{"action":"created","comment":{"url":"https://api.github.com/repos/ilastik/ilastik4ij/pulls/comments/170955907","pull_request_review_id":99716305,"id":170955907,"diff_hunk":"@@ -0,0 +1,174 @@\n+/*\r\n+ * To change this license header, choose License Headers in Project Properties.\r\n+ * To change this template file, choose Tools | Templates\r\n+ * and open the template in the editor.\r\n+ */\r\n+package org.ilastik.ilastik4ij;\r\n+\r\n+import org.junit.After;\r\n+import org.junit.AfterClass;\r\n+import org.junit.Before;\r\n+import org.junit.BeforeClass;\r\n+import org.junit.Test;\r\n+import static org.junit.Assert.*;\r\n+import java.io.File;\r\n+import io.scif.services.DatasetIOService;\r\n+import net.imagej.DatasetService;\r\n+import net.imagej.ImgPlus;\r\n+import net.imagej.axis.Axes;\r\n+import net.imglib2.type.numeric.integer.UnsignedByteType;\r\n+import net.imglib2.type.numeric.integer.UnsignedShortType;\r\n+import org.scijava.log.LogService;\r\n+import net.imagej.Dataset;\r\n+import net.imglib2.RandomAccess;\r\n+import net.imagej.ImageJ;\r\n+import org.scijava.Context;\r\n+import net.imglib2.type.numeric.ARGBType;\r\n+import net.imglib2.converter.Converters;\r\n+import net.imglib2.converter.RealARGBConverter;\r\n+import net.imglib2.RandomAccessibleInterval;\r\n+import net.imglib2.img.Img;\r\n+import net.imglib2.img.ImgView; \r\n+import org.ilastik.ilastik4ij.hdf5.Hdf5DataSetReader;\r\n+import org.ilastik.ilastik4ij.hdf5.Hdf5DataSetWriterFromImgPlus;\r\n+\r\n+/**\r\n+ *\r\n+ * @author Ashis Ravindran\r\n+ */\r\n+public class Hdf5DataSetReaderTest {\r\n+    \r\n+    \r\n+    public Hdf5DataSetReader hdf5Reader;\r\n+    final ImageJ ij = new ImageJ();\r\n+    public Context context = ij.getContext();\r\n+    public DatasetService ds = context.getService(DatasetService.class);\r\n+    public LogService log = context.getService(LogService.class);\r\n+    public String filename = \"src/test/resources/test.h5\";\r\n+    public Hdf5DataSetReaderTest() {\r\n+    }\r\n+    \r\n+    @BeforeClass\r\n+    public static void setUpClass()  {\r\n+    }\r\n+    \r\n+    @AfterClass\r\n+    public static void tearDownClass() {\r\n+         System.out.println(\"In tear down class\");\r\n+         new File(\"src/test/resources/chocolate.h5\").delete();\r\n+         new File(\"src/test/resources/chocolateARGB.h5\").delete();\r\n+         System.out.println(\"File(s) deleted\"); \r\n+    }\r\n+    \r\n+    @Before\r\n+    public void setUp() {\r\n+                System.out.println(\"In SetUp\");\r\n+        \r\n+    }\r\n+    \r\n+    @After\r\n+    public void tearDown() {\r\n+\r\n+        System.out.println(\"In tear down\");\r\n+    }\r\n+\r\n+    /**\r\n+     * Test of read method, of class Hdf5DataSetReader.\r\n+     */\r\n+    @Test\r\n+    public void testReadAxes() {\r\n+        System.out.println(\"Loading file in tzyxc order\");\r\n+        hdf5Reader = new Hdf5DataSetReader(filename, \"exported_data\", \"tzyxc\", log, ds); //\r\n+        ImgPlus image= hdf5Reader.read();\r\n+        assertEquals(\"Bits should be 16\",image.getValidBits(),16);\r\n+        assertEquals(\"DimX should be 4\",4,image.getImg().dimension(0));\r\n+        assertEquals(\"DimY should be 5\",5,image.getImg().dimension(1));\r\n+        assertEquals(\"DimC should be 3\",3,image.getImg().dimension(2));\r\n+        assertEquals(\"DimZ should be 6\",6,image.getImg().dimension(3));\r\n+        assertEquals(\"DimT should be 7\",7,image.getImg().dimension(4));\r\n+        \r\n+        System.out.println(\"Loading file in ztyxc order\");\r\n+        hdf5Reader = new Hdf5DataSetReader(filename, \"exported_data\", \"ztyxc\", log, ds); //\r\n+        image= hdf5Reader.read();\r\n+        assertEquals(\"Bits should be 16\",image.getValidBits(),16);\r\n+        assertEquals(\"DimX should be 4\",4,image.getImg().dimension(0));\r\n+        assertEquals(\"DimY should be 5\",5,image.getImg().dimension(1));\r\n+        assertEquals(\"DimC should be 3\",3,image.getImg().dimension(2));\r\n+        assertEquals(\"DimZ should be 7\",7,image.getImg().dimension(3));\r\n+        assertEquals(\"DimT should be 6\",6,image.getImg().dimension(4));\r\n+                        \r\n+        System.out.println(\"Loading file in ztycx order\");\r\n+        hdf5Reader = new Hdf5DataSetReader(filename, \"exported_data\", \"ztycx\", log, ds); //\r\n+        image= hdf5Reader.read();\r\n+        assertEquals(\"Bits should be 16\",image.getValidBits(),16);\r\n+        assertEquals(\"DimX should be 3\",3,image.getImg().dimension(0));\r\n+        assertEquals(\"DimY should be 5\",5,image.getImg().dimension(1));\r\n+        assertEquals(\"DimC should be 4\",4,image.getImg().dimension(2));\r\n+        assertEquals(\"DimZ should be 7\",7,image.getImg().dimension(3));\r\n+        assertEquals(\"DimT should be 6\",6,image.getImg().dimension(4));\r\n+    }\r\n+    \r\n+    @Test\r\n+    public void testImageContents(){\r\n+        System.out.println(\"Loading file in tzyxc order\");\r\n+        hdf5Reader = new Hdf5DataSetReader(filename, \"exported_data\", \"tzyxc\", log, ds); \r\n+        ImgPlus image= hdf5Reader.read();\r\n+        assertEquals(\"DimX\",0,image.dimensionIndex(Axes.X));\r\n+        assertEquals(\"DimY\",1,image.dimensionIndex(Axes.Y));\r\n+        assertEquals(\"DimC\",2,image.dimensionIndex(Axes.CHANNEL));\r\n+        assertEquals(\"DimZ\",3,image.dimensionIndex(Axes.Z));\r\n+        assertEquals(\"DimT\",4,image.dimensionIndex(Axes.TIME));\r\n+        \r\n+        RandomAccess rai = image.randomAccess();\r\n+        rai.setPosition(1,image.dimensionIndex(Axes.CHANNEL));\r\n+        rai.setPosition(0,image.dimensionIndex(Axes.Y));\r\n+        rai.setPosition(0,image.dimensionIndex(Axes.X));\r\n+        rai.setPosition(5,image.dimensionIndex(Axes.Z));\r\n+        rai.setPosition(6,image.dimensionIndex(Axes.TIME));\r\n+        UnsignedShortType f = (UnsignedShortType)rai.get();\r\n+        assertEquals(\"CHANNEL value should be 200\", 200, f.get());\r\n+        rai.setPosition(5,image.dimensionIndex(Axes.TIME));\r\n+        f = (UnsignedShortType)rai.get();\r\n+        assertEquals(\"CHANNEL value should be 0\", 0, f.get());\r\n+        rai.setPosition(6,image.dimensionIndex(Axes.TIME));\r\n+        rai.setPosition(4,image.dimensionIndex(Axes.Z));\r\n+        f = (UnsignedShortType)rai.get();\r\n+        assertEquals(\"CHANNEL value should be 200\", 200, f.get());\r\n+    }\r\n+    \r\n+    @Test\r\n+    public void testWriteHDF5Positive() throws Exception{\r\n+       String filename_HDF5 =\"src/test/resources/chocolate.h5\";\r\n+       DatasetIOService datasetIOService = context.getService(DatasetIOService.class);\r\n+       Dataset input = datasetIOService.open(\"src/test/resources/chocolate21.jpg\");\r\n+       new Hdf5DataSetWriterFromImgPlus(input.getImgPlus(),filename_HDF5 , \"exported_data\", 0, log).write();\r","path":"src/test/java/org/ilastik/ilastik4ij/Hdf5DataSetReaderTest.java","position":144,"original_position":144,"commit_id":"46438bbd76705c809c1533d7cf39e38a4b81984b","original_commit_id":"46438bbd76705c809c1533d7cf39e38a4b81984b","user":{"login":"wolny","id":706781,"avatar_url":"https://avatars2.githubusercontent.com/u/706781?v=4","gravatar_id":"","url":"https://api.github.com/users/wolny","html_url":"https://github.com/wolny","followers_url":"https://api.github.com/users/wolny/followers","following_url":"https://api.github.com/users/wolny/following{/other_user}","gists_url":"https://api.github.com/users/wolny/gists{/gist_id}","starred_url":"https://api.github.com/users/wolny/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wolny/subscriptions","organizations_url":"https://api.github.com/users/wolny/orgs","repos_url":"https://api.github.com/users/wolny/repos","events_url":"https://api.github.com/users/wolny/events{/privacy}","received_events_url":"https://api.github.com/users/wolny/received_events","type":"User","site_admin":false},"body":"space missing after `getImgPlus(),`. Try reformatting you code with the IDE before committing ","created_at":"2018-02-27T15:16:26Z","updated_at":"2018-02-27T15:17:27Z","html_url":"https://github.com/ilastik/ilastik4ij/pull/5#discussion_r170955907","pull_request_url":"https://api.github.com/repos/ilastik/ilastik4ij/pulls/5","author_association":"NONE","_links":{"self":{"href":"https://api.github.com/repos/ilastik/ilastik4ij/pulls/comments/170955907"},"html":{"href":"https://github.com/ilastik/ilastik4ij/pull/5#discussion_r170955907"},"pull_request":{"href":"https://api.github.com/repos/ilastik/ilastik4ij/pulls/5"}}},"pull_request":{"url":"https://api.github.com/repos/ilastik/ilastik4ij/pulls/5","id":171669897,"html_url":"https://github.com/ilastik/ilastik4ij/pull/5","diff_url":"https://github.com/ilastik/ilastik4ij/pull/5.diff","patch_url":"https://github.com/ilastik/ilastik4ij/pull/5.patch","issue_url":"https://api.github.com/repos/ilastik/ilastik4ij/issues/5","number":5,"state":"open","locked":false,"title":"Junit cases 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