Merge pull request #65 from oscarbranson/dev

0.3.21

CHANGELOG.md

@@ -1,7 +1,16 @@
 # Changelog
 All significant changes to the software will be documented here.
 
-## [0.3.20]
+## [0.3.21] 25/05/2021
+
+### Changed
+- Mass fraction calculation functions updated to work with analyte ratio names.
+- Reproduce now correctly handles mass fraction calculation.
+
+### Flags
+- Mass fraction calculation won't work well (at all?!) with multiple internal standards.
+
+## [0.3.20] 24/05/2021
 
 ### New
 - Integrated long file splitting into analysis function.

latools/D_obj.py

@@ -578,8 +578,6 @@ def calibrate(self, calib_ps, analyte_ratios=None):
         return
 
     def calc_mass_fraction(self, internal_standard_conc, analytes=None, analyte_masses=None):
-        if analytes is None:
-            analytes = self.analytes.difference(self.internal_standard)
         if 'mass_fraction' not in self.data.keys():
             self.data['mass_fraction'] = Bunch()
 
@@ -588,12 +586,17 @@ def calc_mass_fraction(self, internal_standard_conc, analytes=None, analyte_mass
 
         if np.isnan(internal_standard_conc):
             for a in analytes:
-                self.data['mass_fraction'][a] = np.full(self.data['calibrated'][a].shape, np.nan)
+                num, denom = a.split('_')
+                self.data['mass_fraction'][num] = np.full(self.data['calibrated'][a].shape, np.nan)
         else:
             for a in analytes:
-                self.data['mass_fraction'][a] = to_mass_fraction(self.data['calibrated'][a], internal_standard_conc,
-                                                                analyte_masses[a], analyte_masses[self.internal_standard])
-
+                num, denom = a.split('_')
+                self.data['mass_fraction'][num] = to_mass_fraction(molar_ratio=self.data['calibrated'][a], massfrac_denominator=internal_standard_conc,
+                                                                   numerator_mass=analyte_masses[num], denominator_mass=analyte_masses[denom])
+                if denom not in self.data['mass_fraction']:
+                    self.data['mass_fraction'][denom] = np.full(self.data['calibrated'][a].shape, np.nan)
+                    self.data['mass_fraction'][denom][~np.isnan(un.nominal_values(self.data['mass_fraction'][num]))] = internal_standard_conc
+
         self.setfocus('mass_fraction')
 
 
@@ -669,15 +672,16 @@ def ablation_times(self):
             ats[n - 1] = t.max() - t.min()
         return ats
 
-    def get_individual_ablations(self, analytes=None, focus_stage=None):
+    def get_individual_ablations(self, analytes=None, filt=True, focus_stage=None):
         analytes = self._analyte_checker(analytes)
         if focus_stage is None:
             focus_stage = self.focus_stage
         out = []
+        ind = self.filt.grab_filt(filt)
         for n in range(1, self.n + 1):
             sub = {}
             for a in analytes:
-                sub[a] = self.data[focus_stage][a][self.ns == n]
+                sub[a] = self.data[focus_stage][a][(self.ns == n) & ind]
             out.append(sub)
         return out
 

latools/__init__.py

@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.20'
+__version__ = '0.3.21'
 
 def cite(output='text'):
     """

latools/helpers/chemistry.py

@@ -139,15 +139,17 @@ def analyte_mass(analyte, in_name=True):
         If True, numbers in the analyte name are preferred.
     """
     if isinstance(analyte, str):
+        if '_' in analyte:
+            return analyte_mass(analyte.split('_'))
         nums = re.findall('[0-9]+', analyte)
         if in_name and nums:
-            return float(nums[0])
+            return {analyte: float(nums[0])}
         else:
-            return calc_M(re.findall('[A-z]+', analyte)[0])
+            return {analyte: calc_M(re.findall('[A-z]+', analyte)[0])}
     else:
         masses = {}
         for i, a in enumerate(analyte):
-            masses[a] = analyte_mass(a, in_name)
+            masses.update(analyte_mass(a, in_name))
         return masses
 
 

latools/helpers/helpers.py

@@ -130,7 +130,10 @@ def unitpicker(a, denominator=None, focus_stage=None):
     a = abs(a)
     order = np.log10(a)
     m = np.ceil(-order / 3) * 3
-    return float(10**m), udict[m]
+    if np.isnan(m):
+        return 1, ''
+    else:
+        return float(10**m), udict[m]
 
 def collate_data(in_dir, extension='.csv', out_dir=None):
     """

latools/helpers/plot.py

@@ -344,6 +344,10 @@ def crossplot(dat, keys=None, lognorm=True, bins=25, figsize=(12, 12),
     # determine ranges for all analytes
     rdict = {a: (np.nanmin(focus[a] * udict[a][0]),
                  np.nanmax(focus[a] * udict[a][0])) for a in keys}
+    # check for nans
+    for k, v in rdict.items():
+        if any(np.isnan(v)):
+            rdict[k] = (-1,1)
 
     for i, j in tqdm(zip(*np.triu_indices_from(axes, k=1)), desc='Drawing Plots',
                      total=sum(range(len(keys)))):