First commit, working code.

issfile/__init__.py

@@ -0,0 +1,109 @@
+import sys
+import zipfile
+import xml.etree.ElementTree as ET
+import numpy as np
+import re
+from struct import unpack
+from tiffwrite import IJTiffFile
+from tqdm.auto import tqdm
+from itertools import product
+from yaml import safe_load
+
+
+class IssTrack:
+    def __init__(self, file):
+        self.zip = zipfile.ZipFile(file)
+        self.data = self.zip.open('data/PrimaryDecayData.bin')
+        self.metadata = ET.fromstring(self.zip.read('dataProps/Core.xml'))
+        dimensions = self.metadata.find('Dimensions')
+        size_t = int(dimensions.find('TimeSeriesCount').text)
+        size_c = int(dimensions.find('ChannelCount').text)
+        size_y = int(dimensions.find('FrameHeight').text)
+        size_x = int(dimensions.find('FrameWidth').text)
+        # X, Y, channels, n_images, n_carpets
+        self.shape = size_x, size_y, size_c, size_t // 2 + size_t % 2, size_t // 2
+        self.exposure_time = float(self.metadata.find('FrameIntervalTime').text)
+        self.pxsize = float(self.metadata.find('Boundary').find('FrameWidth').text) / self.shape[0]
+
+        self.alba_metadata = safe_load('\n'.join([IssTrack.parse_line(line)
+            for line in self.metadata.find('AlbaSystemSettings').find('withComments').text.splitlines()]))
+        particle_tracking = self.alba_metadata['ParticleTracking']
+        self.points_per_orbit = particle_tracking['ScanCirclePointCount']
+        self.n_orbits = particle_tracking['OrbitCountPerTrack']
+        self.orbit_time = particle_tracking['PacketTrackTime_ms']
+        self.start_times = [float(re.match(r'[.\d]+', value).group(0))
+                            for key, value in self.alba_metadata.items()
+                            if re.match(r'Time Series (\d+) started at', key)]
+        self.time_interval = np.mean(np.diff(self.start_times)[1::2])
+        self.delta = self.shape[2] * 2 ** int(np.ceil(np.log2(self.time_interval * 1000 / self.orbit_time)))
+        self.delta = 768  # TODO: figure out if this number is the same for all files
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args, **kwargs):
+        self.close()
+
+    def close(self):
+        try:
+            self.data.close()
+        finally:
+            self.zip.close()
+
+    def get_image(self, c, t):
+        assert c < self.shape[2] and t < self.shape[3], \
+            f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[3]}'
+        frame = c + 2 * t * self.shape[2]
+        frame_bytes = self.shape[0] * self.shape[1] * self.delta
+        data = []
+        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)))
+        return np.reshape(data, self.shape[:2])
+
+    def get_carpet(self, c, t):
+        assert c < self.shape[2] and t < 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_bytes = self.shape[0] * self.shape[1] * self.delta
+        data = []
+        self.data.seek(frame * frame_bytes)
+        for i in range(frame_bytes // (2 * self.points_per_orbit * self.n_orbits)):
+            line = [unpack('<H', self.data.read(2))[0] for _ in range(self.points_per_orbit * self.n_orbits)]
+            if np.any(line):
+                data.append(line)
+            else:
+                break
+        return np.vstack(data)
+
+    def save_images_as_tiff(self, file):
+        with IJTiffFile(file, (self.shape[2], 1, self.shape[3]),
+                        pxsize=self.pxsize, comment=ET.tostring(self.metadata)) as tif:
+            for c, t in tqdm(product(range(self.shape[2]), range(self.shape[3])), total=self.shape[2] * self.shape[3]):
+                tif.save(self.get_image(c, t), c, 0, t)
+
+    def save_carpets_as_tiff(self, file):
+        with IJTiffFile(file, (self.shape[2], 1, self.shape[4]),
+                        pxsize=self.pxsize, comment=ET.tostring(self.metadata)) as tif:
+            for c, t in tqdm(product(range(self.shape[2]), range(self.shape[4])), total=self.shape[2] * self.shape[4]):
+                tif.save(self.get_carpet(c, t), c, 0, t)
+
+    @staticmethod
+    def parse_line(line):
+        line = re.sub(r'^(\s*)\[([^\[\]]+)]', r'\1\2:', line)
+        line = re.sub(r'\s+:', r':', line)
+        line = re.sub(r'\t', r'', line)
+        line = re.sub(r'\s*-\s*:', r':', line)
+        line = re.sub(r'\s*=\s*', r' ', line)
+        return line
+
+
+def main():
+    for file in sys.argv[1:]:
+        with IssTrack(file) as iss_file:
+            iss_file.save_images_as_tiff(file.replace('.iss-pt', '.tif'))
+            iss_file.save_carpets_as_tiff(file.replace('.iss-pt', '.carpet.tif'))
+
+
+if __name__ == '__main__':
+    main()

setup.py

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+import setuptools
+
+with open('README.md', 'r') as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name='issfile',
+    version='2022.10.12',
+    author='Wim Pomp @ Lenstra lab NKI',
+    author_email='w.pomp@nki.nl',
+    description='Open ISS files.',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    url='https://github.com/wimpomp/issfile',
+    packages=setuptools.find_packages(),
+    classifiers=[
+        'Programming Language :: Python :: 3',
+        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+        'Operating System :: OS Independent',
+    ],
+    python_requires='>=3.8',
+    install_requires=['numpy', 'tiffwrite>=2022.10.0'],
+    entry_points={'console_scripts': ['iss2tiff=issfile:main']}
+)