From ba055f61579b471d4879b18b6fafbc1ce59fb968 Mon Sep 17 00:00:00 2001
From: Simon Humpohl <simon.humpohl@rwth-aachen.de>
Date: Wed, 8 Mar 2023 11:44:07 +0100
Subject: [PATCH] Use tifffile to read the image
---
pyproject.toml | 1 +
qutil/image.py | 24 ++++++++----------------
2 files changed, 9 insertions(+), 16 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 0a2f1657..178a43f4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -61,6 +61,7 @@ qcodes = [
]
image = [
"moviepy",
+ "tifffile[all]"
]
doc = [
"sphinx",
diff --git a/qutil/image.py b/qutil/image.py
index 2f9daeac..d3627159 100644
--- a/qutil/image.py
+++ b/qutil/image.py
@@ -3,12 +3,9 @@ import pathlib
from typing import Optional, Union, Literal
import numpy as np
-from PIL import Image, ImageSequence
+import tifffile
from moviepy.editor import ImageSequenceClip
-from qutil.misc import filter_warnings
-from qutil.itertools import ignore_exceptions
-
try:
from numpy.typing import NDArray
except ImportError:
@@ -17,15 +14,6 @@ except ImportError:
_pathT = Union[str, os.PathLike]
-def read_tiff(path: _pathT) -> NDArray:
- """Read a (multipage) .tif image and return it as an array."""
- # Catch the following error for files generated by the Thorlabs Camera:
- # OSError: Corrupt EXIF data. Expecting to read 2 bytes but only got 0.
- with Image.open(path) as im, filter_warnings('error', UserWarning):
- frames = list(ignore_exceptions(ImageSequence.Iterator(im), UserWarning))
- return np.array(frames)
-
-
def convert_tiff(file: _pathT, fps: float, format: str = '.mp4', threads: Optional[int] = None,
out: Optional[_pathT] = None, logger: Optional[Literal['bar']] = None):
"""Converts a multipage .tif file to `format` and writes it to disk.
@@ -63,7 +51,11 @@ def convert_tiff(file: _pathT, fps: float, format: str = '.mp4', threads: Option
threads=os.cpu_count())
"""
- file = pathlib.Path(file).with_suffix('.tif')
- clip = ImageSequenceClip(read_tiff(file), fps=fps)
- clip.write_videofile((out or file).with_suffix(format), fps, audio=False, threads=threads,
+ in_name = pathlib.Path(file).with_suffix('.tif')
+ out_name = (out or in_name).with_suffix(format)
+
+ data = tifffile.imread(str(in_name))
+ clip = ImageSequenceClip(list(data), fps=fps)
+
+ clip.write_videofile(out_name, fps, audio=False, threads=threads,
logger=logger)
--
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