Merge branch 'ucl-bug:main' into sp/4-bug_line_elements

Author: stellaprins

.github/workflows/unit_tests.yml

@@ -0,0 +1,50 @@
+name: Run unit tests
+
+on:
+  push:
+    branches:
+       - main
+  pull_request:
+    branches:
+       - main
+
+jobs:
+  unit-tests:
+    name: Run unit tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v2
+        with:
+          products: Signal_Processing_Toolbox
+          cache: true
+
+      - name: Run unit tests
+        uses: matlab-actions/run-command@v2
+        with:
+          command: |
+            addpath("${{ github.workspace }}/k-Wave");
+            cd("${{ github.workspace }}/k-Wave/testing/unit");
+            test_struct = runUnitTests("",false);
+            save('test_struct.mat', 'test_struct');
+          startup-options: -nojvm -logfile output.log
+
+      - name: Show test results & create artifact
+        uses: matlab-actions/run-command@v2
+        with:
+          command: |
+            addpath("${{ github.workspace }}/k-Wave");
+            cd("${{ github.workspace }}/k-Wave/testing/unit");
+            load('test_struct.mat', 'test_struct');
+            runUnitTests_show_results(test_struct);
+            runUnitTests_artifact(test_struct);
+          startup-options: -nojvm 
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: unit_test_results
+          path: ${{ github.workspace }}/k-Wave/testing/unit/test_results.json

k-Wave/acousticFieldPropagator.m

@@ -115,7 +115,7 @@
 %#ok<*UNRCH>
 
 % start the timer
-start_time = clock;
+start_time = datetime('now');
 
 % =========================================================================
 % DEFINE LITERALS
@@ -436,7 +436,7 @@
     end
 
     % update command line status
-    disp(['  computation completed in ' scaleTime(etime(clock, start_time))]);
+    disp(['  computation completed in ' scaleTime(seconds(datetime('now') - start_time))]);
 
     % stop evaluation
     return
@@ -555,7 +555,7 @@
 end
 
 % update command line status
-disp(['  computation completed in ' scaleTime(etime(clock, start_time))]);
+disp(['  computation completed in ' scaleTime(seconds(datetime('now') - start_time))]);
 
 % plot the propagator
 if plot_propagator

k-Wave/acousticFieldPropagatorC.m

@@ -66,7 +66,7 @@
 %#ok<*AGROW>
 
 % start time
-global_start_time = clock;
+global_start_time = datetime('now');
 
 % check the inputs are 3D
 if numDim(amp_in) ~= 3
@@ -224,10 +224,10 @@
 acousticFieldPropagator(amp_in, phase_in, dx, f0, c0, 'SaveToDisk', input_filename, input_args{:});
 
 % store time to save input
-compute_time.save_input = etime(clock, global_start_time);
+compute_time.save_input = seconds(datetime('now') - global_start_time);
 
 % start timer
-compute_start_time = clock;
+compute_start_time = datetime('now');
 
 % run the simulation in C++ and print outputs to the MATLAB command line
 if isunix
@@ -250,10 +250,10 @@
 end
 
 % store time to run simulation
-compute_time.simulation = etime(clock, compute_start_time);
+compute_time.simulation = seconds(datetime('now') - compute_start_time);
 
 % start timer
-load_start_time = clock;
+load_start_time = datetime('now');
 
 % load the C++ data back from disk using h5read
 pressure = h5read(output_filename, '/pressure_out');
@@ -274,10 +274,10 @@
 end
 
 % store time to load output
-compute_time.load_output = etime(clock, load_start_time);
+compute_time.load_output = seconds(datetime('now') - load_start_time);
 
 % store total time
-compute_time.total = etime(clock, global_start_time);
+compute_time.total = seconds(datetime('now') - global_start_time);
 
 % assign outputs
 switch nargout

k-Wave/angularSpectrum.m

@@ -134,7 +134,7 @@
 % along with k-Wave. If not, see <http://www.gnu.org/licenses/>.
 
 % start timer
-start_time = clock;
+start_time = datetime('now');
 
 % =========================================================================
 % INPUT CHECKING
@@ -278,7 +278,7 @@
 
 % update command line status
 disp('Running angular spectrum projection...');
-disp(['  start time: ' datestr(start_time)]);
+disp(['  start time: ' char(start_time)]);
 disp(['  input plane size: ' num2str(Nx) ' by ' num2str(Ny) ' grid points (' num2str(scale * Nx * dx) ' by ' num2str(scale * Ny * dx) prefix 'm)']);
 disp(['  grid expansion: ' num2str(grid_expansion) ' grid points']);
 
@@ -399,8 +399,8 @@
 end
 
 % update command line status
-loop_start_time = clock;
-disp(['  precomputation completed in ' scaleTime(etime(loop_start_time, start_time))]);
+loop_start_time = datetime('now');
+disp(['  precomputation completed in ' scaleTime(seconds(loop_start_time-start_time))]);
 disp('  starting z-step loop...');
 
 % loop over z-positions
@@ -494,7 +494,7 @@
 
         % update command line status
         if z_index == loops_for_time_est
-            disp(['  estimated simulation time ' scaleTime(etime(clock, loop_start_time) * Nz / z_index) '...']);
+            disp(['  estimated simulation time ' scaleTime(seconds(datetime('now') - loop_start_time) * Nz / z_index) '...']);
         end
 
         % plot updates
@@ -522,7 +522,7 @@
 end
 
 % update command line status
-disp(['  simulation completed in ' scaleTime(etime(clock, loop_start_time))]);
+disp(['  simulation completed in ' scaleTime(seconds(datetime('now') - loop_start_time))]);
 
 % =========================================================================
 % POST PROCESSING
@@ -576,4 +576,4 @@
 end
 
 % update command line status
-disp(['  total computation time ' scaleTime(etime(clock, start_time))]);
+disp(['  total computation time ' scaleTime(seconds(datetime('now') - start_time))]);

k-Wave/angularSpectrumCW.m

@@ -106,7 +106,7 @@
 % along with k-Wave. If not, see <http://www.gnu.org/licenses/>.
 
 % start timer
-start_time = clock;
+start_time = datetime('now');
 
 % =========================================================================
 % INPUT CHECKING
@@ -256,7 +256,7 @@
 
 % update command line status
 disp('Running CW angular spectrum projection...');
-disp(['  start time: ' datestr(start_time)]);
+disp(['  start time: ' char(start_time)]);
 disp(['  input plane size: ' num2str(Nx) ' by ' num2str(Ny) ' grid points (' num2str(scale * Nx * dx) ' by ' num2str(scale * Ny * dx) prefix 'm)']);
 disp(['  grid expansion: ' num2str(grid_expansion) ' grid points']);
 
@@ -347,8 +347,8 @@
 % =========================================================================
 
 % update command line status
-loop_start_time = clock;
-disp(['  precomputation completed in ' scaleTime(etime(loop_start_time, start_time))]);
+loop_start_time = datetime('now');
+disp(['  precomputation completed in ' scaleTime(seconds(loop_start_time - start_time))]);
 disp('  starting time loop...');
 
 % loop over z-positions
@@ -395,13 +395,13 @@
 
     % update command line status
     if z_index == loops_for_time_est
-        disp(['  estimated simulation time ' scaleTime(etime(clock, loop_start_time) * Nz / z_index) '...']);
+        disp(['  estimated simulation time ' scaleTime(seconds(datetime('now') - loop_start_time) * Nz / z_index) '...']);
     end
 
 end
 
 % update command line status
-disp(['  simulation completed in ' scaleTime(etime(clock, loop_start_time))]);
+disp(['  simulation completed in ' scaleTime(seconds(datetime('now') - loop_start_time))]);
 
 % =========================================================================
 % POST PROCESSING
@@ -427,4 +427,4 @@
 end
 
 % update command line status
-disp(['  total computation time ' scaleTime(etime(clock, start_time))]);
+disp(['  total computation time ' scaleTime(seconds(datetime('now') - start_time))]);

k-Wave/getAffineMatrix.m

@@ -12,7 +12,7 @@
 %     translation         - translation given as [dx, dy] in 2D and 
 %                           [dx, dy, dz] in 3D
 %     rotation            - rotation angle/s in degrees given as 
-%                           [th] in 2D (counter-clockwise) and 
+%                           [th] in 2D (counter-clockwise)and 
 %                           [x_th, y_th, z_th] in 3D (rotate about x
 %                           then y' then z'') [degrees] 
 %

k-Wave/getDateString.m

@@ -3,8 +3,7 @@
 %
 % DESCRIPTION:
 %     getDateString returns a string of the current date and time using
-%     datestr but replacing the white space and : character with an en
-%     dash.
+%     datetime in the following format: 'dd-MMM-yyyy-HH-mm-ss'.
 %
 % USAGE:
 %     date_string = getDateString()
@@ -17,8 +16,7 @@
 % This function is part of the k-Wave Toolbox (http://www.k-wave.org)
 % Copyright (C) 2009-2017 Bradley Treeby
 %
-% See also clock, date, datestr
-
+% See also: datetime
 % This file is part of k-Wave. k-Wave is free software: you can
 % redistribute it and/or modify it under the terms of the GNU Lesser
 % General Public License as published by the Free Software Foundation,
@@ -33,8 +31,4 @@
 % along with k-Wave. If not, see <http://www.gnu.org/licenses/>. 
 
 % get the current time
-date_string = datestr(clock);
-
-% replace the space and : characters with -
-date_string = strrep(date_string, ' ', '-');
-date_string = strrep(date_string, ':', '-');
+date_string = char(datetime("now", "Format", "dd-MMM-yyyy-HH-mm-ss"));

k-Wave/helpfiles/example_at_array_as_sensor.html

@@ -12,11 +12,15 @@
 <h1>Defining A Sensor Using An Array Transducer Example</h1>
 
 <p>This example provides a demonstration of using the <code><a href="kWaveArray.html">kWaveArray</a></code> class to define an array transducer with 20 arc-shaped elements which is then used as a receiver array. It builds on the <a href="example_at_array_as_source.html">Defining A Source Using An Array Transducer Example</a>.</p>
-<p>
-    <ul>
-        <li><a href="matlab:edit([getkWavePath('examples') 'example_at_array_as_sensor.m']);" target="_top">Open the file in the MATLAB Editor</a></li>
-        <li><a href="matlab:run([getkWavePath('examples') 'example_at_array_as_sensor']);" target="_top">Run the file in MATLAB</a></li>
-    </ul>
+
+To open the file in MATLAB, enter the following command in the MATLAB Command Window.
+<pre class="codeinput">
+edit([getkWavePath('examples') 'example_at_array_as_sensor.m']);
+</pre>
+To run the file, enter the following command in the MATLAB Command Window.
+<pre class="codeinput">
+run([getkWavePath('examples') 'example_at_array_as_sensor']);
+</pre>
 </p>
 
 <h2>Contents</h2>

k-Wave/helpfiles/example_at_array_as_source.html

@@ -12,11 +12,15 @@
 <h1>Defining A Source Using An Array Transducer Example</h1>
 
 <p>This example provides a demonstration of using the <code><a href="kWaveArray.html">kWaveArray</a></code> class to define an array transducer with three arc-shaped elements without staircasing errors.</p>
-<p>
-    <ul>
-        <li><a href="matlab:edit([getkWavePath('examples') 'example_at_array_as_source.m']);" target="_top">Open the file in the MATLAB Editor</a></li>
-        <li><a href="matlab:run([getkWavePath('examples') 'example_at_array_as_source']);" target="_top">Run the file in MATLAB</a></li>
-    </ul>
+
+To open the file in MATLAB, enter the following command in the MATLAB Command Window.
+<pre class="codeinput">
+edit([getkWavePath('examples') 'example_at_array_as_source.m']);
+</pre>
+To run the file, enter the following command in the MATLAB Command Window.
+<pre class="codeinput">
+run([getkWavePath('examples') 'example_at_array_as_source']);
+</pre>
 </p>
 
 <p>For a more detailed discussion of this example and the underlying techniques, see  E. S. Wise, B. T. Cox, J. Jaros, & B. E. Treeby (2019). Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods. <em>The Journal of the Acoustical Society of America</em>, 146(1), 278-288. <a href="https://doi.org/10.1121/1.5116132">https://doi.org/10.1121/1.5116132</a>.</p>

k-Wave/helpfiles/example_at_linear_array_transducer.html

@@ -12,11 +12,15 @@
 <h1>Modelling A Linear Array Transducer Example</h1>
 
 <p>This example provides a demonstration of using the <code><a href="kWaveArray.html">kWaveArray</a></code> class to define a linear array transducer with 15 rectangular elements. Electronic focusing is then used to transmit an ultrasound pulse. It builds on the <a href="example_at_array_as_source.html">Defining A Source Using An Array Transducer Example</a>.</p>
-<p>
-    <ul>
-        <li><a href="matlab:edit([getkWavePath('examples') 'example_at_linear_array_transducer.m']);" target="_top">Open the file in the MATLAB Editor</a></li>
-        <li><a href="matlab:run([getkWavePath('examples') 'example_at_linear_array_transducer']);" target="_top">Run the file in MATLAB</a></li>
-    </ul>
+
+To open the file in MATLAB, enter the following command in the MATLAB Command Window.
+<pre class="codeinput">
+edit([getkWavePath('examples') 'example_at_linear_array_transducer.m']);
+</pre>
+To run the file, enter the following command in the MATLAB Command Window.
+<pre class="codeinput">
+run([getkWavePath('examples') 'example_at_linear_array_transducer']);
+</pre>
 </p>
 
 <h2>Contents</h2>