Merge pull request #158 from melissalinkert/biotek-regex

BioTek: refine field and channel name regexes

src/main/java/com/glencoesoftware/bioformats2raw/BioTekReader.java

@@ -60,8 +60,8 @@ public class BioTekReader extends FormatReader {
   private static final Logger LOGGER =
     LoggerFactory.getLogger(BioTekReader.class);
   private static final String BIOTEK_MAGIC = "BTIImageMetaData";
-  private static final String WELL_REGEX = "([A-Z]{1,2})(\\d{1,2})_(\\d+)";
-  private static final String ALPHANUM = "([A-Za-z0-9 ]+)";
+  private static final String WELL_REGEX = "([A-Z]{1,2})(\\d{1,2})_(-?\\d+)";
+  private static final String ALPHANUM = "([A-Za-z0-9 ,\\[\\]]+)";
   private static final String SUFFIX = ".tif[f]?";
   private static final String TIFF_REGEX_A =
     WELL_REGEX + "_(\\d+)_(\\d+)_" + ALPHANUM + "_(\\d+)" + SUFFIX;

src/test/java/com/glencoesoftware/bioformats2raw/test/BioTekTest.java

@@ -0,0 +1,244 @@
+/**
+ * Copyright (c) 2019 Glencoe Software, Inc. All rights reserved.
+ *
+ * This software is distributed under the terms described by the LICENSE.txt
+ * file you can find at the root of the distribution bundle.  If the file is
+ * missing please request a copy by contacting [email protected]
+ */
+package com.glencoesoftware.bioformats2raw.test;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.stream.Stream;
+
+import com.glencoesoftware.bioformats2raw.BioTekReader;
+import loci.common.LogbackTools;
+import loci.common.services.ServiceFactory;
+import loci.formats.services.OMEXMLService;
+import loci.formats.ome.OMEXMLMetadata;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+/**
+ * Tests specific to the BioTek reader included with bioformats2raw.
+ */
+public class BioTekTest {
+
+  /** Temporary directory containing an artificial BioTek plate. */
+  Path input;
+
+  /**
+   * Set logging to warn before all methods and create a new temporary
+   * directory to copy input data.
+   * This gets called once per test, before the test itself is run.
+   *
+   * @param tmp temporary directory for input data
+   */
+  @BeforeEach
+  public void setup(@TempDir Path tmp) throws Exception {
+    input = tmp.resolve("test-input");
+    input.toFile().mkdirs();
+    LogbackTools.setRootLevel("warn");
+  }
+
+  /**
+   * Given a list of file paths that make up a plate, copy the minimal test TIFF
+   * in bioformats2raw/src/test/resources/... to each path. This creates an
+   * artificial BioTek plate that can be initialized by the reader.
+   *
+   * @param filenames relative paths to be created
+   * @throws IOException if file copying fails
+   */
+  void createPlate(String[] filenames) throws IOException {
+    // test file in repository is not real data, but the result of:
+    // $ bfconvert "test&sizeX=2&sizeY=2.fake" test.tiff
+    // $ tiffset -u 270 test.tiff
+    //
+    // the "tiffset" command removes the TIFF comment, because
+    // bfconvert stores ImageJ-style dimension information there,
+    // but BioTekReader expects either no comment or BioTek-specific XML
+    Path testTiff = getTestFile("test.tiff");
+
+    for (String f : filenames) {
+      Files.copy(testTiff, input.resolve(f));
+    }
+
+    // reset the input path to the first file in the list
+    // the reader cannot initialize from a directory
+    input = input.resolve(filenames[0]);
+  }
+
+  /**
+   * Create an artificial single well BioTek plate with the given
+   * list of file names.
+   * Checks that the correct well row/column and ZCT sizes are detected.
+   *
+   * This test will be run once for each Arguments object
+   * returned by getTestCases below.
+   *
+   * @param paths path to each file in the plate
+   * @param wellRow well row index (from 0)
+   * @param wellColumn well column index (from 0)
+   * @param fields number of fields in the well
+   * @param sizeZ number of Z sections
+   * @param sizeC number of channels
+   * @param sizeT number of timepoints
+   */
+  @ParameterizedTest
+  @MethodSource("getTestCases")
+  public void testBioTek(String[] paths, int wellRow, int wellColumn,
+    int fields, int sizeZ, int sizeC, int sizeT) throws Exception
+  {
+    // set up the artificial plate
+    createPlate(paths);
+
+    try (BioTekReader reader = new BioTekReader()) {
+      // initialize the reader, making sure that OME-XML metadata is populated
+      // so that we can check plate/well metadata
+      OMEXMLMetadata metadata = getOMEMetadata();
+      reader.setMetadataStore(metadata);
+      // if file name detection were to break, setId is likely to throw
+      // an exception which would fail the test
+      reader.setId(input.toString());
+
+      // the number of OME Images should match the expected field count
+      // this should be the same as the series count
+      assertEquals(metadata.getImageCount(), fields);
+      assertEquals(metadata.getImageCount(), reader.getSeriesCount());
+      // there should be exactly one plate, with exactly one well
+      assertEquals(metadata.getPlateCount(), 1);
+      assertEquals(metadata.getWellCount(0), 1);
+      // the well's row and column indexes should match expectations
+      // this is especially important for "sparse" plates where the first
+      // row and/or column in the plate are missing
+      assertEquals(metadata.getWellRow(0, 0).getValue(), wellRow);
+      assertEquals(metadata.getWellColumn(0, 0).getValue(), wellColumn);
+      // all of the Images should be linked to the well
+      assertEquals(metadata.getWellSampleCount(0, 0), fields);
+      for (int f=0; f<fields; f++) {
+        // sanity check that the Images are linked to the
+        // well in the correct order
+        assertEquals(metadata.getWellSampleImageRef(0, 0, f), "Image:" + f);
+        // check that the number of Z sections, channels, and timepoints
+        // all match expectations
+        assertEquals(metadata.getPixelsSizeZ(f).getValue(), sizeZ);
+        assertEquals(metadata.getPixelsSizeC(f).getValue(), sizeC);
+        assertEquals(metadata.getPixelsSizeT(f).getValue(), sizeT);
+      }
+    }
+  }
+
+  /**
+   * Make sure that a TIFF file that doesn't follow the expected BioTek naming
+   * conventions is not read by the BioTek reader.
+   */
+  @Test
+  public void testInvalidPath() throws IOException {
+    // this is the same test file that we copy to make artifical plates
+    // just without a name that matches what we expect for BioTek data
+    Path testTiff = getTestFile("test.tiff");
+
+    try (BioTekReader reader = new BioTekReader()) {
+      // make sure the reader recognizes that this is not a BioTek file
+      assertFalse(reader.isThisType(testTiff.toString()));
+
+      // make sure that an exception is thrown if we try to force
+      // the reader to read it anyway
+      assertThrows(IllegalArgumentException.class, () -> {
+        reader.setId(testTiff.toString());
+      });
+    }
+  }
+
+  /**
+   * Generate test cases that are given to testBioTek(...) above.
+   * A list of file names, the well row and column index, number of fields,
+   * and ZCT dimensions are all specified here.
+   *
+   * These are all names taken from real-world data, with minor sanitization
+   * of some of the channel names and wavelengths.
+   *
+   * @return BioTek plate test cases
+   */
+  static Stream<Arguments> getTestCases() {
+    return Stream.of(
+      Arguments.of(new String[] {
+        "A1_-1_1_1_Tsf[Phase Contrast]_001.tif"
+      }, 0, 0, 1, 1, 1, 1),
+      Arguments.of(new String[] {
+        "A1_01_1_1_Phase Contrast_001.tif",
+        "A1_01_1_2_Phase Contrast_001.tif",
+        "A1_01_1_3_Phase Contrast_001.tif",
+        "A1_01_1_4_Phase Contrast_001.tif",
+        "A1_01_1_5_Phase Contrast_001.tif",
+        "A1_01_1_6_Phase Contrast_001.tif",
+        "A1_01_1_7_Phase Contrast_001.tif",
+        "A1_01_1_8_Phase Contrast_001.tif",
+        "A1_01_1_9_Phase Contrast_001.tif",
+      }, 0, 0, 9, 1, 1, 1),
+      Arguments.of(new String[] {
+        "P24_1_Bright Field_1_001_02.tif"
+      }, 15, 23, 1, 1, 1, 1),
+      Arguments.of(new String[] {
+        "B2_1_Bright Field_1_001_02.tif"
+      }, 1, 1, 1, 1, 1, 1),
+      Arguments.of(new String[] {
+        "A1_1_Stitched[AandB_Phase Contrast]_1_001_-1.tif"
+      }, 0, 0, 1, 1, 1, 1),
+      Arguments.of(new String[] {
+        "A1_1Z0_DAPI_1_001_.tif",
+        "A1_1Z1_DAPI_1_001_.tif",
+        "A1_1Z2_DAPI_1_001_.tif",
+        "A1_1Z3_DAPI_1_001_.tif",
+        "A1_1Z4_DAPI_1_001_.tif"
+      }, 0, 0, 1, 5, 1, 1),
+      Arguments.of(new String[] {
+        "A1_-1_1_1_Stitched[Channel1 300,400]_001.tif",
+        "A1_-1_2_1_Stitched[Channel2 500,600]_001.tif",
+        "A1_-1_3_1_Stitched[Channel 3 600,650]_001.tif"
+      }, 0, 0, 1, 1, 3, 1),
+      Arguments.of(new String[] {
+        "A1_-2_1_1_Tsf[Stitched[Channel1 300,400]]_001.tif",
+        "A1_-2_2_1_Tsf[Stitched[Channel2 500,600]]_001.tif",
+        "A1_-2_3_1_Tsf[Stitched[Channel 3 600,650]]_001.tif"
+      }, 0, 0, 1, 1, 3, 1)
+    );
+  }
+
+  /**
+   * Get the absolute path to a resource for this class.
+   *
+   * @param resourceName a relative name for something in
+   *                     bioformats2raw/src/test/resources/...
+   * @return Path object corresponding to the named resource
+   * @throws IOException if the resource could not be located
+   */
+  private Path getTestFile(String resourceName) throws IOException {
+    try {
+      return Paths.get(this.getClass().getResource(resourceName).toURI());
+    }
+    catch (Exception e) {
+      throw new IOException(e);
+    }
+  }
+
+  /**
+   * @return an empty OMEXMLMetadata object that the BioTek reader can fill up
+   */
+  private OMEXMLMetadata getOMEMetadata() throws Exception {
+    ServiceFactory sf = new ServiceFactory();
+    OMEXMLService xmlService = sf.getInstance(OMEXMLService.class);
+    return xmlService.createOMEXMLMetadata();
+  }
+}