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- make it work on Linux again too

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Wim Pomp
2022-10-17 20:16:28 +02:00
parent c3c0c65b06
commit c5ac6346bc
3 changed files with 7 additions and 6 deletions
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2
README.md
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@@ -21,7 +21,7 @@ Metadata is also saved in the tiffs in the description tag.
with IssFile(file) as iss: with IssFile(file) as iss:
image = iss.get_image(c=1, t=5) image = iss.get_image(c=1, t=5)
carpet = iss.get_carpet(c=1, t=5) carpet, (time, x, y, z) = iss.get_carpet(c=1, t=5)
plt.figure() plt.figure()
plt.imshow(image) plt.imshow(image)

9
issfile/__init__.py
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@@ -17,7 +17,7 @@ class TiffFile(IJTiffFile):
if 'processes' not in kwargs: if 'processes' not in kwargs:
kwargs['processes'] = 'all' kwargs['processes'] = 'all'
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
self.iss = iss self.iss = pickle.dumps(iss) # force iss to be transferred to other processes in pickled state
self.bar = bar self.bar = bar
def __getstate__(self): def __getstate__(self):
@@ -27,6 +27,8 @@ class TiffFile(IJTiffFile):
self.bar.update() self.bar.update()
def compress_frame(self, frame): def compress_frame(self, frame):
if isinstance(self.iss, bytes):
self.iss = pickle.loads(self.iss)
if frame[0]: if frame[0]:
frame, metadata = self.iss.get_carpet(*frame[1:]) frame, metadata = self.iss.get_carpet(*frame[1:])
ifd, offsets = super().compress_frame(frame.astype(self.dtype)) ifd, offsets = super().compress_frame(frame.astype(self.dtype))
@@ -89,10 +91,9 @@ class IssFile:
def get_image(self, c, t): def get_image(self, c, t):
assert c < self.shape[2] and t < self.shape[3], \ assert c < self.shape[2] and t < self.shape[3], \
f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[3]}' f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[3]}'
frame = c + 2 * t * self.shape[2] frame = int(c) + 2 * int(t) * self.shape[2]
frame_bytes = self.shape[0] * self.shape[1] * self.delta frame_bytes = self.shape[0] * self.shape[1] * self.delta
data = [] data = []
# TODO: RuntimeWarning: overflow encountered in long_scalars for big files in next line
for address in range(frame * frame_bytes, (frame + 1) * frame_bytes, self.delta): for address in range(frame * frame_bytes, (frame + 1) * frame_bytes, self.delta):
self.data.seek(address) self.data.seek(address)
data.append(unpack('<I', self.data.read(4))) data.append(unpack('<I', self.data.read(4)))
@@ -101,7 +102,7 @@ class IssFile:
def get_carpet(self, c, t, min_n_lines=1): def get_carpet(self, c, t, min_n_lines=1):
assert c < self.shape[2] and t < self.shape[4], \ assert c < self.shape[2] and t < self.shape[4], \
f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[4]}' f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[4]}'
frame = c + (2 * t + 1) * self.shape[2] frame = int(c) + (2 * int(t) + 1) * self.shape[2]
frame_bytes = self.shape[0] * self.shape[1] * self.delta frame_bytes = self.shape[0] * self.shape[1] * self.delta
data, metadata = [], [] data, metadata = [], []
self.data.seek(frame * frame_bytes) self.data.seek(frame * frame_bytes)

2
setup.py
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@@ -5,7 +5,7 @@ with open('README.md', 'r') as fh:
setuptools.setup( setuptools.setup(
name='issfile', name='issfile',
version='2022.10.3', version='2022.10.4',
author='Wim Pomp @ Lenstra lab NKI', author='Wim Pomp @ Lenstra lab NKI',
author_email='w.pomp@nki.nl', author_email='w.pomp@nki.nl',
description='Open ISS files.', description='Open ISS files.',