0)
+    def testInvariantLowGuinier(self):
+        """ test the invariant value for data extrapolated low range using guinier"""
+        q_star_min = self.I.get_qstar_min( data= self.data, model= self.guinier, npts=10)
+        self.assertAlmostEquals(q_star_min, 4.89783e-8)
+        self.assertAlmostEquals(self.I.q_star_min, q_star_min)
+    def testInvariantLowPower(self):
+        """ test the invariant value for data extrapolated low range using pow_law"""
+        q_star_min = self.I.get_qstar_min( data= self.data, model= self.power_law, npts=10)
+        self.assertFalse(numpy.isfinite(q_star_min))
+        self.assertEquals(self.I.q_star_min, q_star_min)
+    def testInvariantHigh(self):
+        """ test the invariant value for data extrapolated high range"""
+        q_star_max = self.I.get_qstar_max( self.data, model=self.power_law, npts=10)
+        self.assertAlmostEquals(q_star_max, 4.066202e-6)
+        self.assertAlmostEquals(self.I0.q_star_max, q_star_max)
+    def test_computation(self):
+        """
+            Test identity smearing
+        """
+        vol = self.I0.get_volume_fraction(contrast=2.6e-6)
+        surface = self.I0.get_surface(contrast=2.6e-6, porod_const=20)
+    def testInvariantTotal(self):
+        """ test the total invariant value for data extrapolated"""
+        self.assertAlmostEquals(self.I.q_star_total, 7.88981e-5)
+        # TODO: Need to test output values
+        #self.assertAlmostEquals(vol, 0)
+        #self.assertAlmostEquals(surface, 0)
+        vol = self.I1.get_volume_fraction(contrast=5.3e-6)
+        surface = self.I1.get_surface(contrast=5.3e-6, porod_const=20)
+        # TODO: Need to test output values
+        #self.assertAlmostEquals(vol, 0)
+        #self.assertAlmostEquals(surface, 0)
+        vol = self.I2.get_volume_fraction(contrast=5.3e-6)
+        surface = self.I2.get_surface(contrast=5.3e-6, porod_const=20)
+        # TODO: Need to test output values
+        self.assertAlmostEquals(vol, 0)
+        self.assertAlmostEquals(surface, 0)
+    def testVolume(self):
+        """ test volume fraction for data extrapolated"""
+        volume = self.I.get_volume_fraction(contrast=2.6e-6)
+        self.assert_(volume > 0 and volume <=1)
+        self.assertAlmostEqual(volume ,0.01)
+    def testSurface(self):
+        """ test surface for data extrapolated"""
+        surface = self.I.get_surface(contrast=2.6e-6, porod_const=20)
+        self.assertAlmostEqual(surface,0.01)
 if __name__ == '__main__':
     unittest.main()

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DataLoader/invariant.py

DataLoader/test/utest_invariant.py

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