Merge pull request #1168 from girder/parse-vendor-info

Parse qptiff and imagej vendor information.

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Change Log
 
+## 1.21.1
+
+### Improvements
+- Parse qptiff and imagej vendor information ([#1168](../../pull/1168))
+
 ## 1.21.0
 
 ### Improvements

sources/tiff/large_image_source_tiff/__init__.py

@@ -169,6 +169,7 @@ def __init__(self, path, **kwargs):  # noqa
         self.sizeX = highest.imageWidth
         self.sizeY = highest.imageHeight
         self._checkForInefficientDirectories()
+        self._checkForVendorSpecificTags()
 
     def _scanDirectories(self):
         lastException = None
@@ -347,6 +348,7 @@ def _initWithTiffTools(self):  # noqa
             for idx in range(self.levels - 1)]
         self._tiffDirectories.append(dir0)
         self._checkForInefficientDirectories()
+        self._checkForVendorSpecificTags()
         return True
 
     def _checkForInefficientDirectories(self, warn=True):
@@ -396,6 +398,27 @@ def _reorient_numpy_image(self, image, orientation):
             image = image[::, ::-1, ::]
         return image
 
+    def _checkForVendorSpecificTags(self):
+        if not hasattr(self, '_frames') or len(self._frames) <= 1:
+            return
+        if self._frames[0].get('frame', {}).get('IndexC'):
+            return
+        dir = self._tiffDirectories[-1]
+        if not hasattr(dir, '_description_record'):
+            return
+        if dir._description_record.get('PerkinElmer-QPI-ImageDescription', {}).get('Biomarker'):
+            channels = []
+            for frame in range(len(self._frames)):
+                dir = self._getDirFromCache(*self._frames[frame]['dirs'][-1])
+                channels.append(dir._description_record.get(
+                    'PerkinElmer-QPI-ImageDescription', {}).get('Biomarker'))
+                if channels[-1] is None:
+                    return
+            self._frames[0]['channels'] = channels
+            for idx, frame in enumerate(self._frames):
+                frame.setdefault('frame', {})
+                frame['frame']['IndexC'] = idx
+
     def _addAssociatedImage(self, largeImagePath, directoryNum, mustBeTiled=False, topImage=None):
         """
         Check if the specified TIFF directory contains an image with a sensible

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -1,3 +1,4 @@
+import json
 import logging
 import math
 import os
@@ -76,6 +77,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     _tileSize = 512
     _minImageSize = 128
     _minTileSize = 128
+    _singleTileSize = 1024
     _maxTileSize = 2048
     _minAssociatedImageSize = 64
     _maxAssociatedImageSize = 8192
@@ -102,6 +104,8 @@ def __init__(self, path, **kwargs):
         self.tileWidth = self.tileHeight = self._tileSize
         s = self._tf.series[maxseries]
         self._baseSeries = s
+        if len(s.levels) == 1:
+            self.tileWidth = self.tileHeight = self._singleTileSize
         page = s.pages[0]
         if ('TileWidth' in page.tags and
                 self._minTileSize <= page.tags['TileWidth'].value <= self._maxTileSize):
@@ -243,6 +247,15 @@ def _findAssociatedImages(self):
                         max(entry['width'], entry['height']) >= self._minAssociatedImageSize):
                     self._associatedImages[id] = entry
 
+    def _handle_imagej(self):
+        try:
+            ijm = self._tf.pages[0].tags['IJMetadata'].value
+            if (ijm['Labels'] and len(ijm['Labels']) == self._framecount and
+                    not getattr(self, '_channels', None)):
+                self._channels = ijm['Labels']
+        except Exception:
+            pass
+
     def _handle_scn(self):  # noqa
         """
         For SCN files, parse the xml and possibly adjust how associated images
@@ -359,7 +372,8 @@ def getInternalMetadata(self, **kwargs):
         pages.extend([page for page in self._tf.pages if page not in pagesInSeries])
         for page in pages:
             for tag in getattr(page, 'tags', []):
-                if tag.dtype_name == 'ASCII' and tag.value:
+                if (tag.dtype_name == 'ASCII' or (
+                        tag.dtype_name == 'BYTE' and isinstance(tag.value, dict))) and tag.value:
                     key = basekey = tag.name
                     suffix = 0
                     while key in result:
@@ -368,6 +382,13 @@ def getInternalMetadata(self, **kwargs):
                         suffix += 1
                         key = '%s_%d' % (basekey, suffix)
                     result[key] = tag.value
+                    if isinstance(result[key], dict):
+                        result[key] = result[key].copy()
+                        for subkey in list(result[key]):
+                            try:
+                                json.dumps(result[key][subkey])
+                            except Exception:
+                                del result[key][subkey]
         if hasattr(self, '_xml') and 'xml' not in result:
             result.pop('ImageDescription', None)
             result['xml'] = self._xml
@@ -420,11 +441,13 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
             if sidx not in self._zarrcache:
                 if len(self._zarrcache) > 10:
                     self._zarrcache = {}
-                self._zarrcache[sidx] = zarr.open(series.aszarr(), mode='r')
-            za = self._zarrcache[sidx]
+                za = zarr.open(series.aszarr(), mode='r')
+                hasgbs = hasattr(za[0], 'get_basic_selection')
+                self._zarrcache[sidx] = (za, hasgbs)
+            za, hasgbs = self._zarrcache[sidx]
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
-        if hasattr(za[0], 'get_basic_selection'):
+        if hasgbs:
             bza = za[0]
             # we could cache this
             for ll in range(len(series.levels) - 1, 0, -1):