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Commit 55e30eb

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author
akramhar
committed
Removed unecessary constructor & added params list to every analyzer
1 parent ec138f4 commit 55e30eb

5 files changed

Lines changed: 156 additions & 115 deletions

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‎src/main/java/edu/umassmed/omega/commons/runnable/OmegaDiffusivityAnalyzer.java‎

Lines changed: 0 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -82,16 +82,6 @@ public OmegaDiffusivityAnalyzer(
8282
null);
8383
}
8484

85-
public OmegaDiffusivityAnalyzer(
86-
final OmegaMessageDisplayerPanelInterface displayerPanel,
87-
final double physicalT,
88-
final OmegaTrajectoriesSegmentationRun segmRun,
89-
final Map<OmegaTrajectory, List<OmegaSegment>> segments,
90-
final List<OmegaParameter> params, final OmegaSNRRun snrRun) {
91-
this(displayerPanel, physicalT, segmRun, segments, params, snrRun,
92-
null, null);
93-
}
94-
9585
public OmegaDiffusivityAnalyzer(
9686
final OmegaMessageDisplayerPanelInterface displayerPanel,
9787
final double physicalT,

‎src/main/java/edu/umassmed/omega/commons/runnable/OmegaIntensityAnalyzer.java‎

Lines changed: 29 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,8 @@
77

88
import javax.swing.SwingUtilities;
99

10+
import edu.umassmed.omega.commons.constants.OmegaConstants;
11+
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaParameter;
1012
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaSNRRun;
1113
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaTrajectoriesSegmentationRun;
1214
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
@@ -45,23 +47,32 @@ public class OmegaIntensityAnalyzer implements Runnable {
4547
private final OmegaTrajectoriesSegmentationRun segmRun;
4648

4749
private final List<OmegaElement> selections;
50+
51+
private final List<OmegaParameter> params;
52+
53+
private boolean useSNR;
4854

4955
public OmegaIntensityAnalyzer(
5056
final OmegaTrajectoriesSegmentationRun segmRun,
51-
final Map<OmegaTrajectory, List<OmegaSegment>> segments) {
52-
this(null, segmRun, segments, null);
57+
final Map<OmegaTrajectory, List<OmegaSegment>> segments,
58+
final List<OmegaParameter> params) {
59+
this(null, segmRun, segments, params, null);
5360
}
5461

5562
public OmegaIntensityAnalyzer(
5663
final OmegaMessageDisplayerPanelInterface displayerPanel,
5764
final OmegaTrajectoriesSegmentationRun segmRun,
5865
final Map<OmegaTrajectory, List<OmegaSegment>> segments,
66+
final List<OmegaParameter> params,
5967
final List<OmegaElement> selections) {
6068
this.displayerPanel = displayerPanel;
6169

6270
this.segmRun = segmRun;
71+
this.params = params;
6372
this.selections = selections;
6473

74+
this.useSNR = false;
75+
6576
this.segments = new LinkedHashMap<OmegaTrajectory, List<OmegaSegment>>(
6677
segments);
6778
this.peakSignalsMap = new LinkedHashMap<OmegaSegment, Double[]>();
@@ -108,8 +119,19 @@ private void findMinMax(final Double[] array, final Double val) {
108119
}
109120
}
110121

122+
private void initializeParameters() {
123+
for (final OmegaParameter param : this.params) {
124+
if (param.getName().equals(OmegaConstants.PARAMETER_SNR_USE)) {
125+
if (param.getStringValue() == String.valueOf(true)) {
126+
this.useSNR = true;
127+
}
128+
}
129+
}
130+
}
131+
111132
@Override
112133
public void run() {
134+
this.initializeParameters();
113135
int counter = 1;
114136
final int max = this.segments.keySet().size();
115137
for (final OmegaTrajectory track : this.segments.keySet()) {
@@ -166,7 +188,7 @@ public void run() {
166188
}
167189

168190
// SNR related START
169-
if (this.snrRun != null) {
191+
if (this.useSNR && (this.snrRun != null)) {
170192
// Integer centerSignal =
171193
// snrRun.getResultingLocalCenterSignals().get(roi);
172194
final Double meanSignal = this.snrRun
@@ -253,6 +275,10 @@ public void run() {
253275
false);
254276
}
255277
}
278+
279+
public List<OmegaParameter> getParameters() {
280+
return this.params;
281+
}
256282

257283
public List<OmegaElement> getSelections() {
258284
return this.selections;

‎src/main/java/edu/umassmed/omega/commons/runnable/OmegaMobilityAnalyzer.java‎

Lines changed: 18 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
88

99
import javax.swing.SwingUtilities;
1010

11+
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaParameter;
1112
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaTrajectoriesSegmentationRun;
1213
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
1314
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaROI;
@@ -28,30 +29,42 @@ public class OmegaMobilityAnalyzer implements Runnable {
2829
private final Map<OmegaSegment, List<Double>> displacementsFromOriginMap;
2930
private final Map<OmegaSegment, Double> maxDisplacementesFromOriginMap;
3031
private final Map<OmegaSegment, List<Double>> timeTraveledMap;
32+
private final Map<OmegaSegment, Double> confinementRatio;
3133
private final Map<OmegaSegment, List<Double>> confinementRatioMap;
3234
private final Map<OmegaSegment, List<Double[]>> anglesAndDirectionalChangesMap;
3335

3436
private final OmegaTrajectoriesSegmentationRun segmRun;
3537
private final List<OmegaElement> selections;
3638

39+
private final List<OmegaParameter> params;
40+
41+
public OmegaMobilityAnalyzer(final double physicalT, final int tMax,
42+
final OmegaTrajectoriesSegmentationRun segmRun,
43+
final Map<OmegaTrajectory, List<OmegaSegment>> segments,
44+
final List<OmegaParameter> params) {
45+
this(null, physicalT, tMax, segmRun, segments, params, null);
46+
}
47+
3748
public OmegaMobilityAnalyzer(final double physicalT, final int tMax,
3849
final OmegaTrajectoriesSegmentationRun segmRun,
3950
final Map<OmegaTrajectory, List<OmegaSegment>> segments) {
40-
this(null, physicalT, tMax, segmRun, segments, null);
51+
this(null, physicalT, tMax, segmRun, segments, null, null);
4152
}
4253

4354
public OmegaMobilityAnalyzer(
4455
final OmegaMessageDisplayerPanelInterface displayerPanel,
4556
final double physicalT, final int tMax,
4657
final OmegaTrajectoriesSegmentationRun segmRun,
4758
final Map<OmegaTrajectory, List<OmegaSegment>> segments,
59+
final List<OmegaParameter> params,
4860
final List<OmegaElement> selections) {
4961

5062
this.displayerPanel = displayerPanel;
5163
this.physicalT = physicalT;
5264
this.tMax = tMax;
5365

5466
this.segmRun = segmRun;
67+
this.params = params;
5568
this.selections = selections;
5669

5770
this.segments = new LinkedHashMap<OmegaTrajectory, List<OmegaSegment>>(
@@ -61,6 +74,7 @@ public OmegaMobilityAnalyzer(
6174
this.displacementsFromOriginMap = new LinkedHashMap<OmegaSegment, List<Double>>();
6275
this.maxDisplacementesFromOriginMap = new LinkedHashMap<OmegaSegment, Double>();
6376
this.timeTraveledMap = new LinkedHashMap<OmegaSegment, List<Double>>();
77+
this.confinementRatio = new LinkedHashMap<OmegaSegment, Double>();
6478
this.confinementRatioMap = new LinkedHashMap<OmegaSegment, List<Double>>();
6579
this.anglesAndDirectionalChangesMap = new LinkedHashMap<OmegaSegment, List<Double[]>>();
6680
}
@@ -137,6 +151,9 @@ public void run() {
137151
anglesAndDirectionalChanges.add(angleAndDirectionalChange);
138152
timeTraveled.add(localTimeTraveled);
139153
}
154+
155+
// TODO compute confinment ratio global and put it in the map
156+
140157
this.distancesMap.put(segment, distances);
141158
this.distancesFromOriginMap.put(segment, distancesFromOrigin);
142159
this.displacementsFromOriginMap.put(segment,

‎src/main/java/edu/umassmed/omega/commons/runnable/OmegaVelocityAnalyzer.java‎

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
88

99
import javax.swing.SwingUtilities;
1010

11+
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaParameter;
1112
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaTrajectoriesSegmentationRun;
1213
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
1314
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaROI;
@@ -33,21 +34,25 @@ public class OmegaVelocityAnalyzer implements Runnable {
3334
private final OmegaTrajectoriesSegmentationRun segmRun;
3435
private final List<OmegaElement> selections;
3536

37+
private final List<OmegaParameter> params;
38+
3639
public OmegaVelocityAnalyzer(final double physicalT, final int tMax,
3740
final OmegaTrajectoriesSegmentationRun segmRun,
3841
final Map<OmegaTrajectory, List<OmegaSegment>> segments) {
39-
this(null, physicalT, tMax, segmRun, segments, null);
42+
this(null, physicalT, tMax, segmRun, segments, null, null);
4043
}
4144

4245
public OmegaVelocityAnalyzer(
4346
final OmegaMessageDisplayerPanelInterface displayerPanel,
4447
final double physicalT, final int tMax,
4548
final OmegaTrajectoriesSegmentationRun segmRun,
4649
final Map<OmegaTrajectory, List<OmegaSegment>> segments,
50+
final List<OmegaParameter> params,
4751
final List<OmegaElement> selections) {
4852
this.displayerPanel = displayerPanel;
4953

5054
this.segmRun = segmRun;
55+
this.params = params;
5156
this.selections = selections;
5257

5358
this.tMax = tMax;

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