Created
September 11, 2024 08:24
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Tool to extract raw data from NeXus formatted HDF5 files to "raw" memory mapped data files
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| import os | |
| import sys | |
| import tqdm | |
| import hdf5plugin | |
| import h5py | |
| def extract(nxs, template, start=None, end=None): | |
| """Extract data from the /entry/data/data dataset in nxs to | |
| individual frames following template, from start to end (range-style)""" | |
| with h5py.File(nxs, "r") as f: | |
| d = f["/entry/data/data"] | |
| s = d.shape | |
| if start is None: | |
| start = 0 | |
| if end is None: | |
| end = s[0] | |
| if end > s[0]: | |
| raise ValueError(f"{end} beyond end of data set ({s[0]})") | |
| print(f"Source dataset shape is: {s}") | |
| for j in tqdm.tqdm(range(start, end)): | |
| i = d[j, :, :] | |
| i.tofile(template % j) | |
| def main(filename): | |
| if not filename.endswith(".nxs"): | |
| raise ValueError(f"{filename} is not NeXus") | |
| template = os.path.split(filename)[-1].replace(".nxs", "_%06d.raw") | |
| extract(filename, template) | |
| if __name__ == "__main__": | |
| main(sys.argv[1]) |
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