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- use css colors to convert color names into rgb values

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Wim Pomp
2025-08-21 22:11:45 +02:00
parent b09f804a3f
commit 067368e06c
7 changed files with 149 additions and 85 deletions
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155
py/tiffwrite/__init__.py
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@@ -9,13 +9,12 @@ 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
from tqdm.auto import tqdm
from . import tiffwrite_rs as rs # noqa
__all__ = ['IJTiffFile', 'IJTiffParallel', 'FrameInfo', 'Tag', 'tiffwrite']
__all__ = ["IJTiffFile", "IJTiffParallel", "FrameInfo", "Tag", "tiffwrite"]
try:
__version__ = version(Path(__file__).parent.name)
@@ -27,11 +26,11 @@ FrameInfo = tuple[ArrayLike, int, int, int]
class Header:
""" deprecated """
"""deprecated"""
class IFD(dict):
""" deprecated """
"""deprecated"""
class TiffWriteWarning(UserWarning):
@@ -39,31 +38,40 @@ class TiffWriteWarning(UserWarning):
class IJTiffFile(rs.IJTiffFile):
""" Writes a tiff file in a format that the BioFormats reader in Fiji understands.
Zstd compression is done in parallel using Rust.
path: path to the new tiff file
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
compression: ('zstd', level) for zstd with compression level: -7 to 22, 'deflate' for deflate compresion
comment: comment to be saved in tif
extratags: other tags to be saved, example: (Tag.ascii(315, 'John Doe'), Tag.bytes(4567, [400, 500])
or (Tag.ascii(33432, 'Made by me'),).
"""Writes a tiff file in a format that the BioFormats reader in Fiji understands.
Zstd compression is done in parallel using Rust.
path: path to the new tiff file
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
compression: ('zstd', level) for zstd with compression level: -7 to 22, 'deflate' for deflate compresion
comment: comment to be saved in tif
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, *, dtype: DTypeLike = 'uint16',
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
deltaz: float = None, timeinterval: float = None,
compression: int | str | tuple[int, int] | tuple[str, int] = None, comment: str = None,
extratags: Sequence[Tag] = None) -> None:
def __init__(
self,
path: str | Path,
*,
dtype: DTypeLike = "uint16",
colors: Sequence[str] = None,
colormap: str = None,
pxsize: float = None,
deltaz: float = None,
timeinterval: float = None,
compression: int | str | tuple[int, int] | tuple[str, int] = None,
comment: str = None,
extratags: Sequence[Tag] = None,
) -> None:
def get_codec(idx: int | str):
codecs = {'z': 50000, 'd': 8, 8: 8, 50000: 50000}
codecs = {"z": 50000, "d": 8, 8: 8, 50000: 50000}
if isinstance(idx, str):
return codecs.get(idx[0].lower(), 50000)
else:
@@ -78,7 +86,7 @@ class IJTiffFile(rs.IJTiffFile):
compression = get_codec(compression), 22
self.set_compression(*compression)
if colors is not None:
self.colors = np.array([get_color(color) for color in colors])
self.colors = [str(color) for color in colors]
if colormap is not None:
self.colormap = get_colormap(colormap)
if pxsize is not None:
@@ -93,10 +101,13 @@ class IJTiffFile(rs.IJTiffFile):
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)
warn(
"Fiji will not interpret colors saved in an (u)int8 tif, save as (u)int16 instead.",
TiffWriteWarning,
stacklevel=2,
)
if colors is not None and colormap is not None:
warn('Cannot have colors and colormap simultaneously.', TiffWriteWarning, stacklevel=2)
warn("Cannot have colors and colormap simultaneously.", TiffWriteWarning, stacklevel=2)
def __enter__(self) -> IJTiffFile:
return self
@@ -105,7 +116,7 @@ class IJTiffFile(rs.IJTiffFile):
self.close()
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 """
"""save a 2d numpy array to the tiff at channel=c, slice=z, time=t, with optional extra tif tags"""
frame = np.asarray(frame).astype(self.dtype)
match self.dtype:
case np.uint8:
@@ -129,51 +140,67 @@ class IJTiffFile(rs.IJTiffFile):
case np.float64:
self.save_f64(frame, c, z, t)
case _:
raise TypeError(f'Cannot save type {self.dtype}')
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 get_colormap(colormap: str) -> np.ndarray:
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'):
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'):
if colormap.startswith("glasbey") or colormap.endswith("glasbey"):
cm[0] = 255, 255, 255
cm[-1] = 0, 0, 0
else:
cmap = matplotlib.colormaps.get_cmap(colormap)
if cmap.N < 256:
cm = (255 * np.vstack(((1, 1, 1),
matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(1, 254),
cmap).to_rgba(np.arange(1, 254))[:, :3],
(0, 0, 0)))).astype('uint8')
cm = (
255
* np.vstack(
(
(1, 1, 1),
matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(1, 254), cmap).to_rgba(
np.arange(1, 254)
)[:, :3],
(0, 0, 0),
)
)
).astype("uint8")
else:
cm = (255 * matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(0, 255), cmap)
.to_rgba(np.arange(256))[:, :3]).astype('uint8')
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')
def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCYX', dtype: DTypeLike = None, bar: bool = False,
*args: Any, **kwargs: Any) -> None:
""" file: string; filename of the new tiff file
data: 2 to 5D numpy array
axes: string; order of dimensions in data, default: TZCYX for 5D, ZCYX for 4D, CYX for 3D, YX for 2D data
dtype: string; datatype to use when saving to tiff
bar: bool; whether to show a progress bar
other args: see IJTiffFile
def tiffwrite(
file: str | Path,
data: np.ndarray,
axes: str = "TZCYX",
dtype: DTypeLike = None,
bar: bool = False,
*args: Any,
**kwargs: Any,
) -> None:
"""file: string; filename of the new tiff file
data: 2 to 5D numpy array
axes: string; order of dimensions in data, default: TZCYX for 5D, ZCYX for 4D, CYX for 3D, YX for 2D data
dtype: string; datatype to use when saving to tiff
bar: bool; whether to show a progress bar
other args: see IJTiffFile
"""
axes = axes[-np.ndim(data):].upper()
if not axes == 'CZTYX':
axes_shuffle = [axes.find(i) for i in 'CZTYX']
axes = axes[-np.ndim(data) :].upper()
if not axes == "CZTYX":
axes_shuffle = [axes.find(i) for i in "CZTYX"]
axes_add = [i for i, j in enumerate(axes_shuffle) if j < 0]
axes_shuffle = [i for i in axes_shuffle if i >= 0]
data = np.transpose(data, axes_shuffle)
@@ -182,8 +209,12 @@ def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCYX', dtype: DT
shape = data.shape[:3]
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):
for n in tqdm(
product(*[range(i) for i in shape]),
total=np.prod(shape), # type: ignore
desc="Saving tiff",
disable=not bar,
):
f.save(data[n], *n)
@@ -193,7 +224,6 @@ try:
from parfor import ParPool, Task
class Pool(ParPool):
def __init__(self, ijtifffile: IJTiffFile, parallel: Callable[[Any], Sequence[FrameInfo]]):
self.ijtifffile = ijtifffile
@@ -211,14 +241,13 @@ try:
super().close()
self.ijtifffile.close()
class IJTiffParallel(metaclass=ABCMeta):
""" wraps IJTiffFile.save in a parallel pool, the method 'parallel' needs to be overloaded """
"""wraps IJTiffFile.save in a parallel pool, the method 'parallel' needs to be overloaded"""
@abstractmethod
def parallel(self, frame: Any) -> Sequence[FrameInfo]:
""" does something with frame in a parallel process,
and returns a sequence of frames and offsets to c, z and t to save in the tif """
"""does something with frame in a parallel process,
and returns a sequence of frames and offsets to c, z and t to save in the tif"""
@wraps(IJTiffFile.__init__)
def __init__(self, *args: Any, **kwargs: Any) -> None: