Merge branch 'develop' of https://github.com/mianalysis/mia into develop

mianalysis · Nov 7, 2023 · d280a16 · d280a16
2 parents 3d0ed78 + a2944ad
commit d280a16
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Showing 5 changed files with 17 additions and 12 deletions.
diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/parameters/text/DoubleP.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/parameters/text/DoubleP.java
@@ -44,10 +44,14 @@ public void setValue(String value) throws NumberFormatException {
                 this.value = value;
             } catch (NumberFormatException e) {
                 MIA.log.writeWarning("Module \"" + module.getName() + "\", parameter \"" + getName()
-                        + " \". Must either:" + "\n    - Be a double-precision number"
-                        + "\n    - Be a global variable handle (e.g. V{name}) "
-                        + "\n    - Contain a calculation (e.g. C{3-6}.  "
-                        + "\nNote: Global variables and calculations can be combined (e.g. C{V{name1} + V{name2} - 4})");
+                        + " \". Must either:" 
+                        + "\n    - A double-precision value,"
+                        + "\n    - A global variable handle in the form V{[VARIABLE NAME]} (e.g. V{name}),"
+                        + "\n    - Contain a calculation in the form CD{[EQUATION]} for double-precision outputs or CI{[EQUATION]} for integer-precision outputs (e.g. CD{3/4}),"
+                        + "\n    - Contain an image measurement in the form Im{[IMAGE NAME|MEASUREMENT NAME]} (e.g. Im{RedChannel|DIMENSIONS // WIDTH}),"
+                        + "\n    - Contain an object collection measurement statistic in the form Os{[OBJECTS NAME|MEASUREMENT NAME|STATISTIC]} (e.g. Os{Nuclei|SHAPE // N_VOXELS|MEAN}),"
+                        + "\n    - Contain an object count in the form Oc{[OBJECTS NAME]} (e.g. Os{Nuclei}),"
+                        + "\nNote: Global variables, dynamic values and calculations can be combined (e.g. CD{V{name1} + Oc{name2} - 4})");
             }
         }
     }

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/parameters/text/IntegerP.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/parameters/text/IntegerP.java
@@ -44,10 +44,11 @@ public void setValue(String value) {
                 this.value = value;
             } catch (NumberFormatException e) {
                 MIA.log.writeWarning("Module \"" + module.getName() + "\", parameter \"" + getName()
-                        + " \". Must either:" + "\n    - Be an integer number"
-                        + "\n    - Be a global variable handle (e.g. V{name}) "
-                        + "\n    - Contain a calculation (e.g. C{3-6}."
-                        + "\nNote: Global variables and calculations can be combined (e.g. C{V{name1} + V{name2} - 4})");
+                + " \". Must either:" 
+                + "\n    - An integer-precision value,"
+                + "\n    - A global variable handle in the form V{[VARIABLE NAME]} (e.g. V{name}),"
+                + "\n    - Contain a calculation in the form CI{[EQUATION]} (e.g. CI{3-4}),"
+                + "\nNote: Global variables and calculations can be combined (e.g. CI{V{name1} + V{name2} - 4})");
             }
         }
     }

diff --git a/mia-gui-swing/src/main/resources/plugins.config b/mia-gui-swing/src/main/resources/plugins.config
@@ -1 +1 @@
-Plugins>ModularImageAnalysis (MIA), "MIA",io.github.mianalysis.MIA.MIA
+Plugins>ModularImageAnalysis (MIA), "MIA",io.github.mianalysis.mia.MIAGUI
diff --git a/mia-headless/src/main/resources/plugins.config b/mia-headless/src/main/resources/plugins.config
@@ -1 +1 @@
-Plugins>ModularImageAnalysis (MIA), "MIA (headless)",io.github.mianalysis.MIA.MIAHeadless
+Plugins>ModularImageAnalysis (MIA), "MIA (headless)",io.github.mianalysis.mia.MIAHeadless
diff --git a/mia-plugin/pom.xml b/mia-plugin/pom.xml
@@ -163,7 +163,7 @@
 
     <build>
         <plugins>
-            <!-- <plugin>
+            <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
                 <version>2.6</version>
@@ -177,7 +177,7 @@
                         </manifest>
                     </archive>
                 </configuration>
-            </plugin> -->
+            </plugin>
 
             <!-- To be uncommented when creating release -->
             <!-- <plugin>