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Merge pull request #450 from girder/ometiff-variations
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Read more OME Tiff files.
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@manthey
manthey authored Jun 4, 2020
2 parents d1f4f89 + 6b237f8 commit d53274e
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Showing 3 changed files with 89 additions and 29 deletions.
63 changes: 37 additions & 26 deletions sources/ometiff/large_image_source_ometiff/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
# limitations under the License.
##############################################################################

import copy
import math
import numpy
import PIL.Image
Expand Down Expand Up @@ -101,30 +102,7 @@ def __init__(self, path, **kwargs):
raise TileSourceException('Not an OME Tiff')
self._omeinfo = info['OME']
self._checkForOMEZLoop(largeImagePath)
if isinstance(self._omeinfo['Image'], dict):
self._omeinfo['Image'] = [self._omeinfo['Image']]
for img in self._omeinfo['Image']:
if isinstance(img['Pixels'].get('TiffData'), dict):
img['Pixels']['TiffData'] = [img['Pixels']['TiffData']]
if isinstance(img['Pixels'].get('Plane'), dict):
img['Pixels']['Plane'] = [img['Pixels']['Plane']]
try:
self._omebase = self._omeinfo['Image'][0]['Pixels']
if ((not len(self._omebase['TiffData']) or (
len(self._omebase['TiffData']) == 1 and
self._omebase['TiffData'][0] == {})) and
len(self._omebase['Plane'])):
self._omebase['TiffData'] = self._omebase['Plane']
if len({entry.get('UUID', {}).get('FileName', '')
for entry in self._omebase['TiffData']}) > 1:
raise TileSourceException('OME Tiff references multiple files')
if (len(self._omebase['TiffData']) != int(self._omebase['SizeC']) *
int(self._omebase['SizeT']) * int(self._omebase['SizeZ']) or
len(self._omebase['TiffData']) != len(
self._omebase.get('Plane', self._omebase['TiffData']))):
raise TileSourceException('OME Tiff contains frames that contain multiple planes')
except (KeyError, ValueError, IndexError):
raise TileSourceException('OME Tiff does not contain an expected record')
self._parseOMEInfo()
omeimages = [
entry['Pixels'] for entry in self._omeinfo['Image'] if
len(entry['Pixels']['TiffData']) == len(self._omebase['TiffData'])]
Expand Down Expand Up @@ -206,6 +184,39 @@ def _checkForOMEZLoop(self, largeImagePath):
info['Image']['Pixels']['PlanesFromZloop'] = 'true'
info['Image']['Pixels']['SizeZ'] = str(zloop)

def _parseOMEInfo(self):
if isinstance(self._omeinfo['Image'], dict):
self._omeinfo['Image'] = [self._omeinfo['Image']]
for img in self._omeinfo['Image']:
if isinstance(img['Pixels'].get('TiffData'), dict):
img['Pixels']['TiffData'] = [img['Pixels']['TiffData']]
if isinstance(img['Pixels'].get('Plane'), dict):
img['Pixels']['Plane'] = [img['Pixels']['Plane']]
try:
self._omebase = self._omeinfo['Image'][0]['Pixels']
if ((not len(self._omebase['TiffData']) or
len(self._omebase['TiffData']) == 1) and
len(self._omebase['Plane'])):
if not len(self._omebase['TiffData']) or self._omebase['TiffData'][0] == {}:
self._omebase['TiffData'] = self._omebase['Plane']
elif (int(self._omebase['TiffData'][0].get('PlaneCount', 0)) ==
len(self._omebase['Plane'])):
planes = copy.deepcopy(self._omebase['Plane'])
for idx, plane in enumerate(planes):
plane['IFD'] = plane.get(
'IFD', int(self._omebase['TiffData'][0].get('IFD', 0)) + idx)
self._omebase['TiffData'] = planes
if len({entry.get('UUID', {}).get('FileName', '')
for entry in self._omebase['TiffData']}) > 1:
raise TileSourceException('OME Tiff references multiple files')
if (len(self._omebase['TiffData']) != int(self._omebase['SizeC']) *
int(self._omebase['SizeT']) * int(self._omebase['SizeZ']) or
len(self._omebase['TiffData']) != len(
self._omebase.get('Plane', self._omebase['TiffData']))):
raise TileSourceException('OME Tiff contains frames that contain multiple planes')
except (KeyError, ValueError, IndexError):
raise TileSourceException('OME Tiff does not contain an expected record')

def getMetadata(self):
"""
Return a dictionary of metadata containing levels, sizeX, sizeY,
Expand Down Expand Up @@ -238,8 +249,8 @@ def getMetadata(self):
for key in reftbl:
if key in frame and not reftbl[key] in frame:
frame[reftbl[key]] = int(frame[key])
if frame[reftbl[key]] + 1 > maxref.get(reftbl[key], 0):
maxref[reftbl[key]] = frame[reftbl[key]] + 1
if reftbl[key] in frame and frame[reftbl[key]] + 1 > maxref.get(reftbl[key], 0):
maxref[reftbl[key]] = frame[reftbl[key]] + 1
frame['Frame'] = idx
if (idx and (
frame.get('IndexV') != result['frames'][idx - 1].get('IndexV') or
Expand Down
25 changes: 22 additions & 3 deletions sources/tiff/large_image_source_tiff/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,14 @@ class TiffFileTileSource(FileTileSource):
'image/x-ptif': SourcePriority.PREFERRED,
}

# When getting tiles for otherwise empty directories (missing powers of
# two), we composite the tile from higher resolution levels. This can use
# excessive memory if there are too many missing levels. For instance, if
# there are six missing levels and the tile size is 1024 square RGBA, then
# 16 Gb are needed for the composited tile at a minimum. By setting
# _maxSkippedLevels, such large gaps are composited in stages.
_maxSkippedLevels = 3

def __init__(self, path, **kwargs):
"""
Initialize the tile class. See the base class for other available
Expand Down Expand Up @@ -272,9 +280,13 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
try:
allowStyle = True
if self._tiffDirectories[z] is None:
if sparseFallback:
raise IOTiffException('Missing z level %d' % z)
tile = self.getTileFromEmptyDirectory(x, y, z, **kwargs)
try:
tile = self.getTileFromEmptyDirectory(x, y, z, **kwargs)
except Exception:
if sparseFallback:
raise IOTiffException('Missing z level %d' % z)
else:
raise
allowStyle = False
format = TILE_FORMAT_PIL
else:
Expand Down Expand Up @@ -327,10 +339,14 @@ def getTileFromEmptyDirectory(self, x, y, z, **kwargs):
:param z: original level.
:returns: tile in PIL format.
"""
basez = z
scale = 1
while self._tiffDirectories[z] is None:
scale *= 2
z += 1
while z - basez > self._maxSkippedLevels:
z -= self._maxSkippedLevels
scale = int(scale / 2 ** self._maxSkippedLevels)
tile = PIL.Image.new(
'RGBA', (self.tileWidth * scale, self.tileHeight * scale))
maxX = 2.0 ** (z + 1 - self.levels) * self.sizeX / self.tileWidth
Expand Down Expand Up @@ -361,8 +377,11 @@ def getPreferredLevel(self, level):
:returns level: a level with actual data that is no lower resolution.
"""
level = max(0, min(level, self.levels - 1))
baselevel = level
while self._tiffDirectories[level] is None and level < self.levels - 1:
level += 1
while level - baselevel > self._maxSkippedLevels:
level -= self._maxSkippedLevels
return level

def getAssociatedImagesList(self):
Expand Down
30 changes: 30 additions & 0 deletions test/test_source_ometiff.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,10 @@

import json
import numpy
from xml.etree import cElementTree

from large_image.constants import TILE_FORMAT_NUMPY
from large_image.tilesource import etreeToDict
import large_image_source_ometiff

from . import utilities
Expand Down Expand Up @@ -81,3 +83,31 @@ def testInternalMetadata():
source = large_image_source_ometiff.OMETiffFileTileSource(imagePath)
metadata = source.getInternalMetadata()
assert 'omeinfo' in metadata


def testXMLParsing():
samples = [{
'xml': """<?xml version='1.0' encoding='utf-8'?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:1ae9b229-162c-4431-8be0-1833b52302e5" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" PhysicalSizeX="0.32499998807907104" PhysicalSizeXUnit="µm" PhysicalSizeY="0.32499998807907104" PhysicalSizeYUnit="µm" SizeC="3" SizeT="1" SizeX="57346" SizeY="54325" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" Name="Red" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:1" Name="Green" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:2" Name="Blue" SamplesPerPixel="1"><LightPath /></Channel><TiffData IFD="0" PlaneCount="3" /><Plane TheC="0" TheT="0" TheZ="0" /><Plane TheC="1" TheT="0" TheZ="0" /><Plane TheC="2" TheT="0" TheZ="0" /></Pixels></Image></OME>""", # noqa
'checks': {
'frames': 3,
'IndexRange': {'IndexC': 3},
'IndexStride': {'IndexC': 1},
'channelmap': {'Blue': 2, 'Green': 1, 'Red': 0},
'channels': ['Red', 'Green', 'Blue'],
}
}]
# Create a source so we can use internal functions for testing
imagePath = utilities.externaldata('data/sample.ome.tif.sha512')
source = large_image_source_ometiff.OMETiffFileTileSource(imagePath)
for sample in samples:
xml = cElementTree.fromstring(sample['xml'])
info = etreeToDict(xml)
source._omeinfo = info['OME']
source._parseOMEInfo()
metadata = source.getMetadata()
for key, value in sample['checks'].items():
if key in {'frames'}:
assert len(metadata[key]) == value
else:
assert metadata[key] == value

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