wim/tiffwrite
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- compression option

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- comment option
This commit is contained in:
Wim Pomp
2022-10-11 16:34:00 +02:00
parent 41006c62bc
commit 1e0c897e4c
2 changed files with 13 additions and 4 deletions
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2
setup.py
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@@ -5,7 +5,7 @@ with open('README.md', 'r') as fh:
setuptools.setup( setuptools.setup(
name='tiffwrite', name='tiffwrite',
version='2022.6.0', version='2022.10.0',
author='Wim Pomp @ Lenstra lab NKI', author='Wim Pomp @ Lenstra lab NKI',
author_email='w.pomp@nki.nl', author_email='w.pomp@nki.nl',
description='Parallel tiff writer compatible with ImageJ.', description='Parallel tiff writer compatible with ImageJ.',

15
tiffwrite/__init__.py
View File

@@ -331,7 +331,7 @@ class IJTiffFile:
wp@tl20200214 wp@tl20200214
""" """
def __init__(self, path, shape, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None, def __init__(self, path, shape, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
timeinterval=None, **extratags): timeinterval=None, compression=(8, 9), comment=None, **extratags):
assert len(shape) >= 3, 'please specify all c, z, t for the shape' assert len(shape) >= 3, 'please specify all c, z, t for the shape'
assert len(shape) <= 3, 'please specify only c, z, t for the shape' assert len(shape) <= 3, 'please specify only c, z, t for the shape'
assert np.dtype(dtype).char in 'BbHhf', 'datatype not supported' assert np.dtype(dtype).char in 'BbHhf', 'datatype not supported'
@@ -345,6 +345,8 @@ class IJTiffFile:
self.pxsize = pxsize self.pxsize = pxsize
self.deltaz = deltaz self.deltaz = deltaz
self.timeinterval = timeinterval self.timeinterval = timeinterval
self.compression = compression
self.comment = comment
self.extratags = {} if extratags is None else Tag.to_tags(extratags) self.extratags = {} if extratags is None else Tag.to_tags(extratags)
if pxsize is not None: if pxsize is not None:
pxsize = Tag.fraction(pxsize) pxsize = Tag.fraction(pxsize)
@@ -381,7 +383,7 @@ class IJTiffFile:
with BytesIO() as framedata: with BytesIO() as framedata:
with tifffile.TiffWriter(framedata, bigtiff=self.header.bigtiff, byteorder=self.header.byteorder) as t: with tifffile.TiffWriter(framedata, bigtiff=self.header.bigtiff, byteorder=self.header.byteorder) as t:
# predictor=True might save a few bytes, but requires the package imagecodes to save floats # predictor=True might save a few bytes, but requires the package imagecodes to save floats
t.write(frame, compression=(8, 9), contiguous=True, predictor=False) t.write(frame, compression=self.compression, contiguous=True, predictor=False)
return framedata.getvalue() return framedata.getvalue()
def save(self, frame, c, z, t, **extratags): def save(self, frame, c, z, t, **extratags):
@@ -450,7 +452,14 @@ class IJTiffFile:
desc.append(f'spacing={self.deltaz}') desc.append(f'spacing={self.deltaz}')
if self.timeinterval is not None: if self.timeinterval is not None:
desc.append(f'finterval={self.timeinterval}') desc.append(f'finterval={self.timeinterval}')
return bytes('\n'.join(desc), 'ascii') desc = [bytes(d, 'ascii') for d in desc]
if self.comment is not None:
desc.append(b'')
if isinstance(self.comment, bytes):
desc.append(self.comment)
else:
desc.append(bytes(self.comment, 'ascii'))
return b'\n'.join(desc)
@cached_property @cached_property
def empty_frame(self): def empty_frame(self):