Merge pull request #12 from SINTEF/release_jan23

Release jan23

AutoActive.prj

@@ -1,5 +1,5 @@
 <deployment-project plugin="plugin.toolbox" plugin-version="1.0">
-  <configuration build-checksum="3654827594" file="C:\Repositories\AutoActive-Matlab-toolbox\AutoActive.prj" location="C:\Repositories\AutoActive-Matlab-toolbox" name="AutoActive" target="target.toolbox" target-name="Package Toolbox">
+  <configuration build-checksum="179251027" file="C:\Users\aliv\work\autoactive\AutoActive-Matlab-toolbox\AutoActive.prj" location="C:\Users\aliv\work\autoactive\AutoActive-Matlab-toolbox" name="AutoActive" target="target.toolbox" target-name="Package Toolbox">
     <param.appname>AutoActive MATLAB Toolbox</param.appname>
     <param.authnamewatermark>Anders Liverud</param.authnamewatermark>
     <param.email>[email protected]</param.email>
@@ -44,11 +44,8 @@ Key Features
 %
 % example_data/*
 % example_data/raw_data/*
-% example_data/raw_data/
-example_data/*
-example_data/raw_data/*
-example_data/raw_data/</param.exclude.filters>
-    <param.exclude.pcodedmfiles>true</param.exclude.pcodedmfiles>
+% example_data/raw_data/</param.exclude.filters>
+    <param.exclude.pcodedmfiles>false</param.exclude.pcodedmfiles>
     <param.examples>&lt;?xml version="1.0" encoding="utf-8"?&gt;
 &lt;examples&gt;
    &lt;exampleCategory name="cross_country_skiing_IMU_and_video"&gt;
@@ -57,6 +54,7 @@ example_data/raw_data/</param.exclude.filters>
          &lt;file type="main"&gt;/examples/cross_country_skiing_IMU_and_video/activityPresenter_cycles_examples.m&lt;/file&gt;
          &lt;file type="thumbnail"&gt;/examples/cross_country_skiing_IMU_and_video/html/activityPresenter_cycles_examples.png&lt;/file&gt;
          &lt;file type="image"&gt;/examples/cross_country_skiing_IMU_and_video/html/activityPresenter_cycles_examples_01.png&lt;/file&gt;
+         &lt;file type="image"&gt;/examples/cross_country_skiing_IMU_and_video/html/activityPresenter_cycles_examples_02.png&lt;/file&gt;
       &lt;/example&gt;
    &lt;/exampleCategory&gt;
 &lt;/examples&gt;</param.examples>
@@ -65,11 +63,7 @@ example_data/raw_data/</param.exclude.filters>
     <param.registered.apps />
     <param.docs>${PROJECT_ROOT}\MatlabToolbox\info.xml</param.docs>
     <param.getting.started.guide>${PROJECT_ROOT}\MatlabToolbox\doc\GettingStarted.mlx</param.getting.started.guide>
-    <param.matlabpath.excludes>
-      <item>/external/Physilog5MatlabToolKit_v1_5_0</item>
-      <item>/external/Physilog5MatlabToolKit_v1_5_0/help_p_files</item>
-      <item>/external/Physilog5MatlabToolKit_v1_4_0/help_p_files</item>
-    </param.matlabpath.excludes>
+    <param.matlabpath.excludes />
     <param.javaclasspath.excludes />
     <param.exported.on.package>true</param.exported.on.package>
     <param.required.addons />
@@ -94,10 +88,10 @@ example_data/raw_data/</param.exclude.filters>
       <param.products.id />
       <param.products.version />
       <param.platforms />
-      <param.exclude.pcodedmfiles />
       <param.demosxml />
       <param.apps />
       <param.registered.apps />
+      <param.matlabpath.excludes />
       <param.javaclasspath.excludes />
       <param.required.addons />
       <param.matlab.project.id />
@@ -127,20 +121,57 @@ example_data/raw_data/</param.exclude.filters>
       <file>${PROJECT_ROOT}\MatlabToolbox\info.xml</file>
       <file>${PROJECT_ROOT}\MatlabToolbox\jar</file>
       <file>${PROJECT_ROOT}\MatlabToolbox\lib</file>
+      <file>${PROJECT_ROOT}\MatlabToolbox\matlab-annot-new.aaz</file>
+      <file>${PROJECT_ROOT}\MatlabToolbox\matlab-annot.aaz</file>
       <file>${PROJECT_ROOT}\MatlabToolbox\testSine.aaz</file>
     </fileset.rootfiles>
     <fileset.depfun.included />
-    <fileset.depfun.excluded>
-      <file>C:\Repositories\skiviewer\devJT\microParam\llh2ecef.m</file>
-    </fileset.depfun.excluded>
+    <fileset.depfun.excluded />
     <fileset.package />
     <build-deliverables>
-      <file location="${PROJECT_ROOT}" name="AutoActive MATLAB Toolbox.mltbx" optional="false">C:\Repositories\AutoActive-Matlab-toolbox\AutoActive MATLAB Toolbox.mltbx</file>
+      <file location="${PROJECT_ROOT}" name="AutoActive MATLAB Toolbox.mltbx" optional="false">C:\Users\aliv\work\autoactive\AutoActive-Matlab-toolbox\AutoActive MATLAB Toolbox.mltbx</file>
     </build-deliverables>
     <workflow />
     <matlab>
-      <root>C:\Program Files\MATLAB\R2020a</root>
-      <toolboxes />
+      <root>C:\Program Files\MATLAB\R2022b</root>
+      <toolboxes>
+        <toolbox name="matlabcoder" />
+        <toolbox name="embeddedcoder" />
+        <toolbox name="gpucoder" />
+        <toolbox name="fixedpoint" />
+        <toolbox name="matlabhdlcoder" />
+        <toolbox name="neuralnetwork" />
+      </toolboxes>
+      <toolbox>
+        <matlabcoder>
+          <enabled>true</enabled>
+        </matlabcoder>
+      </toolbox>
+      <toolbox>
+        <embeddedcoder>
+          <enabled>true</enabled>
+        </embeddedcoder>
+      </toolbox>
+      <toolbox>
+        <gpucoder>
+          <enabled>true</enabled>
+        </gpucoder>
+      </toolbox>
+      <toolbox>
+        <fixedpoint>
+          <enabled>true</enabled>
+        </fixedpoint>
+      </toolbox>
+      <toolbox>
+        <matlabhdlcoder>
+          <enabled>true</enabled>
+        </matlabhdlcoder>
+      </toolbox>
+      <toolbox>
+        <neuralnetwork>
+          <enabled>true</enabled>
+        </neuralnetwork>
+      </toolbox>
     </matlab>
     <platform>
       <unix>false</unix>

CHANGELOG_Toolbox.txt

@@ -1,8 +1,9 @@
 # Changelog
-## [2.1.0] - 2022-08-08
+## [2.1.0] - 2023-01-20
 ### Changed
     - Added example with cross country skiing
-    - Updated documentation of toolbox to include examples	
+    - Updated documentation of toolbox to include examples
+    - Redistributed Physlog5 files in package to avoid external depencency.
 ## [2.0.0] - 2022-06-03
 ### Changed
     - Added annotation support

Java/pom.xml

@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>no.sintef.autoactive</groupId>
   <artifactId>java-file-interface</artifactId>
-  <version>2.0.0</version>
+  <version>2.0.1</version>
   <dependencies>
   	<dependency>
   		<groupId>org.apache.parquet</groupId>

Java/src/main/java/no/sintef/autoactive/matlab/Version.java

@@ -10,7 +10,7 @@
  * @author steffend
  */
 public class Version {
-    private final static String versionString = "Java-file-interface v2.0.0";
+    private final static String versionString = "Java-file-interface v2.0.1";
 
     public static String getVersionString() {
             return versionString;

MatlabToolbox/+autoactive/MatlabVersion.m

@@ -1,5 +1,5 @@
 function versionString = ToolboxVersion()
 
-	versionString = 'Autoactive matlab v2.0.0';
+	versionString = 'Autoactive matlab v2.1.0';
 end
 

MatlabToolbox/examples/annotations/annotationReadWrite.m

@@ -12,7 +12,7 @@
 
     % Add the compiled .jar file of the Activity Presenter Toolbox
     jar_file = dir('../../jar/'); javaaddpath(['../../jar/',jar_file(3).name])
-%     javaaddpath('.\MatlabToolbox\jar\java-file-interface-1.0.0-jar-with-dependencies.jar')
+%     javaaddpath('.\MatlabToolbox\jar\java-file-interface-2.0.1-jar-with-dependencies.jar')
 end
 
 %% Read aaz file created in 'create_annotations.m'

MatlabToolbox/examples/annotations/create_annotations.m

@@ -12,7 +12,7 @@
 
     % Add the compiled .jar file of the Activity Presenter Toolbox
     jar_file = dir('../../jar/'); javaaddpath(['../../jar/',jar_file(3).name])
-%     javaaddpath('.\MatlabToolbox\jar\java-file-interface-1.0.0-jar-with-dependencies.jar')
+%     javaaddpath('.\MatlabToolbox\jar\java-file-interface-2.0.1-jar-with-dependencies.jar')
 end
 
 %%

MatlabToolbox/examples/cross_country_skiing_IMU_and_video/activityPresenter_cycles_examples.m

@@ -46,12 +46,14 @@
 % *Known issues when running this script*:
 %
 % * You need to be in the same "current folder" as the activityPresenter_cycles_examples.m script when running in MATLAB
-% * You need to install the Physilog 5 Matlab Tool Kit by downloading from https://media.gaitup.com/Physilog5MatlabToolKit_v1_5_0.zip and put the extracted folder in the \AutoActive-Matlab-toolbox\MatlabToolbox\external folder
-% * You need to have Python installed and awailable to MATLAB. Follow instructions on https://se.mathworks.com/help/matlab/matlab_external/install-supported-python-implementation.html
+% * You need to install the Physilog 5 Matlab Tool Kit by downloading from:
+% https://media.gaitup.com/Physilog5MatlabToolKit_v1_5_0.zip and put the extracted folder in the \AutoActive-Matlab-toolbox\MatlabToolbox\external folder 
+% (Not needed for AutoActive Matlab toolbox 2.1 and later)
+% * You need to have Python installed and available to MATLAB. Follow instructions on https://se.mathworks.com/help/matlab/matlab_external/install-supported-python-implementation.html
 %
 % Author: Ole Marius Hoel Rindal ([email protected])
 % Date: April 2022
-% Latest update: 14.11.2022
+% Latest update: 20.01.2023
 %
 %% Set up paths, download and unzip data
 % We will first set up the necessary paths for the toolbox and the
@@ -101,13 +103,12 @@
 h_2 = gaussfilter(15);
 
 % Analyze the filter responses of the two lowpass filters.
-[h1,w1] = freqz(h,1,256,fs);hold all;
-[h2,w2] = freqz(h_2,1,256,fs,'r');hold all;
-figure(1);clf;
-plot(w1,db(abs(h1)),'LineWidth',2); hold all;
-plot(w2,db(abs(h2)),'LineWidth',2);
-ylim([-90 0]); ylabel('Magnitude [dB]');xlabel('Frequency [Hz]');
-title('Response of the lowpass filters');
+fft_length = 1024; 
+x_axis = linspace(-fs/2,fs/2,fft_length);
+figure;
+plot(x_axis,fftshift(20*log10(abs((fft(h,fft_length))))),'LineWidth',2);hold on; 
+plot(x_axis,fftshift(20*log10(abs((fft(h_2,fft_length))))),'LineWidth',2);
+xlim([0 50]);ylabel('Magnitude [dB]');xlabel('Frequency [Hz]');
 legend('Hard lowpass filter','Softer lowpass filter');
 set(gca,'FontSize',15)
 

MatlabToolbox/examples/cross_country_skiing_IMU_and_video/html/activityPresenter_cycles_examples.html

@@ -6,8 +6,8 @@
    <!--
 This HTML was auto-generated from MATLAB code.
 To make changes, update the MATLAB code and republish this document.
-      --><title>Cross country skiing example with ActivityPresenter</title><meta name="generator" content="MATLAB 9.8"><link rel="schema.DC" href="http://purl.org/dc/elements/1.1/"><meta name="DC.date" content="2022-11-14"><meta name="DC.source" content="activityPresenter_cycles_examples.m"><style type="text/css">
-html,body,div,span,applet,object,iframe,h1,h2,h3,h4,h5,h6,p,blockquote,pre,a,abbr,acronym,address,big,cite,code,del,dfn,em,font,img,ins,kbd,q,s,samp,small,strike,strong,sub,sup,tt,var,b,u,i,center,dl,dt,dd,ol,ul,li,fieldset,form,label,legend,table,caption,tbody,tfoot,thead,tr,th,td{margin:0;padding:0;border:0;outline:0;font-size:100%;vertical-align:baseline;background:transparent}body{line-height:1}ol,ul{list-style:none}blockquote,q{quotes:none}blockquote:before,blockquote:after,q:before,q:after{content:'';content:none}:focus{outine:0}ins{text-decoration:none}del{text-decoration:line-through}table{border-collapse:collapse;border-spacing:0}
+      --><title>Cross country skiing example with ActivityPresenter</title><meta name="generator" content="MATLAB 9.13"><link rel="schema.DC" href="http://purl.org/dc/elements/1.1/"><meta name="DC.date" content="2023-01-20"><meta name="DC.source" content="activityPresenter_cycles_examples.m"><style type="text/css">
+html,body,div,span,applet,object,iframe,h1,h2,h3,h4,h5,h6,p,blockquote,pre,a,abbr,acronym,address,big,cite,code,del,dfn,em,font,img,ins,kbd,q,s,samp,small,strike,strong,tt,var,b,u,i,center,dl,dt,dd,ol,ul,li,fieldset,form,label,legend,table,caption,tbody,tfoot,thead,tr,th,td{margin:0;padding:0;border:0;outline:0;font-size:100%;vertical-align:baseline;background:transparent}body{line-height:1}ol,ul{list-style:none}blockquote,q{quotes:none}blockquote:before,blockquote:after,q:before,q:after{content:'';content:none}:focus{outine:0}ins{text-decoration:none}del{text-decoration:line-through}table{border-collapse:collapse;border-spacing:0}
 
 html { min-height:100%; margin-bottom:1px; }
 html body { height:100%; margin:0px; font-family:Arial, Helvetica, sans-serif; font-size:10px; color:#000; line-height:140%; background:#fff none; overflow-y:scroll; }
@@ -146,13 +146,12 @@
 h_2 = gaussfilter(15);
 
 <span class="comment">% Analyze the filter responses of the two lowpass filters.</span>
-[h1,w1] = freqz(h,1,256,fs);hold <span class="string">all</span>;
-[h2,w2] = freqz(h_2,1,256,fs,<span class="string">'r'</span>);hold <span class="string">all</span>;
-figure(1);clf;
-plot(w1,db(abs(h1)),<span class="string">'LineWidth'</span>,2); hold <span class="string">all</span>;
-plot(w2,db(abs(h2)),<span class="string">'LineWidth'</span>,2);
-ylim([-90 0]); ylabel(<span class="string">'Magnitude [dB]'</span>);xlabel(<span class="string">'Frequency [Hz]'</span>);
-title(<span class="string">'Response of the lowpass filters'</span>);
+fft_length = 1024;
+x_axis = linspace(-fs/2,fs/2,fft_length);
+figure;
+plot(x_axis,fftshift(20*log10(abs((fft(h,fft_length))))),<span class="string">'LineWidth'</span>,2);hold <span class="string">on</span>;
+plot(x_axis,fftshift(20*log10(abs((fft(h_2,fft_length))))),<span class="string">'LineWidth'</span>,2);
+xlim([0 50]);ylabel(<span class="string">'Magnitude [dB]'</span>);xlabel(<span class="string">'Frequency [Hz]'</span>);
 legend(<span class="string">'Hard lowpass filter'</span>,<span class="string">'Softer lowpass filter'</span>);
 set(gca,<span class="string">'FontSize'</span>,15)
 
@@ -277,12 +276,12 @@
 clear <span class="string">aw</span>;
 </pre><pre class="codeoutput">ArchiveWriter &lt;XC_skiing_with_cycles.aaz&gt; - Open
 Session &lt;XC Skiing&gt; - Writing data
-autoactive.ArchiveWriter: Saving table &lt;35625232-ae0e-4e29-b4f6-07b2ecd4884a/cycle_indicator.parquet&gt;
-autoactive.ArchiveWriter: Saving table &lt;35625232-ae0e-4e29-b4f6-07b2ecd4884a/filtered_acc_chest.parquet&gt;
-Saving file to &lt;35625232-ae0e-4e29-b4f6-07b2ecd4884a/video/dataset_1_OMHR_compressed.mp4&gt;
-autoactive.ArchiveWriter: Saving data &lt;35625232-ae0e-4e29-b4f6-07b2ecd4884a/video/dataset_1_OMHR_compressed.mp4&gt; from &lt;example_data/raw_data/dataset_1_OMHR_compressed.mp4&gt;
-autoactive.ArchiveWriter: Saving textdata &lt;35625232-ae0e-4e29-b4f6-07b2ecd4884a/Annotations/Annotations.json&gt;
-autoactive.ArchiveWriter: Saving metadata &lt;35625232-ae0e-4e29-b4f6-07b2ecd4884a/AUTOACTIVE_SESSION.json&gt;
+autoactive.ArchiveWriter: Saving table &lt;7a3ab2c1-997f-43a2-b51c-b1702de6c18d/cycle_indicator.parquet&gt;
+autoactive.ArchiveWriter: Saving table &lt;7a3ab2c1-997f-43a2-b51c-b1702de6c18d/filtered_acc_chest.parquet&gt;
+Saving file to &lt;7a3ab2c1-997f-43a2-b51c-b1702de6c18d/video/dataset_1_OMHR_compressed.mp4&gt;
+autoactive.ArchiveWriter: Saving data &lt;7a3ab2c1-997f-43a2-b51c-b1702de6c18d/video/dataset_1_OMHR_compressed.mp4&gt; from &lt;example_data/raw_data/dataset_1_OMHR_compressed.mp4&gt;
+autoactive.ArchiveWriter: Saving textdata &lt;7a3ab2c1-997f-43a2-b51c-b1702de6c18d/Annotations/Annotations.json&gt;
+autoactive.ArchiveWriter: Saving metadata &lt;7a3ab2c1-997f-43a2-b51c-b1702de6c18d/AUTOACTIVE_SESSION.json&gt;
 Session &lt;XC Skiing&gt; - End
 autoactive.ArchiveWriter: ArchiveWriter &lt;XC_skiing_with_cycles.aaz&gt; - Closing
 </pre><h2 id="9">Implementation of the Gaussian lowpass filter used</h2><p>The lowpass filter used in this is example is included for simplicity. It is a simple Gaussian lowpass filter used at two different cutoff frequencies.</p><pre class="codeinput"><span class="keyword">function</span> gaussFilter = gaussfilter(sigma)
@@ -291,7 +290,7 @@
     gaussFilter = exp(-x .^ 2 / (2 * sigma ^ 2));
     gaussFilter = gaussFilter / sum (gaussFilter); <span class="comment">% normalize</span>
 <span class="keyword">end</span>
-</pre><p class="footer"><br><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2020a</a><br></p></div><!--
+</pre><p class="footer"><br><a href="https://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2022b</a><br></p></div><!--
 ##### SOURCE BEGIN #####
 %% Cross country skiing example with ActivityPresenter
 % Data from wearable microsensors such as inertial movement sensors (IMUs) 
@@ -396,13 +395,12 @@
 h_2 = gaussfilter(15);
 
 % Analyze the filter responses of the two lowpass filters.
-[h1,w1] = freqz(h,1,256,fs);hold all;
-[h2,w2] = freqz(h_2,1,256,fs,'r');hold all;
-figure(1);clf;
-plot(w1,db(abs(h1)),'LineWidth',2); hold all;
-plot(w2,db(abs(h2)),'LineWidth',2);
-ylim([-90 0]); ylabel('Magnitude [dB]');xlabel('Frequency [Hz]');
-title('Response of the lowpass filters');
+fft_length = 1024; 
+x_axis = linspace(-fs/2,fs/2,fft_length);
+figure;
+plot(x_axis,fftshift(20*log10(abs((fft(h,fft_length))))),'LineWidth',2);hold on; 
+plot(x_axis,fftshift(20*log10(abs((fft(h_2,fft_length))))),'LineWidth',2);
+xlim([0 50]);ylabel('Magnitude [dB]');xlabel('Frequency [Hz]');
 legend('Hard lowpass filter','Softer lowpass filter');
 set(gca,'FontSize',15)
 

MatlabToolbox/examples/gait_example/write_gaitup_garmin_video_data.m

@@ -3,13 +3,13 @@
 % *Known issues when running this script*:
 %
 % * You need to be in the same "current folder" as this script when running in MATLAB (Different from GettingStarted.mlx where MatlabToolbox should be current folder!!)
-% * You need to install the Physilog 5 Matlab Tool Kit by downloading from https://media.gaitup.com/Physilog5MatlabToolKit_v1_5_0.zip and put the extracted folder in the \AutoActive-Matlab-toolbox\MatlabToolbox\external folder
 
 addpath(genpath('../../../../AutoActive-Matlab-toolbox/'));
 % Please be sure that you have downloaded the Physilog 5 Matlab Tool Kit
 % from https://research.gaitup.com/support/
 % or https://media.gaitup.com/Physilog5MatlabToolKit_v1_5_0.zip and put it
-% in the external folder
+% in the external folder (Not needed for AutoActive Matlab toolbox 2.1 and
+% later)
 addpath('../../external/Physilog5MatlabToolKit_v1_5_0/');
 
 UserFolder = pwd; % the current folder path (should be the AutoActive Matlab Toolbox folder for this example)

MatlabToolbox/examples/test_sine/read_archive_sine_sync.m

@@ -8,7 +8,7 @@
 % * You need to be in the same "current folder" as the activityPresenter_cycles_examples.m script when running in MATLAB
 
 
-% javaaddpath('.\MatlabToolbox\jar\java-file-interface-1.0.0-jar-with-dependencies.jar')
+% javaaddpath('.\MatlabToolbox\jar\java-file-interface-2.0.1-jar-with-dependencies.jar')
 jar_file = dir('../../jar/'); javaaddpath(['../../jar/',jar_file(3).name])
 
 % Read table and metadata from original AutoActive Archive

MatlabToolbox/examples/test_sine/test_archive_sine.m

@@ -9,7 +9,7 @@
 
 
 
-% javaaddpath('.\MatlabToolbox\jar\java-file-interface-1.0.0-jar-with-dependencies.jar')
+% javaaddpath('.\MatlabToolbox\jar\java-file-interface-2.0.1-jar-with-dependencies.jar')
 jar_file = dir('../../jar/'); javaaddpath(['../../jar/',jar_file(3).name])
 
 %************ Fetch source code and put it into a source object ************

MatlabToolbox/examples/video_sync/SyncMultipleVideosInSession.m

@@ -1,5 +1,5 @@
 close all, clear all, clc
-javaaddpath('.\MatlabToolbox\jar\java-file-interface-1.0.0-jar-with-dependencies.jar')
+javaaddpath('.\MatlabToolbox\jar\java-file-interface-2.0.1-jar-with-dependencies.jar')
 addpath('C:\YourWorkPath')
 %Read Data from existing archive
 ar = autoactive.ArchiveReader('YourArchive.aaz');

README.md

@@ -1,5 +1,5 @@
 # AutoActive Matlab toolbox
-Updated 03 June 2022
+Updated 04 January 2023
 
 SINTEF - https://www.sintef.com
 
@@ -58,7 +58,7 @@ There is two java projects that contributes to the toolbox.
 ## How to update the MatlabToolbox
 1) Code to be included is located in the 'MatlabToolbox' folder
 2) Download Gaitup Matlab ToolKit for Physilog®5 from https://research.gaitup.com/support/ and uncompress and copy the folder 
-   Physilog5MatlabToolKit_vx_y_z with all files to MatlabToolbox\external
+   Physilog5MatlabToolKit_vx_y_z with all files to MatlabToolbox\external (included in the toolbox from version 2.1, currently not available from GaitUp)
 3) Update the Matlab toolkit source code with any changes
 4) Update the version information in 'MatlabToolbox/+autoactive/MatlabVersion.m'
 5) Start Matlab R2022a and make autoactive-matlab-toolbox active folder