139 lines
4.8 KiB
Python
139 lines
4.8 KiB
Python
import h5py
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import numpy as np
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META_MATRIX = ("UB")
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META_CELL = ("cell")
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META_STR = ("name")
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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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if section in ("detector parameters", "crystal"):
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content[section] = {}
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else:
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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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if section in ("detector parameters", "crystal"):
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if "=" in line:
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variable, value = line.split("=", 1)
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variable = variable.strip()
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value = value.strip()
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if variable in META_STR:
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pass
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elif variable in META_CELL:
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value = np.array(value.split(",")[:6], dtype=np.float)
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elif variable in META_MATRIX:
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value = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
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else: # default is a single float number
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value = float(value)
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content[section][variable] = value
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else:
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content[section].append(line)
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return content
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def read_detector_data(filepath, cami_meta=None):
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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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det_data["original_filename"] = filepath
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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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# overwrite zebra_mode from cami
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if cami_meta is not None:
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if "zebra_mode" in cami_meta:
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det_data["zebra_mode"] = cami_meta["zebra_mode"][0]
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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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det_data["name"] = h5f["/entry1/sample/name"][0].decode()
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det_data["cell"] = h5f["/entry1/sample/cell"][:]
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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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# overwrite metadata from .cami
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if cami_meta is not None:
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if "crystal" in cami_meta:
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cami_meta_crystal = cami_meta["crystal"]
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if "name" in cami_meta_crystal:
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det_data["name"] = cami_meta_crystal["name"]
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if "UB" in cami_meta_crystal:
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det_data["ub"] = cami_meta_crystal["UB"]
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if "cell" in cami_meta_crystal:
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det_data["cell"] = cami_meta_crystal["cell"]
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if "lambda" in cami_meta_crystal:
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det_data["wave"] = cami_meta_crystal["lambda"]
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if "detector parameters" in cami_meta:
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cami_meta_detparam = cami_meta["detector parameters"]
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if "dist1" in cami_meta_detparam:
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det_data["ddist"] = cami_meta_detparam["dist1"]
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return det_data
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