Patch 1 changes

plugins/import_data/icpmsImport.py

@@ -182,4 +182,25 @@ def add_Ft_comb(self, analysis_obj, Fts):
         Ft_comb_dict= {'value': Ft_comb, 'error': None,
                        'type': {'parameter': 'Combined Ft', 'unit': ''},
                        'analysis': analysis_obj}
-        self.db.load_data('datum', Ft_comb_dict)
+        self.db.load_data('datum', Ft_comb_dict)
+# Here we will caluclate ESR_Ft and it's associated uncertainty. It will call upon FT_constants defined in picking_specs.yaml 
+# which are material (mineral) and isotope specific. I'll refer to these as S_238, etc, but they will need to vary depending on the mineral.
+Sbar = a_238*S_238 + a_232*S_232 + (1-a_238-a_235)*S_235
+S_R = 1.681-2.428*FT_comb+1.153*(Ft_comb^2)-0.406*(Ft_comb^3)
+ESR_Ft = Sbar/S_R
+IF Mineral (material?) = 'apatite'
+    IF shape = 'Hexagonal'
+        ESR_Ft_Corr = 0.93*ESR_Ft
+        ESR_Ft_Corr_err = 0.06*ESR_Ft_Corr
+    IF shape = 'ellipsoid'
+        ESR_Ft_Corr = 0.85*ESR_Ft
+        ESR_Ft_Corr_err = 0.10*ESR_Ft_Corr
+IF Mineral (material?) = 'zircon'
+    IF shape = 'Hexagonal'
+        ESR_Ft_Corr = 0.92*ESR_Ft
+        ESR_Ft_Corr_err = 0.08*ESR_Ft_Corr
+    IF shape = 'ellipsoid'
+        ESR_Ft_Corr = 0.98*ESR_Ft
+        ESR_Ft_Corr_err = 0.08*ESR_Ft_Corr
+IF Mineral is otherwise...
+

plugins/import_data/pickingImport.py

@@ -18,6 +18,9 @@
 
 # Replicates Ketcham et al., 2011 for Ft calculation
 def get_Ft(l1, w1, l2, w2, Np, shape, Ft_constants, material):
+# We need to make sure that we know the maximum width. I think we should define that here as
+Wmax = Greater(w1,w2)
+
     Ft_dat = {}
     for iso in ['238U', '235U','232Th', '147Sm']:
         R = Ft_constants[material][iso]
@@ -63,6 +66,66 @@ def get_Ft(l1, w1, l2, w2, Np, shape, Ft_constants, material):
     Ft_dat['Rs'] = Rs
     return Ft_dat
 
+# First correct the Volume (V) values. This depends upon the mineral and the geometry. Right now we have this for apatite and zircon, so if
+# the material is something else then Vcorr should just equal V, and Vcorr_err should be XX.
+IF Mineral (material?) = zircon
+    IF shape == 'Orthorhombic'
+        Then    Vcorr = 0.81*V
+                Vcorr_err = 0.13*VCorr
+    IF shape == 'Ellipsoid'
+        Then    Vcorr = 1.04*V
+                VCorr_err = 0.21*VCorr
+IF Mineral (material?) = apatite
+    IF shape == 'Hexagonal'
+        Then    Vcorr = 0.83*V
+                Vcorr_err = 0.20*VCorr
+    IF shape == 'Ellipsoid'
+        Then    Vcorr = 0.74*V
+                VCorr_err = 0.23*VCorr
+
+# Now correct the Ft. This will depend upon the material, geometry, and maximum width.
+IF Mineral (material?) = 'zircon'
+    IF shape = 'Orthorhombic'
+            Then    238Ftcorr = 0.97*238Ft
+                        IF Wmax < 100, Then 238Fterr = 0.03*238Ftcorr, else 238Fterr = 0.02*238Ftcorr
+                    235Ftcorr = 0.97*235Ft
+                        IF Wmax < 100, Then 235Fterr = 0.04*235Ftcorr, else 235Fterr = 0.03*235Fterr
+                    232Ftcorr = 0.97*232Ft
+                        IF Wmax < 100, Then 232Fterr = 0.05*232Ftcorr, else 232Fterr = 0.02*232Fterr
+                    147Ftcorr = 0.96*147Ft
+                        147Fterr = 0.01*147Ftcorr
+    IF shape = 'Ellipsoid'
+            Then    238Ftcorr = 238Ft
+                        238Fterr = 0.03*238Ftcorr
+                    235Ftcorr = 235Ft
+                        235Fterr = 0.04*235Ftcorr
+                    232Ftcorr = 232Ft
+                        232Fterr = 0.04*232Ftcorr
+                    147Ftcorr = 147Ft
+                        147Fterr = 0.01*147Ftcorr
+
+IF Mineral (material?) = 'apatite'
+    IF shape = 'Orthorhombic'
+            Then    238Ftcorr = 0.97*238Ft
+                        IF Wmax < 100, Then 238Fterr = 0.03*238Ftcorr, else 238Fterr = 0.02*238Ftcorr
+                    235Ftcorr = 0.96*235Ft
+                        IF Wmax < 100, Then 235Fterr = 0.04*235Ftcorr, else 235Fterr = 0.02*235Fterr
+                    232Ftcorr = 0.96*232Ft
+                        IF Wmax < 100, Then 232Fterr = 0.04*232Ftcorr, else 232Fterr = 0.02*232Fterr
+                    147Ftcorr = 0.99*147Ft
+                        147Fterr = 0.01*147Ftcorr
+    IF shape = 'Ellipsoid'
+            Then    238Ftcorr = 0.92*238Ft
+                        238Fterr = 0.05*238Ftcorr
+                    235Ftcorr = 0.91*235Ft
+                        235Fterr = 0.06*235Ftcorr
+                    232Ftcorr = 0.91*232Ft
+                        232Fterr = 0.06*232Ftcorr
+                    147Ftcorr = 0.97*147Ft
+                        147Fterr = 0.01*147Ftcorr                      
+
+
+
 # Function to make datum
 def make_datum(datum, error, parameter, unit):
     return {'value': datum, 'error': error,
@@ -144,10 +207,11 @@ def import_datafile(self, fn, rec, **kwargs):
                 geometry = data.iloc[d][self.picking_specs['Metadata']['Crystal geometry']]
 
                 # Generate Ft and dimensional mass
+                # This needs to be modified to use Vcorr values as described above. I changed that
                 Fts = get_Ft(length1, width1, length2, width2,
                              int(terminations), self.picking_specs['geometry_key'][geometry],
                              self.picking_specs['Ft_constants'], material)
-                dimensional_mass = self.picking_specs['Ft_constants'][material]['density']*Fts['V']/1e6
+                dimensional_mass = self.picking_specs['Ft_constants'][material]['density']*Fts['Vcorr']/1e6
 
                 # create datum and attributes for shape analysis
                 shape_data = []
@@ -189,6 +253,8 @@ def import_datafile(self, fn, rec, **kwargs):
             # make analysis dictionary, exclude missing data if shards
             if shard != 'Y' and shard != 'y':
                 # First, get uncertainty for each derived parameter
+                # We have defined some of these already. Ft_err is defined in my calcs above, and dim_mass_err should just be dim_mass*(Vcorrerr/Vcorr). Rs_err
+                # will be done on the ICPMS import phase
                 for l in chars_attributes:
                     for i in l:
                         # get derived data uncertainties for later
@@ -257,4 +323,4 @@ def import_datafile(self, fn, rec, **kwargs):
                         })
 
             print('')
-            self.db.load_data('sample', sample_schema, strict=True)
+            self.db.load_data('sample', sample_schema, strict=True)

plugins/manipulate_data/dataReduction.py

@@ -142,6 +142,8 @@ def get_input_data(self, d):
                       .filter_by(sample_id=d,
                                  technique='Dates and other derived data')
                       .all())
+# The Ft values and uncertainties below should reference Ft_Corr and Ft_corr_err for each isotope now if the mineral is apatite or zircon. If the mineral is
+# something else, then we need to note that we aren't using corrected values. The values we calculated earlier though are 1s.
         if len(Ft_session) > 0:
             get_corrected = True
             Ft238_datum = self.query_ID(sample_obj.lab_id, '238U Ft (±2σ)')
@@ -166,6 +168,7 @@ def get_input_data(self, d):
 
     def calculate_date(self, He4, He4_s, U238, U238_s, Th232, Th232_s, Sm147, Sm147_s,
                        Ft238, Ft238_s, Ft235, Ft235_s, Ft232, Ft232_s, Ft147, Ft147_s, get_corrected, d, sample_obj):
+        #This is a typo, but I don't know if it matters. Should be U238_mol_per_ng not 328
         U328_mol_per_ng = 1/(238.03*1e9)
         Th232_mol_per_ng = 1/(232*1e9)
         Sm147_mol_per_ng = 1/(157*1e9)
@@ -240,7 +243,7 @@ def calculate_date(self, He4, He4_s, U238, U238_s, Th232, Th232_s, Sm147, Sm147_
             '235Ft-147Ft': Ft235_s*Ft147_s,
             '232Ft-147Ft': Ft232_s*Ft147_s
         }
-
+        # These also need to be referencing the corrected valyes and proper uncertainties
         date = hecalc.get_date(He4_mol, U238=U238_mol, U235=None, Th232=Th232_mol, Sm147=Sm147_mol,
                               Ft238=Ft238, Ft235=Ft235, Ft232=Ft232, Ft147=Ft147)
 
@@ -362,4 +365,4 @@ def calculate_date(self, He4, He4_s, U238, U238_s, Th232, Th232_s, Sm147, Sm147_
                     }]
                 }
             session_dict['sample'] = sample_obj
-            self.db.load_data('session', session_dict)
+            self.db.load_data('session', session_dict)