Merge pull request micro-manager#1956 from nicost/metaDataWriter

MultipageTiff writer: warn against killing MM while filesets are being closed.

mmstudio/src/main/java/org/micromanager/data/internal/multipagetiff/FileSet.java

@@ -21,6 +21,7 @@
 
 package org.micromanager.data.internal.multipagetiff;
 
+import java.awt.GraphicsEnvironment;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
@@ -38,6 +39,7 @@
 import org.micromanager.data.internal.DefaultMetadata;
 import org.micromanager.data.internal.DefaultSummaryMetadata;
 import org.micromanager.internal.propertymap.NonPropertyMapJSONFormats;
+import org.micromanager.internal.utils.ProgressBar;
 import org.micromanager.internal.utils.ReportingUtils;
 
 
@@ -112,9 +114,20 @@ public void finished(String omeXML, String ijDescription) throws IOException {
       // only need to finish last one here because previous ones in set are finished
       // as they fill up with images
       tiffWriters_.getLast().finish();
-      //  close all
+      //  close all, this can be time-consuming ,so use a ProgressBar
+      ProgressBar pb = null;
+      if (!GraphicsEnvironment.isHeadless() && tiffWriters_.size() > 4) {
+         pb = new ProgressBar(null, "Closing files", 0, tiffWriters_.size());
+      }
+      int count = 0;
       for (MultipageTiffWriter w : tiffWriters_) {
          w.close(omeXML, ijDescription);
+         if (pb != null) {
+            pb.setProgress(count++);
+         }
+      }
+      if (pb != null) {
+         pb.setVisible(false);
       }
       omeMetadata_ = null;
       masterStorage_ = null;

mmstudio/src/main/java/org/micromanager/data/internal/multipagetiff/StorageMultipageTiff.java

@@ -239,7 +239,6 @@ private void openExistingDataSet() {
       MultipageTiffReader reader = null;
       File dir = new File(directory_);
 
-      ProgressBar tmpProgressBar = null;
       // Allow operation in headless mode.
       File[] listFiles = dir.listFiles();
       ProgressBar progressBar = null;
@@ -254,7 +253,7 @@ private void openExistingDataSet() {
       if (listFiles != null) {
          for (File f : listFiles) {
             // Heuristics to only read tiff files, and not files created by the
-            // OS (starting with ".")
+            // OS (starting with "._")
             String fileName = f.getName();
             if (fileName.endsWith(".tif") || fileName.endsWith(".TIF")) {
                if (!fileName.startsWith("._")) {
@@ -484,14 +483,14 @@ public synchronized void finished() {
       }
       ProgressBar progressBar = null;
       if (!GraphicsEnvironment.isHeadless()) {
-         // progressBar = new ProgressBar(parent_, "Finishing Files", 0,
-         //        positionToFileSet_.size());
+         progressBar = new ProgressBar(parent_,
+                 "Important: do not close Micro-Manager until files are finished writing.",
+                 0, positionToFileSet_.size());
       }
       try {
          int count = 0;
          if (progressBar != null) {
             progressBar.setProgress(count);
-            progressBar.setVisible(true);
          }
          for (FileSet p : positionToFileSet_.values()) {
             p.finishAbortedAcqIfNeeded();
@@ -525,10 +524,6 @@ public synchronized void finished() {
                filename = p.getCurrentFilename();
                p.finished(fullOMEXMLMetadata, ijDescription);
                master = p;
-               count++;
-               if (progressBar != null) {
-                  progressBar.setProgress(count);
-               }
                break;
             }
          }
@@ -557,10 +552,10 @@ public synchronized void finished() {
                progressBar.setProgress(count);
             }
          }
-         //shut down writing executor--pause here until all tasks have finished
-         //writing so that no attempt is made to close the dataset (and thus
-         //the FileChannel) before everything has finished writing mkae sure
-         //all images have finished writing if they are on seperate thread
+         // shut down writing executor--pause here until all tasks have finished
+         // writing so that no attempt is made to close the dataset (and thus
+         // the FileChannel) before everything has finished writing make sure
+         // all images have finished writing if they are on separate thread
          if (writingExecutor_ != null && !writingExecutor_.isShutdown()) {
             writingExecutor_.shutdown();
             try {
@@ -580,7 +575,8 @@ public synchronized void finished() {
          ReportingUtils.logError(ex);
       } finally {
          if (progressBar != null) {
-            progressBar.setVisible(false);
+            final ProgressBar pb = progressBar;
+            SwingUtilities.invokeLater(() -> pb.setVisible(false));
          }
          // release resources
          omeMetadata_ = null;

mmstudio/src/main/java/org/micromanager/internal/utils/ProgressBar.java

@@ -34,8 +34,7 @@
 /**
  * Utility class to show a ProgressBar.
  * Construction of the ProgressBar is done on the EDT, on the first call of
- * SetProgress.  Thus, it is safe to call this class from any thread, with the
- * possible exception of a call to setVisible(false) from a non-EDT thread.
+ * SetProgress.  Thus, it is safe to call this class from any thread.
  */
 public final class ProgressBar extends JPanel {
    private static final long serialVersionUID = 1L;
@@ -122,7 +121,12 @@ public void setVisible(boolean visible) {
          });
          return;
       }
-      frame_.setVisible(visible);
+      if (visible && frame_ == null) {
+         initialize();
+      }
+      if (frame_ != null) {
+         frame_.setVisible(visible);
+      }
    }
 
    public void setRange(int min, int max) {