wim/tiffwrite
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

- start some color(map) support in python

Browse Source 
- compress_frame function in python for backwards compatibility
- save all extra tags in a single hashmap
- construct tags from references
- store frames by c, z, t
- save px_size in tiff
- some getters and setters in py.rs
This commit is contained in:
Wim Pomp
2024-10-10 15:28:14 +02:00
parent 7678585bba
commit 1197806a6f
5 changed files with 681 additions and 293 deletions
Download Patch File Download Diff File Expand all files Collapse all files

83
py/tiffwrite/__init__.py
View File

@@ -4,7 +4,9 @@ from itertools import product
from pathlib import Path
from typing import Any, Sequence
import colorcet
import numpy as np
from matplotlib import colors as mpl_colors
from numpy.typing import ArrayLike, DTypeLike
from tqdm.auto import tqdm
@@ -27,29 +29,29 @@ class Tag(rs.Tag):
Strip = tuple[list[int], list[int]]
CZT = tuple[int, int, int]
FrameInfo = tuple[IFD, Strip, CZT]
FrameInfo = tuple[np.ndarray, None, CZT]
class IJTiffFile(rs.IJTiffFile):
def __new__(cls, path: str | Path, shape: tuple[int, int, int], dtype: DTypeLike = 'uint16',
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
deltaz: float = None, timeinterval: float = None, comment: str = None,
**extratags: Tag.Value | Tag) -> IJTiffFile:
**extratags: Tag) -> IJTiffFile:
new = super().__new__(cls, str(path), shape)
if colors is not None:
new = new.with_colors(colors)
new.colors = np.array([get_color(color) for color in colors])
if colormap is not None:
new = new.with_colormap(colormap)
new.colormap = get_colormap(colormap)
if pxsize is not None:
new = new.with_pxsize(pxsize)
new.px_size = float(pxsize)
if deltaz is not None:
new = new.with_deltaz(deltaz)
new.delta_z = float(deltaz)
if timeinterval is not None:
new = new.with_timeinterval(timeinterval)
new.time_interval = float(timeinterval)
if comment is not None:
new = new.with_comment(comment)
if extratags:
new = new.extend_extratags(extratags)
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], dtype: DTypeLike = 'uint16', # noqa
@@ -66,30 +68,43 @@ class IJTiffFile(rs.IJTiffFile):
self.close()
def save(self, frame: ArrayLike, c: int, z: int, t: int) -> None:
frame = np.asarray(frame).astype(self.dtype)
match self.dtype:
case np.uint8:
self.save_u8(frame, c, z, t)
case np.uint16:
self.save_u16(frame, c, z, t)
case np.uint32:
self.save_u32(frame, c, z, t)
case np.uint64:
self.save_u64(frame, c, z, t)
case np.int8:
self.save_i8(frame, c, z, t)
case np.int16:
self.save_i16(frame, c, z, t)
case np.int32:
self.save_i32(frame, c, z, t)
case np.int64:
self.save_i64(frame, c, z, t)
case np.float32:
self.save_f32(frame, c, z, t)
case np.float64:
self.save_f64(frame, c, z, t)
case _:
raise TypeError(f'Cannot save type {self.dtype}')
for frame, _, (cn, zn, tn) in self.compress_frame(frame):
frame = np.asarray(frame).astype(self.dtype)
match self.dtype:
case np.uint8:
self.save_u8(frame, c + cn, z + zn, t + tn)
case np.uint16:
self.save_u16(frame, c + cn, z + zn, t + tn)
case np.uint32:
self.save_u32(frame, c + cn, z + zn, t + tn)
case np.uint64:
self.save_u64(frame, c + cn, z + zn, t + tn)
case np.int8:
self.save_i8(frame, c + cn, z + zn, t + tn)
case np.int16:
self.save_i16(frame, c + cn, z + zn, t + tn)
case np.int32:
self.save_i32(frame, c + cn, z + zn, t + tn)
case np.int64:
self.save_i64(frame, c + cn, z + zn, t + tn)
case np.float32:
self.save_f32(frame, c + cn, z + zn, t + tn)
case np.float64:
self.save_f64(frame, c + cn, z + zn, t + tn)
case _:
raise TypeError(f'Cannot save type {self.dtype}')
def compress_frame(self, frame: ArrayLike) -> tuple[FrameInfo]: # noqa
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')
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 = 'TZCXY', dtype: DTypeLike = None, bar: bool = False,