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From "ASF GitHub Bot (Jira)" <j...@apache.org>
Subject [jira] [Work logged] (IMAGING-265) ArrayIndexOutOfBoundsException on reading simple GeoTIFF
Date Tue, 22 Sep 2020 03:23:00 GMT

     [ https://issues.apache.org/jira/browse/IMAGING-265?focusedWorklogId=487625&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-487625
]

ASF GitHub Bot logged work on IMAGING-265:
------------------------------------------

                Author: ASF GitHub Bot
            Created on: 22/Sep/20 03:22
            Start Date: 22/Sep/20 03:22
    Worklog Time Spent: 10m 
      Work Description: gwlucastrig commented on a change in pull request #98:
URL: https://github.com/apache/commons-imaging/pull/98#discussion_r491751220



##########
File path: src/main/java/org/apache/commons/imaging/formats/tiff/datareaders/DataReaderStrips.java
##########
@@ -291,25 +318,50 @@ public BufferedImage readImageData(final Rectangle subImage)
         //        or working
         final ImageBuilder workingBuilder =
                 new ImageBuilder(width, workingHeight, false);
-
-        for (int strip = strip0; strip <= strip1; strip++) {
-            final long rowsPerStripLong = 0xFFFFffffL & rowsPerStrip;
-            final long rowsRemaining = height - (strip * rowsPerStripLong);
-            final long rowsInThisStrip = Math.min(rowsRemaining, rowsPerStripLong);
-            final long bytesPerRow = (bitsPerPixel * width + 7) / 8;
-            final long bytesPerStrip = rowsInThisStrip * bytesPerRow;
-            final long pixelsPerStrip = rowsInThisStrip * width;
-
-            final byte[] compressed = imageData.getImageData(strip).getData();
-
-            final byte[] decompressed = decompress(compressed, compression,
-                    (int) bytesPerStrip, width, (int) rowsInThisStrip);
-
-            interpretStrip(
-                    workingBuilder,
-                    decompressed,
-                    (int) pixelsPerStrip,
-                    yLimit);
+        if (planarConfiguration != 2) {
+            for (int strip = strip0; strip <= strip1; strip++) {
+                final long rowsPerStripLong = 0xFFFFffffL & rowsPerStrip;
+                final long rowsRemaining = height - (strip * rowsPerStripLong);
+                final long rowsInThisStrip = Math.min(rowsRemaining, rowsPerStripLong);
+                final long bytesPerRow = (bitsPerPixel * width + 7) / 8;
+                final long bytesPerStrip = rowsInThisStrip * bytesPerRow;
+                final long pixelsPerStrip = rowsInThisStrip * width;
+
+                final byte[] compressed = imageData.getImageData(strip).getData();
+
+                final byte[] decompressed = decompress(compressed, compression,
+                  (int) bytesPerStrip, width, (int) rowsInThisStrip);
+
+                interpretStrip(
+                  workingBuilder,
+                  decompressed,
+                  (int) pixelsPerStrip,
+                  yLimit);
+            }
+        } else {
+            int nStripsInPlane = imageData.getImageDataLength() / 3;
+            for (int strip = strip0; strip <= strip1; strip++) {
+                final long rowsPerStripLong = 0xFFFFffffL & rowsPerStrip;
+                final long rowsRemaining = height - (strip * rowsPerStripLong);
+                final long rowsInThisStrip = Math.min(rowsRemaining, rowsPerStripLong);
+                final long bytesPerRow = (bitsPerPixel * width + 7) / 8;
+                final long bytesPerStrip = rowsInThisStrip * bytesPerRow;
+                final long pixelsPerStrip = rowsInThisStrip * width;
+
+                byte[] b = new byte[(int) bytesPerStrip];
+                for (int iPlane = 0; iPlane < 3; iPlane++) {
+                    int planeStrip = iPlane * nStripsInPlane + strip;
+                    final byte[] compressed = imageData.getImageData(planeStrip).getData();
+                    final byte[] decompressed = decompress(compressed, compression,
+                      (int) bytesPerStrip, width, (int) rowsInThisStrip);
+                    int index = iPlane;
+                    for (int i = 0; i < decompressed.length; i++) {
+                        b[index] = decompressed[i];
+                        index += 3;
+                    }
+                }
+                interpretStrip(workingBuilder, b, (int) pixelsPerStrip, height);
+            }

Review comment:
       These are two methods have a lot of redundancy and it would be better to combine them
into one.  Unfortunately, they are both public APIs, so I'm not sure we could change their
external appearance.   Of course, we could create a single, consolidated method that does
the processing. Then we could rewrite the existing methods to be "wrapper" methods that called
the new consolidated method.
   
   I think it might be better to treat that change as a separate pull request.
   
   I contributed the "sub-image" logic a number of years ago. At the time, there was a certain
amount of resistance to the idea of a sub-image API, but I thought it was necessary because
may GeoTIFFs are huge (I'd been working with some that are 20000-by-20000 pixels large). 
Anyway, I think I left the original method in place because the code was simpler than the
sub-image code and I thought it would serve as a reference for anyone who was trying to figure
out how it worked.  But I think you are right and the time has come to clean things up. 

##########
File path: src/main/java/org/apache/commons/imaging/formats/tiff/TiffImageData.java
##########
@@ -140,8 +145,8 @@ public ImageDataReader getDataReader(final TiffDirectory directory,
     public abstract ImageDataReader getDataReader(TiffDirectory directory,
             PhotometricInterpreter photometricInterpreter, int bitsPerPixel,
             int[] bitsPerSample, int predictor, int samplesPerPixel, int width,
-            int height, int compression, ByteOrder byteOrder) throws IOException,
-            ImageReadException;
+      int height, int compression, int planarConfiguration,
+      ByteOrder byteOrder) throws IOException,            ImageReadException;

Review comment:
       Some of the spacing got accidentally modified when I edited file.  I thought I cleaned
them all, but I missed this one. Sorry.

##########
File path: src/main/java/org/apache/commons/imaging/formats/tiff/datareaders/DataReaderStrips.java
##########
@@ -237,27 +240,51 @@ private void interpretStrip(
 
     @Override
     public void readImageData(final ImageBuilder imageBuilder)
-            throws ImageReadException, IOException {
-        for (int strip = 0; strip < imageData.getImageDataLength(); strip++) {
-            final long rowsPerStripLong = 0xFFFFffffL & rowsPerStrip;
-            final long rowsRemaining = height - (strip * rowsPerStripLong);
-            final long rowsInThisStrip = Math.min(rowsRemaining, rowsPerStripLong);
-            final long bytesPerRow = (bitsPerPixel * width + 7) / 8;
-            final long bytesPerStrip = rowsInThisStrip * bytesPerRow;
-            final long pixelsPerStrip = rowsInThisStrip * width;
-
-            final byte[] compressed = imageData.getImageData(strip).getData();
-
-            final byte[] decompressed = decompress(compressed, compression,
-                    (int) bytesPerStrip, width, (int) rowsInThisStrip);
-
-            interpretStrip(
-                    imageBuilder,
-                    decompressed,
-                    (int) pixelsPerStrip,
-                    height);
-
+      throws ImageReadException, IOException {
+        if (planarConfiguration != 2) {

Review comment:
       You are absolutely right about using the TiffTagConstant values in the places you cited.
 Actually, I wanted to make line 244 test for planarConfiguration == "Chunky" rather than
!= "Planar", but I was afraid that there might be places in the code where the planarConfiguration
variable didn't get set correctly.  So I thought this would be safer.
   
   If we ever get our hands on some additional test files, I might revisit this.  But that
may be unlikely...  The Tiff Specification itself describes planar-configuration 2 as follows:
_PlanarConfiguration=2 is not currently in widespread use and it is not recommended for general
interchange. It is used an extension and Baseline TIFF readers are not required to support
it._

##########
File path: src/test/java/org/apache/commons/imaging/formats/tiff/datareaders/DataReaderStripsTest.java
##########
@@ -24,7 +24,7 @@
     @Test
     public void testApplyPredictor() throws Exception {
         final int[] bitsPerPixel = {1,2,3};
-        final DataReaderStrips strips = new DataReaderStrips(null, null, 3, bitsPerPixel,
2, 4, 0, 3, 1, 1, null, 2, null);
+        final DataReaderStrips strips = new DataReaderStrips(null, null, 3, bitsPerPixel,
2, 4, 0, 3, 1, 1, 1, null, 2, null);

Review comment:
       Agreed. Good catch.

##########
File path: src/main/java/org/apache/commons/imaging/formats/tiff/datareaders/DataReaderStrips.java
##########
@@ -291,25 +318,50 @@ public BufferedImage readImageData(final Rectangle subImage)
         //        or working
         final ImageBuilder workingBuilder =
                 new ImageBuilder(width, workingHeight, false);
-
-        for (int strip = strip0; strip <= strip1; strip++) {
-            final long rowsPerStripLong = 0xFFFFffffL & rowsPerStrip;
-            final long rowsRemaining = height - (strip * rowsPerStripLong);
-            final long rowsInThisStrip = Math.min(rowsRemaining, rowsPerStripLong);
-            final long bytesPerRow = (bitsPerPixel * width + 7) / 8;
-            final long bytesPerStrip = rowsInThisStrip * bytesPerRow;
-            final long pixelsPerStrip = rowsInThisStrip * width;
-
-            final byte[] compressed = imageData.getImageData(strip).getData();
-
-            final byte[] decompressed = decompress(compressed, compression,
-                    (int) bytesPerStrip, width, (int) rowsInThisStrip);
-
-            interpretStrip(
-                    workingBuilder,
-                    decompressed,
-                    (int) pixelsPerStrip,
-                    yLimit);
+        if (planarConfiguration != 2) {

Review comment:
       Agreed. Good catch.

##########
File path: src/main/java/org/apache/commons/imaging/formats/tiff/TiffImageParser.java
##########
@@ -898,7 +921,7 @@ TiffRasterData getFloatingPointRasterData(
 
         final ImageDataReader dataReader = imageData.getDataReader(directory,
             photometricInterpreter, bitsPerPixel, bitsPerSample, predictor,
-            samplesPerPixel, width, height, compression, byteOrder);
+          samplesPerPixel, width, height, compression, 1, byteOrder);

Review comment:
        Agreed. Good catch.




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Issue Time Tracking
-------------------

    Worklog Id:     (was: 487625)
    Time Spent: 1h 40m  (was: 1.5h)

> ArrayIndexOutOfBoundsException on reading simple GeoTIFF
> --------------------------------------------------------
>
>                 Key: IMAGING-265
>                 URL: https://issues.apache.org/jira/browse/IMAGING-265
>             Project: Commons Imaging
>          Issue Type: Bug
>          Components: Format: TIFF
>    Affects Versions: 1.0-alpha2
>            Reporter: edgar soldin
>            Assignee: Bruno P. Kinoshita
>            Priority: Major
>         Attachments: small_world.tif, small_world_split.jpg
>
>          Time Spent: 1h 40m
>  Remaining Estimate: 0h
>
> hi,
>  
> we on the OpenJUMP project cannot open some GeoTIFFs with commons.imaging . for details
you may find a ticket in our bug tracker [https://sourceforge.net/p/jump-pilot/bugs/498/] .
>  
> the gist is: on loading the attached file getBufferedImage() fails with this stack
> Caused by: java.lang.ArrayIndexOutOfBoundsException: 8000Caused by: java.lang.ArrayIndexOutOfBoundsException:
8000 at org.apache.commons.imaging.formats.tiff.datareaders.DataReaderStrips.interpretStrip(DataReaderStrips.java:196)
at org.apache.commons.imaging.formats.tiff.datareaders.DataReaderStrips.readImageData(DataReaderStrips.java:254)
at org.apache.commons.imaging.formats.tiff.TiffImageParser.getBufferedImage(TiffImageParser.java:665)
at org.apache.commons.imaging.formats.tiff.TiffDirectory.getTiffImage(TiffDirectory.java:254)
at org.apache.commons.imaging.formats.tiff.TiffImageParser.getBufferedImage(TiffImageParser.java:469)
at org.apache.commons.imaging.Imaging.getBufferedImage(Imaging.java:1442) at org.apache.commons.imaging.Imaging.getBufferedImage(Imaging.java:1335)
at org.apache.commons.imaging.Imaging.getBufferedImage(Imaging.java:1304) at com.vividsolutions.jump.workbench.imagery.graphic.CommonsImage.initImage(CommonsImage.java:108)



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