Merge e4b134b into 99eed25

fitbenchmarking/fitbenchmark_one_problem.py

@@ -7,11 +7,11 @@
 import sys
 import numpy as np
 
-from fitting import prerequisites as prereq
-from fitting import misc
-from fitting.plotting import plots
+from fitbenchmarking.fitting import prerequisites as prereq
+from fitbenchmarking.fitting import misc
+from fitbenchmarking.fitting.plotting import plots
 
-from utils.logging_setup import logger
+from fitbenchmarking.utils.logging_setup import logger
 
 
 def fitbm_one_prob(user_input, problem):

fitbenchmarking/fitting/mantid/__init__.py

@@ -1 +0,0 @@
-

fitbenchmarking/fitting/mantid/externals.py

@@ -6,21 +6,22 @@
 from __future__ import (absolute_import, division, print_function)
 
 import mantid.simpleapi as msapi
-from utils.logging_setup import logger
+from fitbenchmarking.utils.logging_setup import logger
 
 
 def gen_func_obj(function_name, params_set):
     """
     Generates a mantid function object.
 
     @param function_name :: the name of the function to be generated
-    @params_set :: set of parameters per function extracted from the problem definition file
+    @params_set :: set of parameters per function extracted from the
+        problem definition file
 
     @returns :: mantid function object that can be called in python
     """
     params_set = (params_set.split(', ties'))[0]
 
-    exec "function_object = msapi." + function_name + "("+ params_set +")"
+    exec "function_object = msapi." + function_name + "(" + params_set + ")"
 
     return function_object
 
@@ -39,12 +40,12 @@ def set_ties(function_object, ties):
         for tie in ties_per_func:
             """
             param_str is a string of the parameter name in the mantid format
-            For a Mantid Composite Function, a formatted parameter name would 
+            For a Mantid Composite Function, a formatted parameter name would
             start with the function number and end with the parameter name.
-            For instance, f0.A would refer to a parameter A of the first 
+            For instance, f0.A would refer to a parameter A of the first
             function is a Composite Function.
             """
-            param_str = 'f'+str(idx)+'.'+(tie.split("'"))[0]
+            param_str = 'f' + str(idx) + '.' + (tie.split("'"))[0]
             function_object.fix(param_str)
 
     return function_object

fitbenchmarking/fitting/mantid/main.py

@@ -9,9 +9,9 @@
 import numpy as np
 import mantid.simpleapi as msapi
 
-from utils.logging_setup import logger
-from fitting import misc
-from fitting.plotting import plot_helper
+from fitbenchmarking.utils.logging_setup import logger
+from fitbenchmarking.fitting import misc
+from fitbenchmarking.fitting.plotting import plot_helper
 
 
 MAX_FLOAT = sys.float_info.max
@@ -41,13 +41,14 @@ def benchmark(problem, wks_created, function, minimizers, cost_function):
         chi_sq, min_chi_sq, best_fit = \
             chisq(status, fit_wks, min_chi_sq, best_fit, minimizer)
         individual_result = \
-            misc.create_result_entry(problem, status, chi_sq, runtime, minimizer,
-                                     function, fin_function_def)
+            misc.create_result_entry(problem, status, chi_sq, runtime,
+                                     minimizer, function, fin_function_def)
 
         results_problem.append(individual_result)
 
     return results_problem, best_fit
 
+
 def fit(problem, wks_created, function, minimizer,
         cost_function='Least squares'):
     """
@@ -65,8 +66,6 @@ def fit(problem, wks_created, function, minimizer,
                 the final function definition
                 and how much time it took for the fit to finish (float)
     """
-
-
     fit_result, t_start, t_end = None, None, None
     try:
         ignore_invalid = get_ignore_invalid(problem, cost_function)
@@ -127,7 +126,7 @@ def parse_result(fit_result, t_start, t_end):
 
     status = 'failed'
     fit_wks, fin_function_def, runtime = None, None, np.nan
-    if not fit_result is None:
+    if fit_result is not None:
         status = fit_result.OutputStatus
         fit_wks = fit_result.OutputWorkspace
         fin_function_def = str(fit_result.Function)

fitbenchmarking/fitting/mantid/prepare_data.py

@@ -4,12 +4,9 @@
 
 from __future__ import (absolute_import, division, print_function)
 
-import copy
 import numpy as np
 import mantid.simpleapi as msapi
 
-from utils.logging_setup import logger
-
 
 def wks_cost_function(problem, use_errors=True):
     """
@@ -38,6 +35,7 @@ def wks_cost_function(problem, use_errors=True):
 
     return wks_created, cost_function
 
+
 def setup_errors(problem):
     """
     Gets errors on the data points from the problem object if there are
@@ -57,6 +55,7 @@ def setup_errors(problem):
         # True errors
         return problem.data_e
 
+
 def convert_back(wks_used, problem, use_errors):
     """
     Convert back so data is of equal lengths.

fitbenchmarking/fitting/mantid/tests/__init__.py

@@ -1 +0,0 @@
-

fitbenchmarking/fitting/mantid/tests/test_func_def.py

@@ -1,135 +1,132 @@
 from __future__ import (absolute_import, division, print_function)
 
 import unittest
-import os
 import numpy as np
 import mantid.simpleapi as msapi
 
-import sys
-test_dir = os.path.dirname(os.path.realpath(__file__))
-parent_dir = os.path.dirname(os.path.normpath(test_dir))
-parent_dir = os.path.dirname(os.path.normpath(parent_dir))
-main_dir = os.path.dirname(os.path.normpath(parent_dir))
-sys.path.insert(0, main_dir)
+from fitbenchmarking.fitting.mantid.func_def import (
+    function_definitions
+)
+from fitbenchmarking.fitting.mantid.func_def import (
+    parse_function_definitions
+)
 
-from fitting.mantid.func_def import function_definitions
-from fitting.mantid.func_def import parse_function_definitions
+from fitbenchmarking.parsing.parse_nist_data import (
+    FittingProblem as NISTFittingProblem
+)
+from fitbenchmarking.parsing.parse_fitbenchmark_data import (
+    FittingProblem as FBFittingProblem
+)
+from fitbenchmarking.mock_problem_files.get_problem_files import get_file
 
-from parsing.parse_nist_data import FittingProblem as NISTFittingProblem
-from parsing.parse_fitbenchmark_data import FittingProblem as FBFittingProblem
-from mock_problem_files.get_problem_files import get_file
 
 class MantidTests(unittest.TestCase):
-
-  def NIST_problem(self):
-    """
-    Helper function.
-    Sets up the problem object for the nist problem file Misra1a.dat
-    """
-
-    data_pattern = np.array([[10.07, 77.6],
-                             [14.73, 114.9],
-                             [17.94, 141.1],
-                             [23.93, 190.8],
-                             [29.61, 239.9],
-                             [35.18, 289.0],
-                             [40.02, 332.8],
-                             [44.82, 378.4],
-                             [50.76, 434.8],
-                             [55.05, 477.3],
-                             [61.01, 536.8],
-                             [66.40, 593.1],
-                             [75.47, 689.1],
-                             [81.78, 760.0]])
-
-    fname = get_file('NIST_Misra1a.dat')
-    prob = NISTFittingProblem(fname)
-    prob.name = 'Misra1a'
-    prob.equation = 'b1*(1-exp(-b2*x))'
-    prob.starting_values = [['b1', [500.0, 250.0]],
-                            ['b2', [0.0001, 0.0005]]]
-    prob.data_x = data_pattern[:, 1]
-    prob.data_y = data_pattern[:, 0]
-
-    return prob
-
-  def Neutron_problem(self):
-    """
-    Sets up the problem object for the neutron problem file:
-    ENGINX193749_calibration_peak19.txt
-    """
-
-    fname = get_file('FB_ENGINX193749_calibration_peak19.txt')
-    prob = FBFittingProblem(fname)
-    prob.name = 'ENGINX 193749 calibration, spectrum 651, peak 19'
-    prob.equation = ("name=LinearBackground,A0=0,A1=0;"
-                     "name=BackToBackExponential,"
-                     "I=597.076,A=1,B=0.05,X0=24027.5,S=22.9096")
-    prob.starting_values = None
-    prob.start_x = 23919.5789114
-    prob.end_x = 24189.3183142
-
-    return prob
-
-  def create_wks_NIST_problem_with_errors(self):
-    """
-    Helper function.
-    Creates a mantid workspace using the data provided by the
-    NIST problem Misra1a.
-    """
-
-    prob = self.NIST_problem()
-    data_e = np.sqrt(abs(prob.data_y))
-    wks_exp = msapi.CreateWorkspace(DataX=prob.data_x, DataY=prob.data_y,
-                                    DataE=data_e)
-    return wks_exp
-
-  def create_wks_NIST_problem_without_errors(self):
-    """
-    Helper function.
-    Creates a mantid workspace using the data provided by the
-    NIST problem Misra1a.
-    """
-
-    prob = self.NIST_problem()
-    wks_exp = msapi.CreateWorkspace(DataX=prob.data_x, DataY=prob.data_y)
-    return wks_exp
-
-  def test_functionDefinitions_return_NIST_functions(self):
-
-    prob = self.NIST_problem()
-
-    function_defs = function_definitions(prob)
-    function_defs_expected = \
-        ["name=fitFunction,b1=500.0,b2=0.0001",
-         "name=fitFunction,b1=250.0,b2=0.0005"]
-
-    self.assertListEqual(function_defs_expected, function_defs)
-
-  def test_functionDefinitions_return_neutron_function(self):
-
-    prob = self.Neutron_problem()
-
-    function_defs = function_definitions(prob)
-    function_defs = [str(function_defs[0])]
-    function_defs_expected = \
-        [("name=LinearBackground,A0=0,A1=0;name=BackToBackExponential,"
-          "I=597.076,A=1,B=0.05,X0=24027.5,S=22.9096")]
-
-    self.assertListEqual(function_defs_expected, function_defs)
-
-  def test_parseNistFunctionDefinitions_get_true_function(self):
-
-    prob = self.NIST_problem()
-    nb_start_vals = 2
-
-    function_defs = parse_function_definitions(prob, nb_start_vals)
-    function_defs_expected = \
-        ["name=fitFunction,b1=500.0,b2=0.0001",
-         "name=fitFunction,b1=250.0,b2=0.0005"]
-
-    self.assertListEqual(function_defs_expected, function_defs)
+    def NIST_problem(self):
+        """
+        Helper function.
+        Sets up the problem object for the nist problem file Misra1a.dat
+        """
+
+        data_pattern = np.array([[10.07, 77.6],
+                                 [14.73, 114.9],
+                                 [17.94, 141.1],
+                                 [23.93, 190.8],
+                                 [29.61, 239.9],
+                                 [35.18, 289.0],
+                                 [40.02, 332.8],
+                                 [44.82, 378.4],
+                                 [50.76, 434.8],
+                                 [55.05, 477.3],
+                                 [61.01, 536.8],
+                                 [66.40, 593.1],
+                                 [75.47, 689.1],
+                                 [81.78, 760.0]])
+
+        fname = get_file('NIST_Misra1a.dat')
+        prob = NISTFittingProblem(fname)
+        prob.name = 'Misra1a'
+        prob.equation = 'b1*(1-exp(-b2*x))'
+        prob.starting_values = [['b1', [500.0, 250.0]],
+                                ['b2', [0.0001, 0.0005]]]
+        prob.data_x = data_pattern[:, 1]
+        prob.data_y = data_pattern[:, 0]
+
+        return prob
+
+    def Neutron_problem(self):
+        """
+        Sets up the problem object for the neutron problem file:
+        ENGINX193749_calibration_peak19.txt
+        """
+
+        fname = get_file('FB_ENGINX193749_calibration_peak19.txt')
+        prob = FBFittingProblem(fname)
+        prob.name = 'ENGINX 193749 calibration, spectrum 651, peak 19'
+        prob.equation = ("name=LinearBackground,A0=0,A1=0;"
+                         "name=BackToBackExponential,"
+                         "I=597.076,A=1,B=0.05,X0=24027.5,S=22.9096")
+        prob.starting_values = None
+        prob.start_x = 23919.5789114
+        prob.end_x = 24189.3183142
+
+        return prob
+
+    def create_wks_NIST_problem_with_errors(self):
+        """
+        Helper function.
+        Creates a mantid workspace using the data provided by the
+        NIST problem Misra1a.
+        """
+
+        prob = self.NIST_problem()
+        data_e = np.sqrt(abs(prob.data_y))
+        wks_exp = msapi.CreateWorkspace(DataX=prob.data_x, DataY=prob.data_y,
+                                        DataE=data_e)
+        return wks_exp
+
+    def create_wks_NIST_problem_without_errors(self):
+        """
+        Helper function.
+        Creates a mantid workspace using the data provided by the
+        NIST problem Misra1a.
+        """
+
+        prob = self.NIST_problem()
+        wks_exp = msapi.CreateWorkspace(DataX=prob.data_x, DataY=prob.data_y)
+        return wks_exp
+
+    def test_functionDefinitions_return_NIST_functions(self):
+        prob = self.NIST_problem()
+
+        function_defs = function_definitions(prob)
+        function_defs_expected = \
+            ["name=fitFunction,b1=500.0,b2=0.0001",
+             "name=fitFunction,b1=250.0,b2=0.0005"]
+
+        self.assertListEqual(function_defs_expected, function_defs)
+
+    def test_functionDefinitions_return_neutron_function(self):
+        prob = self.Neutron_problem()
+
+        function_defs = function_definitions(prob)
+        function_defs = [str(function_defs[0])]
+        function_defs_expected = \
+            [("name=LinearBackground,A0=0,A1=0;name=BackToBackExponential,"
+              "I=597.076,A=1,B=0.05,X0=24027.5,S=22.9096")]
+
+        self.assertListEqual(function_defs_expected, function_defs)
+
+    def test_parseNistFunctionDefinitions_get_true_function(self):
+        prob = self.NIST_problem()
+        nb_start_vals = 2
+
+        function_defs = parse_function_definitions(prob, nb_start_vals)
+        function_defs_expected = \
+            ["name=fitFunction,b1=500.0,b2=0.0001",
+             "name=fitFunction,b1=250.0,b2=0.0005"]
+
+        self.assertListEqual(function_defs_expected, function_defs)
 
 
 if __name__ == "__main__":
-  unittest.main()
+    unittest.main()