Skip to content

Commit 063678d

Browse files
sjcrosssjcross
authored
Merge pull request #208 from mianalysis/develop
Moving to v1.6.11
2 parents 5c15cdc + 17c144b commit 063678d

File tree

87 files changed

+115
-114
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

87 files changed

+115
-114
lines changed

‎.vscode/tasks.json

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212
{
1313
"label": "maven: package-quick",
1414
"type": "shell",
15-
"command": "mvn clean package -Dscp=provided -D enforcer.skip -D maven.test.skip -D maven.javadoc.skip",
15+
"command": "mvn clean package -Dscp=provided -D enforcer.skip -D maven.test.skip -D maven.javadoc.skip -T 1C",
1616
"group": {
1717
"kind": "build",
1818
"isDefault": false
@@ -39,7 +39,7 @@
3939
{
4040
"label": "maven: package-complete",
4141
"type": "shell",
42-
"command": "mvn clean package -Dscp=provided site -e",
42+
"command": "mvn clean package -Dscp=provided site -e -T 1C -Dparallel=all -DperCoreThreadCount=true",
4343
"group": {
4444
"kind": "build",
4545
"isDefault": true

‎mia-algorithms/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-algorithms</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-algorithms</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-algorithms/src/main/java/io/github/mianalysis/mia/process/system/Folder.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -224,8 +224,8 @@ public int compare(File o1, File o2) {
224224
if (matcher1.matches() && matcher2.matches()) {
225225
// The regex format has been found for both name types
226226
if (matcher1.group(1).equals(matcher2.group(1)))
227-
// The non-numeric parts match
228-
if (matcher1.groupCount() > 2 && matcher2.groupCount() > 2)
227+
// The non-numeric parts match
228+
if (matcher1.group(2) != null && matcher2.group(2) != null)
229229
// There are numeric parts to these filenames
230230
if (matcher1.group(2).equals(matcher2.group(2)))
231231
// Numeric parts are also equal, so compare based on extension
@@ -234,7 +234,7 @@ public int compare(File o1, File o2) {
234234
// Numeric parts are different, so compare based on these
235235
return Integer.parseInt(matcher1.group(2)) - Integer.parseInt(matcher2.group(2));
236236
else {
237-
// They don't have numeric parts to compare, so compare based on extensions
237+
// They don't both have numeric parts to compare, so compare based on extensions
238238
return o1.getName().compareTo(o2.getName());
239239
}
240240

‎mia-bonej/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-bonej</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-bonej</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-coordinates/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-coordinates</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-coordinates</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-core/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-core</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-core</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-core/src/main/java/io/github/mianalysis/mia/module/objects/filter/AbstractObjectFilter.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -44,7 +44,7 @@ public interface FilterModes {
4444

4545
}
4646

47-
static void processRemoval(Obj inputObject, @Nullable Objs outputObjects, Iterator<Obj> iterator) {
47+
protected static void processRemoval(Obj inputObject, @Nullable Objs outputObjects, Iterator<Obj> iterator) {
4848
// Getting existing relationships
4949
LinkedHashMap<String, Objs> children = inputObject.getChildren();
5050
LinkedHashMap<String, Obj> parents = inputObject.getParents(true);

‎mia-core/src/main/java/io/github/mianalysis/mia/process/exporting/Exporter.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -910,7 +910,7 @@ private void prepareObjectsXLS(SXSSFWorkbook workbook, Workspaces workspaces, Mo
910910
// Running through each Workspace, adding rows
911911
for (Workspace workspace : workspaces) {
912912
for (String objectName : workspace.getObjects().keySet()) {
913-
Objs objects = workspace.getObjects().get(objectName);
913+
Objs objects = workspace.getObjects(objectName);
914914

915915
if (!modules.objectsExportMeasurements(objectName) &! modules.objectsExportMetadata(objectName))
916916
continue;

‎mia-deepimagej/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-deepimagej</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-deepimagej</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-macros/pom.xml

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-macros</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-macros</name>
1717
<url>https://github.com/mianalysis/mia</url>
@@ -127,13 +127,13 @@
127127
<dependency>
128128
<groupId>io.github.mianalysis</groupId>
129129
<artifactId>mia-core</artifactId>
130-
<version>1.6.10</version>
130+
<version>1.6.11</version>
131131
</dependency>
132132

133133
<dependency>
134134
<groupId>io.github.mianalysis</groupId>
135135
<artifactId>mia-modules</artifactId>
136-
<version>1.6.10</version>
136+
<version>1.6.11</version>
137137
</dependency>
138138
</dependencies>
139139

‎mia-modules/pom.xml

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.6.10</version>
9+
<version>1.6.11</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-modules</artifactId>
14-
<version>1.6.10</version>
14+
<version>1.6.11</version>
1515
<packaging>jar</packaging>
1616
<name>mia-modules</name>
1717
<url>https://github.com/mianalysis/mia</url>
@@ -127,7 +127,7 @@
127127
<dependency>
128128
<groupId>io.github.mianalysis</groupId>
129129
<artifactId>mia-core</artifactId>
130-
<version>1.6.10</version>
130+
<version>1.6.11</version>
131131
</dependency>
132132

133133
<dependency>

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/images/measure/MeasureImageColocalisation.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -522,7 +522,7 @@ public Status process(Workspace workspace) {
522522
Image maskImage = (Image) workspace.getImage(maskImageName);
523523
String imageMaskLogic = parameters.getValue(IMAGE_MASK_LOGIC,workspace);
524524
String objectName = parameters.getValue(INPUT_OBJECTS,workspace);
525-
Objs objects = workspace.getObjects().get(objectName);
525+
Objs objects = workspace.getObjects(objectName);
526526
String objectMaskLogic = parameters.getValue(OBJECT_MASK_LOGIC,workspace);
527527
String thresholdingMode = parameters.getValue(THRESHOLDING_MODE,workspace);
528528
String imageMeasurementName1 = parameters.getValue(IMAGE_MEASUREMENT_1,workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/convert/ConvertObjectsToImage.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -233,7 +233,7 @@ public Status process(Workspace workspace) {
233233
String parentForColour = parameters.getValue(PARENT_OBJECT_FOR_COLOUR, workspace);
234234
String partnerForColour = parameters.getValue(PARTNER_OBJECTS_FOR_COLOUR, workspace);
235235

236-
Objs inputObjects = workspace.getObjects().get(objectName);
236+
Objs inputObjects = workspace.getObjects(objectName);
237237

238238
// Generating colours for each object
239239
HashMap<Integer, Float> hues = null;

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByChildren.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ public String getDescription() {
6666
protected Status process(Workspace workspace) {
6767
// Getting input objects
6868
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
69-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
69+
Objs inputObjects = workspace.getObjects(inputObjectsName);
7070

7171
// Getting parameters
7272
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMeasurement.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ public String getDescription() {
6767
protected Status process(Workspace workspace) {
6868
// Getting input objects
6969
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
70-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
70+
Objs inputObjects = workspace.getObjects(inputObjectsName);
7171

7272
// Getting parameters
7373
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMeasurementExtremes.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -212,7 +212,7 @@ public String getDescription() {
212212
protected Status process(Workspace workspace) {
213213
// Getting input objects
214214
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
215-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
215+
Objs inputObjects = workspace.getObjects(inputObjectsName);
216216

217217
// Getting parameters
218218
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMetadata.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -64,7 +64,7 @@ public String getDescription() {
6464
protected Status process(Workspace workspace) {
6565
// Getting input objects
6666
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
67-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
67+
Objs inputObjects = workspace.getObjects(inputObjectsName);
6868

6969
// Getting parameters
7070
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByPartners.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ public String getDescription() {
6767
protected Status process(Workspace workspace) {
6868
// Getting input objects
6969
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
70-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
70+
Objs inputObjects = workspace.getObjects(inputObjectsName);
7171

7272
// Getting parameters
7373
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByProximity.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -176,7 +176,7 @@ public String getDescription() {
176176
protected Status process(Workspace workspace) {
177177
// Getting input objects
178178
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
179-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
179+
Objs inputObjects = workspace.getObjects(inputObjectsName);
180180

181181
// Getting parameters
182182
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -519,7 +519,7 @@ public String getDescription() {
519519
public Status process(Workspace workspace) {
520520
// Getting input objects
521521
String inputObjectsName = parameters.getValue(INPUT_OBJECTS,workspace);
522-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
522+
Objs inputObjects = workspace.getObjects(inputObjectsName);
523523

524524
// Getting parameters
525525
String filterMode = parameters.getValue(FILTER_MODE,workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -200,7 +200,7 @@ public String getDescription() {
200200
protected Status process(Workspace workspace) {
201201
// Getting input objects
202202
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
203-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
203+
Objs inputObjects = workspace.getObjects(inputObjectsName);
204204

205205
// Getting parameters
206206
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterSpecificObjectIDs.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -202,7 +202,7 @@ public String getDescription() {
202202
protected Status process(Workspace workspace) {
203203
// Getting input objects
204204
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
205-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
205+
Objs inputObjects = workspace.getObjects(inputObjectsName);
206206

207207
// Getting parameters
208208
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutMeasurement.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@ public String getDescription() {
109109
protected Status process(Workspace workspace) {
110110
// Getting input objects
111111
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
112-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
112+
Objs inputObjects = workspace.getObjects(inputObjectsName);
113113

114114
// Getting parameters
115115
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutMetadata.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@ public String getDescription() {
109109
protected Status process(Workspace workspace) {
110110
// Getting input objects
111111
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
112-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
112+
Objs inputObjects = workspace.getObjects(inputObjectsName);
113113

114114
// Getting parameters
115115
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutParent.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -108,7 +108,7 @@ public String getDescription() {
108108
protected Status process(Workspace workspace) {
109109
// Getting input objects
110110
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
111-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
111+
Objs inputObjects = workspace.getObjects(inputObjectsName);
112112

113113
// Getting parameters
114114
String filterMode = parameters.getValue(FILTER_MODE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureIntensityAlongPath.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -323,7 +323,7 @@ public String getDescription() {
323323
public Status process(Workspace workspace) {
324324
// Getting objects to measure
325325
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
326-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
326+
Objs inputObjects = workspace.getObjects(inputObjectsName);
327327

328328
// Getting parameters
329329
ParameterGroup inputImages = parameters.getParameter(MEASURE_ANOTHER_IMAGE);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectColocalisation.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -222,7 +222,7 @@ public Status process(Workspace workspace) {
222222

223223
// Getting parameters
224224
String objectName = parameters.getValue(INPUT_OBJECTS, workspace);
225-
Objs objects = workspace.getObjects().get(objectName);
225+
Objs objects = workspace.getObjects(objectName);
226226
String thresholdingMode = parameters.getValue(THRESHOLDING_MODE, workspace);
227227
String imageMeasurementName1 = parameters.getValue(IMAGE_MEASUREMENT_1, workspace);
228228
String imageMeasurementName2 = parameters.getValue(IMAGE_MEASUREMENT_2, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectGiniCoefficient.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -88,7 +88,7 @@ public Status process(Workspace workspace) {
8888
// Getting input objects
8989
String inputImageName = parameters.getValue(INPUT_IMAGE, workspace);
9090
String objectName = parameters.getValue(INPUT_OBJECTS, workspace);
91-
Objs objects = workspace.getObjects().get(objectName);
91+
Objs objects = workspace.getObjects(objectName);
9292

9393
Image inputImage = workspace.getImage(inputImageName);
9494
String measurementName = getFullName(inputImageName);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectGreyscaleKFunction.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -125,7 +125,7 @@ public Status process(Workspace workspace) {
125125
// Getting input objects
126126
String inputImageName = parameters.getValue(INPUT_IMAGE, workspace);
127127
String objectName = parameters.getValue(INPUT_OBJECTS, workspace);
128-
Objs objects = workspace.getObjects().get(objectName);
128+
Objs objects = workspace.getObjects(objectName);
129129

130130
int minRadius = parameters.getValue(MINIMUM_RADIUS_PX, workspace);
131131
int maxRadius = parameters.getValue(MAXIMUM_RADIUS_PX, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectIntensity.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -274,7 +274,7 @@ public String getDescription() {
274274
public Status process(Workspace workspace) {
275275
// Getting input objects
276276
String objectName = parameters.getValue(INPUT_OBJECTS, workspace);
277-
Objs objects = workspace.getObjects().get(objectName);
277+
Objs objects = workspace.getObjects(objectName);
278278

279279
// Getting input image
280280
String imageName = parameters.getValue(INPUT_IMAGE, workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureObjectTexture.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -188,7 +188,7 @@ public Status process(Workspace workspace) {
188188

189189
// Getting input objects
190190
String inputObjectsName = parameters.getValue(INPUT_OBJECTS,workspace);
191-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
191+
Objs inputObjects = workspace.getObjects(inputObjectsName);
192192

193193
// If no objects were detected, skipping this module
194194
if (inputObjects.size() == 0)

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureSpotIntensity.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -184,7 +184,7 @@ public Status process(Workspace workspace) {
184184

185185
// Getting objects to measure
186186
String inputObjectsName = parameters.getValue(INPUT_OBJECTS,workspace);
187-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
187+
Objs inputObjects = workspace.getObjects(inputObjectsName);
188188

189189
// Getting parameters
190190
double radius = parameters.getValue(FIXED_VALUE,workspace);

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/intensity/MeasureTextureAlongPath.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -171,7 +171,7 @@ public Status process(Workspace workspace) {
171171

172172
// Getting input objects
173173
String inputObjectsName = parameters.getValue(INPUT_OBJECTS,workspace);
174-
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
174+
Objs inputObjects = workspace.getObjects(inputObjectsName);
175175

176176
// If no objects were detected, skipping this module
177177
if (inputObjects.size() == 0)

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/measure/miscellaneous/AdoptParentMeasurement.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -91,7 +91,7 @@ public Status process(Workspace workspace) {
9191
String parentObjectsName = parameters.getValue(PARENT_OBJECT, workspace);
9292
LinkedHashMap<Integer, Parameters> collections = parameters.getValue(ADD_MEASUREMENT, workspace);
9393

94-
Objs objects = workspace.getObjects().get(objectName);
94+
Objs objects = workspace.getObjects(objectName);
9595

9696
if (objects == null)
9797
return Status.PASS;

0 commit comments

Comments
 (0)