From 08a1543e95df781b547eac2ce487b036f5a51343 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Fri, 12 Feb 2010 15:32:10 +0000
Subject: [PATCH] Added BD Pathway reader, courtesy of Shawn Garbett.  Closes
 #389.

---
 .../src/loci/formats/in/BDReader.java         | 371 ++++++++++++++++++
 .../bio-formats/src/loci/formats/readers.txt  |   3 +
 2 files changed, 374 insertions(+)
 create mode 100644 components/bio-formats/src/loci/formats/in/BDReader.java

diff --git a/components/bio-formats/src/loci/formats/in/BDReader.java b/components/bio-formats/src/loci/formats/in/BDReader.java
new file mode 100644
index 00000000000..3d335560033
--- /dev/null
+++ b/components/bio-formats/src/loci/formats/in/BDReader.java
@@ -0,0 +1,371 @@
+//
+// BDReader.java
+//
+
+/*
+OME Bio-Formats package for reading and converting biological file formats.
+Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
+Copyright (C) 2009-@year@ Vanderbilt Integrative Cancer Center.
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+*/
+
+package loci.formats.in;
+
+import java.io.*;
+import java.util.*;
+
+import loci.common.DataTools;
+import loci.common.Location;
+import loci.common.RandomAccessInputStream;
+import loci.common.XMLTools;
+import loci.common.IniList;
+import loci.common.IniParser;
+import loci.formats.CoreMetadata;
+import loci.formats.FormatException;
+import loci.formats.FormatReader;
+import loci.formats.FormatTools;
+import loci.formats.MetadataTools;
+import loci.formats.meta.FilterMetadata;
+import loci.formats.meta.MetadataStore;
+import loci.formats.tiff.IFD;
+import loci.formats.tiff.TiffParser;
+
+/**
+ * BDReader is the file format reader for BD Pathway datasets.
+ *
+ * <dl><dt><b>Source code:</b></dt>
+ * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/src/loci/formats/in/BDReader.java">Trac</a>,
+ * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/bio-formats/src/loci/formats/in/BDReader.java">SVN</a></dd></dl>
+ *
+ * @author Shawn Garbett  Shawn.Garbett a t Vanderbilt.edu
+ */
+public class BDReader extends FormatReader {
+
+  // -- Constants --
+  private static final String EXPERIMENT_FILE = "Experiment.exp";
+  private static final String[] META_EXT = {"drt","dye","exp","plt"};
+
+  // -- Fields --
+  private Vector<String> metadataFiles = new Vector<String>();
+  private Vector<String> channelNames = new Vector<String>();
+  private Vector<String> wellLabels = new Vector<String>();
+  private String plateName;
+  private String[] tiffs;
+  private MinimalTiffReader reader;
+
+  // -- Constructor --
+
+  /** Constructs a new ScanR reader. */
+  public BDReader() {
+    super("BD Pathway", new String[] {"exp", "tif"});
+    domains = new String[] {FormatTools.HCS_DOMAIN};
+    suffixSufficient = false;
+  }
+
+  // -- IFormatReader API methods --
+
+  /* @see loci.formats.IFormatReader#isThisType(String, boolean) */
+  public boolean isThisType(String name, boolean open) {
+    String id = new Location(name).getAbsolutePath();
+    try {
+      id = locateExperimentFile(id);
+    }
+    catch (FormatException f) {
+      return false;
+    }
+    catch (IOException f) {
+      return false;
+    }
+
+    if (id.endsWith(EXPERIMENT_FILE)) { return true; }
+
+    return super.isThisType(name, open);
+  }
+
+  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
+  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
+    TiffParser p = new TiffParser(stream);
+    IFD ifd = p.getFirstIFD();
+    if (ifd == null) return false;
+
+    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
+
+    return software.trim().startsWith("MATROX Imaging Library");
+  }
+
+  /* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
+  public String[] getSeriesUsedFiles(boolean noPixels) {
+    FormatTools.assertId(currentId, true, 1);
+
+    Vector<String> files = new Vector<String>();
+    for (String file : metadataFiles) {
+      if (file != null) files.add(file);
+    }
+
+    if (!noPixels && tiffs != null) {
+      int offset = getSeries() * getImageCount();
+      for (int i = 0; i<getImageCount(); i++) {
+        if (tiffs[offset + i] != null) { files.add(tiffs[offset + i]); }
+      }
+    }
+
+    return files.toArray(new String[files.size()]);
+  }
+
+  /* @see loci.formats.IFormatReader#close(boolean) */
+  public void close(boolean fileOnly) throws IOException {
+    super.close(fileOnly);
+    if (!fileOnly) {
+      if (reader != null) reader.close();
+      reader = null;
+      tiffs = null;
+      plateName = null;
+      channelNames.clear();
+      metadataFiles.clear();
+      wellLabels.clear();
+    }
+  }
+
+  /* @see IFormatReader#fileGroupOption(String) */
+  public int fileGroupOption(String id) throws FormatException, IOException {
+    return FormatTools.MUST_GROUP;
+  }
+
+  /**
+   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
+   */
+  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
+    throws FormatException, IOException
+  {
+    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
+
+    int index = getSeries() * getImageCount() + no;
+    if (tiffs[index] != null) {
+      reader.setId(tiffs[index]);
+      reader.openBytes(0, buf, x, y, w, h);
+      reader.close();
+    }
+
+    return buf;
+  }
+
+  // -- Internal FormatReader API methods --
+  public IniList readMetaData(String id) throws IOException {
+    IniList exp = (new IniParser()).parseINI(
+      new BufferedReader(new FileReader(id)));
+    IniList plate = null;
+    // Read Plate File
+    for (String filename : metadataFiles) {
+      if (filename.endsWith(".plt")) {
+        plate = (new IniParser()).parseINI(
+          new BufferedReader(new FileReader(filename)));
+        break;
+      }
+    }
+    if (plate == null) throw new IOException("No Plate File");
+
+    plateName = plate.getTable("PlateType").get("Brand");
+
+    Location dir = new Location(id).getParentFile();
+    for (String filename :  dir.list()) {
+      if (filename.startsWith("Well ")) {
+        wellLabels.add(filename.substring(5,8));
+      }
+    }
+
+    core = new CoreMetadata[wellLabels.size()];
+
+    core[0] = new CoreMetadata();
+
+
+// Hack for current testing/development purposes
+// Not all channels have the same Z!!! How to handle???
+// FIXME FIXME FIXME
+    core[0].sizeZ=1;
+// FIXME FIXME FIXME
+// END OF HACK
+
+    core[0].sizeC = Integer.parseInt(exp.getTable("General").get("Dyes"));
+
+    for (int i=1; i<=core[0].sizeC; i++) {
+      channelNames.add(exp.getTable("Dyes").get(Integer.toString(i)));
+    }
+
+    // Count Images
+    core[0].sizeT = 0;
+    Location well = new Location(dir.getAbsolutePath(),
+      "Well " + wellLabels.get(1));
+    for (String filename : well.list()) {
+      if (filename.startsWith(channelNames.get(0)) &&
+         filename.endsWith(".tif"))
+      {
+        core[0].sizeT++;
+      }
+    }
+    return exp;
+  }
+
+  /* @see loci.formats.FormatReader#initFile(String) */
+  protected void initFile(String id) throws FormatException, IOException {
+    // make sure we have the experiment file
+    id = locateExperimentFile(id);
+    super.initFile(id);
+    Location dir = new Location(id).getAbsoluteFile().getParentFile();
+
+    for (String file : dir.list(true)) {
+      Location f = new Location(dir, file);
+      if (!f.isDirectory()) {
+        for (String ext : META_EXT) {
+          if (checkSuffix(id, ext)) {
+            metadataFiles.add(f.getAbsolutePath());
+          }
+        }
+      }
+    }
+
+    // parse Experiment metadata
+    IniList experiment = readMetaData(id);
+    Vector<String> uniqueRows = new Vector<String>();
+    Vector<String> uniqueColumns = new Vector<String>();
+
+    for (String well : wellLabels) {
+      String row = well.substring(0, 1).trim();
+      String column = well.substring(1, 3).trim();
+
+      if (!uniqueRows.contains(row) && row.length() > 0) uniqueRows.add(row);
+      if (!uniqueColumns.contains(column) && column.length() > 0) {
+        uniqueColumns.add(column);
+      }
+    }
+
+    int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
+    int nTimepoints = getSizeT();
+    int nWells = wellLabels.size();
+    int nChannels = getSizeC() == 0 ? channelNames.size() : getSizeC();
+    if (nChannels == 0) nChannels = 1;
+
+    tiffs = getTiffs(dir.getAbsoluteFile().toString());
+
+    // []   files = new String[nChannels * nWells * nTimepoints * nSlices];
+
+    reader = new MinimalTiffReader();
+    reader.setId(tiffs[0]);
+
+    int sizeX = reader.getSizeX();
+    int sizeY = reader.getSizeY();
+    int pixelType = reader.getPixelType();
+    boolean rgb = reader.isRGB();
+    boolean interleaved = reader.isInterleaved();
+    boolean indexed = reader.isIndexed();
+    boolean littleEndian = reader.isLittleEndian();
+
+    reader.close();
+
+    for (int i=0; i<getSeriesCount(); i++) {
+      core[i] = new CoreMetadata();
+      core[i].sizeC = nChannels;
+      core[i].sizeZ = nSlices;
+      core[i].sizeT = nTimepoints;
+      core[i].sizeX = sizeX;
+      core[i].sizeY = sizeY;
+      core[i].pixelType = pixelType;
+      core[i].rgb = rgb;
+      core[i].interleaved = interleaved;
+      core[i].indexed = indexed;
+      core[i].littleEndian = littleEndian;
+      core[i].dimensionOrder = "XYZTC";
+      core[i].imageCount = nSlices * nTimepoints * nChannels;
+    }
+
+    MetadataStore store =
+      new FilterMetadata(getMetadataStore(), isMetadataFiltered());
+    MetadataTools.populatePixels(store, this);
+
+    // populate LogicalChannel data
+    for (int i=0; i<getSeriesCount(); i++) {
+      for (int c=0; c<getSizeC(); c++) {
+        store.setLogicalChannelName(channelNames.get(c), i, c);
+      }
+    }
+
+    store.setPlateRowNamingConvention("A", 0);
+    store.setPlateColumnNamingConvention("01", 0);
+    store.setPlateName(plateName, 0);
+
+    for (int i=0; i<getSeriesCount(); i++) {
+      MetadataTools.setDefaultCreationDate(store, id, i);
+
+      String name = wellLabels.get(i);
+      String row = name.substring(0, 1);
+      Integer col = Integer.parseInt(name.substring(1, 3));
+
+      store.setWellColumn(col, 0, i);
+      store.setWellRow(row.charAt(0)-'A', 0, i);
+
+      store.setWellSampleIndex(new Integer(i), 0, i, 1);
+      store.setImageName(name, i);
+    }
+  }
+
+  /* Locate the experiment file given any file in set */
+  private String locateExperimentFile(String id)
+    throws FormatException, IOException
+  {
+    if (!checkSuffix(id, "exp")) {
+      Location parent = new Location(id).getAbsoluteFile().getParentFile();
+      if (checkSuffix(id, "tif")) parent = parent.getParentFile();
+      for (String file : parent.list()) {
+        if (file.equals(EXPERIMENT_FILE)) {
+          id = new Location(parent, file).getAbsolutePath();
+          break;
+        }
+      }
+      if (!checkSuffix(id, "exp")) {
+        throw new FormatException("Could not find " + EXPERIMENT_FILE +
+          " in " + parent.getAbsolutePath());
+      }
+    }
+    return id;
+  }
+
+  public String[] getTiffs(String dir) {
+    LinkedList<String> files = new LinkedList<String>();
+    FileFilter wellDirFilter = new FileFilter() {
+      public boolean accept(File file) {
+          return file.isDirectory() && file.getName().startsWith("Well ");
+      }
+    };
+    FileFilter tiffFilter = new FileFilter() {
+      public boolean accept(File file) {
+        return file.getName().matches(".* - n\\d\\d\\d\\d\\d\\d\\.tif");
+      }
+    };
+
+    File[] dirs = (new File(dir)).listFiles(wellDirFilter);
+
+    Arrays.sort(dirs);
+
+    for (File well : dirs) {
+      File[] found = well.listFiles(tiffFilter);
+      Arrays.sort(found);
+      for (File file : found) {
+        files.add(file.getAbsolutePath());
+      }
+    }
+
+    return files.toArray(new String[files.size()]);
+  }
+}
diff --git a/components/bio-formats/src/loci/formats/readers.txt b/components/bio-formats/src/loci/formats/readers.txt
index 92afd79f8ba..1e1dee4132a 100644
--- a/components/bio-formats/src/loci/formats/readers.txt
+++ b/components/bio-formats/src/loci/formats/readers.txt
@@ -68,6 +68,7 @@ loci.formats.in.ARFReader             # arf
 loci.formats.in.CellomicsReader       # c01
 loci.formats.in.LiFlimReader          # fli
 loci.formats.in.TargaReader           # tga
+loci.formats.in.OxfordInstrumentsReader # top
 loci.formats.in.FakeReader            # fake
 
 # multi-extension messes
@@ -79,6 +80,7 @@ loci.formats.in.ICSReader             # ics, ids
 loci.formats.in.PerkinElmerReader     # rec, ano, csv, htm, tim, zpo, 2, 3, ...
 loci.formats.in.AmiraReader           # am, amiramesh, grey, hx, labels, ...
 loci.formats.in.ScanrReader           # dat, xml, tif
+loci.formats.in.BDReader              # exp, tif
 
 # standard PIC reader must go last (it accepts any PIC)
 loci.formats.in.BioRadReader          # pic
@@ -115,6 +117,7 @@ loci.formats.in.ImprovisionTiffReader # tif
 loci.formats.in.MetamorphTiffReader   # tif
 loci.formats.in.NikonTiffReader       # tif
 loci.formats.in.OMETiffReader         # tif
+loci.formats.in.PhotoshopTiffReader   # tif
 
 # standard TIFF reader must go last (it accepts any TIFF)
 loci.formats.in.TiffDelegateReader    # tif, tiff