From 55a43e2e1695e451ac37433d4921f16f5f65b220 Mon Sep 17 00:00:00 2001
From: Nicolas Chiaruttini <nicolas.chiaruttini@epfl.ch>
Date: Tue, 17 Sep 2024 17:15:27 +0200
Subject: [PATCH] Important: removes scijava parameter names with upper case

---
 .../img/bioformats/command/OpenSampleCommand.java    | 12 ++++++------
 .../command/CreateBdvDatasetQuPathCommand.java       | 10 +++++-----
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/main/java/ch/epfl/biop/bdv/img/bioformats/command/OpenSampleCommand.java b/src/main/java/ch/epfl/biop/bdv/img/bioformats/command/OpenSampleCommand.java
index 3dc59c0..9a739e1 100644
--- a/src/main/java/ch/epfl/biop/bdv/img/bioformats/command/OpenSampleCommand.java
+++ b/src/main/java/ch/epfl/biop/bdv/img/bioformats/command/OpenSampleCommand.java
@@ -49,7 +49,7 @@ public class OpenSampleCommand implements Command {
 	@Parameter(label = "Choose a sample dataset", choices = { "VSI", "JPG_RGB",
 		"OLYMPUS_OIR", "LIF", "TIF_TIMELAPSE_3D", "ND2_20X", "ND2_60X",
 		"BOTH_ND2" })
-	String datasetName;
+	String datasetname;
 
 	@Parameter(type = ItemIO.OUTPUT)
 	AbstractSpimData<?> spimData;
@@ -57,7 +57,7 @@ public class OpenSampleCommand implements Command {
 	public void run() {
 		// Find the datasetname through reflection
 		Field[] fields = DatasetHelper.class.getFields();
-		if (datasetName.equals("BOTH_ND2")) {
+		if (datasetname.equals("BOTH_ND2")) {
 			File f20 = DatasetHelper.getDataset(DatasetHelper.ND2_20X);
 			File f60 = DatasetHelper.getDataset(DatasetHelper.ND2_60X);
 
@@ -99,16 +99,16 @@ public void run() {
 			return;
 		}
 		for (Field f : fields) {
-			if (f.getName().equals(datasetName.toUpperCase())) {
+			if (f.getName().equals(datasetname.toUpperCase())) {
 				try {
 					// Dataset found
-					datasetName = (String) f.get(null);
+					datasetname = (String) f.get(null);
 					//System.out.println(datasetName);
-					if (datasetName.equals(DatasetHelper.VSI)) {
+					if (datasetname.equals(DatasetHelper.VSI)) {
 						DatasetHelper.getSampleVSIDataset();
 					}
 
-					File file = DatasetHelper.getDataset(datasetName);
+					File file = DatasetHelper.getDataset(datasetname);
 
 					spimData = OpenersToSpimData.getSpimData(new OpenerSettings().location(file).voxSizeReferenceFrameLength(
 							new Length(1, UNITS.MILLIMETER)).positionReferenceFrameLength(
diff --git a/src/main/java/ch/epfl/biop/bdv/img/qupath/command/CreateBdvDatasetQuPathCommand.java b/src/main/java/ch/epfl/biop/bdv/img/qupath/command/CreateBdvDatasetQuPathCommand.java
index 3085fe2..d7190e6 100644
--- a/src/main/java/ch/epfl/biop/bdv/img/qupath/command/CreateBdvDatasetQuPathCommand.java
+++ b/src/main/java/ch/epfl/biop/bdv/img/qupath/command/CreateBdvDatasetQuPathCommand.java
@@ -54,7 +54,7 @@ public class CreateBdvDatasetQuPathCommand implements Command
 		CreateBdvDatasetQuPathCommand.class);
 
 	@Parameter
-	File quPathProject;
+	File qupath_project;
 
 	@Parameter
 	Context context;
@@ -83,7 +83,7 @@ public void run() {
 
 		try {
 			// Deserialize the QuPath project
-			JsonObject projectJson = ProjectIO.loadRawProject(new File(quPathProject.toURI()));
+			JsonObject projectJson = ProjectIO.loadRawProject(new File(qupath_project.toURI()));
 			Gson gson = new Gson();
 			MinimalQuPathProject project = gson.fromJson(projectJson, MinimalQuPathProject.class);
 			logger.debug("Opening QuPath project " + project.uri);
@@ -95,7 +95,7 @@ public void run() {
 				OpenerSettings openerSettings =
 						OpenerSettings.QuPath()
 								.splitRGBChannels(split_rgb_channels)
-								.location(quPathProject.getAbsolutePath())
+								.location(qupath_project.getAbsolutePath())
 								.setEntry(image.entryID)
 								.unit(unit)
 								.positionConvention(plane_origin_convention)
@@ -108,8 +108,8 @@ public void run() {
 
 			spimData = OpenersToSpimData.getSpimData(openerSettingsList);
 
-			if (datasetname.equals("")) {
-				datasetname = quPathProject.getParentFile().getName();
+			if (datasetname.isEmpty()) {
+				datasetname = qupath_project.getParentFile().getName();
 			}
 
 		} catch (Exception e) {