Merge pull request #108 from ImperialCollegeLondon/fix/spectrum-psd-o…

…ne-sensor

fix: Spectrum and PSD support one sensor only

.env

@@ -1 +1 @@
-MAG_DATA_VISUALIZATION_VERSION=7.2.0
+MAG_DATA_VISUALIZATION_VERSION=7.2.1

app/core/+mag/+app/+manage/ToolbarManager.m

@@ -158,28 +158,10 @@ function debugToggleToolOff(this)
 
         function helpPushToolClicked(this)
 
-            % Show progress bar.
-            closeProgressBar = this.App.AppNotificationHandler.overlayProgressBar("Generating diagnostics..."); %#ok<NASGU>
+            web("https://github.com/ImperialCollegeLondon/MAG-Data-Visualization-Toolbox/issues/new/choose");
 
-            % Instantiate variables to save.
-            model = this.App.Model;
-
-            % Create folder to zip.
-            statusFolder = tempname();
-            zipFolder = statusFolder + ".zip";
-
-            mkdir(statusFolder);
-            deleteFolder = onCleanup(@() rmdir(statusFolder, "s"));
-
-            % Create MAT file with variables.
-            save(fullfile(statusFolder, "data.mat"), "model");
-            exportapp(this.App.UIFigure, fullfile(statusFolder, "app.png"));
-
-            zip(zipFolder, statusFolder);
-            clipboard("copy", zipFolder);
-
-            % Show dialog.
-            this.App.AppNotificationHandler.displayAlert(compose("Share ZIP file ""%s""" + newline() + "with the developer. Path copied to clipboard.", zipFolder), "Share Diagnostics", "info");
+            this.App.AppNotificationHandler.displayAlert("Create issue on GitHub to share feedback, report issues and ask questions.", ...
+                "Create GitHub Issue", "info");
         end
     end
 end

resources/release-notes.md

@@ -3,24 +3,8 @@
 
 ## App
 
-- Add option to set breakpoint for error identifier (as well as error source)
+- Replace diagnostics sharing with link to GitHub for creating an issue when help button is pressed
 
 ## Software
 
-- Add support for IMAP I-ALiRT data with one sensor only
-- Add range and 24-bit scaling for HelioSwarm science data
-- Use SPICE to convert time from MET (equivalent to SCLK, but in seconds) to UTC
-- Remove unnecessary `fullfile`s in `mag.imap.Analysis` default values
-- Remove unnecessary description of processing steps
-- Fix issue with `mag.imap.view.Field` not coping with one sensor science data missing, but its temperature being available
-
-## Build
-
-- Use `matlab.addons.toolbox.ToolboxOptions` to replace toolbox template
-
-## CI
-
-- Separate CI tests and packaging into separate GitHub workflows
-- `main` branch is no longer "special" and is not packaged up on push
-- Tags can be used to create new releases
-- Install support packages required for MATLAB tests
+- IMAP spectrogram and PSD support only one sensor

src/mission/imap/+mag/+imap/+view/PSD.m

@@ -8,6 +8,11 @@
         Duration (1, 1) duration = hours(1)
     end
 
+    properties (Hidden)
+        % TRANSFORMATION Transformation for calculating PSD.
+        Transformation (1, 1) mag.transform.PSD = mag.transform.PSD()
+    end
+
     methods
 
         function this = PSD(results, options)
@@ -29,42 +34,80 @@ function visualize(this)
             primary = this.Results.Primary;
             secondary = this.Results.Secondary;
 
-            % PSD.
-            if ismissing(this.Start) || ~isbetween(this.Start, primary.Time(1), primary.Time(end))
-                psdStart = primary.Time(1);
+            numPSDs = 0;
+            yLine = mag.graphics.chart.Line(Axis = "y", Value = 0.01, Style = "--", Label = "10 pT Hz^{-0.5}");
+
+            % Primary.
+            if ~isempty(primary) && primary.HasData
+
+                numPSDs = numPSDs + 1;
+
+                primaryPSD = this.computePSD(primary);
+                primaryCharts = this.getPSDCharts(primaryPSD, primarySensor, yLine);
             else
-                psdStart = this.Start;
+                primaryCharts = {};
             end
 
-            if (this.Duration > (primary.Time(end) - psdStart))
-                psdDuration = primary.Time(end) - psdStart;
+            % Secondary.
+            if ~isempty(secondary) && secondary.HasData
+
+                numPSDs = numPSDs + 1;
+
+                secondaryPSD = this.computePSD(secondary);
+                secondaryCharts = this.getPSDCharts(secondaryPSD, secondarySensor, yLine);
             else
-                psdDuration = this.Duration;
+                secondaryCharts = {};
             end
 
-            psdPrimary = mag.psd(primary, Start = psdStart, Duration = psdDuration);
-            psdSecondary = mag.psd(secondary, Start = psdStart, Duration = psdDuration);
-
-            yLine = mag.graphics.chart.Line(Axis = "y", Value = 0.01, Style = "--", Label = "10 pT Hz^{-0.5}");
+            % Plot.
+            if isempty(primaryCharts) && isempty(secondaryCharts)
+                return;
+            end
 
             this.Figures = this.Factory.assemble( ...
-                psdPrimary, mag.graphics.style.Default(Title = compose("%s PSD", primarySensor), XLabel = this.FLabel, YLabel = this.PSDLabel, XScale = "log", YScale = "log", Legend = ["x", "y", "z"], Charts = [mag.graphics.chart.Plot(XVariable = "Frequency", YVariables = ["X", "Y", "Z"]), yLine]), ...
-                psdSecondary, mag.graphics.style.Default(Title = compose("%s PSD", secondarySensor), XLabel = this.FLabel, YLabel = this.PSDLabel, XScale = "log", YScale = "log", Legend = ["x", "y", "z"], Charts = [mag.graphics.chart.Plot(XVariable = "Frequency", YVariables = ["X", "Y", "Z"]), yLine]), ...
-                Title = this.getPSDFigureTitle(primary, secondary, psdStart, psdDuration), ...
-                Name = this.getPSDFigureName(primary, secondary, psdStart), ...
-                Arrangement = [2, 1], ...
+                primaryCharts{:}, ...
+                secondaryCharts{:}, ...
+                Title = this.getPSDFigureTitle(primary, secondary), ...
+                Name = this.getPSDFigureName(primary, secondary), ...
+                Arrangement = [numPSDs, 1], ...
                 WindowState = "maximized");
         end
     end
 
     methods (Access = private)
 
-        function value = getPSDFigureTitle(this, primary, secondary, psdStart, psdDuration)
-            value = compose("Start: %s - Duration: %s - (%s, %s)", this.date2str(psdStart), psdDuration, this.getDataFrequency(primary.MetaData), this.getDataFrequency(secondary.MetaData));
+        function psd = computePSD(this, science)
+
+            transformation = this.Transformation;
+
+            if ismissing(this.Start) || ~isbetween(this.Start, science.Time(1), science.Time(end))
+                transformation.Start = science.Time(1);
+            else
+                transformation.Start = this.Start;
+            end
+
+            if (this.Duration > (science.Time(end) - transformation.Start))
+                transformation.Duration = science.Time(end) - psdStart;
+            else
+                transformation.Duration = this.Duration;
+            end
+
+            psd = transformation.apply(science);
+        end
+
+        function charts = getPSDCharts(this, psd, sensor, yLine)
+
+            charts = {psd, ...
+                mag.graphics.style.Default(Title = compose("%s PSD", sensor), XLabel = this.FLabel, YLabel = this.PSDLabel, XScale = "log", YScale = "log", Legend = ["x", "y", "z"], ...
+                Charts = [mag.graphics.chart.Plot(XVariable = "Frequency", YVariables = ["X", "Y", "Z"]), yLine])};
+        end
+
+        function value = getPSDFigureTitle(this, primary, secondary)
+            value = compose("Start: %s - Duration: %s - (%s, %s)", this.date2str(this.Transformation.Start), this.Transformation.Duration, this.getDataFrequency(primary.MetaData), this.getDataFrequency(secondary.MetaData));
         end
 
-        function value = getPSDFigureName(this, primary, secondary, psdStart)
-            value = compose("%s (%s, %s) PSD (%s)", primary.MetaData.getDisplay("Mode"), this.getDataFrequency(primary.MetaData), this.getDataFrequency(secondary.MetaData), this.date2str(psdStart));
+        function value = getPSDFigureName(this, primary, secondary)
+            value = compose("%s (%s, %s) PSD (%s)", primary.MetaData.getDisplay("Mode"), this.getDataFrequency(primary.MetaData), this.getDataFrequency(secondary.MetaData), this.date2str(this.Transformation.Start));
         end
     end
 end

src/mission/imap/+mag/+imap/+view/Spectrogram.m

@@ -15,6 +15,11 @@
         Overlap (1, 1) double = missing()
     end
 
+    properties (Hidden)
+        % TRANSFORMATION Transformation for calculating spectrogram.
+        Transformation (1, 1) mag.transform.Spectrogram = mag.transform.Spectrogram()
+    end
+
     methods
 
         function this = Spectrogram(results, options)
@@ -36,23 +41,41 @@ function visualize(this)
             primary = this.Results.Primary;
             secondary = this.Results.Secondary;
 
-            % Spectrogram.
-            primarySpectrum = mag.spectrogram(primary, FrequencyLimits = this.FrequencyLimits, FrequencyPoints = this.FrequencyPoints, ...
-                Normalize = this.Normalize, Window = this.Window, Overlap = this.Overlap);
+            numSpectra = 0;
+
+            % Primary.
+            if ~isempty(primary) && primary.HasData
+
+                numSpectra = numSpectra + 1;
 
-            secondarySpectrum = mag.spectrogram(secondary, FrequencyLimits = this.FrequencyLimits, FrequencyPoints = this.FrequencyPoints, ...
-                Normalize = this.Normalize, Window = this.Window, Overlap = this.Overlap);
+                primarySpectrum = this.computeSpectrogram(primary);
+                primaryCharts = this.getSpectrogramCharts(primary, primarySpectrum, primarySensor, "left");
+            else
+                primaryCharts = {};
+            end
+
+            % Secondary.
+            if ~isempty(secondary) && secondary.HasData
 
-            % Field and spectrogram.
-            primaryCharts = this.getFrequencyCharts(primary, primarySpectrum, primarySensor, "left");
-            secondaryCharts = this.getFrequencyCharts(secondary, secondarySpectrum, secondarySensor, "right");
+                numSpectra = numSpectra + 1;
+
+                secondarySpectrum = this.computeSpectrogram(secondary);
+                secondaryCharts = this.getSpectrogramCharts(secondary, secondarySpectrum, secondarySensor, "right");
+            else
+                secondaryCharts = {};
+            end
+
+            % Plot.
+            if isempty(primaryCharts) && isempty(secondaryCharts)
+                return;
+            end
 
             this.Figures = this.Factory.assemble( ...
                 primaryCharts{:}, ...
                 secondaryCharts{:}, ...
-                Title = this.getFrequencyFigureTitle(primary, secondary), ...
-                Name = this.getFrequencyFigureName(primary, secondary), ...
-                Arrangement = [9, 2], ...
+                Title = this.getSpectrogramFigureTitle(primary, secondary), ...
+                Name = this.getSpectrogramFigureName(primary, secondary), ...
+                Arrangement = [9, numSpectra], ...
                 LinkXAxes = true, ...
                 TileIndexing = "columnmajor", ...
                 WindowState = "maximized");
@@ -61,7 +84,20 @@ function visualize(this)
 
     methods (Access = private)
 
-        function charts = getFrequencyCharts(this, science, spectrum, name, axisLocation)
+        function spectrum = computeSpectrogram(this, science)
+
+            transformation = this.Transformation;
+
+            transformation.FrequencyLimits = this.FrequencyLimits;
+            transformation.FrequencyPoints = this.FrequencyPoints;
+            transformation.Normalize = this.Normalize; 
+            transformation.Window = this.Window;
+            transformation.Overlap = this.Overlap;
+
+            spectrum = transformation.apply(science);
+        end
+
+        function charts = getSpectrogramCharts(this, science, spectrum, name, axisLocation)
 
             charts = { ...
                 science, mag.graphics.style.Default(Title = compose("%s x", name), YLabel = "[nT]", YAxisLocation = axisLocation, Charts = mag.graphics.chart.Plot(YVariables = "X")), ...
@@ -72,12 +108,12 @@ function visualize(this)
                 spectrum, mag.graphics.style.Colormap(YLabel = this.FLabel, CLabel = this.PLabel, YLimits = "tight", Layout = [2, 1], Charts = mag.graphics.chart.Spectrogram(YVariables = "Z"))};
         end
 
-        function value = getFrequencyFigureTitle(this, primary, secondary)
+        function value = getSpectrogramFigureTitle(this, primary, secondary)
             value = compose("%s (%s, %s)", primary.MetaData.getDisplay("Mode"), this.getDataFrequency(primary.MetaData), this.getDataFrequency(secondary.MetaData));
         end
 
-        function value = getFrequencyFigureName(this, primary, secondary)
-            value = this.getFrequencyFigureTitle(primary, secondary) + compose(" Frequency (%s)", this.date2str(primary.MetaData.Timestamp));
+        function value = getSpectrogramFigureName(this, primary, secondary)
+            value = this.getSpectrogramFigureTitle(primary, secondary) + compose(" Frequency (%s)", this.date2str(primary.MetaData.Timestamp));
         end
     end
 end

tests/system/analyze/tIMAPAnalysis.m

@@ -11,6 +11,10 @@ function skipOnGitHub(testCase)
             testCase.assumeTrue(isempty(getenv("GITHUB_ACTIONS")), "Tests cannot run on GitHub CI runner.");
         end
 
+        function checkMICEToolbox(testCase)
+            testCase.assumeTrue(exist("mice", "file") == 3, "MICE Toolbox not installed. Test skipped.");
+        end
+
         function useMATLABR2024bOrAbove(testCase)
             testCase.assumeTrue(matlabRelease().Release >= "R2024b", "Only MATLAB older than R2024b is supported for this test.");
         end

tests/unit/analyze/tSpice.m

@@ -1,6 +1,14 @@
 classdef tSpice < MAGAnalysisTestCase
 % TSPICE Unit tests for "mag.process.Spice" classes.
 
+    methods (TestClassSetup)
+
+        % Check that MICE Toolbox is installed.
+        function checkMICEToolbox(testCase)
+            testCase.assumeTrue(exist("mice", "file") == 3, "MICE Toolbox not installed. Test skipped.");
+        end
+    end
+
     methods (Test)
 
         % Test that conversion from MET to UTC is correct.

tests/unit/io/tScienceCSVIn.m

@@ -9,7 +9,7 @@
     methods (TestClassSetup)
 
         % Check that MICE Toolbox is installed.
-        function checkSPDFCDFToolbox(testCase)
+        function checkMICEToolbox(testCase)
             testCase.assumeTrue(exist("mice", "file") == 3, "MICE Toolbox not installed. Test skipped.");
         end
     end

tests/unit/visualize/view/MAGViewTestCase.m

@@ -10,7 +10,7 @@
             testCase.assertNumElements(actualInputs, numel(expectedInputs), "Number of inputs should be as expected.");
 
             for i = 1:numel(expectedInputs)
-                testCase.verifyEqual(expectedInputs{i}, actualInputs{i}, compose("Input #%i should match expectation.", i));
+                testCase.verifyEqual(actualInputs{i}, expectedInputs{i}, compose("Input #%i should match expectation.", i));
             end
         end
 
@@ -48,7 +48,7 @@
             end
 
             % Create instrument meta data.
-            metaInstrument = mag.meta.Instrument(ASW = "5.01", BSW = "0.02", GSE = "10.5.4", Model = "FM", Timestamp = datetime("now", TimeZone = "UTC"));
+            metaInstrument = mag.meta.Instrument(Mission = "IMAP", ASW = "5.01", BSW = "0.02", GSE = "10.5.4", Model = "FM", Timestamp = datetime("now", TimeZone = "UTC"));
 
             % Create science data.
             setup1 = mag.meta.Setup(Can = "None", FEE = "FEE2", Harness = "Some cable", Model = "EM4");