Merge branch 'develop'

README.md

@@ -6,11 +6,11 @@
 
 ![TomoBEAR Social Media Logo Image](images/TomoBEAR_gitlogo.png)
 
-Implementation details and benchmarks you can find in our preprint:
-</br> Balyschew N, Yushkevich A, Mikirtumov V, Sanchez RM, Sprink T, Kudryashev M. Streamlined Structure Determination by Cryo-Electron Tomography and Subtomogram Averaging using TomoBEAR. **[Preprint]** 2023. bioRxiv doi: [10.1101/2023.01.10.523437](https://www.biorxiv.org/content/10.1101/2023.01.10.523437v1)
+Implementation details and benchmarks you can find in our publication:
+</br> Balyschew N, Yushkevich A, Mikirtumov V, Sanchez RM, Sprink T, Kudryashev M. Streamlined Structure Determination by Cryo-Electron Tomography and Subtomogram Averaging using TomoBEAR. *Nat Commun* **14**, 6543 (2023). doi: [10.1038/s41467-023-42085-w](https://www.nature.com/articles/s41467-023-42085-w)
 
 > **Warning**
-> <br/> This software is currently in pre-release state. New features may still appear and refactoring may still take place between all the current and future 0.x.y versions until 1.0.0 will be ready to be released.
+> <br/> This software is currently in pre-release state. New features may still appear and refactoring may still take place between all the current and future 0.x.y versions until 1.0.0 will be ready to be released. Binaries are not currently shipped.
 
 ## Contents
 
@@ -36,7 +36,7 @@ We have prepared a range of short (8-12 min) video-tutorials explaining setup, u
 
 In the following picture you can see a flow chart of the main `TomoBEAR` processing steps. As the basic input data you can use raw frame movies or already assembled tilt stacks. More on input formats you [can read here](https://github.com/KudryashevLab/TomoBEAR/wiki/Usage.md#input-data-file-formats).
 
-![Schematic Pipeline Image](images/pipeline_simplified.png)
+![Schematic Pipeline Image](images/pipeline_upd.png)
 
 Blue boxes outline the steps that are performed fully automatically, green boxes may require human intervention. The steps encapsulated in the red frame represent the functionality of live data processing. More detailed diagram [is located on wiki](https://github.com/KudryashevLab/TomoBEAR/wiki).
 

modules/AreTomo.m

@@ -94,7 +94,7 @@
                 if obj.configuration.correct_pretilt_flag ~= -1
                     tilt_axis_offset_command_snippet = " -TiltCor " + num2str(obj.configuration.correct_pretilt_flag);
                     pretilt_angle_to_use = -obj.configuration.pretilt_tilt_axis;
-                    if pretilt_angle_to_use == 0
+                    if pretilt_angle_to_use ~= 0
                         tilt_axis_offset_command_snippet = tilt_axis_offset_command_snippet + " " + num2str(pretilt_angle_to_use);
                     end
                 else
@@ -125,7 +125,7 @@
                     + ") is lower than required input_stack_binning (=" + num2str(obj.configuration.input_stack_binning) + ") !");
             end
 
-            stack_source = string(tilt_stacks(obj.configuration.set_up.adjusted_j).folder) + string(filesep) + string(tilt_stacks(obj.configuration.set_up.adjusted_j).name);
+            stack_source = string(tilt_stacks(obj.configuration.set_up.j).folder) + string(filesep) + string(tilt_stacks(obj.configuration.set_up.j).name);
 
             % Generate aligned stack of the requested binning level
             stack_destination = obj.output_path + filesep + obj.name + ".ali";
@@ -194,7 +194,7 @@
             % Generate aligned unbinned stack using alignment parameters
             % previously detected at the requested binning level
             tilt_stacks = getTiltStacksFromStandardFolder(obj.configuration, true);
-            stack_source = string(tilt_stacks(obj.configuration.set_up.adjusted_j).folder) + string(filesep) + string(tilt_stacks(obj.configuration.set_up.adjusted_j).name);
+            stack_source = string(tilt_stacks(obj.configuration.set_up.j).folder) + string(filesep) + string(tilt_stacks(obj.configuration.set_up.j).name);
             stack_destination_unbinned = obj.output_path + filesep + obj.name + "_bin_" + num2str(1) + ".ali";
 
             if obj.configuration.use_previous_alignment == false

modules/BinStacks.m

@@ -246,10 +246,15 @@
                     if obj.configuration.run_ctf_phaseflip == true
                         tlt_file = getFilePathsFromLastBatchruntomoRun(obj.configuration, "rawtlt");
                         defocus_file = getFilePathsFromLastBatchruntomoRun(obj.configuration, "defocus");
-                        splitted_tilt_stack_path_name = strsplit(stack_output_path, ".");
-                        ctf_corrected_stack_destination = splitted_tilt_stack_path_name(1)...
+
+                        [stack_filepath, stack_filename, stack_ext] = fileparts(stack_output_path);
+                        %splitted_tilt_stack_path_name = strsplit(stack_output_path, ".");
+                        %ctf_corrected_stack_destination = splitted_tilt_stack_path_name(1)...
+                        %    + "_" + obj.configuration.ctf_corrected_stack_suffix...
+                        %    + "." + splitted_tilt_stack_path_name(2);
+                        ctf_corrected_stack_destination = stack_filepath + filesep + stack_filename...
                             + "_" + obj.configuration.ctf_corrected_stack_suffix...
-                            + "." + splitted_tilt_stack_path_name(2);
+                            + stack_ext;
 
                         command = "ctfphaseflip -input " + stack_output_path...
                             + " -output " + ctf_corrected_stack_destination...
@@ -263,9 +268,12 @@
                             + " -cs " + obj.configuration.spherical_aberation...
                             + " -ampContrast " + obj.configuration.ampContrast;
 
-                        if obj.configuration.use_aligned_stack == false
-                            command = command + " -xform " + xf_file_destination;
-                        end
+                        % NOTE: if stack is aligned, no need to transform
+                        % NOTE: if stack is non-aligned, no need to
+                        % transform since it was not requested
+                        %if obj.configuration.use_aligned_stack == false
+                        %    command = command + " -xform " + xf_file_destination;
+                        %end
 
                         if obj.configuration.set_up.gpu > 0 && versionGreaterThan(obj.configuration.environment_properties.imod_version, "4.10.9")
                             command = command + " -gpu " + obj.configuration.set_up.gpu;

modules/Reconstruct.m

@@ -304,15 +304,14 @@
                 tlt_out = fopen(tlt_out_name, "w");
 
                 if obj.configuration.correct_angles == "center"
-                    tlt_in = fopen(tlt_file{1}, "r");
-
-                    tlt_out_name = obj.output_path + string(filesep) + name + ".tlt";
-                    tlt_out = fopen(tlt_out_name, "w");
-
-                    high_tilt = fgetl(tlt_in);
+                    high_tilt = str2double(fgetl(tlt_in));
                     % TODO:DIRTY -> code clean
+                    low_tilt = high_tilt;
                     while ~feof(tlt_in)
-                        low_tilt = fgetl(tlt_in);
+                        low_tilt_new = str2double(fgetl(tlt_in));
+                        if ~isnan(low_tilt_new)
+                            low_tilt = low_tilt_new;
+                        end
                     end
                     fclose(tlt_in);
 
@@ -321,7 +320,7 @@
                     tlt_in = fopen(tlt_file{1}, "r");
                     while ~feof(tlt_in)
                         % TODO: needs to be tested
-                        tilt_adjusted = num2str(fgetl(tlt_in)) + shift;
+                        tilt_adjusted = str2double(fgetl(tlt_in)) + shift;
                         fprintf(tlt_out, "%.2f\n", tilt_adjusted);
                     end
                 elseif obj.configuration.correct_angles == "subtract"