wim/tiffwrite
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- Switch to zstd compression as default.

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- Only warn if frames are missing when the file is closed, allowing the user to debug the error causing missing frames.
This commit is contained in:
Wim Pomp
2024-02-14 14:54:13 +01:00
parent e736770512
commit 43b6a48049
3 changed files with 55 additions and 41 deletions
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9
pyproject.toml
View File

@@ -1,6 +1,6 @@
[tool.poetry]
name = "tiffwrite"
version = "2023.8.0"
version = "2024.2.0"
description = "Parallel tiff writer compatible with ImageJ."
authors = ["Wim Pomp, Lenstra lab NKI <w.pomp@nki.nl>"]
license = "GPL-3.0-or-later"
@@ -9,18 +9,21 @@ packages = [{include = "tiffwrite"}]
repository = "https://github.com/wimpomp/tiffwrite"
[tool.poetry.dependencies]
python = "^3.7"
python = "^3.8"
tifffile = "*"
numpy = "*"
tqdm = "*"
colorcet = "*"
matplotlib = "*"
parfor = ">=2023.8.3"
parfor = ">=2023.10.1"
pytest = { version = "*", optional = true }
[tool.poetry.extras]
test = ["pytest"]
[tool.pytest.ini_options]
filterwarnings = ["ignore:::(?!tiffwrite)"]
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

4
tests/test_multiple.py
View File

@@ -10,8 +10,8 @@ def test_mult(tmp_path):
shape = (2, 3, 5)
paths = [tmp_path / f'test{i}.tif' for i in range(6)]
with ExitStack() as stack:
tifs = [stack.enter_context(IJTiffFile(path, shape)) for path in paths]
for c, z, t in tqdm(product(range(shape[0]), range(shape[1]), range(shape[2])), total=np.prod(shape)):
tifs = [stack.enter_context(IJTiffFile(path, shape)) for path in paths] # noqa
for c, z, t in tqdm(product(range(shape[0]), range(shape[1]), range(shape[2])), total=np.prod(shape)): # noqa
for tif in tifs:
tif.save(np.random.randint(0, 255, (64, 64)), c, z, t)
assert all([path.exists() for path in paths])

83
tiffwrite/__init__.py
View File

@@ -1,5 +1,6 @@
import os
import struct
import warnings
from collections.abc import Iterable
from contextlib import contextmanager
from datetime import datetime
@@ -23,7 +24,7 @@ __all__ = ["IJTiffFile", "Tag", "tiffwrite"]
try:
__version__ = version("tiffwrite")
except Exception:
except Exception: # noqa
__version__ = "unknown"
@@ -48,9 +49,9 @@ def tiffwrite(file, data, axes='TZCXY', dtype=None, bar=False, *args, **kwargs):
shape = data.shape[:3]
with IJTiffFile(file, shape, data.dtype if dtype is None else dtype, *args, **kwargs) as f:
at_least_one = False
for n in tqdm(product(*[range(i) for i in shape]), total=np.prod(shape), desc='Saving tiff', disable=not bar):
if np.any(data[n]) or not at_least_one:
f.save(data[n], *n)
for n in tqdm(product(*[range(i) for i in shape]), total=np.prod(shape), desc='Saving tiff', disable=not bar): # noqa
if np.any(data[n]) or not at_least_one: # noqa
f.save(data[n], *n) # noqa
at_least_one = True
@@ -116,6 +117,9 @@ class Tag:
(denominator is not None and denominator < 0) else 32) - 1)
def __init__(self, ttype, value=None, offset=None):
self.fh = None
self.header = None
self.bytes_data = None
if value is None:
self.value = ttype
if all([isinstance(value, int) for value in self.value]):
@@ -182,7 +186,7 @@ class Tag:
return self.value, len(self.value) // struct.calcsize(self.dtype)
elif self.ttype in (2, 14):
if isinstance(self.value, str):
bytes_value = self.value.encode('ascii') + b'\x00'
bytes_value = self.value.encode('ascii') + b'\x00' # noqa
else:
bytes_value = b'\x00'.join([value.encode('ascii') for value in self.value]) + b'\x00'
return bytes_value, len(bytes_value)
@@ -240,6 +244,10 @@ class Tag:
class IFD(dict):
def __init__(self, fh=None):
super().__init__()
self.fh = fh
self.header = None
self.offset = None
self.where_to_write_next_ifd_offset = None
if fh is not None:
header = Header(fh)
fh.seek(header.offset)
@@ -280,7 +288,7 @@ class IFD(dict):
value = [struct.unpack(header.byteorder + dtype, fh.read(dtypelen))[0] for _ in range(count)]
if toolong:
fh.seek(cp)
fh.seek(cp) # noqa
self[code] = Tag(ttype, value, pos)
fh.seek(header.offset)
@@ -338,7 +346,7 @@ class IJTiffFile:
wp@tl20200214
"""
def __init__(self, path, shape, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
timeinterval=None, compression=(8, 9), comment=None, **extratags):
timeinterval=None, compression=(50000, 22), comment=None, **extratags):
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 np.dtype(dtype).char in 'BbHhf', 'datatype not supported'
@@ -418,7 +426,7 @@ class IJTiffFile:
if self.deltaz is not None:
desc.append(f'spacing={self.deltaz}')
if self.timeinterval is not None:
desc.append(f'finterval={self.timeinterval}')
desc.append(f'interval={self.timeinterval}')
desc = [bytes(d, 'ascii') for d in desc]
if self.comment is not None:
desc.append(b'')
@@ -465,26 +473,33 @@ class IJTiffFile:
for c, color in enumerate(self.colors_bytes):
ifds[c][320] = Tag('SHORT', color)
ifds[c][262] = Tag('SHORT', 3)
if 306 not in ifds[0]:
if 0 in ifds and 306 not in ifds[0]:
ifds[0][306] = Tag('ASCII', datetime.now().strftime('%Y:%m:%d %H:%M:%S'))
wrn = False
for framenr in range(self.nframes):
stripbyteoffsets, stripbytecounts = zip(*[strips[(framenr, channel)]
for channel in range(self.spp)])
ifds[framenr][258].value = self.spp * ifds[framenr][258].value
ifds[framenr][270] = Tag('ASCII', self.description)
ifds[framenr][273] = Tag('LONG8', sum(stripbyteoffsets, []))
ifds[framenr][277] = Tag('SHORT', self.spp)
ifds[framenr][279] = Tag('LONG8', sum(stripbytecounts, []))
ifds[framenr][305] = Tag('ASCII', 'tiffwrite_tllab_NKI')
if self.extratags is not None:
ifds[framenr].update(self.extratags)
if self.colormap is None and self.colors is None and self.shape[0] > 1:
ifds[framenr][284] = Tag('SHORT', 2)
ifds[framenr].write(fh, self.header, self.write)
if framenr:
ifds[framenr].write_offset(ifds[framenr - 1].where_to_write_next_ifd_offset)
if framenr in ifds and all([(framenr, channel) in strips for channel in range(self.spp)]):
stripbyteoffsets, stripbytecounts = zip(*[strips[(framenr, channel)]
for channel in range(self.spp)])
ifds[framenr][258].value = self.spp * ifds[framenr][258].value
ifds[framenr][270] = Tag('ASCII', self.description)
ifds[framenr][273] = Tag('LONG8', sum(stripbyteoffsets, []))
ifds[framenr][277] = Tag('SHORT', self.spp)
ifds[framenr][279] = Tag('LONG8', sum(stripbytecounts, []))
ifds[framenr][305] = Tag('ASCII', 'tiffwrite_tllab_NKI')
if self.extratags is not None:
ifds[framenr].update(self.extratags)
if self.colormap is None and self.colors is None and self.shape[0] > 1:
ifds[framenr][284] = Tag('SHORT', 2)
ifds[framenr].write(fh, self.header, self.write)
if framenr:
ifds[framenr].write_offset(ifds[framenr - 1].where_to_write_next_ifd_offset)
else:
ifds[framenr].write_offset(self.header.offset - self.header.offsetsize)
else:
ifds[framenr].write_offset(self.header.offset - self.header.offsetsize)
wrn = True
if wrn:
warnings.warn('Some frames were not added to the tif file, either you forgot them, '
'or an error occured and the tif file was closed prematurely.')
def __enter__(self):
return self
@@ -548,14 +563,10 @@ class FileHandle:
@contextmanager
def lock(self):
self._lock.acquire()
f = None
try:
f = open(self.name, 'rb+')
f.seek(self._pos.value)
yield f
finally:
if f is not None:
self._pos.value = f.tell()
f.close()
self._lock.release()
with self._lock:
with open(self.name, 'rb+') as f:
try:
f.seek(self._pos.value)
yield f
finally:
self._pos.value = f.tell()