From d0dec52020f7e6bb58d573624a682fb72b4fa6f2 Mon Sep 17 00:00:00 2001
From: Curtis Rueden <ctrueden@wisc.edu>
Date: Thu, 2 Sep 2010 20:29:39 +0000
Subject: [PATCH] Better series handling when number of series is extremely
 large.

---
 .../src/loci/plugins/in/ImportProcess.java    |  42 ++++++
 .../src/loci/plugins/in/ImporterOptions.java  |  27 ++--
 .../src/loci/plugins/in/SeriesDialog.java     | 130 ++++++++++--------
 .../src/loci/plugins/in/importer-options.txt  |   5 -
 4 files changed, 123 insertions(+), 81 deletions(-)

diff --git a/components/loci-plugins/src/loci/plugins/in/ImportProcess.java b/components/loci-plugins/src/loci/plugins/in/ImportProcess.java
index 4a0f24d5208..8a74a6bcb5f 100644
--- a/components/loci-plugins/src/loci/plugins/in/ImportProcess.java
+++ b/components/loci-plugins/src/loci/plugins/in/ImportProcess.java
@@ -28,6 +28,7 @@ Data Browser and Stack Slicer. Copyright (C) 2005-@year@ Melissa Linkert,
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.StringTokenizer;
 
 import loci.common.Location;
 import loci.common.Region;
@@ -181,6 +182,47 @@ public boolean isWindowless() {
     return baseReader != null && LociPrefs.isWindowless(baseReader);
   }
 
+  public void setSeriesList(String seriesList) {
+    final int seriesCount = getSeriesCount();
+    options.clearSeries();
+
+    // remove illegal characters
+    seriesList = seriesList.replaceAll("[^\\d,\\-]", "");
+
+    // parse series list
+    StringTokenizer st = new StringTokenizer(seriesList, ",");
+    while (st.hasMoreTokens()) {
+      final String token = st.nextToken();
+      int dash = token.indexOf("-");
+      if (dash < 0) {
+        // single number
+        try {
+          final int s = Integer.parseInt(token) - 1;
+          options.setSeriesOn(s, true);
+        }
+        catch (NumberFormatException exc) {
+          // skip invalid series number
+        }
+      }
+      else {
+        // numerical range
+        final String firstString = token.substring(0, dash);
+        final String lastString = token.substring(dash + 1);
+        try {
+          final int first = Integer.parseInt(firstString) - 1;
+          final int last = Integer.parseInt(lastString) - 1;
+          for (int s = first; s <= last; s++) {
+            if (s >= seriesCount) break; // skip out of bounds series
+            options.setSeriesOn(s, true);
+          }
+        }
+        catch (NumberFormatException exc) {
+          // skip invalid numerical range
+        }
+      }
+    }
+  }
+
   // -- ImportProcess methods - post-READER --
 
   /** Valid only after {@link ImportStep#READER}. */
diff --git a/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java b/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java
index 32f901e7790..ee43b9513a2 100644
--- a/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java
+++ b/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java
@@ -64,7 +64,6 @@ public class ImporterOptions extends OptionsList {
   public static final String KEY_OPEN_ALL_SERIES = "openAllSeries";
   public static final String KEY_QUIET           = "quiet";
   //public static final String KEY_RECORD          = "record";
-  public static final String KEY_SERIES          = "series";
   public static final String KEY_SHOW_METADATA   = "showMetadata";
   public static final String KEY_SHOW_OME_XML    = "showOMEXML";
   public static final String KEY_SHOW_ROIS       = "showROIs";
@@ -195,26 +194,26 @@ public void parseArg(String arg) {
 
   /** Handles obsolete macro keys, for backward compatibility. */
   public void checkObsoleteOptions() {
-    String options = Macro.getOptions();
+    final String macroOptions = Macro.getOptions();
 
     // NB: It would be nice to remove the Standard ImageJ option someday;
     // when that happens, the following code provides support for old macros.
     // check obsolete view options
-    //String stackFormat = options == null ?
-    //  null : Macro.getValue(options, "view", null);
+    //String stackFormat = macroOptions == null ?
+    //  null : Macro.getValue(macroOptions, "view", null);
     //final String viewStandard = "Standard ImageJ";
     //if (viewStandard.equals(stackFormat)) {
     //  // Standard ImageJ -> Hyperstack
-    //  options = options.replaceFirst(
+    //  macroOptions = macroOptions.replaceFirst(
     //    "\\[" + viewStandard + "\\]", VIEW_HYPERSTACK);
-    //  Macro.setOptions(options);
+    //  Macro.setOptions(macroOptions);
     //  setStackFormat(VIEW_HYPERSTACK);
     //}
 
     // check obsolete color options
-    boolean mergeChannels = checkKey(options, "merge_channels");
-    boolean rgbColorize = checkKey(options, "rgb_colorize");
-    boolean customColorize = checkKey(options, "custom_colorize");
+    final boolean mergeChannels = checkKey(macroOptions, "merge_channels");
+    final boolean rgbColorize = checkKey(macroOptions, "rgb_colorize");
+    final boolean customColorize = checkKey(macroOptions, "custom_colorize");
     if (mergeChannels) setColorMode(COLOR_MODE_COMPOSITE);
     else if (rgbColorize) setColorMode(COLOR_MODE_COLORIZED);
     else if (customColorize) setColorMode(COLOR_MODE_CUSTOM);
@@ -306,11 +305,6 @@ public boolean isColorModeCustom() {
   //public boolean isRecord() { return isSet(KEY_RECORD); }
   //public void setRecord(boolean b) { setValue(KEY_RECORD, b); }
 
-  // series
-  public String getSeriesInfo() { return getInfo(KEY_SERIES); }
-  public String getSeries() { return getValue(KEY_SERIES); }
-  public void setSeries(String s) { setValue(KEY_SERIES, s); }
-
   // showMetadata
   public String getShowMetadataInfo() { return getInfo(KEY_SHOW_METADATA); }
   public boolean isShowMetadata() { return isSet(KEY_SHOW_METADATA); }
@@ -404,6 +398,9 @@ public boolean isSeriesOn(int s) {
   public void setSeriesOn(int s, boolean value) {
     set(seriesOn, s, value, false);
   }
+  public void clearSeries() {
+    seriesOn.clear();
+  }
 
   // swap options
   public String getInputOrder(int s) { return get(inputOrder, s, null); }
@@ -485,7 +482,7 @@ private <T extends Object> T get(List<T> list, int index, T defaultValue) {
   }
 
   /** Tests whether the given boolean key is set in the specified options. */
-  private boolean checkKey(String options, String key) {
+  protected boolean checkKey(String options, String key) {
     if (options == null) return false;
 
     // delete anything inside square brackets, for simplicity
diff --git a/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java b/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java
index c174dea63fe..cf9196068f7 100644
--- a/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java
+++ b/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java
@@ -29,6 +29,7 @@ Data Browser and Stack Slicer. Copyright (C) 2005-@year@ Melissa Linkert,
 import com.jgoodies.forms.layout.CellConstraints;
 import com.jgoodies.forms.layout.FormLayout;
 
+import ij.Macro;
 import ij.gui.GenericDialog;
 
 import java.awt.Button;
@@ -41,7 +42,6 @@ Data Browser and Stack Slicer. Copyright (C) 2005-@year@ Melissa Linkert,
 import java.awt.Panel;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.StringTokenizer;
 
 import javax.swing.Box;
 import javax.swing.JPanel;
@@ -62,6 +62,7 @@ public class SeriesDialog extends ImporterDialog implements ActionListener {
 
   public static final int MAX_COMPONENTS = 256;
   public static final int MAX_SERIES_THUMBS = 200;
+  public static final int MAX_SERIES_TOGGLES = MAX_SERIES_THUMBS;
 
   // -- Fields --
 
@@ -80,40 +81,12 @@ public SeriesDialog(ImportProcess process) {
 
   @Override
   protected boolean needPrompt() {
-    // CTR FIXME - eliminate weird handling of series string here
-    String seriesString = options.getSeries();
-    if (process.isWindowless()) {
-      if (seriesString != null) {
-        if (seriesString.startsWith("[")) {
-          seriesString = seriesString.substring(1, seriesString.length() - 2);
-        }
-
-        // default all series to false
-        final int seriesCount = process.getSeriesCount();
-        for (int s=0; s<seriesCount; s++) options.setSeriesOn(s, false);
-
-        // extract enabled series values from series string
-        StringTokenizer tokens = new StringTokenizer(seriesString, " ");
-        while (tokens.hasMoreTokens()) {
-          String token = tokens.nextToken().trim();
-          int n = Integer.parseInt(token);
-          if (n < seriesCount) options.setSeriesOn(n, true);
-        }
-      }
-      options.setSeries(seriesString);
-      return false;
-    }
-
-    return process.getSeriesCount() > 1 &&
+    return !process.isWindowless() && process.getSeriesCount() > 1 &&
       !options.openAllSeries() && !options.isViewNone();
   }
 
   @Override
   protected GenericDialog constructDialog() {
-    // -- CTR FIXME - refactor series-related options into SeriesOptions class
-    // has a normalize(IFormatReader) method
-    // call both before and after the dialog here...
-
     final int seriesCount = process.getSeriesCount();
 
     // NB: Load thumbnails only when series count is modest.
@@ -138,31 +111,44 @@ protected GenericDialog constructDialog() {
 
     GenericDialog gd = new GenericDialog("Bio-Formats Series Options");
 
-    // NB: We need to add the checkboxes in groups, to prevent an
-    // exception from being thrown if there are more than 512 series.
-    // See also:
-    //   https://skyking.microscopy.wisc.edu/trac/java/ticket/408 and
-    //   http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980
-
-    final int nGroups = (seriesCount + MAX_COMPONENTS - 1) / MAX_COMPONENTS;
-    int nextSeries = 0;
-    for (int i=0; i<nGroups; i++) {
-      final int nRows = Math.min(MAX_COMPONENTS, seriesCount - nextSeries);
-      final String[] labels = new String[nRows];
-      final boolean[] defaultValues = new boolean[nRows];
-      for (int row=0; row<nRows; row++) {
-        labels[row] = process.getSeriesLabel(nextSeries);
-        defaultValues[row] = options.isSeriesOn(nextSeries);
-        nextSeries++;
+    // NB: Provide individual checkboxes only when series count is manageable.
+    if (seriesCount < MAX_SERIES_TOGGLES) {
+      // NB: We need to add the checkboxes in groups, to prevent an
+      // exception from being thrown if there are more than 512 series.
+      // See also:
+      //   https://skyking.microscopy.wisc.edu/trac/java/ticket/408 and
+      //   http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980
+
+      final int nGroups = (seriesCount + MAX_COMPONENTS - 1) / MAX_COMPONENTS;
+      int nextSeries = 0;
+      for (int i=0; i<nGroups; i++) {
+        final int nRows = Math.min(MAX_COMPONENTS, seriesCount - nextSeries);
+        final String[] labels = new String[nRows];
+        final boolean[] defaultValues = new boolean[nRows];
+        for (int row=0; row<nRows; row++) {
+          labels[row] = process.getSeriesLabel(nextSeries);
+          defaultValues[row] = options.isSeriesOn(nextSeries);
+          nextSeries++;
+        }
+        gd.addCheckboxGroup(nRows, 1, labels, defaultValues);
       }
-      gd.addCheckboxGroup(nRows, 1, labels, defaultValues);
-    }
 
-    // extract checkboxes, for "Select All" and "Deselect All" functions
-    boxes = WindowTools.getCheckboxes(gd).toArray(new Checkbox[0]);
+      // extract checkboxes, for "Select All" and "Deselect All" functions
+      boxes = WindowTools.getCheckboxes(gd).toArray(new Checkbox[0]);
 
-    // rebuild dialog so that the thumbnails and checkboxes line up correctly
-    rebuildDialog(gd, nGroups);
+      // rebuild dialog so that the thumbnails and checkboxes line up correctly
+      rebuildDialog(gd, nGroups);
+    }
+    else {
+      // too many series; display a simple text field for specifying series
+      gd.addMessage(
+        "Please specify the image series you wish to import.\n" +
+        "Use commas to list multiple series. You can also use\n" +
+        "a dash to represent a range of series. For example,\n" +
+        "to import series 1, 3, 4, 5, 7, 8, 9, 12, 15 & 16,\n" +
+        "you could write: 1, 3-5, 7-9, 12, 15-16");
+      gd.addStringField("Series_list: ", "1");
+    }
 
     return gd;
   }
@@ -182,21 +168,43 @@ protected boolean displayDialog(GenericDialog gd) {
   @Override
   protected boolean harvestResults(GenericDialog gd) {
     final int seriesCount = process.getSeriesCount();
-    String seriesString = "[";
-    for (int i=0; i<seriesCount; i++) {
-      boolean on = gd.getNextBoolean();
-      options.setSeriesOn(i, on);
-      if (on) seriesString += i + " ";
+    options.clearSeries();
+
+    // examine series key regardless of number of series
+    final String macroOptions = Macro.getOptions();
+    final String macroSeriesList = macroOptions == null ? null :
+      Macro.getValue(macroOptions, "series_list", null);
+    if (macroSeriesList != null) process.setSeriesList(macroSeriesList);
+
+    if (seriesCount < MAX_SERIES_TOGGLES) {
+      // harvest individual checkbox values
+      for (int i=0; i<seriesCount; i++) {
+        final boolean on = gd.getNextBoolean();
+        if (on) options.setSeriesOn(i, on);
+      }
+    }
+    else {
+      // harvest series string
+      final String seriesList = gd.getNextString();
+      process.setSeriesList(seriesList);
     }
-    seriesString += "]";
-    options.setSeries(seriesString);
+
+    // examine series_XX keys regardless of number of series
+    if (macroOptions != null) {
+      for (int i=0; i<seriesCount; i++) {
+        final String seriesKey = "series_" + (i + 1);
+        final boolean on = options.checkKey(macroOptions, seriesKey);
+        if (on) options.setSeriesOn(i, on);
+      }
+    }
+
     return true;
   }
 
   // -- ActionListener methods --
 
   public void actionPerformed(ActionEvent e) {
-    String cmd = e.getActionCommand();
+    final String cmd = e.getActionCommand();
     if ("select".equals(cmd)) {
       for (int i=0; i<boxes.length; i++) boxes[i].setState(true);
       updateIfGlitched();
@@ -218,7 +226,7 @@ private void updateIfGlitched() {
   }
 
   private void rebuildDialog(GenericDialog gd, int buttonRow) {
-    // rebuild dialog using FormLayout to organize things more nicely
+    // rebuild dialog to organize things more nicely
 
     final String cols = p == null ? "pref" : "pref, 3dlu, pref";
 
diff --git a/components/loci-plugins/src/loci/plugins/in/importer-options.txt b/components/loci-plugins/src/loci/plugins/in/importer-options.txt
index 93c316cb153..1daf0774f93 100644
--- a/components/loci-plugins/src/loci/plugins/in/importer-options.txt
+++ b/components/loci-plugins/src/loci/plugins/in/importer-options.txt
@@ -173,11 +173,6 @@ default = false
 #  more like a normal, fully memory-resident image stack.
 #default = false
 
-[series]
-type = string
-label = series
-default = 0
-
 [showMetadata]
 type = boolean
 label = Display_metadata