Legacy ND2 removal

[dgault]

Opening this PR as a fresh version of #4049, this PR should keep the history of NativeND2Reader when using git log --follow -p ND2Reader.java

This the follow up to #4030

• LegacyND2Reader has been removed
• ND2Reader has been removed
• NativeND2Reader has been moved to ND2Reader and deprecation flags removed
• Options to use the LegacyReader in Bio-Formats Plugins have been removed
• lib/LegacyND2Reader.dll has been removed

Remaining decision on renaming nativend2.chunkmap to nd2.chunkmap

[dgault]

The remaining issue is the handling of nativend2.chunkmap. Renaming this to nd2.chunkmap absolutely makes sense to me.

The only users who I can see be impacted by the renaming will be those using the command line tools, were you will be supplying the raw String value rather than using ND2Reader.USE_CHUNKMAP_KEY. Do we want to retain functionality for the old String or is renaming suitable for a major version?

[melissalinkert]

Looks good to me, and confirmed that git log -p --follow ND2Reader.java now shows the history as expected. I think I'm fine with renaming nativend2.chunkmap to nd2.chunkmap.

[sbesson]

On the ND2 chunkmap option, my preference would be to rename the key as nd2.chunkmap with a slight preference for adding some backwards compatibility for the existing option as we did not notify of the breaking change in Bio-Formats 6.x.

Locally, the following changes on top of the current branch were sufficient to allow existing code using the nativend2.chunkmap string explicitly to keep working with a warning.

diff --git a/components/formats-gpl/src/loci/formats/in/ND2Reader.java b/components/formats-gpl/src/loci/formats/in/ND2Reader.java
index 4cd74eceec..01e7ce6ccd 100644
--- a/components/formats-gpl/src/loci/formats/in/ND2Reader.java
+++ b/components/formats-gpl/src/loci/formats/in/ND2Reader.java
@@ -80,7 +80,10 @@ public class ND2Reader extends SubResolutionFormatReader {
   public static final long ND2_MAGIC_BYTES_2 = 0x6a502020L;
   private static final int BUFFER_SIZE = 32 * 1024;
 
-  public static final String USE_CHUNKMAP_KEY = "nativend2.chunkmap";
+  /** Legacy chunkmap option key will be removed in Bio-Formats 8.0.0. */
+  @Deprecated
+  public static final String USE_CHUNKMAP_LEGACY_KEY = "nativend2.chunkmap";
+  public static final String USE_CHUNKMAP_KEY = "nd2.chunkmap";
   public static final boolean USE_CHUNKMAP_DEFAULT = true;
 
   // -- Fields --
@@ -150,8 +153,14 @@ public class ND2Reader extends SubResolutionFormatReader {
   public boolean useChunkMap() {
     MetadataOptions options = getMetadataOptions();
     if (options instanceof DynamicMetadataOptions) {
+      if (((DynamicMetadataOptions) options).get(USE_CHUNKMAP_LEGACY_KEY) != null) {
+        LOGGER.warn("Legacy chunkmap option detected use {} instead",
+          USE_CHUNKMAP_KEY);
+      }
+      Boolean defaultValue = ((DynamicMetadataOptions) options).getBoolean(
+        USE_CHUNKMAP_LEGACY_KEY, USE_CHUNKMAP_DEFAULT);
       return ((DynamicMetadataOptions) options).getBoolean(
-        USE_CHUNKMAP_KEY, USE_CHUNKMAP_DEFAULT);
+        USE_CHUNKMAP_KEY, defaultValue);
     }
     return USE_CHUNKMAP_DEFAULT;
   }

[sbesson]

Quickly retested the chunkmap options (renamed & legacy) using a public ND2 sample:

build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -version
Version: 7.0.0-SNAPSHOT
Build date: 20 July 2023
VCS revision: f68d57bfe9a1a38e0b3e74bb2fac5077589de3aa
build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -nopix BF007.nd2 -debug | grep chunk
Attempting to use chunk map = true
build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -nopix BF007.nd2 -debug -option nd2.chunkmap true | grep chunk
Attempting to use chunk map = true
build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -nopix BF007.nd2 -debug -option nd2.chunkmap false | grep chunk
Attempting to use chunk map = false
Adding non-chunkmap offset 73744, nameLength = 4072, dataLength = 51145
build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -nopix BF007.nd2 -debug -option nativend2.chunkmap false | grep chunk
Legacy chunkmap option detected use nd2.chunkmap instead
Attempting to use chunk map = false
Adding non-chunkmap offset 73744, nameLength = 4072, dataLength = 51145
build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -nopix BF007.nd2 -debug -option nativend2.chunkmap true | grep chunk
Legacy chunkmap option detected use nd2.chunkmap instead
Attempting to use chunk map = true
build@42fe18ce620d:/uod/idr/repos/curated/nd2/public/maxime$ showinf -nopix BF007.nd2 -debug -option nativend2.chunkmap true -option nd2.chunkmap false | grep chunk
Legacy chunkmap option detected use nd2.chunkmap instead
Attempting to use chunk map = false
Adding non-chunkmap offset 73744, nameLength = 4072, dataLength = 51145

I think the nightly CI repository failures are unrelated to this change. If so, this looks good to merge from my perspective

[dgault]

Yeah, repo test failure is related to a new operetta sample file I added