fix a bug due to wrong scaling factor applied to f_ideal

jackey-qiu · May 20, 2021 · 8c88a69 · 8c88a69
1 parent 88f1d3b
commit 8c88a69
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Showing 10 changed files with 1,807 additions and 63 deletions.
diff --git a/EnginePool/models/setup_domain_hematite_rcut.py b/EnginePool/models/setup_domain_hematite_rcut.py
@@ -320,10 +320,10 @@ def setup_raxr_pars_new(NUMBER_SPECTRA,F1F2_FILE):
         F1F2=np.loadtxt(os.path.join(F1F2_FILE))
         rgh_raxr=UserVars()
         for i in range(NUMBER_SPECTRA):
-            rgh_raxr.new_var('a'+str(i+1),0.0)
-            rgh_raxr.new_var('b'+str(i+1),0.0)
-            rgh_raxr.new_var('c'+str(i+1),0.0)
-            rgh_raxr.new_var('A_'+str(i+1),2.0)
+            rgh_raxr.new_var('a'+str(i+1),1.0)
+            rgh_raxr.new_var('b'+str(i+1),1.0)
+            rgh_raxr.new_var('c'+str(i+1),1.0)
+            rgh_raxr.new_var('A_'+str(i+1),0.2)
             rgh_raxr.new_var('P_'+str(i+1),0.0) 
     else:
         rgh_raxr=None

diff --git a/EnginePool/models/structure_tools/__pycache__/sxrd_dafy.cal_fs_numba-174.py38.2.nbc b/EnginePool/models/structure_tools/__pycache__/sxrd_dafy.cal_fs_numba-174.py38.2.nbc
diff --git a/EnginePool/models/structure_tools/__pycache__/sxrd_dafy.cal_fs_numba-174.py38.nbi b/EnginePool/models/structure_tools/__pycache__/sxrd_dafy.cal_fs_numba-174.py38.nbi
diff --git a/FilterPool/data_superrod.py b/FilterPool/data_superrod.py
@@ -562,6 +562,7 @@ def concatenate_all_ctr_datasets(self):
         all_ctr_data = []
         self.ctr_data_info = {}
         self.scaling_tag = []
+        self.scaling_tag_raxs = []
         self.data_sequence = []
         for i,each in enumerate(self.items):
             if hasattr(each,'mask'):
@@ -572,6 +573,10 @@ def concatenate_all_ctr_datasets(self):
             if x[0]>100:#x column is energy for raxs (in ev); but x column is L for CTR (smaller than 10 usually)
                 data_type_tag = 100+i#datasets with tag>100 are raxs data 
                 self.data_sequence.append(data_type_tag)
+                if int(h[0])==0 and int(k[0])==0:
+                    self.scaling_tag_raxs.append('specular_rod')
+                else:
+                    self.scaling_tag_raxs.append('nonspecular_rod')
             else:
                 data_type_tag = 1+i#datasets with tag>1 but <100 are ctr data
                 self.data_sequence.append(data_type_tag)

diff --git a/examples/hematite_rcut_AD/test.rod b/examples/hematite_rcut_AD/test.rod
diff --git a/examples/hematite_rcut_AD/test_data.csv b/examples/hematite_rcut_AD/test_data.csv
diff --git a/examples/hematite_rcut_AD/test_data.xlsx b/examples/hematite_rcut_AD/test_data.xlsx
diff --git a/projects/superrod/SuPerRod_GUI.py b/projects/superrod/SuPerRod_GUI.py
@@ -1004,7 +1004,10 @@ def calc_f_ideal(self):
         self.f_ideal = []
         for i in range(len(self.model.data)):
             each = self.model.data[i]
-            self.f_ideal.append(self.model.script_module.sample.calc_f_ideal(each.extra_data['h'], each.extra_data['k'], each.x)**2)
+            if each.x[0]>1000:#indicate energy column
+                self.f_ideal.append(self.model.script_module.sample.calc_f_ideal(each.extra_data['h'], each.extra_data['k'], each.extra_data['Y'])**2)
+            else:
+                self.f_ideal.append(self.model.script_module.sample.calc_f_ideal(each.extra_data['h'], each.extra_data['k'], each.x)**2)
 
     def update_plot_data_view(self):
         """update views of all figures if script is compiled, while only plot data profiles if otherwise"""
@@ -1128,7 +1131,8 @@ def _get_index(index_in_use):
 
                 #plot ideal structure factor
                 try:
-                    scale_factor = [self.model.script_module.rgh.scale_nonspecular_rods,self.model.script_module.rgh.scale_specular_rod][int("00L" in self.model.data[i].name)]
+                    specular_condition = int(round(self.model.data[_get_index(i+offset)].extra_data['h'][0],0))==0 and int(round(self.model.data[_get_index(i+offset)].extra_data['k'][0],0))==0
+                    scale_factor = [self.model.script_module.rgh.scale_nonspecular_rods,self.model.script_module.rgh.scale_specular_rod][int(specular_condition)]
                     h_, k_ = int(round(self.model.data[_get_index(i+offset)].extra_data['h'][0],0)),int(round(self.model.data[_get_index(i+offset)].extra_data['k'][0],0))
                     extra_scale_factor = 'scale_factor_{}{}L'.format(h_,k_)
                     if hasattr(self.model.script_module.rgh,extra_scale_factor):

diff --git a/projects/superrod/standard_scripts/template_script_hematite_rcut.py b/projects/superrod/standard_scripts/template_script_hematite_rcut.py
@@ -10,7 +10,7 @@
 
 import models.setup_domain_hematite_rcut as setup_domain_hematite_rcut
 from accessory_functions.data_formating.data_formating import format_hkl
-from UtilityFunctions import config_file_parser_bv, update_O_NUMBER
+from UtilityFunctions import config_file_parser_bv, update_O_NUMBER, setup_raxr_pars_new
 from FitEnginePool import bond_valence_constraint
 
 model_type = 'ctr'
@@ -23,7 +23,7 @@
 F1F2_FILE='As_K_edge_March28_2018.f1f2'
 #/raxs/end#
 if NUMBER_SPECTRA!=0:
-    rgh_raxs,F1F2=setup_domain_hematite_rcut.setup_raxr_pars_new(NUMBER_SPECTRA, F1F2_FILE)
+    rgh_raxs,F1F2 = setup_raxr_pars_new(NUMBER_SPECTRA, F1F2_FILE)
 else:
     rgh_raxs, F1F2 = None, []
 
@@ -235,8 +235,8 @@ def Sim(data,VARS=vars()):
         sub_sets, data_info = data.split_used_dataset(F_, data_type = 'RAXS')
         F_ = data.insert_datasets(full_set = F_all, sub_sets = sub_sets, data_info = data_info, data_type = 'RAXS')
         #you need to edit the list of extra scaling factor accordingly
-        #scaling_factors = [[rgh.scale_nonspecular_rods, rgh.scale_specular_rod][int(each=='specular_rod')] for each in data.scaling_tag]
-        F_raxs = data.split_fullset(F_,scale_factors=1, data_type = 'RAXS')
+        scaling_factors = [[rgh.scale_nonspecular_rods, rgh.scale_specular_rod][int(each=='specular_rod')] for each in data.scaling_tag_raxs]
+        F_raxs = data.split_fullset(F_,scale_factors=scaling_factors, data_type = 'RAXS')
     else:
         F_raxs=data.split_fullset(data.ctr_data_all[condition_raxs][:,0]*0,scale_factors=1, data_type = 'RAXS')
 
@@ -251,56 +251,3 @@ def Sim(data,VARS=vars()):
             bv += VARS['bv_constraint_domain{}'.format(i+1)].cal_distance()
 
     return F,1+bv,fom_scaler
-'''
-def Sim(data,VARS=vars()):
-    F =[]
-    fom_scaler=[]
-    beta=rgh.beta
-
-    #/update_sorbate/begin#
-    for i in range(num_sorbate_slabs):
-        VARS['{}{}'.format(VARS['sorbate_instance_head'],i+1)].set_coordinate_all_rgh()
-    #/update_sorbate/end#
-
-    #normalize the domain weight to make total = 1
-    wt_list = [getattr(rgh_wt, 'wt_domain{}'.format(i+1)) for i in range(num_surface_slabs)]
-    total_wt = sum(wt_list)
-    for i in range(num_surface_slabs):
-        sample.domain['domain{}'.format(i+1)]['wt']=wt_list[i]/total_wt
-
-    #faster solution(a factor of two faster than using loop)
-    #ctr datasets
-    condition_ctr = data.ctr_data_all[:,-1]<100
-    h_, k_, x_,LB_,dL_ = data.ctr_data_all[condition_ctr][:,0], data.ctr_data_all[condition_ctr][:,1], data.ctr_data_all[condition_ctr][:,2],data.ctr_data_all[condition_ctr][:,4],data.ctr_data_all[condition_ctr][:,5]
-    rough_ = (1-beta)/((1-beta)**2 + 4*beta*np.sin(np.pi*(x_-LB_)/dL_)**2)**0.5
-    f_ = rough_*sample.calc_f_all(h_, k_, x_)
-    F_ = abs(f_*f_)
-    #you need to edit the list of extra scaling factor accordingly
-    scaling_factors = [[rgh.scale_nonspecular_rods, rgh.scale_specular_rod][int(each=='specular_rod')] for each in data.scaling_tag]
-    F_ctr = data.split_fullset(F_,scaling_factors)
-
-    #raxs datasets
-    condition_raxs = data.ctr_data_all[:,-1]>=100
-    if True in list(condition_raxs):
-        h_, k_, E_, l_, LB_,dL_ = data.ctr_data_all[condition_raxs][:,0], data.ctr_data_all[condition_raxs][:,1], data.ctr_data_all[condition_raxs][:,2],data.ctr_data_all[condition_raxs][:,3], data.ctr_data_all[condition_raxs][:,4],data.ctr_data_all[condition_raxs][:,5]
-        rough_ = (1-beta)/((1-beta)**2 + 4*beta*np.sin(np.pi*(l_-LB_)/dL_)**2)**0.5
-        f_ = rough_*sample.calc_f_all_RAXS(h_, k_, l_, E_)
-        F_ = abs(f_*f_)
-        #you need to edit the list of extra scaling factor accordingly
-        #scaling_factors = [[rgh.scale_nonspecular_rods, rgh.scale_specular_rod][int(each=='specular_rod')] for each in data.scaling_tag]
-        F_raxs = data.split_fullset(F_,scale_factors=1, data_type = 'RAXS')
-    else:
-        F_raxs = []
-
-    #Now merge both datasets together
-    F = data.merge_datasets(ctr_datasets = F_ctr, raxs_datasets = F_raxs)    
-    fom_scaler = [1]*len(F)
-
-    #calculate bv panelty factor
-    bv = 0
-    if USE_BV:
-        for i in range(num_surface_slabs):
-            bv += VARS['bv_constraint_domain{}'.format(i+1)].cal_distance()
-
-    return F,1+bv,fom_scaler
-'''
diff --git a/util/UtilityFunctions.py b/util/UtilityFunctions.py
@@ -28,12 +28,28 @@
 currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
 DaFy_Path = os.path.dirname(currentdir)
 sys.path.append(os.path.join(DaFy_Path,'EnginePool'))
+from models.utils import UserVars
 import FitEnginePool
 import matplotlib.pyplot as pyplot
 #make compatibility of py 2 and py 3#
 if (sys.version_info > (3, 0)):
     raw_input = input
 
+def setup_raxr_pars_new(NUMBER_SPECTRA,F1F2_FILE):
+    if NUMBER_SPECTRA!=0:
+        F1F2=np.loadtxt(os.path.join(F1F2_FILE))
+        rgh_raxr=UserVars()
+        for i in range(NUMBER_SPECTRA):
+            rgh_raxr.new_var('a'+str(i+1),1.0)
+            rgh_raxr.new_var('b'+str(i+1),1.0)
+            rgh_raxr.new_var('c'+str(i+1),1.0)
+            rgh_raxr.new_var('A_'+str(i+1),0.2)
+            rgh_raxr.new_var('P_'+str(i+1),0.0) 
+    else:
+        rgh_raxr=None
+        F1F2=None
+    return rgh_raxr,F1F2
+
 def config_file_parser_bv(config_file):
     return_lib = {}
     config = configparser.RawConfigParser()