newer FC scripts are working, now older ones fail
This commit is contained in:
parent
3793f67951
commit
29518b9ea0
@ -42,6 +42,7 @@ AppDir:
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- python3.9-minimal
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- python3-numpy
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- python3-scipy
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- gnuplot-nox
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- python3-bsddb3
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- python3-h5py
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- python3-pyqt5
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@ -57,7 +58,6 @@ AppDir:
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- qtbase5-dev-tools
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- qtchooser
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- pyqt5-dev-tools
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- qtchooser
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- libavahi-client3
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- libavahi-common-data
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- libavahi-common3
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@ -2,6 +2,7 @@ from __future__ import annotations
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import pathlib
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from matplotlib import pyplot as plt
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# import matplotlib.pyplot as plt
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from scipy.optimize import curve_fit
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import numpy as np
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@ -14,6 +15,7 @@ from nmreval.utils.utils import get_temperature, roundrobin
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class FCReader:
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def __init__(self, fname: (list | str | pathlib.Path)):
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print('Hello')
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if isinstance(fname, (str, pathlib.Path)):
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self.fnames = [fname]
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else:
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@ -25,8 +27,6 @@ class FCReader:
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self.t_params = {}
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self.f_params = {}
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self._scipt_type = 'old'
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def __call__(self, fname: (list | str | pathlib.Path)):
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if isinstance(fname, (str, pathlib.Path)):
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self.fnames = [fname]
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@ -77,7 +77,14 @@ class FCReader:
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def _read_from_hdf(self, filename: (str | pathlib.Path)) -> dict:
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_temp = {}
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reader = HdfReader(filename)
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mag_directory = 'mag' if self._scipt_type == 'old' else 'Magnetization'
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mag_directory = 'Magnetization'
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for m in ['Magnetization', 'mag']:
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try:
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mag_directory = m
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except KeyError:
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continue
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for mag in reader.get_selected(mag_directory, dtype='points'):
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_temp[mag.value] = mag
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@ -97,21 +104,15 @@ class FCReader:
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return _temp
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@staticmethod
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def _read_signals(filename, region: tuple = None) -> dict:
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def _read_signals(self, filename, region: tuple = None) -> dict:
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reader = HdfReader(filename)
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start = 0
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stop = 30e-5
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# This is one set with attributes to find default start:stop values
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try:
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p = reader.parameters('/ABS_ACC_FID')
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start = p['start']
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stop = p['stop']
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except:
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pass
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# This is one set with attributes to find default start:stop values (with some
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p = reader.parameters('/ABS_ACC_FID')
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start = p.get('stainte') or p.get('start') or 0
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stop = p.get('stointe') or p.get('stop') or 30e-5
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if region is None:
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if region == (None, None) or region is None:
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region = (start, stop)
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if region[0] is None:
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@ -119,15 +120,35 @@ class FCReader:
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if region[1] is None:
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region = (region[0], stop)
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sig = reader.get_selected('/data/B=*/ACC_ABS_FID*', dtype='signal')
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_temp = {}
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for s in sig:
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pts = s.points([region])
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b = s.group
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if b not in _temp:
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_temp[b] = []
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bevo_groups = reader['data'].children
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for grp in bevo_groups.values():
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for k in grp.data():
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print(k)
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if str(k.parent) != 'ACC_ABS_FID_sig (group)':
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continue
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_temp[b].append([s.value, *[pp[1] for pp in pts]])
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print(k.path, k, k.parent, k.parameter['bevo'], k.parameter['tevo'])
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bevo = k.parameter['bevo']
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tevo = k.parameter['tevo']
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s = reader.make_signal(k, flag='fid', value='tevo', group='bevo')
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pts = s.points([region])
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if bevo not in _temp:
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_temp[bevo] = []
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_temp[bevo].append((tevo, *[pp[1] for pp in pts]))
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# sig = reader.get_selected('/data/B=*/ACC_ABS_FID*', dtype='signal')
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# _temp = {}
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# for s in sig:
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# pts = s.points([region])
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# b = s.group
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# if b not in _temp:
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# _temp[b] = []
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#
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# _temp[b].append([s.value, *[pp[1] for pp in pts]])
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for b, m in sorted(_temp.items()):
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m = np.array(m)
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@ -148,9 +169,9 @@ class FCReader:
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fit_path = fname_no_ext.joinpath('fit')
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fit_path.mkdir(parents=True, exist_ok=True)
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# if save_fig:
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# image_path = fname_no_ext.joinpath('png')
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# image_path.mkdir(parents=True, exist_ok=True)
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if save_fig:
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image_path = fname_no_ext.joinpath('png')
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image_path.mkdir(parents=True, exist_ok=True)
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header = 'm0\tt1\tbeta\toff\n'
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@ -189,16 +210,16 @@ class FCReader:
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np.savetxt(fit_path.joinpath(save_name), np.c_[xplot, yplot],
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header=header+'\t'.join([f'{p}+/-{err}' for p, err in zip(p0, perr)]))
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# if save_fig:
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# fig, ax = plt.subplots()
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# ax.set_xlabel('t / s')
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# ax.set_ylabel('M')
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# axheader = f'T1: {p0[2]:.4g}(+/-{perr[2]:.4g}) beta: {p0[3]:.4g}(+/-{perr[3]:.4g})'
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# ax.set_title(f'f = {k:.4g} Hz\n{axheader}')
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# ax.semilogx(v.x, v.y, 'o')
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# ax.semilogx(xplot, yplot, '-')
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# fig.savefig(image_path.joinpath(save_name).with_suffix('.png'))
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# plt.close(fig)
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if save_fig:
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fig, ax = plt.subplots()
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ax.set_xlabel('t / s')
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ax.set_ylabel('M')
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axheader = f'T1: {p0[2]:.4g}(+/-{perr[2]:.4g}) beta: {p0[3]:.4g}(+/-{perr[3]:.4g})'
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ax.set_title(f'f = {k:.4g} Hz\n{axheader}')
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ax.semilogx(v.x, v.y, 'o')
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ax.semilogx(xplot, yplot, '-')
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fig.savefig(image_path.joinpath(save_name).with_suffix('.png'))
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plt.close(fig)
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freqs = np.asanyarray(freqs)
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params = np.asanyarray(params)
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@ -290,45 +311,45 @@ class FCReader:
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path = pathlib.Path(path)
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path.mkdir(parents=True, exist_ok=True)
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# fig_mag, ax_mag = plt.subplots()
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# fig_t1, ax_t1 = plt.subplots()
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# fig_beta, ax_beta = plt.subplots()
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#
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# if kind == 'temp':
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# _params = self.t_params
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# else:
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# _params = self.f_params
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#
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# save_path = path.joinpath(kind)
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# if not save_path.exists():
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# save_path.mkdir(parents=True)
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#
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# for key, par in _params.items():
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# pl, = ax_mag.plot(par[:, 0], par[:, 1], 'o', label=key)
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# ax_mag.plot(par[:, 0], par[:, 3], 's', color=pl.get_color())
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# ax_t1.plot(par[:, 0], par[:, 5], 'o', label=key)
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# ax_beta.plot(par[:, 0], par[:, 7], 'o', label=key)
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#
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# for a in [ax_mag, ax_t1, ax_beta]:
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# if kind == 'freq':
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# a.legend(loc='upper left', bbox_to_anchor=(1, 1), ncol=2)
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# a.set_xlabel('T / K')
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# else:
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# a.set_xscale('log')
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# a.legend(loc='upper left', bbox_to_anchor=(1, 1))
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# a.set_xlabel('f / Hz')
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#
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# ax_t1.set_yscale('log')
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# ax_t1.set_ylabel('T1 / s')
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# ax_beta.set_ylabel('beta')
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# ax_mag.set_ylabel('M0 (squares), Offset (circles)')
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#
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# fig_beta.savefig(path.joinpath(f'beta_{kind}.png'), bbox_inches="tight")
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# fig_mag.savefig(path.joinpath(f'mag_{kind}.png'), bbox_inches="tight")
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# fig_t1.savefig(path.joinpath(f't1_{kind}.png'), bbox_inches="tight")
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# plt.close(fig_mag)
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# plt.close(fig_beta)
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# plt.close(fig_t1)
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fig_mag, ax_mag = plt.subplots()
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fig_t1, ax_t1 = plt.subplots()
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fig_beta, ax_beta = plt.subplots()
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if kind == 'temp':
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_params = self.t_params
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else:
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_params = self.f_params
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save_path = path.joinpath(kind)
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if not save_path.exists():
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save_path.mkdir(parents=True)
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for key, par in _params.items():
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pl, = ax_mag.plot(par[:, 0], par[:, 1], 'o', label=key)
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ax_mag.plot(par[:, 0], par[:, 3], 's', color=pl.get_color())
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ax_t1.plot(par[:, 0], par[:, 5], 'o', label=key)
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ax_beta.plot(par[:, 0], par[:, 7], 'o', label=key)
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for a in [ax_mag, ax_t1, ax_beta]:
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if kind == 'freq':
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a.legend(loc='upper left', bbox_to_anchor=(1, 1), ncol=2)
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a.set_xlabel('T / K')
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else:
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a.set_xscale('log')
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a.legend(loc='upper left', bbox_to_anchor=(1, 1))
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a.set_xlabel('f / Hz')
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ax_t1.set_yscale('log')
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ax_t1.set_ylabel('T1 / s')
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ax_beta.set_ylabel('beta')
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ax_mag.set_ylabel('M0 (squares), Offset (circles)')
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fig_beta.savefig(path.joinpath(f'beta_{kind}.png'), bbox_inches="tight")
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fig_mag.savefig(path.joinpath(f'mag_{kind}.png'), bbox_inches="tight")
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fig_t1.savefig(path.joinpath(f't1_{kind}.png'), bbox_inches="tight")
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plt.close(fig_mag)
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plt.close(fig_beta)
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plt.close(fig_t1)
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def get_parameter(self, parameter='all', kind='freq', path=None, write=True, plot=True):
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param_list = []
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@ -391,99 +412,10 @@ class FCReader:
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return m0 * np.exp(-(x/t1)**beta) + off
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class FCFileReader:
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def __init__(self, fname: str):
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self.filename = pathlib.Path(fname)
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self._is_dir = self.filename.is_dir()
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self._script_type = None
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self.reader = None
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if not self._is_dir:
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self.reader = HdfReader(self.filename)
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if 'mag' in self.reader:
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self._script_type = 'old'
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elif 'Magnetization' in self.reader:
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self._script_type = '2022_09'
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self._temperature = get_temperature(self.filename.stem)
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def load_magnetization(self, region=None):
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if self._is_dir:
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_temp = self._read_from_dir()
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else:
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if region is None:
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_temp = self._read_from_hdf()
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else:
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_temp = self._read_signals(region)
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if not _temp:
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raise OSError(-666, f'No magnetization found for {self.filename.name}.', self.filename.name)
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def _read_from_hdf(self) -> dict:
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_temp = {}
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mag_directory = 'mag' if self._script_type == 'old' else 'Magnetization'
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for mag in self.reader.get_selected(mag_directory, dtype='points'):
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_temp[mag.value] = mag
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return _temp
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def _read_from_dir(self) -> dict:
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fname_no_ext = self.filename.with_suffix('')
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data_path = fname_no_ext / 'data'
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_temp = {}
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for mag in data_path.glob('*.dat'):
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d = AsciiReader(mag).export()
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for v in d:
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_temp[v.value] = v
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break
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return _temp
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def _read_signals(self, region: tuple = None) -> dict:
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start = 0
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stop = 30e-5
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# This is one set with attributes to find default start:stop values
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try:
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p = self.reader.parameters('/ABS_ACC_FID')
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start = p['start']
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stop = p['stop']
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except:
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pass
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if region is None:
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region = (start, stop)
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if region[0] is None:
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region = (start, region[1])
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if region[1] is None:
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region = (region[0], stop)
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sig = self.reader.get_selected('/data/B=*/ACC_ABS_FID*', dtype='signal')
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_temp = {}
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for s in sig:
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pts = s.points([region])
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b = s.group
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if b not in _temp:
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_temp[b] = []
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_temp[b].append([s.value, *[pp[1] for pp in pts]])
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for b, m in sorted(_temp.items()):
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m = np.array(m)
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_temp[b] = Points(x=m[:, 0], y=m[:, 1], value=b, name=f'B={b}').sort()
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return _temp
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if __name__ == '__main__':
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from pprint import pprint
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test = FCReader('/autohome/dominik/nmreval/testdata/fc_test/2022-09-15_1344_new_script.h5')
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# test = FCReader('/autohome/dominik/nmreval/testdata/fc_test/314K_2015-09-03_1605.h5')
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test = FCReader('/autohome/dominik/nmreval/testdata/fc_test/314K_2015-09-03_1605.h5')
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test.load_magnetization(region=(None, None))
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test.load_magnetization()
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test.load_magnetization(region=(0, 10e-6))
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# pprint(test.data)
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# test = FCReader('/autohome/dominik/nmreval/testdata/fc_test/2023-03-16_1423.h5')
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# test.load_magnetization(region=(None, None))
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print(test.data)
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@ -27,7 +27,7 @@ class HdfNode:
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'num_signals', 'num_pts', 'num_grp',
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'title_parameter', 'parameter']
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def __init__(self, name, ref, parent):
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def __init__(self, name: str, ref, parent: HdfNode | None):
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self.name = name
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self.type = 'group'
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self.reference = ref
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@ -59,7 +59,6 @@ class HdfNode:
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return key in self.children
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def clear(self):
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self.name = ''
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self.type = 'group'
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@ -281,16 +280,16 @@ class HdfReader(HdfNode):
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for child in val.data(dtype=dtype):
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try:
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if child.type == 'points':
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ret_val.append(self._make_point(child))
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ret_val.append(self.make_point(child))
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elif child.type == 'signal':
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ret_val.append(self._make_signal(child, flag=flag, value=value, group=group))
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ret_val.append(self.make_signal(child, flag=flag, value=value, group=group))
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except IOError:
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print('something went wrong for ' + child.name)
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continue
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return ret_val
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def _make_point(self, node):
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def make_point(self, node):
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data = self.file[node.reference]
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val = None
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@ -300,7 +299,7 @@ class HdfReader(HdfNode):
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return Points(x=data['x'], y=data['y'], yerr=data['y_err'], name=node.name, value=val)
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def _make_signal(self, node, flag: str = 'fid', value: str = None, group: str = None):
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def make_signal(self, node, flag: str = 'fid', value: str = None, group: str = None):
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if value is None:
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value = self._get_parameter_values(node, node.parameter)
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else:
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