add testSfovStitchForSinglePixelGap to help debug issue in newexport …

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saalfeldlab · Jan 17, 2025 · c28048f · c28048f
1 parent 2c574ad
commit c28048f
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diff --git a/render-app/src/test/java/org/janelia/alignment/ByteRendererTest.java b/render-app/src/test/java/org/janelia/alignment/ByteRendererTest.java
@@ -0,0 +1,61 @@
+package org.janelia.alignment;
+
+import ij.ImagePlus;
+import ij.process.ImageProcessor;
+
+import java.io.File;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Tests the {@link ByteRenderer} class.
+ */
+public class ByteRendererTest {
+
+    private File outputFile;
+
+    @Before
+    public void setup() throws Exception {
+        final SimpleDateFormat TIMESTAMP = new SimpleDateFormat("yyyyMMddHHmmssSSS");
+        final String timestamp = TIMESTAMP.format(new Date());
+        outputFile = new File("test-render-" + timestamp +".jpg").getCanonicalFile();
+    }
+
+    @After
+    public void tearDown() {
+        ArgbRendererTest.deleteTestFile(outputFile);
+    }
+
+    @Test
+    public void testSfovStitchForSinglePixelGap() throws Exception {
+
+        final String[] args = {
+                "--tile_spec_url", "src/test/resources/stitch-test/sfov_stitch_test.json",
+                "--out", outputFile.getAbsolutePath(),
+                "--x", "40000",
+                "--y", "71800",
+                "--width", "200",
+                "--height", "1600",
+                "--scale", "1.0"
+        };
+
+        ByteRenderer.renderUsingCommandLineArguments(args);
+
+        Assert.assertTrue("stitched file " + outputFile.getAbsolutePath() + " not created", outputFile.exists());
+
+        final ImageProcessor renderedIp = new ImagePlus(outputFile.getAbsolutePath()).getProcessor();
+        for (int y = 0; y < renderedIp.getHeight(); y++) {
+          for (int x = 0; x < renderedIp.getWidth(); x++) {
+                final int pixel = renderedIp.get(x, y);
+                if (pixel == 0) {
+                    Assert.fail("pixel at " + x + ", " + y + " is 0");
+                }
+            }
+        }
+    }
+}
diff --git a/render-app/src/test/resources/stitch-test/sfov_032.png b/render-app/src/test/resources/stitch-test/sfov_032.png
diff --git a/render-app/src/test/resources/stitch-test/sfov_053.png b/render-app/src/test/resources/stitch-test/sfov_053.png
diff --git a/render-app/src/test/resources/stitch-test/sfov_stitch_test.json b/render-app/src/test/resources/stitch-test/sfov_stitch_test.json
@@ -0,0 +1,94 @@
+[
+    {
+        "tileId": "w60_magc0399_scan032_m0013_s032",
+        "layout": {
+            "sectionId": "27.0",
+            "imageRow": 52,
+            "imageCol": 39,
+            "stageX": -42969,
+            "stageY": 2421
+        },
+        "z": 27,
+        "minX": 39979,
+        "minY": 71722,
+        "maxX": 41986,
+        "maxY": 73475,
+        "width": 2000,
+        "height": 1748,
+        "minIntensity": 0,
+        "maxIntensity": 255,
+        "mipmapLevels": {
+            "0": {
+                "imageUrl": "src/test/resources/stitch-test/sfov_032.png"
+            }
+        },
+        "filterSpec": {
+            "className": "org.janelia.alignment.filter.LinearIntensityMap8BitFilter",
+            "parameters": {
+                "dataString": "4,4,2,1.0284811399868938,0.029346107192258688,1.023003296603754,0.03663639362344909,1.021907788146802,0.035048851639186474,1.0210199400422122,0.033760535759358404,1.0227874482594197,0.030373077221192632,1.020569279288468,0.0321604087923233,1.019676226282893,0.03169955537725808,1.019472606147438,0.03089711622703571,1.0189979930060649,0.03186246441106026,1.0184807047583027,0.03081228102412721,1.0183532599256808,0.02957112029919836,1.0186777068434212,0.0284266306612502,1.0178016865306736,0.032106451841777184,1.0175032194716653,0.03052295248290758,1.0180689838914496,0.02816628876464062,1.0191685881477346,0.025875590667384953"
+            }
+        },
+        "transforms": {
+            "type": "list",
+            "specList": [
+                {
+                    "type": "leaf",
+                    "className": "org.janelia.alignment.transform.ExponentialFunctionOffsetTransform",
+                    "dataString": "3.164065083689898,0.010223592506552219,0.0,0"
+                },
+                {
+                    "type": "leaf",
+                    "className": "mpicbg.trakem2.transform.AffineModel2D",
+                    "dataString": "1.0009509051913514 -5.040850755104299E-4 -9.192991608458097E-4 1.001892938678442 39984.329672107226 71723.0368157889"
+                }
+            ]
+        },
+        "meshCellSize": 64
+    },
+    {
+        "tileId": "w60_magc0399_scan032_m0013_s053",
+        "layout": {
+            "sectionId": "27.0",
+            "imageRow": 52,
+            "imageCol": 37,
+            "stageX": -44844,
+            "stageY": 2418
+        },
+        "z": 27,
+        "minX": 38082,
+        "minY": 71720,
+        "maxX": 40090,
+        "maxY": 73474,
+        "width": 2000,
+        "height": 1748,
+        "minIntensity": 0,
+        "maxIntensity": 255,
+        "mipmapLevels": {
+            "0": {
+                "imageUrl": "src/test/resources/stitch-test/sfov_053.png"
+            }
+        },
+        "filterSpec": {
+            "className": "org.janelia.alignment.filter.LinearIntensityMap8BitFilter",
+            "parameters": {
+                "dataString": "4,4,2,0.9868704254148127,-0.006959740351722811,0.986046315474171,-0.006405214344341661,0.9851386650740306,-0.007073839421573837,0.9824143338915927,-0.006534357478219284,0.9862019889097078,-0.005924635026674959,0.9859732550832011,-0.006308722814153114,0.9853973791971904,-0.007206494286178981,0.9840303154293883,-0.007510954163011714,0.9852805441771888,-0.0050535654033397985,0.9851081377971626,-0.005667214597788405,0.9852613117950361,-0.007925649969195534,0.9849821985494925,-0.010197616684699182,0.9827460902276816,-0.0015559823323283563,0.9827079796380237,-0.003306014025519244,0.9843605113515159,-0.00865074372417586,0.9845488420496232,-0.012406446695880695"
+            }
+        },
+        "transforms": {
+            "type": "list",
+            "specList": [
+                {
+                    "type": "leaf",
+                    "className": "org.janelia.alignment.transform.ExponentialFunctionOffsetTransform",
+                    "dataString": "3.164065083689898,0.010223592506552219,0.0,0"
+                },
+                {
+                    "type": "leaf",
+                    "className": "mpicbg.trakem2.transform.AffineModel2D",
+                    "dataString": "1.0014295214519409 -3.05675382552633E-4 -9.223349366686741E-4 1.0027697487274574 38087.33559327713 71721.56802309508"
+                }
+            ]
+        },
+        "meshCellSize": 64
+    }
+]