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- some warnings

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- better color(map) support
- make python module optional in rust
- max 48 threads
This commit is contained in:
Wim Pomp
2024-10-12 13:19:22 +02:00
parent 4d31933a38
commit 625b222a0d
9 changed files with 224 additions and 105 deletions
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109
py/tiffwrite/__init__.py
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@@ -3,8 +3,10 @@ from __future__ import annotations
from itertools import product
from pathlib import Path
from typing import Any, Sequence
from warnings import warn
import colorcet
import matplotlib
import numpy as np
from matplotlib import colors as mpl_colors
from numpy.typing import ArrayLike, DTypeLike
@@ -12,13 +14,13 @@ from tqdm.auto import tqdm
from . import tiffwrite_rs as rs # noqa
__all__ = ['Header', 'IJTiffFile', 'IFD', 'FrameInfo', 'Tag', 'Strip', 'tiffwrite']
class Header:
pass
class IFD(dict):
pass
@@ -32,38 +34,60 @@ CZT = tuple[int, int, int]
FrameInfo = tuple[np.ndarray, None, CZT]
class TiffWriteWarning(UserWarning):
pass
class IJTiffFile(rs.IJTiffFile):
def __new__(cls, path: str | Path, shape: tuple[int, int, int] = None, dtype: DTypeLike = 'uint16',
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
deltaz: float = None, timeinterval: float = None, compression: int = None, comment: str = None,
**extratags: Tag) -> IJTiffFile:
new = super().__new__(cls, str(path))
""" Writes a tiff file in a format that the BioFormats reader in Fiji understands.
file: filename of the new tiff file
shape: not used anymore
dtype: datatype to use when saving to tiff
colors: a tuple with a color per channel, chosen from matplotlib.colors, html colors are also possible
colormap: name of a colormap from colorcet
pxsize: pixel size in um
deltaz: z slice interval in um
timeinterval: time between frames in seconds
extratags: other tags to be saved, example: (Tag.ascii(315, 'John Doe'), Tag.bytes(4567, [400, 500])
or (Tag.ascii(33432, 'Made by me'),).
"""
def __new__(cls, path: str | Path, *args, **kwargs) -> IJTiffFile:
return super().__new__(cls, str(path))
def __init__(self, path: str | Path, shape: tuple[int, int, int] = None, dtype: DTypeLike = 'uint16',
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
deltaz: float = None, timeinterval: float = None, compression: int = None, comment: str = None,
extratags: Sequence[Tag] = None) -> None:
self.path = Path(path)
self.shape = shape
self.dtype = np.dtype(dtype)
if compression is not None:
if isinstance(compression, Sequence):
compression = compression[-1]
new.set_compression_level(compression)
self.set_compression_level(compression)
if colors is not None:
new.colors = np.array([get_color(color) for color in colors])
self.colors = np.array([get_color(color) for color in colors])
if colormap is not None:
new.colormap = get_colormap(colormap)
self.colormap = get_colormap(colormap)
if pxsize is not None:
new.px_size = float(pxsize)
self.px_size = float(pxsize)
if deltaz is not None:
new.delta_z = float(deltaz)
self.delta_z = float(deltaz)
if timeinterval is not None:
new.time_interval = float(timeinterval)
self.time_interval = float(timeinterval)
if comment is not None:
new.comment = comment
for extra_tag in extratags:
new.append_extra_tag(extra_tag, None)
return new
def __init__(self, path: str | Path, shape: tuple[int, int, int] = None, dtype: DTypeLike = 'uint16', # noqa
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None, # noqa
deltaz: float = None, timeinterval: float = None, comment: str = None, # noqa
**extratags: Tag.Value | Tag) -> None: # noqa
self.path = Path(path)
self.dtype = np.dtype(dtype)
self.comment = comment
if extratags is not None:
for extra_tag in extratags:
self.append_extra_tag(extra_tag, None)
if self.dtype.itemsize == 1 and colors is not None:
warn('Fiji will not interpret colors saved in an (u)int8 tif, save as (u)int16 instead.',
TiffWriteWarning, stacklevel=2)
if shape is not None:
warn('Providing shape is not needed anymore, the argument will be removed in the future.',
DeprecationWarning, stacklevel=2)
if colors is not None and colormap is not None:
warn('Cannot have colors and colormap simultaneously.', TiffWriteWarning, stacklevel=2)
def __enter__(self) -> IJTiffFile:
return self
@@ -71,7 +95,8 @@ class IJTiffFile(rs.IJTiffFile):
def __exit__(self, exc_type, exc_val, exc_tb):
self.close()
def save(self, frame: ArrayLike, c: int, z: int, t: int) -> None:
def save(self, frame: ArrayLike, c: int, z: int, t: int, extratags: Sequence[Tag] = None) -> None:
""" save a 2d numpy array to the tiff at channel=c, slice=z, time=t, with optional extra tif tags """
for frame, _, (cn, zn, tn) in self.compress_frame(frame):
frame = np.asarray(frame).astype(self.dtype)
match self.dtype:
@@ -97,15 +122,36 @@ class IJTiffFile(rs.IJTiffFile):
self.save_f64(frame, c + cn, z + zn, t + tn)
case _:
raise TypeError(f'Cannot save type {self.dtype}')
if extratags is not None:
for extra_tag in extratags:
self.append_extra_tag(extra_tag, (c, z, t))
def compress_frame(self, frame: ArrayLike) -> tuple[FrameInfo]: # noqa
""" backwards compatibility """
return (frame, None, (0, 0, 0)),
def get_colormap(colormap: str) -> np.ndarray:
colormap = getattr(colorcet, colormap)
colormap[0] = '#ffffff'
colormap[-1] = '#000000'
return np.array([[int(''.join(i), 16) for i in zip(*[iter(s[1:])] * 2)] for s in colormap]).astype('uint8')
if hasattr(colorcet, colormap.rstrip('_r')):
cm = np.array([[int(''.join(i), 16) for i in zip(*[iter(s[1:])] * 2)]
for s in getattr(colorcet, colormap.rstrip('_r'))]).astype('uint8')
if colormap.endswith('_r'):
cm = cm[::-1]
if colormap.startswith('glasbey') or colormap.endswith('glasbey'):
cm[0] = 0, 0, 0
cm[-1] = 255, 255, 255
else:
cmap = matplotlib.colormaps.get_cmap(colormap)
if cmap.N < 256:
cm = (255 * np.vstack(((0, 0, 0),
matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(1, 254),
cmap).to_rgba(np.arange(1, 254))[:, :3],
(1, 1, 1)))).astype('uint8')
else:
cm = (255 * matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(0, 255), cmap)
.to_rgba(np.arange(256))[:, :3]).astype('uint8')
return cm
def get_color(color: str) -> np.ndarray:
return np.array([int(''.join(i), 16) for i in zip(*[iter(mpl_colors.to_hex(color)[1:])] * 2)]).astype('uint8')
@@ -131,10 +177,7 @@ def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCXY', dtype: DT
data = np.expand_dims(data, axis)
shape = data.shape[:3]
with IJTiffFile(file, shape, data.dtype if dtype is None else dtype, *args, **kwargs) as f: # type: ignore
at_least_one = False
with IJTiffFile(file, dtype=data.dtype if dtype is None else dtype, *args, **kwargs) as f:
for n in tqdm(product(*[range(i) for i in shape]), total=np.prod(shape), # type: ignore
desc='Saving tiff', disable=not bar):
if np.any(data[n]) or not at_least_one:
f.save(data[n], *n)
at_least_one = True
f.save(data[n], *n)