Miscellaneous fixes

Added a Long Type to fix errors in the metadata reader caused by reading integers greater than 2^31
Enclosed in  try/catch all decoding of numbers from the yaml files
Added support for sldyz and npyz files, which store the data compressed, using the zstd codecs
Added support of 2D timelapse dats stored in a single file (SFMT -> Single File Multi Timpoint)
Fixed GetVoxelSize to accont for magnification
Fixed bugs in the usage of the string substring method
Fixed allocation of byte buffer to read a plane. Allocation was twice as large as needed.
Added code to import ROI's annotations when Metadata level is not Minimum
Fixed adding Plane Exposure Time to metadata store
Fixed error: "YAMLException: The incoming YAML document exceeds the limit: 3145728 code points." for very large yaml files by using yaml LoaderOptions setCodePointLimit.

Author: nicolapapp

.gitignore

@@ -20,4 +20,5 @@ tools/*.jar
 *.iml
 .*.swp
 *.clean
-.vscode
+.vscode
+components/formats-gpl/src/loci/formats/in/SlideBook6Reader.java

components/formats-bsd/src/loci/formats/in/SlideBook7Reader.java

@@ -48,6 +48,7 @@
 import java.util.List;
 import static java.lang.Integer.max;
 
+import org.yaml.snakeyaml.LoaderOptions;
 import org.yaml.snakeyaml.nodes.MappingNode;
 import org.yaml.snakeyaml.nodes.Node;
 import org.yaml.snakeyaml.nodes.NodeTuple;
@@ -1063,7 +1064,13 @@ public Boolean LoadChannelRecord()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kChannelRecordFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kChannelRecordFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 int theLastIndex = 0;
                 StrIntPair thePair;
@@ -1147,7 +1154,13 @@ public Boolean LoadMaks()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kMaskRecordFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kMaskRecordFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 int theLastIndex = 0;
                 List<NodeTuple> theValueClassList = theNode.getValue();
@@ -1216,7 +1229,13 @@ public Boolean LoadAnnotations()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kAnnotationRecordFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kAnnotationRecordFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 int theLastIndex = 0;
                 CDataTableHeaderRecord70 theDataTableHeaderRecord70 = new CDataTableHeaderRecord70();
@@ -1291,7 +1310,13 @@ public Boolean LoadElapsedTimes()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kElapsedTimesFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kElapsedTimesFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 ScalarNode theKeyNode;
                 Node theCurrentNode;
@@ -1315,7 +1340,13 @@ public Boolean LoadSAPositions()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kSAPositionDataFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kSAPositionDataFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 ScalarNode theKeyNode;
                 Node theCurrentNode;
@@ -1350,7 +1381,13 @@ public Boolean LoadStagePosition()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kStagePositionDataFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kStagePositionDataFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 ScalarNode theKeyNode;
                 Node theCurrentNode;
@@ -1388,7 +1425,14 @@ public Boolean LoadAuxData()
         {
             try (InputStream inputStream = new FileInputStream(mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kAuxDataFilename);
                 Reader inputStreamReader = new InputStreamReader(inputStream);) {
-                Yaml yaml = new Yaml();
+                // making sure that the yaml code limit is big enough for this file
+                String thePath = mFile.GetImageGroupDirectory(mImageTitle) + CSBFile70.kAuxDataFilename;
+                File fil = new File(thePath);
+                long length = fil.length();
+                LoaderOptions loadingConfig = new LoaderOptions();
+                loadingConfig.setCodePointLimit((int)length + 10000);
+                Yaml yaml = new Yaml(loadingConfig);
+                //Yaml yaml = new Yaml();
                 MappingNode theNode = (MappingNode)yaml.compose(inputStreamReader);
                 ScalarNode theKeyNode;
                 Node theCurrentNode;
@@ -3048,7 +3092,7 @@ protected void initFile(String id) throws FormatException, IOException {
 
 									// set exposure time
 									int expTime = theCurrentImageGroup.GetExposureTime(channel);
-									store.setPlaneExposureTime(new Time(Double.valueOf(expTime), UNITS.MILLISECOND), capture, imageIndex);
+									store.setPlaneExposureTime(new Time(new Double(expTime), UNITS.MILLISECOND), capture, imageIndex);
 
 									// set tile xy position
 									double numberX = theCurrentImageGroup.GetXPosition( position);