From 963f8f826957a678b9cfbe15add2aaaa4584a14e Mon Sep 17 00:00:00 2001
From: David Manthey <david.manthey@kitware.com>
Date: Fri, 27 Sep 2019 09:18:07 -0400
Subject: [PATCH] This improves handling tiff files with multiple tiled images.

Before, if there are multiple tiled images (each possibly with a pyramid
of smaller images), the image with the largest tiles was selected.  Now,
the image with the largest tiles that are not the whole image are
selected.

Also, this adds parsing for Optrascan metadata stored as xml within the
pixel space of an uncompressed image.
---
 .../tiff/large_image_source_tiff/__init__.py  | 67 ++++++++++++++++---
 1 file changed, 57 insertions(+), 10 deletions(-)

diff --git a/sources/tiff/large_image_source_tiff/__init__.py b/sources/tiff/large_image_source_tiff/__init__.py
index a1e0724f3..171f1d13b 100644
--- a/sources/tiff/large_image_source_tiff/__init__.py
+++ b/sources/tiff/large_image_source_tiff/__init__.py
@@ -107,7 +107,7 @@ def __init__(self, path, **kwargs):
             if level < 0:
                 continue
             # Store information for sorting with the directory.
-            alldir.append((td.tileWidth * td.tileHeight, level,
+            alldir.append((level > 0, td.tileWidth * td.tileHeight, level,
                            td.imageWidth * td.imageHeight, directoryNum, td))
         # If there are no tiled images, raise an exception.
         if not len(alldir):
@@ -125,9 +125,11 @@ def __init__(self, path, **kwargs):
         # preferred image
         for tdir in alldir:
             td = tdir[-1]
-            level = tdir[1]
+            level = tdir[2]
             if (td.tileWidth != highest.tileWidth or
                     td.tileHeight != highest.tileHeight):
+                if not len(self._associatedImages):
+                    self._addAssociatedImage(largeImagePath, tdir[-2], True, highest)
                 continue
             # If a layer's image is not a multiple of the tile size, it should
             # be near a power of two of the highest resolution image.
@@ -151,19 +153,29 @@ def __init__(self, path, **kwargs):
         self.sizeX = highest.imageWidth
         self.sizeY = highest.imageHeight
 
-    def _addAssociatedImage(self, largeImagePath, directoryNum):
+    def _addAssociatedImage(self, largeImagePath, directoryNum, mustBeTiled=False, topImage=None):
         """
-        Check if the specified TIFF directory contains a non-tiled image with a
-        sensible image description that can be used as an ID.  If so, and if
-        the image isn't too large, add this image as an associated image.
+        Check if the specified TIFF directory contains an image with a sensible
+        image description that can be used as an ID.  If so, and if the image
+        isn't too large, add this image as an associated image.
 
         :param largeImagePath: path to the TIFF file.
         :param directoryNum: libtiff directory number of the image.
+        :param mustBeTiles: if true, use tiled images.  If false, require
+           untiled images.
+        :param topImage: if specified, add image-embedded metadata to this
+           image.
         """
         try:
-            associated = TiledTiffDirectory(largeImagePath, directoryNum, False)
-            id = associated._tiffInfo.get(
-                'imagedescription').strip().split(None, 1)[0].lower()
+            associated = TiledTiffDirectory(largeImagePath, directoryNum, mustBeTiled)
+            id = ''
+            if associated._tiffInfo.get('imagedescription'):
+                id = associated._tiffInfo.get(
+                    'imagedescription').strip().split(None, 1)[0].lower()
+            elif mustBeTiled:
+                id = 'dir%d' % directoryNum
+                if not len(self._associatedImages):
+                    id = 'macro'
             if not isinstance(id, six.text_type):
                 id = id.decode('utf8')
             # Only use this as an associated image if the parsed id is
@@ -172,7 +184,14 @@ def _addAssociatedImage(self, largeImagePath, directoryNum):
             if (id.isalnum() and len(id) > 3 and len(id) <= 20 and
                     associated._pixelInfo['width'] <= 8192 and
                     associated._pixelInfo['height'] <= 8192):
-                self._associatedImages[id] = associated._tiffFile.read_image()
+                image = associated._tiffFile.read_image()
+                # Optrascan scanners are store xml image descriptions in a
+                # "tiled image".  Check if this is the case, and, if so, parse
+                # such data
+                if image.tobytes()[:6] == b'<?xml ':
+                    self._parseImageXml(image.tobytes().rsplit(b'>', 1)[0] + b'>', topImage)
+                    return
+                self._associatedImages[id] = image
         except (TiffException, AttributeError):
             # If we can't validate or read an associated image or it has no
             # useful imagedescription, fail quietly without adding an
@@ -184,6 +203,34 @@ def _addAssociatedImage(self, largeImagePath, directoryNum):
             config.getConfig('logger').exception(
                 'Could not use non-tiled TIFF image as an associated image.')
 
+    def _parseImageXml(self, xml, topImage):
+        """
+        Parse metadata stored in arbitrary xml and associate it with a specific
+        image.
+
+        :params xml: the xml as a string or bytes object.
+        :params topImage: the image to add metadata to.
+        """
+        if not topImage or topImage.pixelInfo.get('magnificaiton'):
+            return
+        topImage.parse_image_description(xml)
+        if not topImage._description_xml:
+            return
+        try:
+            xml = topImage._description_xml
+            # Optrascan metadata
+            scanDetails = xml.get('ScanInfo', xml.get('EncodeInfo'))['ScanDetails']
+            mag = float(scanDetails['Magnification'])
+            # In microns; convert to mm
+            scale = float(scanDetails['PixelResolution']) * 1e-3
+            topImage._pixelInfo = {
+                'magnification': mag,
+                'mm_x': scale,
+                'mm_y': scale,
+            }
+        except Exception:
+            pass
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.