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Update tifffile/tifffile.py
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@cgohlke
cgohlke committed Aug 31, 2024
1 parent ef34fd6 commit 8968a80
Showing 1 changed file with 171 additions and 28 deletions.
199 changes: 171 additions & 28 deletions tifffile/tifffile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@

:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
:License: BSD 3-Clause
:Version: 2024.8.28
:Version: 2024.8.30
:DOI: `10.5281/zenodo.6795860 <https://doi.org/10.5281/zenodo.6795860>`_

Quickstart
Expand Down Expand Up @@ -114,9 +114,13 @@
Revisions
---------

2024.8.28
2024.8.30

- Pass 5096 tests.
- Support writing OME Dataset and some StructuredAnnotations elements.

2024.8.28

- Fix LSM scan types and dimension orders (#269, breaking).
- Use IO[bytes] instead of BinaryIO for typing (#268).

Expand Down Expand Up @@ -630,9 +634,9 @@
... )

Write a multi-dimensional, multi-resolution (pyramidal), multi-series OME-TIFF
file with metadata. Sub-resolution images are written to SubIFDs. Limit
parallel encoding to 2 threads. Write a thumbnail image as a separate image
series:
file with optional metadata. Sub-resolution images are written to SubIFDs.
Limit parallel encoding to 2 threads. Write a thumbnail image as a separate
image series:

>>> data = numpy.random.randint(0, 255, (8, 2, 512, 512, 3), 'uint8')
>>> subresolutions = 2
Expand All @@ -649,6 +653,12 @@
... 'PhysicalSizeYUnit': 'µm',
... 'Channel': {'Name': ['Channel 1', 'Channel 2']},
... 'Plane': {'PositionX': [0.0] * 16, 'PositionXUnit': ['µm'] * 16},
... 'Description': 'A multi-dimensional, multi-resolution image',
... 'MapAnnotation': { # for OMERO
... 'Namespace': 'openmicroscopy.org/PyramidResolution',
... '1': '256 256',
... '2': '128 128',
... },
... }
... options = dict(
... photometric='rgb',
Expand Down Expand Up @@ -748,14 +758,14 @@
to it via the Zarr interface (note: this does not work with compression):

>>> imwrite(
... 'temp.ome.tif',
... 'temp2.ome.tif',
... shape=(8, 800, 600),
... dtype='uint16',
... photometric='minisblack',
... tile=(128, 128),
... metadata={'axes': 'CYX'},
... )
>>> store = imread('temp.ome.tif', mode='r+', aszarr=True)
>>> store = imread('temp2.ome.tif', mode='r+', aszarr=True)
>>> z = zarr.open(store, mode='r+')
>>> z
<zarr.core.Array (8, 800, 600) uint16>
Expand Down Expand Up @@ -815,7 +825,7 @@

from __future__ import annotations

__version__ = '2024.8.28'
__version__ = '2024.8.30'

__all__ = [
'TiffFile',
Expand Down Expand Up @@ -15858,10 +15868,12 @@ class OmeXml:
... axes='CYX',
... Name='First Image',
... PhysicalSizeX=2.0,
... MapAnnotation={'key': 'value'},
... Dataset={'Name': 'FirstDataset'},
... )
>>> xml = omexml.tostring()
>>> xml
'<OME ...<Image ID="Image:0" Name="First Image">...</Image></OME>'
'<OME ...<Image ID="Image:0" Name="First Image">...</Image>...</OME>'
>>> OmeXml.validate(xml)
True

Expand All @@ -15873,8 +15885,8 @@ class OmeXml:
annotations: list[str]
"""OME-XML Annotation elements."""

elements: list[str]
"""Other OME-XML elements."""
datasets: list[str]
"""OME-XML Dataset elements."""

_xml: str
_ifd: int
Expand All @@ -15885,18 +15897,16 @@ def __init__(self, **metadata: Any) -> None:
self._ifd = 0
self.images = []
self.annotations = []
self.elements = []
self.datasets = []
# TODO: parse other OME elements from metadata
# Project
# Dataset
# Folder
# Experiment
# Plate
# Screen
# Experimenter
# ExperimenterGroup
# Instrument
# StructuredAnnotations
# ROI
if 'UUID' in metadata:
uuid = metadata['UUID'].split(':')[-1]
Expand All @@ -15913,10 +15923,10 @@ def __init__(self, **metadata: Any) -> None:
f'<OME xmlns="{schema}" '
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
f'xsi:schemaLocation="{schema} {schema}/ome.xsd" '
f'UUID="urn:uuid:{uuid}" {creator}>'
f'UUID="urn:uuid:{uuid}"{creator}>'
'{datasets}'
'{images}'
'{annotations}'
'{elements}'
'</OME>'
)

Expand Down Expand Up @@ -15957,11 +15967,15 @@ def addimage(
Additional OME-XML attributes or elements to be stored.

Image/Pixels:
Name, AcquisitionDate, Description, DimensionOrder,
Name, Description,
DimensionOrder, TypeDescription,
PhysicalSizeX, PhysicalSizeXUnit,
PhysicalSizeY, PhysicalSizeYUnit,
PhysicalSizeZ, PhysicalSizeZUnit,
TimeIncrement, TimeIncrementUnit.
TimeIncrement, TimeIncrementUnit,
StructuredAnnotations, BooleanAnnotation, DoubleAnnotation,
LongAnnotation, CommentAnnotation, MapAnnotation,
Dataset
Per Plane:
DeltaT, DeltaTUnit,
ExposureTime, ExposureTimeUnit,
Expand All @@ -15980,6 +15994,7 @@ def addimage(

"""
index = len(self.images)
annotation_refs = []

# get Image and Pixels metadata
metadata = metadata.get('OME', metadata)
Expand Down Expand Up @@ -16118,12 +16133,17 @@ def addimage(
'E': 'lambda',
'Q': 'other',
}
axestypedescr = metadata.get('TypeDescription', {})
for i, ax in enumerate(hiaxes):
if ax in 'APRHEQ':
if ax in axestypedescr:
typedescr = f'TypeDescription="{axestypedescr[ax]}" '
else:
typedescr = ''
x = hiaxes[i - 1 : i]
if x and x in 'TZC':
# use previous axis
modulo[x] = axestype[ax], shape[i]
modulo[x] = axestype[ax], shape[i], typedescr
else:
# use next unused axis
for x in 'TZC':
Expand All @@ -16132,7 +16152,7 @@ def addimage(
and x not in hiaxes
and x not in modulo
):
modulo[x] = axestype[ax], shape[i]
modulo[x] = axestype[ax], shape[i], typedescr
dimorder += x
break
else:
Expand All @@ -16144,13 +16164,15 @@ def addimage(

# TODO: use user-specified start, stop, step, or labels
moduloalong = ''.join(
f'<ModuloAlong{ax} Type="{axtype}" '
f'<ModuloAlong{ax} Type="{axtype}" {typedescr}'
f'Start="0" End="{size - 1}"/>'
for ax, (axtype, size) in modulo.items()
for ax, (axtype, size, typedescr) in modulo.items()
)
annotationref = f'<AnnotationRef ID="Annotation:{index}"/>'
annotations = (
f'<XMLAnnotation ID="Annotation:{index}" '
annotation_refs.append(
f'<AnnotationRef ID="Annotation:{len(self.annotations)}"/>'
)
self.annotations.append(
f'<XMLAnnotation ID="Annotation:{len(self.annotations)}" '
'Namespace="openmicroscopy.org/omero/dimension/modulo">'
'<Value>'
'<Modulo namespace='
Expand All @@ -16160,7 +16182,6 @@ def addimage(
'</Value>'
'</XMLAnnotation>'
)
self.annotations.append(annotations)
else:
modulo = {}
annotationref = ''
Expand Down Expand Up @@ -16307,6 +16328,15 @@ def addimage(
else:
interleaved = ''

self._dataset(
metadata.get('Dataset', {}), f'<ImageRef ID="Image:{index}"/>'
)

self._annotations(
metadata.get('StructuredAnnotations', metadata), annotation_refs
)
annotationref = ''.join(annotation_refs)

self.images.append(
f'<Image ID="Image:{index}"{name}>'
f'{elements}'
Expand All @@ -16333,7 +16363,7 @@ def tostring(self, *, declaration: bool = False) -> str:

"""
# TODO: support other top-level elements
elements = ''.join(self.elements)
datasets = ''.join(self.datasets)
images = ''.join(self.images)
annotations = ''.join(self.annotations)
if annotations:
Expand All @@ -16348,7 +16378,7 @@ def tostring(self, *, declaration: bool = False) -> str:
declaration=declaration_str,
images=images,
annotations=annotations,
elements=elements,
datasets=datasets,
)
return xml

Expand Down Expand Up @@ -16452,6 +16482,119 @@ def _attributes(
)
return ''.join(a for a in attributes if a)

def _dataset(self, metadata: dict[str, Any] | None, imageref: str) -> None:
"""Add Dataset element to self.datasets."""
index = len(self.datasets)
if metadata is None:
# dataset explicitly disabled
return None
if not metadata and index == 0:
# no dataset provided yet
return None
if not metadata:
# use previous dataset
index -= 1
if '<AnnotationRef' in self.datasets[index]:
self.datasets[index] = self.datasets[index].replace(
'<AnnotationRef', f'{imageref}<AnnotationRef'
)
else:
self.datasets[index] = self.datasets[index].replace(
'</Dataset>', f'{imageref}</Dataset>'
)
return None

# new dataset
name = metadata.get('Name', '')
if name:
name = f' Name="{OmeXml._escape(name)}"'

description = metadata.get('Description', '')
if description:
description = (
f'<Description>{OmeXml._escape(description)}</Description>'
)

annotation_refs: list[str] = []
self._annotations(metadata, annotation_refs)
annotationref = ''.join(annotation_refs)

self.datasets.append(
f'<Dataset ID="Dataset:{index}"{name}>'
f'{description}'
f'{imageref}'
f'{annotationref}'
'</Dataset>'
)
return None # f'<DatasetRef ID="Dataset:{index}"/>'

def _annotations(
self, metadata: dict[str, Any], annotation_refs: list[str]
) -> None:
"""Add annotations to self.annotations and annotation_refs."""
values: Any
for name, values in metadata.items():
if name not in {
'BooleanAnnotation',
'DoubleAnnotation',
'LongAnnotation',
'CommentAnnotation',
'MapAnnotation',
# 'FileAnnotation',
# 'ListAnnotation',
# 'TimestampAnnotation,
# 'XmlAnnotation',
}:
continue
if not values:
continue
if not isinstance(values, (list, tuple)):
values = [values]
for value in values:
namespace = ''
description = ''
if isinstance(value, dict):
value = value.copy()
description = value.pop('Description', '')
if description:
description = (
'<Description>'
f'{OmeXml._escape(description)}'
'</Description>'
)
namespace = value.pop('Namespace', '')
if namespace:
namespace = f' Namespace="{OmeXml._escape(namespace)}"'
value = value.pop('Value', value)
if name == 'MapAnnotation':
if not isinstance(value, dict):
raise ValueError('MapAnnotation is not a dict')
values = [
f'<M K="{OmeXml._escape(k)}">{OmeXml._escape(v)}</M>'
for k, v in value.items()
]
elif name == 'BooleanAnnotation':
values = [f'{bool(value)}'.lower()]
else:
values = [OmeXml._escape(str(value))]
annotation_refs.append(
f'<AnnotationRef ID="Annotation:{len(self.annotations)}"/>'
)
self.annotations.append(
''.join(
(
f'<{name} '
f'ID="Annotation:{len(self.annotations)}"'
f'{namespace}>',
description,
'<Value>',
''.join(values),
'</Value>',
f'</{name}>',
)
)
)

@staticmethod
def validate(
omexml: str,
Expand Down

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