89 lines
2.6 KiB
Python
89 lines
2.6 KiB
Python
import h5py
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def read_h5meta(filepath):
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"""Open and parse content of a h5meta file.
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Args:
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filepath (str): File path of a h5meta file.
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Returns:
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dict: A dictionary with section names and their content.
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"""
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with open(filepath) as file:
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content = parse_h5meta(file)
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return content
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def parse_h5meta(file):
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content = dict()
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section = None
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for line in file:
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line = line.strip()
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if line.startswith("#begin "):
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section = line[len("#begin ") :]
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content[section] = []
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elif line.startswith("#end"):
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section = None
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elif section:
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content[section].append(line)
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return content
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def read_detector_data(filepath):
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"""Read detector data and angles from an h5 file.
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Args:
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filepath (str): File path of an h5 file.
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Returns:
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ndarray: A 3D array of data, omega, gamma, nu.
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"""
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with h5py.File(filepath, "r") as h5f:
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data = h5f["/entry1/area_detector2/data"][:]
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# reshape data to a correct shape (2006 issue)
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n, cols, rows = data.shape
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data = data.reshape(n, rows, cols)
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det_data = {"data": data}
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if "/entry1/zebra_mode" in h5f:
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det_data["zebra_mode"] = h5f["/entry1/zebra_mode"][0].decode()
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else:
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det_data["zebra_mode"] = "nb"
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# om, sometimes ph
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if det_data["zebra_mode"] == "nb":
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det_data["omega"] = h5f["/entry1/area_detector2/rotation_angle"][:]
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else: # bi
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det_data["omega"] = h5f["/entry1/sample/rotation_angle"][:]
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det_data["gamma"] = h5f["/entry1/ZEBRA/area_detector2/polar_angle"][:] # gammad
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det_data["nu"] = h5f["/entry1/ZEBRA/area_detector2/tilt_angle"][:] # nud
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det_data["ddist"] = h5f["/entry1/ZEBRA/area_detector2/distance"][:]
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det_data["wave"] = h5f["/entry1/ZEBRA/monochromator/wavelength"][:]
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det_data["chi"] = h5f["/entry1/sample/chi"][:] # ch
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det_data["phi"] = h5f["/entry1/sample/phi"][:] # ph
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det_data["ub"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
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for var in ("omega", "gamma", "nu", "chi", "phi"):
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if abs(det_data[var][0] - det_data[var][-1]) > 0.1:
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det_data["scan_motor"] = var
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break
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else:
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raise ValueError("No angles that vary")
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# optional parameters
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if "/entry1/sample/magnetic_field" in h5f:
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det_data["mf"] = h5f["/entry1/sample/magnetic_field"][:]
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if "/entry1/sample/temperature" in h5f:
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det_data["temp"] = h5f["/entry1/sample/temperature"][:]
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return det_data
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