From 4c856c4cad1567200cfc97d54e16d080a65b8be7 Mon Sep 17 00:00:00 2001
From: David Manthey <david.manthey@kitware.com>
Date: Wed, 24 Aug 2022 11:03:23 -0400
Subject: [PATCH] Better ignore tiff directories that aren't part of the
 pyramid.

We had one test file with a "thumbnail" image that was tiled but at a
different resolution than expected.  This was mistakenly used as a level
of the image.
---
 CHANGELOG.md                                     |  1 +
 sources/tiff/large_image_source_tiff/__init__.py | 14 +++++++++++++-
 test/datastore.py                                |  5 ++++-
 test/test_source_base.py                         |  6 +++---
 test/test_source_tiff.py                         |  6 ++++++
 5 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5cacc7e86..480d1eb4b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 ### Bug Fixes
 - Fix iterating tiles where the overlap larger than the tile size ([940](../../pull/940))
+- Better ignore tiff directories that aren't part of the pyramid ([943](../../pull/943))
 
 ## 1.16.1
 
diff --git a/sources/tiff/large_image_source_tiff/__init__.py b/sources/tiff/large_image_source_tiff/__init__.py
index fdee1febd..697df4a51 100644
--- a/sources/tiff/large_image_source_tiff/__init__.py
+++ b/sources/tiff/large_image_source_tiff/__init__.py
@@ -85,7 +85,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
 
     _maxAssociatedImageSize = 8192
 
-    def __init__(self, path, **kwargs):
+    def __init__(self, path, **kwargs):  # noqa
         """
         Initialize the tile class.  See the base class for other available
         parameters.
@@ -141,6 +141,18 @@ def __init__(self, path, **kwargs):
                     ((td.imageHeight % td.tileHeight) and
                         not nearPowerOfTwo(td.imageHeight, highest.imageHeight))):
                 continue
+            # If a layer is a multiple of the tile size, the number of tiles
+            # should be a power of two rounded up from the primary.
+            if (not (td.imageWidth % td.tileWidth) and not (td.imageHeight % td.tileHeight)):
+                htw = highest.imageWidth // td.tileWidth
+                hth = highest.imageHeight // td.tileHeight
+                ttw = td.imageWidth // td.tileWidth
+                tth = td.imageHeight // td.tileHeight
+                while (htw > ttw and htw > 1) or (hth > tth and hth > 1):
+                    htw = (htw + 1) // 2
+                    hth = (hth + 1) // 2
+                if htw != ttw or hth != tth:
+                    continue
             directories[level] = td
         if not len(directories) or (len(directories) < 2 and max(directories.keys()) + 1 > 4):
             raise TileSourceError(
diff --git a/test/datastore.py b/test/datastore.py
index 8c88e6649..fe9f007ba 100644
--- a/test/datastore.py
+++ b/test/datastore.py
@@ -79,7 +79,10 @@
     'TC_NG_SFBay_US_Geo.tif': 'sha512:da2e66528f77a5e10af5de9e496074b77277c3da81dafc69790189510e5a7e18dba9e966329d36c979f1b547f0d36a82fbc4cfccc65ae9ef9e2747b5a9ee77b0',  # noqa
     # Geospatial tiff - cloud optimized
     'TC_NG_SFBay_US_Geo_COG.tif': 'sha512:5e56cdb8fb1a02615698a153862c10d5292b1ad42836a6e8bce5627e93a387dc0d3c9b6cfbd539796500bc2d3e23eafd07550f8c214e9348880bbbc6b3b0ea0c',  # noqa
-
+    # Tiff with extra overview that was originally misinterpreted as a layer
+    # Source: generated from a tifftools dump with the image descriptions and
+    #  topmost layer removed.
+    'extraoverview.tiff': 'sha512:22793cc6285ad11fbb47927c3d546d35e531a73852b79a9248ba489b421792e3a55da61e00079372bcf72a7e11b12e1ee69d553620edf46ff8d86ad2a9da9fc5',  # noqa
 }
 
 
diff --git a/test/test_source_base.py b/test/test_source_base.py
index d3a2ef27b..dbf8ba193 100644
--- a/test/test_source_base.py
+++ b/test/test_source_base.py
@@ -43,11 +43,11 @@
     'openjpeg': {'read': r'\.(jp2)$'},
     'openslide': {
         'read': r'\.(ptif|svs|tif.*)$',
-        'noread': r'(oahu|DDX58_AXL|huron\.image2_jpeg2k|landcover_sample|d042-353\.crop|US_Geo\.)',
+        'noread': r'(oahu|DDX58_AXL|huron\.image2_jpeg2k|landcover_sample|d042-353\.crop|US_Geo\.|extraoverview)',  # noqa
         'skipTiles': r'one_layer_missing'},
     'pil': {
         'read': r'\.(jpeg|png|tif.*)$',
-        'noread': r'(G10-3|JK-kidney|d042-353|huron|one_layer_missing|US_Geo)'},
+        'noread': r'(G10-3|JK-kidney|d042-353|huron|one_layer_missing|US_Geo|extraoverview)'},
     'test': {'any': True, 'skipTiles': r''},
     'tiff': {
         'read': r'\.(ptif|scn|svs|tif.*)$',
@@ -57,7 +57,7 @@
     'vips': {
         'read': r'',
         'noread': r'\.(nc|nd2|yml|yaml|json|czi|png|svs|scn)$',
-        'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles|JK-kidney_B-gal_H3_4C_1-500sec\.jp2)'},  # noqa
+        'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles|JK-kidney_B-gal_H3_4C_1-500sec\.jp2|extraoverview)'},  # noqa
 }
 if sys.version_info >= (3, 7):
     SourceAndFiles.update({
diff --git a/test/test_source_tiff.py b/test/test_source_tiff.py
index a01a8d926..da0f0b239 100644
--- a/test/test_source_tiff.py
+++ b/test/test_source_tiff.py
@@ -868,3 +868,9 @@ def testTileFrames():
     info = tifftools.read_tiff(image)
     assert len(info['ifds']) == 3
     os.unlink(image)
+
+
+def testExtraOverview():
+    imagePath = datastore.fetch('extraoverview.tiff')
+    source = large_image_source_tiff.open(imagePath)
+    assert len([d for d in source._tiffDirectories if d is not None]) == 3