add SIRT and FakeSIRT options

KudryashevLab · Dec 8, 2023 · e097088 · e097088
1 parent ad3ff6d
commit e097088
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Showing 2 changed files with 13 additions and 0 deletions.
diff --git a/configurations/defaults.json b/configurations/defaults.json
@@ -225,6 +225,8 @@
     "Reconstruct": {
         "execution_method": "in_order",
         "reconstruct": "binned",
+        "sirt_iter": -1,
+        "fake_sirt_iter": -1,
         "use_ctf_corrected_stack": true,
         "generate_exact_filtered_tomograms": false,
         "exact_filter_size": 1500,

diff --git a/modules/Reconstruct.m b/modules/Reconstruct.m
@@ -359,6 +359,11 @@
                     + " -TILTFILE " + tlt_out_name...
                     + " -THICKNESS " + obj.configuration.reconstruction_thickness;
 
+                if isfield(obj.configuration, "sirt_iter") && (obj.configuration.sirt_iter >= 1)
+                    command = command + " -SIRTIterations " + obj.configuration.sirt_iter;
+                elseif isfield(obj.configuration, "fake_sirt_iter") && (obj.configuration.fake_sirt_iter >= 1)
+                    command = command + " -FakeSIRTiterations " + obj.configuration.fake_sirt_iter;
+                end
 
                 if obj.configuration.set_up.gpu > 0
                     command = command + " -UseGPU " + obj.configuration.set_up.gpu ;
@@ -442,6 +447,12 @@
                         + " -TILTFILE " + tlt_out_name...
                         + " -THICKNESS " + num2str(obj.configuration.reconstruction_thickness / splitted_binning, '%.f');
 
+                    if isfield(obj.configuration, "sirt_iter") && (obj.configuration.sirt_iter >= 1)
+                        command = command + " -SIRTIterations " + obj.configuration.sirt_iter;
+                    elseif isfield(obj.configuration, "fake_sirt_iter") && (obj.configuration.fake_sirt_iter >= 1)
+                        command = command + " -FakeSIRTiterations " + obj.configuration.fake_sirt_iter;
+                    end
+
                     if isfield(obj.configuration, "exclude_lists") && isfield(obj.configuration.exclude_lists, field_names{obj.configuration.set_up.j})
                         command = command + " -EXCLUDELIST2 " + strjoin(strsplit(num2str(obj.configuration.exclude_lists.(field_names{obj.configuration.set_up.j})')), ",");
                     elseif ~isempty(getFilePathsFromLastBatchruntomoRun(obj.configuration, "fid"))