Merge branch 'read_fc'

AppImageBuilder.yml

@@ -41,6 +41,7 @@ AppDir:
 #      - zsync
 #      - hicolor-icon-theme
       - libatlas3-base
+      - gnuplot-nox
       - python3.9-minimal
       - python3-numpy
       - python3-scipy

src/nmreval/io/fcbatchreader.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
 import pathlib
+import subprocess
+import tempfile
 
 # import matplotlib.pyplot as plt
 from scipy.optimize import curve_fit
@@ -9,6 +11,7 @@ import numpy as np
 from nmreval.data.points import Points
 from nmreval.io.asciireader import AsciiReader
 from nmreval.io.hdfreader import HdfReader
+from nmreval.lib.logger import logger
 from nmreval.utils.utils import get_temperature, roundrobin
 
 
@@ -54,7 +57,7 @@ class FCReader:
                 _temp = self._read_from_dir(filename)
 
             else:
-                raise TypeError
+                raise TypeError(f'{filename} is of unknown type')
 
             if not _temp:
                 raise OSError(-666, f'No magnetization found for {filename.name}.', filename.name)
@@ -178,6 +181,7 @@ class FCReader:
                 fit_path.mkdir(parents=True, exist_ok=True)
 
             if save_fig:
+                data_path = fname_no_ext.joinpath('data')
                 image_path = fname_no_ext.joinpath('png')
                 image_path.mkdir(parents=True, exist_ok=True)
 
@@ -218,16 +222,34 @@ class FCReader:
                         np.savetxt(fit_path.joinpath(save_name), np.c_[xplot, yplot],
                                    header=header+'\t'.join([f'{p}+/-{err}' for p, err in zip(p0, perr)]))
 
-                    # if save_fig:
-                    #     fig, ax = plt.subplots()
-                    #     ax.set_xlabel('t / s')
-                    #     ax.set_ylabel('M')
-                    #     axheader = f'T1: {p0[2]:.4g}(+/-{perr[2]:.4g}) beta: {p0[3]:.4g}(+/-{perr[3]:.4g})'
-                    #     ax.set_title(f'f = {k:.4g} Hz\n{axheader}')
-                    #     ax.semilogx(v.x, v.y, 'o')
-                    #     ax.semilogx(xplot, yplot, '-')
-                    #     fig.savefig(image_path.joinpath(save_name).with_suffix('.png'))
-                    #     plt.close(fig)
+                    if save_fig:
+                        img_file = image_path.joinpath(save_name).with_suffix(".png")
+
+                        gnuplot_args = [
+                            'set terminal png;',
+                            f'set output "{img_file}";',
+                            f'set title "f = {k:.4g} Hz\\n{p0[2]:.4g}(+/-{perr[2]:.4g}) beta: {p0[3]:.4g}(+/-{perr[3]:.4g})";',
+                            'set xlabel "t / s";',
+                            'set logscale x;',
+                            'set format x "10^{{%L}}";',
+                            'set ylabel "M";',
+                            'set key off;',
+                            f'plot "{data_path.joinpath(save_name)}" with points pointtype 5, "{fit_path.joinpath(save_name)}" with lines;',
+                        ]
+
+                        try:
+                            proc = subprocess.Popen(
+                                ['gnuplot', '-p'],
+                                shell=True,
+                                stdin=subprocess.PIPE,
+                                encoding='utf8',
+                            )
+                            for args in gnuplot_args:
+                                proc.stdin.write(args)
+                            proc.stdin.write('quit\n')
+                            proc.stdin.flush()
+                        except Exception as e:
+                            logger.error(f'saving image {save_name} failed', e)
 
             freqs = np.asanyarray(freqs)
             params = np.asanyarray(params)