@@ -164,25 +189,34 @@

SummaryΒΆ

If we put all the preceding steps together:

-
eg = la.analyse('./')
-eg.despike()
-eg.autorange()
-eg.bkg_correct()
-eg.ratio()
-eg.calibrate()
-
-# create a threshold filter at 0.5 mmol/mol Al/Ca
-eg.filter_threshold('Al27', 0.5E-3)
-# turn off the 'above' filter, so only data below the threshold is kept.
-eg.filter_off('Al27_thresh_above')
-
-# calculate sample statistics.
-eg.stat_samples()
-stats = eg.getstats()
-stats.to_csv('reports/stats.csv')
+
    eg = la.analyse(data_folder='./data/',
+                config='DEFAULT',
+                internal_standard='Ca43',
+                srm_identifier='STD')
+eg.despike(expdecay_despiker=True,
+           noise_despiker=True)
+eg.autorange(on_mult=[1.5, 0.8],
+             off_mult=[0.8, 1.5])
+eg.bkg_calc_weightedmean(weight_fwhm=300,
+                         n_min=10)
+    eg.bkg_subtract()
+    eg.ratio()
+eg.calibrate(drift_correct=False,
+             poly_n=0,
+             srms_used=['NIST610', 'NIST612', 'NIST614'])
+
+    # create a threshold filter at 0.1 mmol/mol Al/Ca
+    eg.filter_threshold(analyte='Al27', threshold=0.1e-3)
+    # turn off the 'above' filter, so only data below the threshold is kept.
+    eg.filter_on(filt=0)
+
+    # calculate sample statistics.
+    eg.stat_samples()
+    stats = eg.getstats()
+    stats.to_csv('reports/stats.csv')
 

 

-
Here we processed just 4 files, but the same procedure can be applied to an entire day of analyses, and takes just a few seconds longer.

+
Here we processed just 3 files, but the same procedure can be applied to an entire day of analyses, and takes just a little longer.

 
The processing stage most likely to modify your results is filtering.
 There are a number of filters available, ranging from simple concentration thresholds (filter_threshold(), as above) to advanced multi-dimensional clustering algorithms (filter_clustering()).
 We reccommend you read and understand the section on Filtering & Data Selection before applying filters to your data.

@@ -195,16 +229,19 @@ 
Before You Go
+
diff --git a/docs_source/source/users/beginners/10-summary.rst b/docs_source/source/users/beginners/10-summary.rst index 9bdde3f..1f67ffa 100644 --- a/docs_source/source/users/beginners/10-summary.rst +++ b/docs_source/source/users/beginners/10-summary.rst @@ -6,24 +6,33 @@ Summary If we put all the preceding steps together:: - eg = la.analyse('./') - eg.despike() - eg.autorange() - eg.bkg_correct() + eg = la.analyse(data_folder='./data/', + config='DEFAULT', + internal_standard='Ca43', + srm_identifier='STD') + eg.despike(expdecay_despiker=True, + noise_despiker=True) + eg.autorange(on_mult=[1.5, 0.8], + off_mult=[0.8, 1.5]) + eg.bkg_calc_weightedmean(weight_fwhm=300, + n_min=10) + eg.bkg_subtract() eg.ratio() - eg.calibrate() - - # create a threshold filter at 0.5 mmol/mol Al/Ca - eg.filter_threshold('Al27', 0.5E-3) + eg.calibrate(drift_correct=False, + poly_n=0, + srms_used=['NIST610', 'NIST612', 'NIST614']) + + # create a threshold filter at 0.1 mmol/mol Al/Ca + eg.filter_threshold(analyte='Al27', threshold=0.1e-3) # turn off the 'above' filter, so only data below the threshold is kept. - eg.filter_off('Al27_thresh_above') + eg.filter_on(filt=0) # calculate sample statistics. eg.stat_samples() stats = eg.getstats() stats.to_csv('reports/stats.csv') -Here we processed just 4 files, but the same procedure can be applied to an entire day of analyses, and takes just a few seconds longer. +Here we processed just 3 files, but the same procedure can be applied to an entire day of analyses, and takes just a little longer. The processing stage most likely to modify your results is filtering. There are a number of filters available, ranging from simple concentration thresholds (:meth:`~latools.analyse.filter_threshold`, as above) to advanced multi-dimensional clustering algorithms (:meth:`~latools.analyse.filter_clustering`). diff --git a/docs_source/source/users/installing.rst b/docs_source/source/users/installing.rst index a7a5ecf..25bc213 100644 --- a/docs_source/source/users/installing.rst +++ b/docs_source/source/users/installing.rst @@ -46,7 +46,7 @@ Once git is installed, you can install ``latools`` directly from the online proj This will download and install the latest version of ``latools`` from Github. In the future if you'd like to update ``latools`` to the latest version it's as adding ``--upgrade`` to the end of the code above. -.. Tip:: The ``@master`` at the end of the command installs the most up-to-date version of the software. If you want to install a specific version of ``latools``, replace ``master`` with the version number (e.g. ``v0.2.2a`` will get you the very first release of ``latools``). +.. Tip:: The ``@master`` at the end of the command installs the most up-to-date version of the software. If you want to install a specific version of ``latools``, replace ``@master`` with the version number (e.g. ``@v0.2.2a`` will get you the very first release of ``latools``). ------------------- 2. Pre-built Binary