Warning gantry and couch angles + correct displayed progress #879

lisaseckler · 2025-11-28T09:45:02Z

Warning for different numbers of gantry and couch angles + correct progress displaying of the stf calculation

Copilot

Pull request overview

This PR adds warning/error messages when gantry and couch angles have different counts, and modifies the progress display mechanism during STF (steering file) calculation.

Upgrades angle mismatch warnings to errors with more specific messages
Introduces a new parameter to matRad_progress to differentiate between two progress display scenarios
Modifies progress reporting in the beam generation loop to use different display modes

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 11 comments.

File	Description
matRad/util/matRad_progress.m	Adds a new `scen` parameter to control progress display behavior, replacing the previous backspace-based update mechanism with carriage return and mode-based logic
matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m	Changes angle mismatch warnings to errors, adds error messages for angle count mismatches, and passes display mode parameter to progress function calls

Comments suppressed due to low confidence (1)

matRad/util/matRad_progress.m:9

The new parameter scen is not documented in the function header. The documentation should be updated to include this new parameter, its purpose, and valid values (e.g., 1 for first progress update, 2 for subsequent updates).

% call
%   matRad_progress(currentIndex, totalNumberOfEvaluations)
%
% input
%   currentIndex:               current iteration index
%   totalNumberOfEvaluations:   maximum iteration index

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Copilot · 2025-12-01T08:57:37Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

            if nBeams ~= numel(this.couchAngles)
                matRad_cfg = MatRad_Config.instance();
-                matRad_cfg.dispWarning('For some reason, we have a different number of beam and couch angles!');
+                matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')


Missing semicolon at the end of this statement. In MATLAB, statements without semicolons print their output to the console, which would display the error message twice (once from dispError and once from the return value).

Suggested change

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.');

Copilot · 2025-12-01T08:57:37Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

            if nBeams ~= numel(this.couchAngles)
                matRad_cfg = MatRad_Config.instance();
-                matRad_cfg.dispWarning('For some reason, we have a different number of beam and couch angles!');
+                matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')


The error message is inaccurate. This condition triggers when the number of gantry angles doesn't equal the number of couch angles, not specifically when there are "more gantry angles than couch angles". The message should be more generic to cover both cases (e.g., "The number of gantry angles and couch angles must be equal.").

Suggested change

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

matRad_cfg.dispError('The number of gantry angles and couch angles must be equal.')

Copilot · 2025-12-01T08:57:38Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

                if numel(this.gantryAngles) > numel(this.couchAngles)
+                    matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')
                    %Append Couch angles with zeros
                    this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];                    
                elseif numel(this.couchAngles) > numel(this.gantryAngles)


matRad_cfg variable is used but not defined in this scope. It needs to be instantiated with matRad_cfg = MatRad_Config.instance(); before calling dispError.

Suggested change

if numel(this.gantryAngles) > numel(this.couchAngles)

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

%Append Couch angles with zeros

this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];

elseif numel(this.couchAngles) > numel(this.gantryAngles)

if numel(this.gantryAngles) > numel(this.couchAngles)

matRad_cfg = MatRad_Config.instance();

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

%Append Couch angles with zeros

this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];

elseif numel(this.couchAngles) > numel(this.gantryAngles)

matRad_cfg = MatRad_Config.instance();

Copilot · 2025-12-01T08:57:38Z

matRad/util/matRad_progress.m

+
+% --- first part of the progress ---
+if scen == 1
+    % new line


The comment "new line" is misleading. The \r escape sequence is a carriage return that moves the cursor to the beginning of the current line, not a new line. If a new line is actually needed, use \n instead. If the intent is to overwrite the current line (which seems correct given the context), update the comment to reflect this, e.g., "overwrite current line".

Suggested change

% new line

% overwrite current line

Copilot · 2025-12-01T08:57:38Z

matRad/util/matRad_progress.m

+
+% --- for scenario 2, same line ---
+if scen == 2
+    fprintf('   Progress: %6.2f %%', percent);


The progress display for scen == 2 will append " Progress: X.XX %" to whatever is currently on the console line without proper updating. This will create messy output if called multiple times. Consider using backspace characters (\b) to erase the previous output, or use \r to return to the beginning of the line and overwrite, similar to how scen == 1 works.

Suggested change

fprintf(' Progress: %6.2f %%', percent);

fprintf('\rProgress: %6.2f %%', percent);

Copilot · 2025-12-01T08:57:39Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

            if ~this.lockAngleUpdate
                this.lockAngleUpdate = true;
                if numel(this.gantryAngles) > numel(this.couchAngles)
+                    matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')


Missing semicolon at the end of this statement. In MATLAB, statements without semicolons print their output to the console, which would display the error message twice (once from dispError and once from the return value).

Suggested change

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.');

Copilot · 2025-12-01T08:57:39Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

                if numel(this.gantryAngles) > numel(this.couchAngles)
+                    matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')
                    %Append Couch angles with zeros
                    this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];                    
                elseif numel(this.couchAngles) > numel(this.gantryAngles)


matRad_cfg variable is used but not defined in this scope. It needs to be instantiated with matRad_cfg = MatRad_Config.instance(); before calling dispError.

Suggested change

if numel(this.gantryAngles) > numel(this.couchAngles)

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

%Append Couch angles with zeros

this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];

elseif numel(this.couchAngles) > numel(this.gantryAngles)

if numel(this.gantryAngles) > numel(this.couchAngles)

matRad_cfg = MatRad_Config.instance();

matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')

%Append Couch angles with zeros

this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];

elseif numel(this.couchAngles) > numel(this.gantryAngles)

matRad_cfg = MatRad_Config.instance();

Copilot · 2025-12-01T08:57:39Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

                    %Append Couch angles with zeros
                    this.couchAngles = [this.couchAngles zeros(1,numel(this.gantryAngles)-numel(this.couchAngles))];                    
                elseif numel(this.couchAngles) > numel(this.gantryAngles)
+                    matRad_cfg.dispError('There are more couch angles than gantry angles. They have to have the same size.')


Missing semicolon at the end of this statement. In MATLAB, statements without semicolons print their output to the console, which would display the error message twice (once from dispError and once from the return value).

Suggested change

matRad_cfg.dispError('There are more couch angles than gantry angles. They have to have the same size.')

matRad_cfg.dispError('There are more couch angles than gantry angles. They have to have the same size.');

Copilot · 2025-12-01T08:57:40Z

matRad/util/matRad_progress.m

-function matRad_progress(currentIndex, totalNumberOfEvaluations)
+function matRad_progress(currentIndex, totalNumberOfEvaluations,scen)
 % matRad progress bar
 % 


The new scen parameter breaks backward compatibility with all existing calls to matRad_progress throughout the codebase. Many files call this function with only 2 parameters (see matRad_sampling.m, matRad_DoseEngineBase.m, etc.). Consider making scen an optional parameter with a default value, e.g., function matRad_progress(currentIndex, totalNumberOfEvaluations, scen) with logic like if nargin < 3, scen = 1; end.

Suggested change

%

%

if nargin < 3

scen = 1;

end

Copilot · 2025-12-01T08:57:40Z

matRad/util/matRad_progress.m

+persistent isInitialized
+
+if isempty(isInitialized)
+    isInitialized = true;
 end
-
-if (currentIndex > 1)
-  Length = numel(sprintf('%3.2f %%',(currentIndex-1)/totalNumberOfEvaluations*100));
-  fprintf(repmat('\b',1,Length));
+
+percent = (currentIndex / totalNumberOfEvaluations) * 100;
+
+% --- first part of the progress ---
+if scen == 1
+    % new line
+    fprintf('\rProgress: %6.2f %%', percent);
 end
-
-% Print the progress tool
-fprintf('%3.2f %%',currentIndex/totalNumberOfEvaluations*100);
-
-% After the last iteration print a newline command
-if (currentIndex == totalNumberOfEvaluations)
-    fprintf('\n');
+
+% --- for scenario 2, same line ---
+if scen == 2
+    fprintf('   Progress: %6.2f %%', percent);
 end
-
+
+% --- finish line after the last angle ---
+if currentIndex == totalNumberOfEvaluations && scen == 2
+    fprintf('\n');
+    clear isInitialized


The persistent isInitialized variable is declared and set but never actually used to control any logic. It's only cleared when currentIndex == totalNumberOfEvaluations && scen == 2, but this clearing has no effect since the variable isn't checked anywhere. Consider removing this unused code or implementing the intended initialization logic.

codecov · 2025-12-01T09:05:33Z

Codecov Report

❌ Patch coverage is 6.25000% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 53.81%. Comparing base (162bde8) to head (dae8c3d).

Files with missing lines	Patch %	Lines
matRad/util/matRad_progress.m	0.00%	11 Missing ⚠️
...ring/matRad_StfGeneratorExternalRayBixelAbstract.m	20.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #879      +/-   ##
==========================================
- Coverage   53.88%   53.81%   -0.07%     
==========================================
  Files         308      308              
  Lines       19954    19959       +5     
==========================================
- Hits        10752    10741      -11     
- Misses       9202     9218      +16

☔ View full report in Codecov by Sentry.
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remocristoforetti · 2025-12-01T09:18:22Z

matRad/steering/matRad_StfGeneratorExternalRayBixelAbstract.m

                % Show progress
                if matRad_cfg.logLevel > 2
-                    matRad_progress(i,length(this.gantryAngles));
+                    matRad_progress(i,length(this.gantryAngles),2);


I don't think we need this second call to matRad_progress

github-actions · 2025-12-01T09:22:40Z

Test Results

3 files ±0 3 suites ±0 44m 48s ⏱️ +10s
319 tests ±0 317 ✅ - 2 0 💤 ±0 2 ❌ +2
1 053 runs ±0 1 042 ✅ - 6 5 💤 ±0 6 ❌ +6

For more details on these failures, see this check.

Results for commit dae8c3d. ± Comparison against base commit 162bde8.

remocristoforetti · 2025-12-01T09:22:57Z

matRad/util/matRad_progress.m

-if (currentIndex == 1)
-    fprintf('Progress: ');
+
+persistent isInitialized


I would avoid the use of persistent variables for this as matRad_progress is also called outside of the stf generator. Also seems like it's not used.

remocristoforetti · 2025-12-01T09:25:54Z

matRad/util/matRad_progress.m

+percent = (currentIndex / totalNumberOfEvaluations) * 100;
+
+% --- first part of the progress ---
+if scen == 1


I don't understand why we need a scen input, and seems like the output is never cleared, keeps adding the 'Progress '

github-actions · 2026-01-01T01:50:18Z

This PR was automatically marked as stale it has been open 30 days with no activity. Please review/update/merge this PR.

Warning gantry and couch angles + correct displayed progress

dae8c3d

Warning for different numbers of gantry and couch angles + correct progress displaying of the stf calculation

wahln requested a review from Copilot December 1, 2025 08:52

Copilot started reviewing on behalf of wahln December 1, 2025 08:53 View session

wahln requested review from JenHardt and remocristoforetti December 1, 2025 08:54

Copilot finished reviewing on behalf of wahln December 1, 2025 08:55

Copilot AI reviewed Dec 1, 2025

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remocristoforetti reviewed Dec 1, 2025

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github-actions bot added the stale Automatic label for stale issues label Jan 1, 2026

	matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')
	matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.');

	matRad_cfg.dispError('There are more gantry angles than couch angles. They have to have the same size.')
	matRad_cfg.dispError('The number of gantry angles and couch angles must be equal.')

	fprintf(' Progress: %6.2f %%', percent);
	fprintf('\rProgress: %6.2f %%', percent);

	matRad_cfg.dispError('There are more couch angles than gantry angles. They have to have the same size.')
	matRad_cfg.dispError('There are more couch angles than gantry angles. They have to have the same size.');

-%
+%
+if nargin < 3
+    scen = 1;
+end

Warning gantry and couch angles + correct displayed progress #879

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