diff --git a/configurations/defaults.json b/configurations/defaults.json index b1a59b7..df1a717 100755 --- 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 index a742800..b5967be 100644 --- 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"))