- change to MIT license

- change XY to YX in python tiffwrite.tiffwrite
This commit is contained in:
Wim Pomp
2025-02-19 20:41:28 +01:00
parent 8f4a506d45
commit 9ee8fc1029
7 changed files with 97 additions and 717 deletions

View File

@@ -150,19 +150,19 @@ 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,
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: TZCXY for 5D, ZCXY for 4D, CXY for 3D, XY for 2D data
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 == 'CZTXY':
axes_shuffle = [axes.find(i) for i in 'CZTXY']
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)