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Windows compatibility

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Wim Pomp
2022-10-17 16:56:26 +02:00
parent 9b20e7c657
commit c3c0c65b06
2 changed files with 33 additions and 34 deletions
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61
issfile/__init__.py
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@@ -11,6 +11,33 @@ from yaml import safe_load
from argparse import ArgumentParser
class TiffFile(IJTiffFile):
""" Modify the tiff writer so that it can read from the .iss-pt file by itself in parallel processes. """
def __init__(self, *args, iss, bar, **kwargs):
if 'processes' not in kwargs:
kwargs['processes'] = 'all'
super().__init__(*args, **kwargs)
self.iss = iss
self.bar = bar
def __getstate__(self):
return {key: value for key, value in self.__dict__.items() if key != 'bar'}
def update(self):
self.bar.update()
def compress_frame(self, frame):
if frame[0]:
frame, metadata = self.iss.get_carpet(*frame[1:])
ifd, offsets = super().compress_frame(frame.astype(self.dtype))
# ISS = 9*19*19 = 3249; list of t, x, y, z for each row in carpet
ifd[3249] = Tag('float', metadata.T.flatten())
return ifd, offsets
else:
frame = self.iss.get_image(*frame[1:])
return super().compress_frame(frame.astype(self.dtype))
class IssFile:
def __init__(self, file, version=388):
self.file = file
@@ -65,6 +92,7 @@ class IssFile:
frame = c + 2 * t * self.shape[2]
frame_bytes = self.shape[0] * self.shape[1] * self.delta
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):
self.data.seek(address)
data.append(unpack('<I', self.data.read(4)))
@@ -94,45 +122,16 @@ class IssFile:
index[int(round(j / self.cycle_time))] = i
return data[index], metadata[index].T
@property
def tiff_writer(self):
class TiffFile(IJTiffFile):
""" Modify the tiff writer so that it can read from the .iss-pt file by itself in parallel processes. """
def __init__(self, *args, iss, bar, **kwargs):
if 'processes' not in kwargs:
kwargs['processes'] = 'all'
super().__init__(*args, **kwargs)
self.iss = pickle.dumps(iss)
self.bar = bar
def update(self):
self.bar.update()
def compress_frame(self, frame):
if isinstance(self.iss, bytes):
self.iss = pickle.loads(self.iss)
if frame[0]:
frame, metadata = self.iss.get_carpet(*frame[1:])
ifd, offsets = super().compress_frame(frame.astype(self.dtype))
# ISS = 9*19*19 = 3249; list of t, x, y, z for each row in carpet
ifd[3249] = Tag('float', metadata.T.flatten())
return ifd, offsets
else:
frame = self.iss.get_image(*frame[1:])
return super().compress_frame(frame.astype(self.dtype))
return TiffFile
def save_images_as_tiff(self, file):
with tqdm(total=self.shape[2] * self.shape[3], desc='Writing images') as bar:
with self.tiff_writer(file, (self.shape[2], 1, self.shape[3]), iss=self, bar=bar,
with TiffFile(file, (self.shape[2], 1, self.shape[3]), iss=self, bar=bar,
pxsize=self.pxsize, comment=ET.tostring(self.metadata)) as tif:
for c, t in product(range(self.shape[2]), range(self.shape[3])):
tif.save(np.array((0, c, t)), c, 0, t)
def save_carpets_as_tiff(self, file):
with tqdm(total=self.shape[2] * self.shape[4], desc='Writing carpets') as bar:
with self.tiff_writer(file, (self.shape[2], 1, self.shape[4]), iss=self, bar=bar,
with TiffFile(file, (self.shape[2], 1, self.shape[4]), iss=self, bar=bar,
pxsize=self.orbit_pxsize, comment=ET.tostring(self.metadata)) as tif:
for c, t in product(range(self.shape[2]), range(self.shape[4])):
tif.save(np.array((1, c, t)), c, 0, t)

2
setup.py
View File

@@ -5,7 +5,7 @@ with open('README.md', 'r') as fh:
setuptools.setup(
name='issfile',
version='2022.10.2',
version='2022.10.3',
author='Wim Pomp @ Lenstra lab NKI',
author_email='w.pomp@nki.nl',
description='Open ISS files.',