Temporary OIR fix (related to ome/bioformats#4205)

BIOP · Jul 2, 2024 · ec8888f · ec8888f
1 parent 35dc43b
commit ec8888f
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Showing 4 changed files with 80 additions and 13 deletions.
diff --git a/src/main/java/ch/epfl/biop/kheops/KheopsHelper.java b/src/main/java/ch/epfl/biop/kheops/KheopsHelper.java
@@ -84,7 +84,6 @@ public static SourcesInfo getSourcesFromFile(String path,int tileX,
                             .readerPoolSize(nParallelJobs)
                             .splitRGBChannels(splitRGB)
                             .positionConvention(position_convention)
-                            .cornerPositionConvention()
                             .context(context)
             );
         }

diff --git a/src/main/java/ch/epfl/biop/kheops/command/KheopsBatchCommand.java b/src/main/java/ch/epfl/biop/kheops/command/KheopsBatchCommand.java
@@ -27,7 +27,9 @@
 import ch.epfl.biop.kheops.ometiff.OMETiffExporter;
 import ij.IJ;
 import loci.common.DebugTools;
+import loci.formats.FormatException;
 import loci.formats.IFormatReader;
+import loci.formats.in.OIRReader;
 import loci.formats.meta.IMetadata;
 import org.apache.commons.io.FilenameUtils;
 import org.scijava.Context;
@@ -145,10 +147,29 @@ public void run() {
                             IJ.log("Processing " + input_path);
                             String fileName = input_path.getName();
 
-                            KheopsHelper.SourcesInfo sourcesInfo =
-                                    KheopsHelper
-                                            .getSourcesFromFile(input_path.getAbsolutePath(), tileSize, tileSize, 1,
-                                                    1, false, "CORNER", context);
+                            final KheopsHelper.SourcesInfo sourcesInfo;
+
+                            if (FilenameUtils.isExtension(input_path.getAbsolutePath(),"oir")) {
+                                // We need to read one full plane, otherwise the reader is too bad
+                                // I unfortunately need to initialize a reader to get the size
+                                System.out.println("OIR File detected! Reading full plane.");
+                                OIRReader r = new OIRReader();
+                                try {
+                                    r.setId(input_path.getAbsolutePath());
+                                    sourcesInfo =
+                                        KheopsHelper
+                                                .getSourcesFromFile(input_path.getAbsolutePath(), r.getSizeX(), r.getSizeY(), 1,
+                                                        1, false, "CORNER", context);
+                                } catch (FormatException | IOException e) {
+                                    throw new RuntimeException(e);
+                                }
+                            } else {
+                                sourcesInfo =
+                                        KheopsHelper
+                                                .getSourcesFromFile(input_path.getAbsolutePath(), tileSize, tileSize, 1,
+                                                        1, false, "CORNER", context);
+
+                            }
 
                             int nSeriesOriginal = sourcesInfo.idToSources.keySet().size();
 

diff --git a/src/main/java/ch/epfl/biop/kheops/command/KheopsCommand.java b/src/main/java/ch/epfl/biop/kheops/command/KheopsCommand.java
@@ -27,7 +27,9 @@
 import ch.epfl.biop.kheops.ometiff.OMETiffExporter;
 import ij.IJ;
 import loci.common.DebugTools;
+import loci.formats.FormatException;
 import loci.formats.IFormatReader;
+import loci.formats.in.OIRReader;
 import loci.formats.meta.IMetadata;
 import org.apache.commons.io.FilenameUtils;
 import org.scijava.Context;
@@ -110,7 +112,7 @@ public void run() {
         String fileName = input_path.getName();
 
         //--------------------
-        int tileSize = 512;
+        int tileSize = 1024;
         int nThreads = Math.max(1,Runtime.getRuntime().availableProcessors()-1);
 
         File parent_dir = new File(input_path.getParent());
@@ -125,10 +127,35 @@ public void run() {
 
         int numberOfBlocksComputedInAdvance = 64;
 
-        KheopsHelper.SourcesInfo sourcesInfo =
+        /*KheopsHelper.SourcesInfo sourcesInfo =
                 KheopsHelper
                         .getSourcesFromFile(input_path.getAbsolutePath(), tileSize, tileSize, numberOfBlocksComputedInAdvance,
-                        nThreads,false, "CORNER", context);
+                        nThreads,false, "CORNER", context);*/
+        //String fileName = input_path.getName();
+
+        final KheopsHelper.SourcesInfo sourcesInfo;
+
+        if (FilenameUtils.isExtension(input_path.getAbsolutePath(),"oir")) {
+            // We need to read one full plane, otherwise the reader is too bad
+            // I unfortunately need to initialize a reader to get the size
+            System.out.println("OIR File detected! Reading full plane.");
+            OIRReader r = new OIRReader();
+            try {
+                r.setId(input_path.getAbsolutePath());
+                sourcesInfo =
+                        KheopsHelper
+                                .getSourcesFromFile(input_path.getAbsolutePath(), r.getSizeX(), r.getSizeY(), 6,
+                                        1, false, "CORNER", context);
+            } catch (FormatException | IOException e) {
+                throw new RuntimeException(e);
+            }
+        } else {
+            sourcesInfo =
+                    KheopsHelper
+                            .getSourcesFromFile(input_path.getAbsolutePath(), tileSize, tileSize, numberOfBlocksComputedInAdvance,
+                                    1, false, "CORNER", context);
+
+        }
 
         int nSeriesOriginal = sourcesInfo.idToSources.keySet().size();
 

diff --git a/src/test/java/DemoExport.java b/src/test/java/DemoExport.java
@@ -21,19 +21,27 @@
  */
 import ch.epfl.biop.kheops.ometiff.OMETiffExporter;
 import loci.common.DebugTools;
+import net.imagej.ImageJ;
 import net.imglib2.FinalInterval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.position.FunctionRandomAccessible;
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.view.Views;
+import org.scijava.task.TaskService;
+
+import java.time.Duration;
+import java.time.Instant;
 
 public class DemoExport {
 
     public static void main( String[] args )
     {
+        ImageJ ij = new ImageJ();
+        ij.ui().showUI();
         int sizeInPixelX = 512;
         int sizeInPixelY = 512;
         int tileSize = 512;
+        int nT = 512;
         final FunctionRandomAccessible<ARGBType> checkerboard = new FunctionRandomAccessible<>(
                 2,
                 (location, value) -> {
@@ -49,20 +57,32 @@ public static void main( String[] args )
 
         try {
             //String path = "C:\\Users\\nicol\\Desktop\\ometiff\\ntest-" + sizeInPixelX + "x"+sizeInPixelY+"px-" + tileSize + "tile.ome.tiff";
-            String path = "C:\\kheops\\ntest-" + sizeInPixelX + "x"+sizeInPixelY+"px-" + tileSize + "tile.ome.tiff";
+            String path = "C:\\kheops\\test_x-" + sizeInPixelX + "_y-"+sizeInPixelY+"_tile-" + tileSize + "_nT-"+nT+".ome.tiff";
             System.out.println("Saving "+path);
-            OMETiffExporter.builder()
-                    .putXYZRAI(img)
-                    .putXYZRAI(0,1,img)
-                    .defineMetaData("Image")
+
+            Instant start = Instant.now();
+
+            OMETiffExporter.OMETiffExporterBuilder.Data.DataBuilder dataBuilder = OMETiffExporter.builder();
+
+            for (int t = 0;t<nT;t++) {
+                dataBuilder.putXYZRAI(0,t,img);
+            }
+
+            dataBuilder.defineMetaData("Image")
                     .imageName("Bob")
                     .voxelPhysicalSizeMicrometer(10,10,2)
                     .pixelsTimeIncrementInS(0.35)
                     .defineWriteOptions()
+                    .tileSize(tileSize,tileSize)
+                    .monitor(ij.get(TaskService.class))
                     .savePath(path)
                     .create()
                     .export();
 
+            Instant end = Instant.now();
+
+            System.out.println("Export time (ms) \t"+Duration.between(start,end).toMillis());
+
         } catch (Exception e) {
             // TODO Auto-generated catch block
             e.printStackTrace();