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Commit 6b12e7b

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kotik-coderkotik-coder
committed
AbsorptionModel.java: Moved optimisationVector(…) and assign(…) from Problem class
ADIScheme: Increased default time step to ensure adequate results Calculation.java: - Fixed problem with missing parent when creating a Calculation from a SearchTask. In the copy constructor, the parent is now removed, but the result is preserved. - Fixed incorrect status update in setStatus(…) method. Rules have been created to block status update in certain cases. - Introduced the isBetterThan(…) method, which performs a statistical check (e.g. BIC) plus an F-test, if the latter is possible, and uses this combination to assess which calculations gives a better result. CorrelationBuffer.java: truncate(…) excludes buffer elements which show very close parameter values and therefore negatively affect the correlation tests. CorrelationTest: Changed selector for correlation tests Details: Status may now indicate if the the new results are worse than the previous result. DiathermicMedium: Removed custom default number of data points DifferenceScheme: Added a check to see if the DiscretePulse had already been created. If so, the latter is only updated. This prevents adding superfluous listeners and creating objects DiscretePulse: Added Objects.requireNonNull when accessing the SearchTask ancestor of the Problem instance FTest.java: Added the Fischer test capability to compare two Calculation instances where one model is nested within the other. InstanceDescriptor: Instead of returning false in case if the descriptor is not recognised, the attemptUpdate(…) now throws an IllegalArgumentException. NetzschCSVReader: - Added detector spot size in the list of imported properties. -findLineByLabel now uses reader.mark(…) to keep track of previous valid position. If the search fails, the position of the reader will be reset to this mark. ParticipatingMedium & PenetrationProblem: Removed custom number of data points PenetrationProblem: Moved functionality specific to absoprtion model into the AbsorptionModel class PulseMainMenu: Changed initialisation of the correlation tests and communication of the selector with GUI. ResultTable & ResultTableModel: Added null checks for the result extracted from the Calculation instance ResultTableModel: Heavily modified the addRow(result) method where an entry will not be added to the results table if (a) a previous calculation had been previously completed and (b) the new result is rated worse than the previous result. SearchTask: Added storeCalculation(…) and findBestCalculation(…). TaskManager: Added call to storeCalculation(…) in the execute method, upon successful completion of the CompletableFuture.
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30 files changed

+558
-202
lines changed

‎pom.xml

Copy file name to clipboardExpand all lines: pom.xml
+1-1Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33

44
<groupId>kotik-coder</groupId>
55
<artifactId>PULsE</artifactId>
6-
<version>1.93F</version>
6+
<version>1.94</version>
77
<name>PULsE</name>
88
<description>Processing Unit for Laser flash Experiments</description>
99
<developers>

‎src/main/java/pulse/input/Metadata.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/input/Metadata.java
+2Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222
import pulse.problem.laser.RectangularPulse;
2323
import pulse.properties.NumericProperty;
2424
import pulse.properties.NumericPropertyKeyword;
25+
import static pulse.properties.NumericPropertyKeyword.FOV_OUTER;
2526
import pulse.properties.Property;
2627
import pulse.properties.SampleName;
2728
import pulse.tasks.Identifier;
@@ -199,6 +200,7 @@ public Set<NumericPropertyKeyword> listedKeywords() {
199200
set.add(LASER_ENERGY);
200201
set.add(DETECTOR_GAIN);
201202
set.add(DETECTOR_IRIS);
203+
set.add(FOV_OUTER);
202204
return set;
203205
}
204206

‎src/main/java/pulse/io/readers/NetzschCSVReader.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/io/readers/NetzschCSVReader.java
+25-2Lines changed: 25 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -45,6 +45,7 @@ public class NetzschCSVReader implements CurveReader {
4545
private final static String SHOT_DATA = "Shot_data";
4646
private final static String DETECTOR = "DETECTOR";
4747
private final static String THICKNESS = "Thickness_RT";
48+
private final static String DETECTOR_SPOT_SIZE = "Spotsize";
4849
private final static String DIAMETER = "Diameter";
4950

5051
/**
@@ -109,6 +110,13 @@ public List<ExperimentalData> read(File file) throws IOException {
109110
var format = DecimalFormat.getInstance(locale);
110111
format.setGroupingUsed(false);
111112

113+
var spot = findLineByLabel(reader, DETECTOR_SPOT_SIZE, THICKNESS, delims);
114+
double spotSize = 0;
115+
if(spot != null) {
116+
var spotTokens = spot.split(delims);
117+
spotSize = format.parse(spotTokens[spotTokens.length - 1]).doubleValue() * TO_METRES;
118+
}
119+
112120
var tempTokens = findLineByLabel(reader, THICKNESS, delims).split(delims);
113121

114122
final double thickness = format.parse(tempTokens[tempTokens.length - 1]).doubleValue() * TO_METRES;
@@ -135,7 +143,7 @@ public List<ExperimentalData> read(File file) throws IOException {
135143
var met = new Metadata(derive(TEST_TEMPERATURE, sampleTemperature), shotId);
136144
met.set(NumericPropertyKeyword.THICKNESS, derive(NumericPropertyKeyword.THICKNESS, thickness));
137145
met.set(NumericPropertyKeyword.DIAMETER, derive(NumericPropertyKeyword.DIAMETER, diameter));
138-
met.set(NumericPropertyKeyword.FOV_OUTER, derive(NumericPropertyKeyword.FOV_OUTER, 0.85 * diameter));
146+
met.set(NumericPropertyKeyword.FOV_OUTER, derive(NumericPropertyKeyword.FOV_OUTER, spotSize != 0 ? spotSize : 0.85 * diameter));
139147
met.set(NumericPropertyKeyword.SPOT_DIAMETER, derive(NumericPropertyKeyword.SPOT_DIAMETER, 0.94 * diameter));
140148

141149
curve.setMetadata(met);
@@ -198,29 +206,44 @@ protected static int determineShotID(BufferedReader reader, File file) throws IO
198206
return shotId;
199207

200208
}
201-
209+
202210
protected static String findLineByLabel(BufferedReader reader, String label, String delims) throws IOException {
211+
return findLineByLabel(reader, label, "!!!", delims);
212+
}
213+
214+
protected static String findLineByLabel(BufferedReader reader, String label, String stopLabel, String delims) throws IOException {
203215

204216
String line = "";
205217
String[] tokens;
206218

219+
reader.mark(1000);
220+
207221
//find keyword
208222
outer:
209223
for (line = reader.readLine(); line != null; line = reader.readLine()) {
210224

211225
tokens = line.split(delims);
212226

213227
for (String token : tokens) {
228+
214229
if (token.equalsIgnoreCase(label)) {
215230
break outer;
216231
}
232+
233+
if(token.equalsIgnoreCase(stopLabel)) {
234+
line = null;
235+
reader.reset();
236+
break outer;
237+
}
238+
217239
}
218240

219241
}
220242

221243
return line;
222244

223245
}
246+
224247
/**
225248
* As this class uses the singleton pattern, only one instance is created
226249
* using an empty no-argument constructor.

‎src/main/java/pulse/problem/laser/DiscretePulse.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/problem/laser/DiscretePulse.java
+8-1Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,7 @@
11
package pulse.problem.laser;
22

3+
import java.util.Objects;
4+
import pulse.input.ExperimentalData;
35
import pulse.problem.schemes.Grid;
46
import pulse.problem.statements.Problem;
57
import pulse.problem.statements.Pulse;
@@ -37,14 +39,19 @@ public DiscretePulse(Problem problem, Grid grid) {
3739

3840
recalculate();
3941

40-
var data = ((SearchTask) problem.specificAncestor(SearchTask.class)).getExperimentalCurve();
42+
Object ancestor =
43+
Objects.requireNonNull( problem.specificAncestor(SearchTask.class),
44+
"Problem has not been assigned to a SearchTask");
45+
46+
ExperimentalData data = ((SearchTask)ancestor).getExperimentalCurve();
4147

4248
pulse.getPulseShape().init(data, this);
4349
pulse.addListener(e -> {
4450
timeFactor = problem.getProperties().timeFactor();
4551
recalculate();
4652
pulse.getPulseShape().init(data, this);
4753
});
54+
4855
}
4956

5057
/**

‎src/main/java/pulse/problem/schemes/ADIScheme.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/problem/schemes/ADIScheme.java
+1-1Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ public abstract class ADIScheme extends DifferenceScheme {
1919
* time factor.
2020
*/
2121
public ADIScheme() {
22-
this(derive(GRID_DENSITY, 30), derive(TAU_FACTOR, 1.0));
22+
this(derive(GRID_DENSITY, 30), derive(TAU_FACTOR, 0.5));
2323
}
2424

2525
/**

‎src/main/java/pulse/problem/schemes/DifferenceScheme.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/problem/schemes/DifferenceScheme.java
+5-1Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -108,7 +108,11 @@ public void copyFrom(DifferenceScheme df) {
108108
* @see pulse.problem.schemes.Grid.adjustTo()
109109
*/
110110
protected void prepare(Problem problem) {
111-
discretePulse = problem.discretePulseOn(grid);
111+
if(discretePulse == null)
112+
discretePulse = problem.discretePulseOn(grid);
113+
else
114+
discretePulse.recalculate();
115+
112116
grid.adjustTo(discretePulse);
113117

114118
var hc = problem.getHeatingCurve();

‎src/main/java/pulse/problem/schemes/solvers/ImplicitTranslucentSolver.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/problem/schemes/solvers/ImplicitTranslucentSolver.java
+7-4Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@
1111
import pulse.problem.statements.PenetrationProblem;
1212
import pulse.problem.statements.Problem;
1313
import pulse.problem.statements.model.AbsorptionModel;
14+
import pulse.problem.statements.model.BeerLambertAbsorption;
1415
import pulse.properties.NumericProperty;
1516

1617
public class ImplicitTranslucentSolver extends ImplicitScheme implements Solver<PenetrationProblem> {
@@ -44,14 +45,16 @@ private void prepare(PenetrationProblem problem) {
4445

4546
final double Bi1H = (double) problem.getProperties().getHeatLoss().getValue() * grid.getXStep();
4647
final double hx = grid.getXStep();
48+
49+
absorption = problem.getAbsorptionModel();
50+
4751
HH = hx * hx;
4852
_2Bi1HTAU = 2.0 * Bi1H * tau;
4953
b11 = 1.0 / (1.0 + 2.0 * tau / HH * (1 + Bi1H));
5054

51-
absorption = problem.getAbsorptionModel();
5255
final double EPS = 1E-7;
53-
rearAbsorption = tau * absorption.absorption(LASER, (N - EPS) * hx);
54-
frontAbsorption = tau * absorption.absorption(LASER, 0.0);
56+
rearAbsorption = tau * absorption.absorption(LASER, (N - EPS) * hx);
57+
frontAbsorption = tau * absorption.absorption(LASER, 0.0) + 2.0*tau/hx;
5558

5659
var tridiagonal = new TridiagonalMatrixAlgorithm(grid) {
5760

@@ -61,7 +64,7 @@ public double phi(final int i) {
6164
}
6265

6366
};
64-
67+
6568
// coefficients for difference equation
6669
tridiagonal.setCoefA(1. / HH);
6770
tridiagonal.setCoefB(1. / tau + 2. / HH);

‎src/main/java/pulse/problem/statements/DiathermicMedium.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/problem/statements/DiathermicMedium.java
-2Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -34,11 +34,9 @@
3434
*/
3535
public class DiathermicMedium extends ClassicalProblem {
3636

37-
private final static int DEFAULT_CURVE_POINTS = 300;
3837

3938
public DiathermicMedium() {
4039
super();
41-
getHeatingCurve().setNumPoints(derive(NUMPOINTS, DEFAULT_CURVE_POINTS));
4240
}
4341

4442
public DiathermicMedium(Problem p) {

‎src/main/java/pulse/problem/statements/ParticipatingMedium.java

Copy file name to clipboardExpand all lines: src/main/java/pulse/problem/statements/ParticipatingMedium.java
-3Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -21,11 +21,8 @@
2121

2222
public class ParticipatingMedium extends NonlinearProblem {
2323

24-
private final static int DEFAULT_CURVE_POINTS = 300;
25-
2624
public ParticipatingMedium() {
2725
super();
28-
getHeatingCurve().setNumPoints(derive(NUMPOINTS, DEFAULT_CURVE_POINTS));
2926
setComplexity(ProblemComplexity.HIGH);
3027
}
3128

‎src/main/java/pulse/problem/statements/PenetrationProblem.java

Copy file name to clipboard
+3-55Lines changed: 3 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,8 @@
11
package pulse.problem.statements;
22

3-
import static pulse.math.transforms.StandardTransformations.LOG;
4-
import static pulse.properties.NumericProperties.derive;
5-
import static pulse.properties.NumericPropertyKeyword.NUMPOINTS;
6-
73
import java.util.List;
84

95
import pulse.math.ParameterVector;
10-
import pulse.math.Segment;
11-
import static pulse.math.transforms.StandardTransformations.ABS;
126
import pulse.problem.schemes.DifferenceScheme;
137
import pulse.problem.schemes.solvers.ImplicitTranslucentSolver;
148
import pulse.problem.schemes.solvers.SolverException;
@@ -21,8 +15,6 @@
2115

2216
public class PenetrationProblem extends ClassicalProblem {
2317

24-
private final static int DEFAULT_CURVE_POINTS = 300;
25-
2618
private InstanceDescriptor<AbsorptionModel> instanceDescriptor
2719
= new InstanceDescriptor<AbsorptionModel>(
2820
"Absorption Model Selector", AbsorptionModel.class);
@@ -31,7 +23,6 @@ public class PenetrationProblem extends ClassicalProblem {
3123

3224
public PenetrationProblem() {
3325
super();
34-
getHeatingCurve().setNumPoints(derive(NUMPOINTS, DEFAULT_CURVE_POINTS));
3526
instanceDescriptor.setSelectedDescriptor(BeerLambertAbsorption.class.getSimpleName());
3627
instanceDescriptor.addListener(() -> initAbsorption());
3728
absorption.setParent(this);
@@ -72,56 +63,13 @@ public InstanceDescriptor<AbsorptionModel> getAbsorptionSelector() {
7263
@Override
7364
public void optimisationVector(ParameterVector output, List<Flag> flags) {
7465
super.optimisationVector(output, flags);
75-
76-
for (int i = 0, size = output.dimension(); i < size; i++) {
77-
var key = output.getIndex(i);
78-
double value = 0;
79-
80-
switch (key) {
81-
case LASER_ABSORPTIVITY:
82-
value = (double) (absorption.getLaserAbsorptivity()).getValue();
83-
break;
84-
case THERMAL_ABSORPTIVITY:
85-
value = (double) (absorption.getThermalAbsorptivity()).getValue();
86-
break;
87-
case COMBINED_ABSORPTIVITY:
88-
value = (double) (absorption.getCombinedAbsorptivity()).getValue();
89-
break;
90-
default:
91-
continue;
92-
}
93-
94-
//do this for the listed key values
95-
output.setTransform(i, ABS);
96-
output.set(i, value);
97-
output.setParameterBounds(i, new Segment(1E-2, 1000.0));
98-
99-
}
100-
66+
absorption.optimisationVector(output, flags);
10167
}
10268

10369
@Override
10470
public void assign(ParameterVector params) throws SolverException {
10571
super.assign(params);
106-
107-
double value;
108-
109-
for (int i = 0, size = params.dimension(); i < size; i++) {
110-
var key = params.getIndex(i);
111-
112-
switch (key) {
113-
case LASER_ABSORPTIVITY:
114-
case THERMAL_ABSORPTIVITY:
115-
case COMBINED_ABSORPTIVITY:
116-
value = params.inverseTransform(i);
117-
break;
118-
default:
119-
continue;
120-
}
121-
122-
absorption.set(key, derive(key, value));
123-
124-
}
72+
absorption.assign(params);
12573
}
12674

12775
@Override
@@ -139,4 +87,4 @@ public Problem copy() {
13987
return new PenetrationProblem(this);
14088
}
14189

142-
}
90+
}

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