From 27ae413e094b915b95abaf490f63fee2f3722e78 Mon Sep 17 00:00:00 2001
From: Juan Carlos Farah <juancarlos.farah@epfl.ch>
Date: Tue, 17 Aug 2021 21:16:49 +0200
Subject: [PATCH] feat: allow to set starting step

---
 .../BuildSegmentationConfiguration.m          |  6 ++-
 .../pipelines/BuildSegmentationPipeline.m     |  2 +-
 .../sequences/BuildSegmentationSequence.m     |  2 +-
 src/matlab/classes/Sequence.m                 | 50 +++++++++++++++----
 4 files changed, 48 insertions(+), 12 deletions(-)

diff --git a/src/matlab/builders/configurations/BuildSegmentationConfiguration.m b/src/matlab/builders/configurations/BuildSegmentationConfiguration.m
index 4dcd996..13ae09f 100644
--- a/src/matlab/builders/configurations/BuildSegmentationConfiguration.m
+++ b/src/matlab/builders/configurations/BuildSegmentationConfiguration.m
@@ -32,6 +32,10 @@
 config.parcellation = 'schaefer_2018_400_subc';
 config.parallel = false;
 
+% sequence level configurations
+config.sequence.startStep = 6;
+config.sequence.noCleanUp = true;
+
 
 % step 1: fast
 config.step1.H = 0.25;
@@ -56,7 +60,7 @@
 
 % step 4: binarize
 config.step4.skip = false;
-config.step4.optional = true;
+config.step4.optional = false;
 config.step4.clobber = config.clobber;
 config.step4.verbose = config.verbose;
 
diff --git a/src/matlab/builders/pipelines/BuildSegmentationPipeline.m b/src/matlab/builders/pipelines/BuildSegmentationPipeline.m
index fc9a630..33063d4 100644
--- a/src/matlab/builders/pipelines/BuildSegmentationPipeline.m
+++ b/src/matlab/builders/pipelines/BuildSegmentationPipeline.m
@@ -24,7 +24,7 @@
   pathToIntermediaryOutputs char = '.'
   pathToOutput char = '.'
   numSubjects int8 {mustBeNonnegative} = 0
-  config = {}
+  config = struct()
 end
 
 % names of inputs needed to start the sequence
diff --git a/src/matlab/builders/sequences/BuildSegmentationSequence.m b/src/matlab/builders/sequences/BuildSegmentationSequence.m
index cc3abdf..11476c6 100644
--- a/src/matlab/builders/sequences/BuildSegmentationSequence.m
+++ b/src/matlab/builders/sequences/BuildSegmentationSequence.m
@@ -398,7 +398,7 @@
                     outputs, ...
                     pathToWorkspace, ...
                     pathToOutput, ...
-                    true);
+                    config.sequence);
 
 end
 
diff --git a/src/matlab/classes/Sequence.m b/src/matlab/classes/Sequence.m
index acaf621..b2ba304 100644
--- a/src/matlab/classes/Sequence.m
+++ b/src/matlab/classes/Sequence.m
@@ -8,9 +8,9 @@
     Outputs
     WorkspacePath
     OutputPath
-    NoCleanUp
     Results
     Ready
+    Configuration
   end
 
   methods
@@ -19,17 +19,42 @@
                             outputs, ...
                             workspacePath, ...
                             outputPath, ...
-                            noCleanUp)
+                            config)
       %SEQUENCE Construct an instance of this class
       %   Detailed explanation goes here
+      arguments
+        steps
+        inputs
+        outputs
+        workspacePath
+        outputPath
+        config
+      end
+
+      % default to empty struct if empty cell array is passed
+      if isempty(config)
+        obj.Configuration = struct();
+      else
+        obj.Configuration = config;
+      end
+
+      % add default config options
+      if ~isfield(obj.Configuration, 'noCleanUp')
+         obj.Configuration.noCleanUp = false;
+      end
+      if ~isfield(obj.Configuration, 'startStep')
+         obj.Configuration.startStep = 1;
+      end
+
+
       obj.Steps = steps;
       obj.Inputs = inputs;
       obj.Outputs = outputs;
       obj.WorkspacePath = workspacePath;
       obj.OutputPath = outputPath;
-      obj.NoCleanUp = noCleanUp;
       obj.Results = cell(1, length(steps));
       obj.Ready = false;
+      obj.Configuration = config;
     end
 
     function isValid = validate(obj)
@@ -86,7 +111,7 @@
 
     function [obj, success] = cleanUp(obj)
       success = true;
-      if obj.NoCleanUp
+      if obj.Configuration.noCleanUp
         return
       end
       % remove the workspace
@@ -174,14 +199,21 @@
       for i = 1 : length(obj.Steps)
         step = obj.Steps{i};
 
-        % check if we are skipping this step
+        % check if we are skipping this step using start step
+        startStep = obj.Configuration.startStep;
+        if i < obj.Configuration.startStep
+          warning('start step is %d, skipping step %d', startStep, i);
+          continue;
+        end
+
+        % check if we are skipping this step manually
         skip = isfield(step.Configuration, 'skip') && ...
                        step.Configuration.skip == true;
         if skip
           warning('skipping step %d', i)
           continue;
         end
-        
+
         % check if step is optional
         optional = isfield(step.Configuration, 'optional') && ...
                            step.Configuration.optional == true;
@@ -230,7 +262,7 @@
             return
           else
             warning('ignoring optional step %d after caught error: step %d failed with status %d and message "%s"\n', ...
-                    i, ...      
+                    i, ...
                     i, ...
                     status, ...
                     result);
@@ -242,13 +274,13 @@
 
       % extract outputs
       extractOutputsSuccess = obj.extractOutputs();
-      
+
       if ~extractOutputsSuccess
         success = false;
       end
 
       % clean up
-      if ~obj.NoCleanUp
+      if ~obj.Configuration.noCleanUp
         [~, cleanUpSuccess] = obj.cleanUp();
         if ~cleanUpSuccess
           success = false;