Source code for WrightTools.data._aramis

"""Aramis."""


# --- import --------------------------------------------------------------------------------------


import os
import struct
import pathlib
import warnings

import numpy as np

from ._data import Data
from .. import exceptions as wt_exceptions


# --- define --------------------------------------------------------------------------------------


__all__ = ["from_Aramis"]


# --- from function -------------------------------------------------------------------------------


[docs]def from_Aramis(filepath, name=None, parent=None, verbose=True) -> Data: """Create a data object from Horiba Aramis ngc binary file. Parameters ---------- filepath : path-like Path to .ngc file. Can be either a local or remote file (http/ftp). Can be compressed with gz/bz2, decompression based on file name. name : string (optional) Name to give to the created data object. If None, name is extracted from file. Default is None. parent : WrightTools.Collection (optional) Collection to place new data object within. Default is None. verbose : boolean (optional) Toggle talkback. Default is True. Returns ------- data New data object(s). """ # parse filepath filestr = os.fspath(filepath) filepath = pathlib.Path(filepath) if not ".ngc" in filepath.suffixes: wt_exceptions.WrongFileTypeWarning.warn(filepath, ".ngc") ds = np.DataSource(None) f = ds.open(filestr, "rb") header = f.readline() if header != b"NGSNextGen\x01\x00\x00\x00\x01\x00\x00\x00\n": warnings.warn(f"Unexpected Header {header}, Aramis parsing may not be valid") header = f.read(10) if header != b"DataMatrix": warnings.warn(f"Unexpected Header {header}, Aramis parsing may not be valid") instr = _readstr(f) iname = _readstr(f) # parse name if not name: name = iname # create data kwargs = {"name": name, "kind": "Aramis", "source": filestr} if parent is None: data = Data(**kwargs) else: data = parent.create_data(**kwargs) # array f.seek(4 * 4, 1) # skip 4 integers [~=size, 0, 8, -1] is expected asize = struct.unpack("<i", f.read(4))[0] ndim = struct.unpack("<h", f.read(2))[0] shape = struct.unpack(f"<{'i'*ndim}", f.read(4 * ndim)) f.seek(2 + 4, 1) # skip '0xffff', size in bytes arr = np.fromfile(f, "<f4", np.prod(shape)) arr.shape = shape f.read((asize - arr.size) * 4) while f.read(1) == b"\0": pass f.seek(-1, 1) nlab = struct.unpack("<h", f.read(2))[0] labels = [_readstr(f) for _ in range(nlab)] nunit = struct.unpack("<h", f.read(2))[0] unit_trans = {"1/cm": "wn", "┬Ám": "um", "sec": "s_t", "": None} units = [_readstr(f) for _ in range(nunit)] units = [unit_trans.get(u, u) for u in units] skip = struct.unpack("<h", f.read(2))[0] f.seek(skip, 1) # skip values that were all zero in test data # Which index in the shape aligns whith which label/unit nidx = struct.unpack("<h", f.read(2))[0] idx = struct.unpack(f"<{'h'*2*nidx}", f.read(4 * nidx))[::2] chidx = idx.index(ndim) data.create_channel(labels[chidx], arr, units=units[chidx]) # Endpoints of axes, needed if full array unavailable nend = struct.unpack("<h", f.read(2))[0] end = struct.unpack(f"<{'f'*nend}", f.read(4 * nend)) # Unknown what value means, other than nonzero seems to indicate array present nunk = struct.unpack("<h", f.read(2))[0] unk = struct.unpack(f"<{'i'*nunk}", f.read(4 * nunk)) for i, u in enumerate(unk): if idx[i] < ndim: if u != 0: axissize = struct.unpack("<h", f.read(2))[0] // 4 arr = np.fromfile(f, "<f4", axissize) else: arr = np.linspace(end[2 * i], end[2 * i + 1], shape[idx[i]]) sh = [1] * ndim sh[idx[i]] = shape[idx[i]] arr.shape = tuple(sh) data.create_variable(labels[i], arr, units=units[i], label=labels[i]) data.transform(*[labels[i] for i, ix in enumerate(idx) if ix < ndim]) # finish f.close() if verbose: print("data created at {0}".format(data.fullpath)) print(" axes: {0}".format(data.axis_names)) print(" shape: {0}".format(data.shape)) return data
def _readstr(f): return f.read(ord(f.read(1))).decode("iso-8859-1")