Merge pull request #66 from oscarbranson/dev

0.3.22

CHANGELOG.md

@@ -1,6 +1,11 @@
 # Changelog
 All significant changes to the software will be documented here.
 
+## [0.3.22] 27/05/2021
+
+### Changed
+- Fixes to handling of uncalibrated elements in _analyte_checker, which effects calibration, minimal_export and plotting after calibration.
+
 ## [0.3.21] 25/05/2021
 
 ### Changed

latools/D_obj.py

@@ -127,7 +127,8 @@ def __init__(self, data_file=None, dataformat=None, errorhunt=False, cmap=None,
 
         # set for recording calculated ratios
         self.analyte_ratios = set()
-
+        self.uncalibrated = set()
+
         # calculate total counts
         self.data['total_counts'] = sum(self.data['rawdata'].values())
 

latools/__init__.py

@@ -17,7 +17,7 @@
 from .helpers import chemistry
 from . import preprocessing
 
-__version__ = '0.3.21'
+__version__ = '0.3.22'
 
 def cite(output='text'):
     """

latools/helpers/helpers.py

@@ -515,18 +515,24 @@ def analyte_checker(self, analytes=None, check_ratios=True, single=False):
         analytes = [analytes]
 
     out = set()
-    if self.focus_stage not in ['ratios', 'calibrated'] or not check_ratios:
-        if analytes is None:
-            analytes = self.analytes
-        out = self.analytes.intersection(analytes)
-    else:
+    if self.focus_stage in ['ratios', 'calibrated'] and check_ratios:
         if analytes is None:
             analytes = self.analyte_ratios
         # case 1: provided analytes are an exact match for items in analyte_ratios
         valid1 = self.analyte_ratios.intersection(analytes)
         # case 2: provided analytes are in numerator of ratios
         valid2 = [a for a in self.analyte_ratios if a.split('_')[0] in analytes]
         out = valid1.union(valid2)
+    else:
+        if analytes is None:
+            analytes = self.analytes
+        out = self.analytes.intersection(analytes)
+
+    if len(self.uncalibrated) > 0:
+        if self.focus_stage in ['ratios', 'calibrated'] and check_ratios:
+            out.difference_update(self.uncalibrated)
+        else:
+            out.difference_update([u.split('_')[0] for u in self.uncalibrated])
 
     if len(out) == 0:
         raise ValueError(f'{analytes} does not match any valid analyte names.')
@@ -536,4 +542,14 @@ def analyte_checker(self, analytes=None, check_ratios=True, single=False):
             raise ValueError(f'{analytes} matches more than one valid analyte ({out}). Please be more specific.')
         return out.pop()
 
+    return out
+
+def split_analyte_ratios(ratios):
+    out = set()
+    if isinstance(ratios, str):
+        out.update(ratios.split('_'))
+    elif ratios is None:
+        return out
+    else:
+        out.update(*map(split_analyte_ratios, ratios))
     return out

latools/latools.py

@@ -39,7 +39,7 @@
 from .helpers.helpers import (rolling_window, enumerate_bool,
                       un_interp1d, get_date,
                       unitpicker, rangecalc, Bunch, calc_grads,
-                      get_total_time_span, analyte_checker)
+                      get_total_time_span, analyte_checker, split_analyte_ratios)
 from .helpers import logging
 from .helpers.logging import _log
 from .helpers.config import read_configuration, config_locator
@@ -1560,11 +1560,8 @@ def srm_id_auto(self, srms_used=['NIST610', 'NIST612', 'NIST614'], analytes=None
         # TODO: srm_id_plot!
         if isinstance(srms_used, str):
             srms_used = [srms_used]
-
-        # compile measured SRM data
-        self.srm_compile_measured(n_min)
 
-        # load SRM database
+        # reload SRM database (if reloard_srm_databse=True)
         self.srm_load_database(srms_used, reload_srm_database)
 
         analytes = self._analyte_checker(analytes)
@@ -1651,6 +1648,12 @@ def calibrate(self, analytes=None, drift_correct=True,
         -------
         None
         """
+        # load SRM database
+        self.srm_load_database(srms_used, reload_srm_database)
+
+        # compile measured SRM data
+        self.srm_compile_measured(n_min)
+
         analytes = self._analyte_checker(analytes)
 
         if isinstance(srms_used, str):
@@ -1744,6 +1747,7 @@ def calibrate(self, analytes=None, drift_correct=True,
         with self.pbar.set(total=len(self.data), desc='Applying Calibrations') as prog:
             for d in self.data.values():
                 d.calibrate(self.calib_ps, analytes)
+                d.uncalibrated = self.uncalibrated
                 prog.update()
 
         # record SRMs used for plotting
@@ -1756,7 +1760,6 @@ def calibrate(self, analytes=None, drift_correct=True,
 
         self.stages_complete.update(['calibrated'])
         self.focus_stage = 'calibrated'
-
         return
 
     # data filtering
@@ -1780,6 +1783,7 @@ def get_sample_list(self, save_as=None, overwrite=False):
 
         empty = pd.DataFrame(index=self.samples, columns=['int_stand_massfrac'])
         empty.to_csv(save_as)
+        self.internal_standard_concs = empty
         print(self._wrap_text('Sample List saved to {} \nPlease modify and re-import using read_internal_standard_concs()'.format(save_as)))
 
     def read_internal_standard_concs(self, sample_concs=None):
@@ -2962,10 +2966,7 @@ def get_focus(self, filt=False, samples=None, subset=None, nominal=False):
 
         focus = {'uTime': []}
 
-        if self.focus_stage not in ['ratios', 'calibrated']:
-            columns = self.analytes
-        else:
-            columns = self.analyte_ratios
+        columns = self._analyte_checker()
 
         focus.update({a: [] for a in columns})
 
@@ -4175,9 +4176,7 @@ def minimal_export(self, target_analytes=None, path=None):
             os.mkdir(path)
 
         # parse minimal analytes (exclude ratios, include target_analytes)
-        export_analytes = target_analytes
-        for a in self.minimal_analytes.difference([None]):
-            export_analytes.update(a.split('_'))
+        export_analytes = target_analytes.union(split_analyte_ratios(self.minimal_analytes))
         export_analytes = self.analytes_sorted(export_analytes, check_ratios=False)
 
         # export data