Consolidate HackImageUrlPathClient and BackgroundCorrectedImageUrlClient

saalfeldlab · Dec 13, 2024 · 79fae18 · 79fae18
1 parent dc2af2f
commit 79fae18
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Showing 2 changed files with 51 additions and 157 deletions.
diff --git a/...t/src/main/java/org/janelia/render/client/multisem/BackgroundCorrectedImageUrlClient.java b/...t/src/main/java/org/janelia/render/client/multisem/BackgroundCorrectedImageUrlClient.java
diff --git a/...-java-client/src/main/java/org/janelia/render/client/multisem/HackImageUrlPathClient.java b/...-java-client/src/main/java/org/janelia/render/client/multisem/HackImageUrlPathClient.java
@@ -5,6 +5,7 @@
 
 import java.io.File;
 import java.util.Map;
+import java.util.function.UnaryOperator;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -22,8 +23,11 @@
 
 /**
  * Java client to copy a stack's tiles, changing the image URL paths for all tiles in the resulting stack.
- * In this case, the image URLs are changed to point to images that have been contrast-adjusted using the Hayworth
- * pipeline.
+ * Currently implemented URL transformations:
+ * - HayworthContrastPathTransformation: changes the image URL to point to images that have been contrast-adjusted using
+ *   the Hayworth pipeline.
+ * - BasicBackgroundCorrectionPathTransformation: changes the image URL to point to images that have been
+ *   background-corrected using the BaSiC background correction method.
  *
  * @author Eric Trautman
  */
@@ -48,6 +52,8 @@ public static class Parameters extends CommandLineParameters {
         private String targetStack;
     }
 
+    private static final Logger LOG = LoggerFactory.getLogger(HackImageUrlPathClient.class);
+
     public static void main(final String[] args) {
 
         final ClientRunner clientRunner = new ClientRunner(args) {
@@ -60,20 +66,22 @@ public void runClient(final String[] args)
 
                 LOG.info("runClient: entry, parameters={}", parameters);
 
-                final HackImageUrlPathClient client = new HackImageUrlPathClient(parameters);
+                final UnaryOperator<String> pathTransformation = new BasicBackgroundCorrectionPathTransformation();
+                final HackImageUrlPathClient client = new HackImageUrlPathClient(parameters, pathTransformation);
                 client.fixStackData();
             }
         };
         clientRunner.run();
     }
 
     private final Parameters parameters;
-
     private final RenderDataClient renderDataClient;
+    private final UnaryOperator<String> pathTransformation;
 
-    private HackImageUrlPathClient(final Parameters parameters) {
+    private HackImageUrlPathClient(final Parameters parameters, final UnaryOperator<String> pathTransformation) {
         this.parameters = parameters;
         this.renderDataClient = parameters.renderWeb.getDataClient();
+        this.pathTransformation = pathTransformation;
     }
 
     private void fixStackData() throws Exception {
@@ -96,47 +104,59 @@ private void fixStackData() throws Exception {
     }
 
     private void fixTileSpec(final TileSpec tileSpec) {
-
         final Integer zeroLevelKey = 0;
 
         for (final ChannelSpec channelSpec : tileSpec.getAllChannels()) {
-
             final Map.Entry<Integer, ImageAndMask> entry = channelSpec.getFirstMipmapEntry();
+			if ((entry == null) || !zeroLevelKey.equals(entry.getKey())) {
+                continue;
+			}
 
-            if ((entry != null) && zeroLevelKey.equals(entry.getKey())) {
-
-                final ImageAndMask sourceImageAndMask = entry.getValue();
+			final ImageAndMask sourceImageAndMask = entry.getValue();
 
-                // file:/nrs/hess/data/hess_wafer_53/raw/imaging/msem/scan_001/wafer_53_scan_001_20220427_23-16-30/402_/000005/402_000005_001_2022-04-28T1457426331720.png
-                final String imageUrl = sourceImageAndMask.getImageUrl();
+            final String imageUrl = sourceImageAndMask.getImageUrl();
+            final String transformedUrl = pathTransformation.apply(imageUrl);
 
-                final Matcher m = PATH_PATTERN.matcher(imageUrl);
-                if (m.matches()) {
+            if (transformedUrl == null) {
+                throw new IllegalArgumentException("could not transform image URL: " + imageUrl);
+            }
 
-                    // file:/nrs/hess/data/hess_wafer_53/msem_with_hayworth_contrast/scan_001/402_/000005/402_000005_001_2022-04-28T1457426331720.png
-                    final File hackFile = new File("/nrs/hess/data/hess_wafer_53/msem_with_hayworth_contrast/" +
-                                                   m.group(1) +  m.group(2));
-                    if (! hackFile.exists()) {
-                        throw new IllegalArgumentException("file does not exist: " + hackFile);
-                    }
+            final File hackFile = new File(transformedUrl);
+            if (! hackFile.exists()) {
+                throw new IllegalArgumentException("target file does not exist: " + hackFile);
+            }
 
-                    final ImageAndMask hackedImageAndMask =
-                            sourceImageAndMask.copyWithDerivedUrls("file:" + hackFile.getAbsolutePath(),
-                                                                   sourceImageAndMask.getMaskUrl());
+            final ImageAndMask hackedImageAndMask = sourceImageAndMask.copyWithDerivedUrls("file:" + hackFile.getAbsolutePath(),
+                                                                                           sourceImageAndMask.getMaskUrl());
+            channelSpec.putMipmap(zeroLevelKey, hackedImageAndMask);
+        }
+    }
 
-                    channelSpec.putMipmap(zeroLevelKey, hackedImageAndMask);
 
-                } else {
-                    throw new IllegalArgumentException("invalid image URL: " + imageUrl);
-                }
+    private static class HayworthContrastPathTransformation implements UnaryOperator<String> {
+        private final Pattern PATH_PATTERN = Pattern.compile("^file:/nrs.*/(scan_\\d\\d\\d/)wafer.*/(\\d\\d\\d_/.*png)$");
 
+        // original: file:/nrs/hess/data/hess_wafer_53/raw/imaging/msem/scan_001/wafer_53_scan_001_20220427_23-16-30/402_/000005/402_000005_001_2022-04-28T1457426331720.png
+        // target:   file:/nrs/hess/data/hess_wafer_53/msem_with_hayworth_contrast/scan_001/402_/000005/402_000005_001_2022-04-28T1457426331720.png
+        @Override
+        public String apply(final String path) {
+            final Matcher matcher = PATH_PATTERN.matcher(path);
+            if (matcher.matches()) {
+                return "/nrs/hess/data/hess_wafer_53/msem_with_hayworth_contrast/" + matcher.group(1) + matcher.group(2);
+            } else {
+                return null;
             }
-
         }
-
     }
 
-    private final Pattern PATH_PATTERN = Pattern.compile("^file:/nrs.*/(scan_\\d\\d\\d/)wafer.*/(\\d\\d\\d_/.*png)$");
+    private static class BasicBackgroundCorrectionPathTransformation implements UnaryOperator<String> {
+
+        // original: file:/nrs/hess/ibeammsem/system_02/wafers/wafer_60/acquisition/scans/scan_004/slabs/slab_0399/mfovs/mfov_0000/sfov_001.png
+        // target:   file:/nrs/hess/ibeammsem/system_02/wafers/wafer_60/acquisition/background_corrected/scans/scan_004/slabs/slab_0399/mfovs/mfov_0000/sfov_001.png
+        @Override
+        public String apply(final String path) {
+            return path.substring(5, 62) + "/background_corrected" + path.substring(62);
+        }
+    }
 
-    private static final Logger LOG = LoggerFactory.getLogger(HackImageUrlPathClient.class);
 }