Merge pull request #256 from melissalinkert/phenix-db

Add Phenix INI file support

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

@@ -539,7 +539,8 @@ public void setCompressionProperties(Map<String, Object> properties) {
             "com.glencoesoftware.bioformats2raw.BioTekReader," +
             "com.glencoesoftware.bioformats2raw.ND2PlateReader," +
             "com.glencoesoftware.bioformats2raw.MetaxpressReader," +
-            "com.glencoesoftware.bioformats2raw.MCDReader"
+            "com.glencoesoftware.bioformats2raw.MCDReader," +
+            "com.glencoesoftware.bioformats2raw.PhenixReader"
   )
   public void setExtraReaders(Class<?>[] extraReaderList) {
     if (extraReaderList != null) {

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

@@ -0,0 +1,135 @@
+/**
+ * Copyright (c) 2024 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;
+
+import loci.common.DataTools;
+import loci.common.IniTable;
+
+/**
+ * Represents a single image (one 2D plane) in an Opera Phenix database plate.
+ */
+public class PhenixImage {
+
+  /**
+   * Unique index of this plane.
+   * This is for sorting purposes only, and may not correspond to the
+   * well, field, series, plane, etc.
+   */
+  public int index;
+
+  /**
+   * Non-unique Image ID.
+   * All images in the plate will have the same ID, so this should not be
+   * used for sorting or lookups.
+   */
+  public String id;
+
+  /** Well row, indexed from 1. */
+  public int row;
+
+  /** Well column, indexed from 1. */
+  public int col;
+
+  /** Field, indexed from 1. */
+  public int field;
+
+  /** Calculated series index, from 0. */
+  public int series;
+
+  /** Plane, indexed from 1. */
+  public int plane;
+
+  /** Channel, indexed from 1. */
+  public int channel;
+
+  /** Channel name. */
+  public String channelName;
+
+  /** Exposure time in seconds. */
+  public Double exposureTime;
+
+  /** Filter wavelength in nm. */
+  public Double filterWavelength;
+
+  /** Laser wavelength in nm. */
+  public Double wavelength;
+
+  /** Image acquisition date. */
+  public String acquisitionDate;
+
+  /** Absolute Z position. */
+  public Double zPosition;
+
+  /** Temperature at acquisition. */
+  public Double temperature;
+
+  /** Absolute file path. */
+  public String filename;
+
+  /**
+   * Construct an empty PhenixImage.
+   */
+  public PhenixImage() {
+  }
+
+  /**
+   * Construct a PhenixImage representing a single plane,
+   * using the given INI data.
+   *
+   * @param table INI table containing image metadata
+   */
+  public PhenixImage(IniTable table) {
+    id = table.get("id");
+    index = Integer.parseInt(table.get("index"));
+    row = Integer.parseInt(table.get("row"));
+    col = Integer.parseInt(table.get("col"));
+    field = Integer.parseInt(table.get("field"));
+    series = Integer.parseInt(table.get("series"));
+    plane = Integer.parseInt(table.get("plane"));
+    channel = Integer.parseInt(table.get("channel"));
+    acquisitionDate = table.get("acquisitionDate");
+    zPosition = DataTools.parseDouble(table.get("zPosition"));
+    temperature = DataTools.parseDouble(table.get("temperature"));
+    filename = table.get("filename");
+    channelName = table.get("channelName");
+    exposureTime = DataTools.parseDouble(table.get("exposureTime"));
+    wavelength = DataTools.parseDouble(table.get("laserWavelength"));
+    filterWavelength = DataTools.parseDouble(table.get("filterWavelength"));
+  }
+
+  /**
+   * @return populated INI table representing this image
+   */
+  public IniTable getIniTable() {
+    IniTable table = new IniTable();
+    table.put(IniTable.HEADER_KEY, "Image " + index);
+    table.put("id", id);
+    table.put("index", String.valueOf(index));
+    table.put("row", String.valueOf(row));
+    table.put("col", String.valueOf(col));
+    table.put("field", String.valueOf(field));
+    table.put("series", String.valueOf(series));
+    table.put("plane", String.valueOf(plane));
+    table.put("channel", String.valueOf(channel));
+    table.put("acquisitionDate", acquisitionDate);
+    table.put("zPosition", String.valueOf(zPosition));
+    table.put("temperature", String.valueOf(temperature));
+    table.put("filename", filename);
+    table.put("channelName", channelName);
+    table.put("exposureTime", String.valueOf(exposureTime));
+    table.put("laserWavelength", String.valueOf(wavelength));
+    table.put("filterWavelength", String.valueOf(filterWavelength));
+    return table;
+  }
+
+  @Override
+  public String toString() {
+    return String.format("ID %d: %s", id, filename);
+  }
+
+}