Filter out complex SEs if generated.

Author: MJWester1

MATLAB/+smi/@SMLM/SMLM.m

@@ -297,6 +297,9 @@ function analyzeAll(obj, DatasetList)
         end
         [SMD] = LD.genLocalizations();
 
+        % Filter out any localizations with nonzero imaginary standard errors.
+        SMD = smi_helpers.Filters.filterImag(SMD, obj.Verbose);
+
         % Keep track of why localizations were filtered out.
         obj.SMDPreThresh = smi_core.SingleMoleculeData.catSMD( ...
                               obj.SMDPreThresh, LD.SMDPreThresh, false);

MATLAB/+smi_helpers/@Filters/Filters.m

@@ -18,6 +18,8 @@
    SMD = filterFC(SMD, Verbose, nFC)
    SMD = filterNN(SMD, Verbose, n_NN, MedianMultiplier)
 
+   SMD = filterImag(SMD, Verbose)
+
 end % methods(Static)
 
 end % classdef Filters

MATLAB/+smi_helpers/@Filters/README.md

@@ -25,3 +25,5 @@ static methods:
   filter out localizations representing fewer than nFC frame connections
 - **[filterNN](filterNN.m)**:
   localizations are filtered based on the nearest neighbor distance
+- **[filterImag](filterImag.m)**:
+  filter out _SE SMD fields with non-zero imaginary components

MATLAB/+smi_helpers/@Filters/filterImag.m

@@ -0,0 +1,41 @@
+function SMD = filterImag(SMD, Verbose)
+%filterImag: Filter out _SE SMD fields with non-zero imaginary components.
+%
+% INPUT:
+%    SMD     Single Molecule Data structure
+%    Verbose verbosity flag [DEFAULT = false]
+%
+% OUTPUT:
+%    SMD   modified Single Molecule Data structure
+
+% Created by
+%   Michael J. Wester (5/23/2025)
+
+if ~exist('Verbose', 'var')
+   Verbose = false;
+end
+
+n_prefilter = numel(SMD.X);
+
+% Find SMD fields that contain an SE in their name.
+f = fields(SMD);
+SE = f(contains(f, '_SE'));
+% Eliminate fields that do not contain n_prefilter elements.
+inuse = arrayfun(@(i) numel(SMD.(SE{i})) == n_prefilter, 1:numel(SE));
+SEinuse = SE(inuse);
+
+% Check the fields for nonzero imaginary values.
+complex = [];
+for i = 1 : numel(SEinuse)
+   complex = union(complex, find(imag(SMD.(SE{i})) ~= 0));
+end
+
+noncomplex = setdiff(1:n_prefilter, complex);
+SMD = smi_core.SingleMoleculeData.isolateSubSMD(SMD, noncomplex);
+
+if Verbose >= 2 && numel(SMD.X) ~= n_prefilter
+   fprintf('   Complex standard errors removed = %d out of %d\n', ...
+           n_prefilter - numel(SMD.X), n_prefilter);
+end
+
+end