Update software to v2.5.1

.github/workflows/matlab.yml

@@ -38,7 +38,7 @@ jobs:
     if: github.ref == 'refs/heads/main'
     needs: test
     env:
-      VERSION: "2.5.0"
+      VERSION: "2.5.1"
     steps:
       - name: Check out repository
         uses: actions/checkout@v3

resources/ReleaseNotes.md

@@ -1,23 +1,23 @@
 # App
 
-- Fix issue with default patterns on some computers
+- Fix issue when event, meta data and HK patterns are empty
+- Fix issue with closing invalid figures
 
 # Software
 
-- Add separate classes for each specific HK type
-- Add reference frame to science meta data
-- Make `crop` a method of `mag.TimeSeries`
-- Make magnitude and derivatives dependent properties of `mag.Science`
-- Customize `get` method of `mag.Data` to accept multiple property names
-- Allow charts to have `mag.Data` as input
-- Rename `mag.AutomatedAnalysis` to `mag.IMAPTestingAnalysis`
-- Rename `mag.Result` to `mag.PSD`
-- Remove support for `Filters` in charts
-- Remove implicit conversion methods for `table`, `timetable` and `tabular`
-- Fix issues with setting colors in charts
-- Add tests for `mag.Data`, `mag.Science` and `mag.HK`
-- Add tests for `mag.graphics.chart.Area`, `mag.graphics.chart.Scatter`, `mag.graphics.chart.Stairs` and `mag.graphics.chart.Stem` plots
-
-# GitHub Workflows
-
-- Update dependencies to latest versions
+- Add method to `mag.Instrument` to fill warm-up with `missing` data
+- Add method to `mag.Science` to replace periods with a filler variable
+- Add save/load utility class
+- Separate calculation of spectrogram in separate function
+- Replace last element of file with `missing` to improve plot where data is missing
+- Science object with no data is considered empty in `mag.Instrument`
+- Reintroduce filtering for charts
+- Rename `cropDataBasedOnScience` to `cropToMatch`
+- Make sure derivative is empty when data is empty
+- Remove unnecessary `Sealed` attributes on classes
+- Fix issue with consecutive events of the same type missing a completion message
+- Fix issue when cropping data and no timestamps are selected
+- Fix issue with `mag.graphics.chart.Stem` not showing markers
+- Add tests for `mag.Instrument`, `mag.PSD` and `mag.Science/computePSD`
+- Add tests for `mag.graphics.mixin.mustBeColor`
+- Fix typo in `MarkerSupportTestCase`

src/analyze/+mag/@IMAPTestingAnalysis/IMAPTestingAnalysis.m

@@ -1,9 +1,8 @@
-classdef (Sealed) IMAPTestingAnalysis < matlab.mixin.Copyable & mag.mixin.SetGet
+classdef (Sealed) IMAPTestingAnalysis < matlab.mixin.Copyable & mag.mixin.SetGet & mag.mixin.SaveLoad
 % IMAPTESTINGANALYSIS Automate analysis of an IMAP CPT or SFT folder.
 
-    properties (Constant, Hidden)
-        % VERSION Version number.
-        Version (1, 1) string = mag.version()
+    properties (Constant)
+        Version = mag.version()
     end
 
     properties
@@ -288,7 +287,7 @@ function load(this)
             rampMode.Secondary = this.SecondaryRamp;
 
             if rampMode.HasScience
-                rampMode.cropDataBasedOnScience();
+                rampMode.cropToMatch();
             else
                 rampMode = mag.Instrument.empty();
             end
@@ -400,16 +399,10 @@ function load(this)
                 return;
             end
 
-            result.Primary.Data = result.Primary.Data(primaryPeriod, :);
-            result.Primary.Data.Properties.Events = result.Primary.Data.Properties.Events(primaryPeriod, :);
-
-            result.Secondary.Data = result.Secondary.Data(secondaryPeriod, :);
-            result.Secondary.Data.Properties.Events = result.Secondary.Data.Properties.Events(secondaryPeriod, :);
+            result.crop(primaryPeriod, secondaryPeriod);
 
             if isempty(result.Primary.Data) || isempty(result.Secondary.Data)
                 result = mag.Instrument.empty();
-            else
-                result.cropDataBasedOnScience();
             end
         end
     end
@@ -424,7 +417,7 @@ function load(this)
             elseif isa(object, "struct")
 
                 % Recreate object based on version.
-                if isfield(object, "Outboard")
+                if isequal(object.OriginalVersion, 1.0)
 
                     % Convert object to version 2.0 and recursively
                     % dispatch it.
@@ -447,9 +440,9 @@ function load(this)
                     end
 
                     loadedObject = mag.IMAPTestingAnalysis.loadobj(loadedObject);
-                elseif isfield(object, "PrimaryRamp")
+                elseif isequal(object.OriginalVersion, 2.0)
 
-                    % Convert object directly to version 3.0.
+                    % Convert object directly to version 2.5.
                     loadedObject = mag.IMAPTestingAnalysis();
                     loadedObject.Results = mag.Instrument();
 

src/analyze/+mag/@IMAPTestingAnalysis/loadEventsData.m

@@ -151,6 +151,16 @@ function loadEventsData(this)
         ae = acknowledgeEvents([acknowledgeEvents.timestamp] >= e.CommandTimestamp);
         ce = completedEvents([completedEvents.timestamp] >= e.CommandTimestamp);
 
+        % Remove responses to subsequent commands of the same type.
+        similarSubsequentEvents = events(([events.Type] == e.Type) & ([events.SubType] == e.SubType) & ([events.CommandTimestamp] > e.CommandTimestamp));
+
+        if ~isempty(similarSubsequentEvents)
+
+            ae = ae([ae.timestamp] < similarSubsequentEvents(1).CommandTimestamp);
+            ce = ce([ce.timestamp] < similarSubsequentEvents(1).CommandTimestamp);
+        end
+
+        % Find acknoledgement time.
         if isfield(ae, "type") && isfield(ae, "subtype")
 
             ae = ae((str2double([ae.type]) == e.Type) & (str2double([ae.subtype]) == e.SubType));
@@ -164,6 +174,7 @@ function loadEventsData(this)
             end
         end
 
+        % Find completion time.
         if isfield(ce, "type") && isfield(ce, "subtype")
 
             ce = ce((str2double([ce.type]) == e.Type) & (str2double([ce.subtype]) == e.SubType));

src/analyze/+mag/@IMAPTestingAnalysis/loadScienceData.m

@@ -50,6 +50,11 @@ function loadScienceData(this, primaryMetaData, secondaryMetaData)
             secondary = ps.apply(secondary, smd);
         end
 
+        % Remove last data point, to avoid continuous lines when data is
+        % missing.
+        primary{end, ["x", "y", "z"]} = missing();
+        secondary{end, ["x", "y", "z"]} = missing();
+
         %% Convert to timetable
 
         primaryData = vertcat(primaryData, table2timetable(primary, RowTimes = "t")); %#ok<AGROW>

src/data/+mag/+event/Event.m

@@ -36,13 +36,13 @@
 
     methods (Hidden, Sealed)
 
-        function tableThis = timetable(this)
+        function timetableThis = timetable(this)
         % TIMETABLE Convert events to timetable.
 
             emptyTime = datetime.empty();
             emptyTime.TimeZone = "UTC";
 
-            tableThis = struct2table(struct(Time = emptyTime, ...
+            timetableThis = struct2table(struct(Time = emptyTime, ...
                 Mode = double.empty(0, 1), ...
                 PrimaryRate = double.empty(0, 1), ...
                 SecondaryRate = double.empty(0, 1), ...
@@ -51,21 +51,21 @@
                 Range = double.empty(0, 1), ...
                 Sensor = string.empty(0, 1), ...
                 Label = string.empty(0, 1)));
-            tableThis = table2timetable(tableThis, RowTimes = "Time");
+            timetableThis = table2timetable(timetableThis, RowTimes = "Time");
 
             for t = 1:numel(this)
 
                 tt = this(t).convertToTimeTable();
-                tableThis = outerjoin(tableThis, tt, MergeKeys = true, Keys = ["Time", intersect(tableThis.Properties.VariableNames, tt.Properties.VariableNames)]);
+                timetableThis = outerjoin(timetableThis, tt, MergeKeys = true, Keys = ["Time", intersect(timetableThis.Properties.VariableNames, tt.Properties.VariableNames)]);
             end
 
-            tableThis = sortrows(tableThis);
+            timetableThis = sortrows(timetableThis);
 
-            fillVariables = intersect(["Mode", "PrimaryRate", "SecondaryRate", "PacketFrequency", "Range"], tableThis.Properties.VariableNames);
-            tableThis(:, fillVariables) = fillmissing(tableThis(:, fillVariables), "previous");
+            fillVariables = intersect(["Mode", "PrimaryRate", "SecondaryRate", "PacketFrequency", "Range"], timetableThis.Properties.VariableNames);
+            timetableThis(:, fillVariables) = fillmissing(timetableThis(:, fillVariables), "previous");
 
-            tableThis{contains(tableThis.Label, "Config"), ["PrimaryRate", "SecondaryRate", "PacketFrequency", "Duration"]} = missing();
-            tableThis{contains(tableThis.Label, "Ramp"), "Range"} = missing();
+            timetableThis{contains(timetableThis.Label, "Config"), ["PrimaryRate", "SecondaryRate", "PacketFrequency", "Duration"]} = missing();
+            timetableThis{contains(timetableThis.Label, "Ramp"), "Range"} = missing();
         end
     end
 

src/data/+mag/+hk/Power.m

@@ -1,4 +1,4 @@
-classdef (Sealed) Power < mag.HK
+classdef Power < mag.HK
 % POWER Class containing MAG power HK packet data.
 
     properties (Dependent)

src/data/+mag/+hk/Processor.m

@@ -1,4 +1,4 @@
-classdef (Sealed) Processor < mag.HK
+classdef Processor < mag.HK
 % PROCESSOR Class containing MAG processor HK packet data.
 
     properties (Dependent)

src/data/+mag/+hk/SID15.m

@@ -1,4 +1,4 @@
-classdef (Sealed) SID15 < mag.HK
+classdef SID15 < mag.HK
 % SID15 Class containing MAG SID15 HK packet data.
 
     properties (Dependent)

src/data/+mag/+hk/Status.m

@@ -1,4 +1,4 @@
-classdef (Sealed) Status < mag.HK
+classdef Status < mag.HK
 % STATUS Class containing MAG status HK packet data.
 
     properties (Dependent)

src/data/+mag/HK.m

@@ -51,7 +51,12 @@ function crop(this, timeFilter)
             for i = 1:numel(this)
 
                 this(i).Data = this(i).Data(timeFilter, :);
-                this(i).MetaData.Timestamp = this(i).Time(1);
+
+                if isempty(this(i).Time)
+                    this(i).MetaData.Timestamp = NaT(TimeZone = mag.process.DateTime.TimeZone);
+                else
+                    this(i).MetaData.Timestamp = this(i).Time(1);
+                end
             end
         end
 

src/data/+mag/Instrument.m

@@ -47,7 +47,9 @@
         end
 
         function value = get.HasScience(this)
-            value = ~isempty(this.Primary) && ~isempty(this.Secondary);
+
+            value = ~isempty(this.Primary) && ~isempty(this.Secondary) && ...
+                ~isempty(this.Primary.Data) && ~isempty(this.Secondary.Data);
         end
 
         function value = get.HasHK(this)
@@ -90,6 +92,20 @@
             sensor = supportedSensors(locSelected);
         end
 
+        function fillWarmUp(this, timePeriod, filler)
+        % FILLWARMUP Replace beginning of science mode with filler
+        % variable.
+
+            arguments
+                this (1, 1) mag.Instrument
+                timePeriod (1, 1) duration = minutes(1)
+                filler (1, 1) double = missing()
+            end
+
+            this.Primary.replace(timePeriod, filler);
+            this.Secondary.replace(timePeriod, filler);
+        end
+
         function crop(this, primaryFilter, secondaryFilter)
         % CROP Crop data based on selected filters for primary and
         % secondary science.
@@ -101,7 +117,7 @@ function crop(this, primaryFilter, secondaryFilter)
             end
 
             this.cropScience(primaryFilter, secondaryFilter);
-            this.cropDataBasedOnScience();
+            this.cropToMatch();
         end
 
         function cropScience(this, primaryFilter, secondaryFilter)
@@ -118,22 +134,26 @@ function cropScience(this, primaryFilter, secondaryFilter)
             this.Secondary.crop(secondaryFilter);
         end
 
-        function cropDataBasedOnScience(this)
-        % CROPDATABASEDONSCIENCE Crop meta data, events and HK based on
-        % science timestamps.
+        function cropToMatch(this, startTime, endTime)
+        % CROPTOMATCH Crop meta data, events and HK based on science
+        % timestamps or specified timestamps.
 
-            timeRange = this.TimeRange;
+            arguments
+                this (1, 1) mag.Instrument
+                startTime (1, 1) datetime = this.TimeRange(1)
+                endTime (1, 1) datetime = this.TimeRange(2)
+            end
 
             % Filter events.
             if ~isempty(this.Events)
-                this.Events = this.Events(isbetween([this.Events.CommandTimestamp], timeRange(1), timeRange(2), "closed"));
+                this.Events = this.Events(isbetween([this.Events.CommandTimestamp], startTime, endTime, "closed"));
             end
 
             % Filter HK.
-            this.HK.crop(timerange(timeRange(1), timeRange(2), "closed"));
+            this.HK.crop(timerange(startTime, endTime, "closed"));
 
             % Adjust meta data.
-            this.MetaData.Timestamp = timeRange(1);
+            this.MetaData.Timestamp = startTime;
         end
 
         function resample(this, targetFrequency)

src/data/+mag/Science.m

@@ -1,4 +1,4 @@
-classdef (Sealed) Science < mag.TimeSeries & matlab.mixin.CustomDisplay
+classdef Science < mag.TimeSeries & matlab.mixin.CustomDisplay
 % SCIENCE Class containing MAG science data.
 
     properties (Dependent)
@@ -60,15 +60,15 @@
         end
 
         function dx = get.dX(this)
-            dx = [diff(this.X); missing()];
+            dx = this.computeDerivative(this.X);
         end
 
         function dy = get.dY(this)
-            dy = [diff(this.Y); missing()];
+            dy = this.computeDerivative(this.Y);
         end
 
         function dz = get.dZ(this)
-            dz = [diff(this.Z); missing()];
+            dz = this.computeDerivative(this.Z);
         end
 
         function range = get.Range(this)
@@ -102,7 +102,11 @@ function crop(this, timeFilter)
                 this.Data.Properties.Events = this.Data.Properties.Events(timePeriod, :);
             end
 
-            this.MetaData.Timestamp = this.Time(1);
+            if isempty(this.Time)
+                this.MetaData.Timestamp = NaT(TimeZone = mag.process.DateTime.TimeZone);
+            else
+                this.MetaData.Timestamp = this.Time(1);
+            end
         end
 
         function resample(this, targetFrequency)
@@ -194,6 +198,25 @@ function filter(this, numeratorOrFilter, denominator)
             this.Data{1:numCoefficients, ["x", "y", "z"]} = missing();
         end
 
+        function replace(this, timeFilter, filler)
+        % REPLACE Replace length of data specified by time filter with
+        % filler variable.
+
+            arguments
+                this (1, 1) mag.Science
+                timeFilter (1, 1) {mustBeA(timeFilter, ["duration", "timerange", "withtol"])}
+                filler (1, 1) double = missing()
+            end
+
+            if isa(timeFilter, "duration")
+                timePeriod = timerange(this.Time(1), this.Time(1) + timeFilter, "closed");
+            elseif isa(timeFilter, "timerange") || isa(timeFilter, "withtol")
+                timePeriod = timeFilter;
+            end
+
+            this.Data{timePeriod, ["x", "y", "z"]} = filler;
+        end
+
         function data = computePSD(this, options)
         % COMPUTEPSD Compute the power spectral density of the magnetic
         % field measurements.
@@ -213,11 +236,11 @@ function filter(this, numeratorOrFilter, denominator)
             % Filter out data.
             if isempty(options.Start)
 
-                t = this.Data.t;
+                t = this.Time;
                 locFilter = true(size(this.Data, 1), 1);
             else
 
-                t = (this.Data.t - options.Start);
+                t = (this.Time - options.Start);
 
                 locFilter = t > 0;
 
@@ -229,7 +252,7 @@ function filter(this, numeratorOrFilter, denominator)
             % Compute PSD.
             dt = seconds(median(diff(t(locFilter))));
 
-            [psd, f] = psdtsh(this.Data{locFilter, ["x", "y", "z"]}, dt, options.FFTType, options.NW);
+            [psd, f] = psdtsh(this.XYZ(locFilter, :), dt, options.FFTType, options.NW);
             psd = psd .^ 0.5;
 
             data = mag.PSD(table(f, psd(:, 1), psd(:, 2), psd(:, 3), VariableNames = ["f", "x", "y", "z"]));