Add scripts to plot from CLI
Jeff Moe
parent
6b4d7eccec
commit
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@ -51,12 +51,15 @@ pip install --user --upgrade -r requirements.txt
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# witzit scripts
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* `witzit-load` --- Load and text display data from SciAps or Olympus XRF.
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* `witzit-plot` --- Plot a sample from a SciAps X-555 or Olympus Vanta-M.
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* `witzit-plot2png` --- Plot a sample from a SciAps X-555 or Olympus Vanta-M
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and save to PNG.
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Development is most easily done under Jupyter with Tensorboard
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for training models. These files are in the `notebooks/` directory.
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* `witzit-plot-x555.ipynb` --- witzit Jupyter notebook, plotting application for SciAps X-555 XRF.
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* `witzit-plot-vanta.ipynb` --- witzit Jupyter notebook, plotting application for Olympus Vanta XRF.
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* `witzit-plot.ipynb` --- witzit Jupyter notebook, plotting application for
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SciAps X-555 or Olympus Vanta-M.
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* `witzit-predict.ipynb` --- witzit Jupyter notebook, prediction application.
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* `witzit-train.ipynb` --- witzit Jupyter notebook, training application.
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@ -0,0 +1,87 @@
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#!/usr/bin/python3
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#
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# witzit-plot
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#
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# Copyright (C) 2022, Jeff Moe
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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# witzit-plot
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# Plot a sample from a SciAps X-555 or Olympus Vanta-M.
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#
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# Usage:
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# witzit-plot [data filename]
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#
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# Examples:
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# witzit-plot examples/olympus-vanta.csv
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# witzit-plot examples/sciaps-x555.mca
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import numpy as np
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import pandas as pd
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import seaborn as sns
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import matplotlib.pyplot as plt
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import locale
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import sys
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import re
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locale.setlocale(locale.LC_ALL, "en_US.utf8")
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plt.rcParams['axes.formatter.use_locale'] = True
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# Determine what type of file to load to dataframe
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datafile=(sys.argv[1])
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with open(datafile) as f:
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firstline = f.readline().rstrip()
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if firstline == 'File Version = 2':
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print('SciAps X-555 XRF MCA')
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template = pd.read_csv('template/sciaps-x555-ev.csv', header=0,
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skiprows=0,
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usecols = [0])
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mca = pd.read_csv(datafile, skiprows=21, header=0,
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usecols = [0])
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df=template.join(mca)
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df.rename(columns = {'2048':'Counts'}, inplace = True)
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elif re.match(re.compile('Date,*'), firstline):
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print('Olympus Vanta-M XRF')
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df = pd.read_csv(datafile, header=0,
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skiprows=39,
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names=('energy (eV)', 'Counts'),
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usecols = [0, 1])
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df['energy (eV)'] = df['energy (eV)'] * 1000
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elif re.match(re.compile('"Date",*'), firstline):
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print('Possibly SciAps X-555 XRF CSV, not processed. Use .mca file instead of .csv.')
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exit()
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else:
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print('Unknown file type.')
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exit()
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# Plot
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sns.set_theme()
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plt.figure(facecolor='xkcd:off white', figsize=(15, 8))
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g=sns.lineplot(x="energy (eV)", y="Counts", data=df, linestyle='-', linewidth=1, color='xkcd:pale orange')
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g.set_title('XRF Spectrum'.format('seaborn'), color='xkcd:cornflower blue', fontsize='large', fontweight='bold')
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g.set_xlabel('energy (eV)', color='xkcd:goldenrod', fontsize='large', fontweight='bold')
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g.set_ylabel('Counts', color='xkcd:cerulean', fontsize='large', fontweight='bold')
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g.patch.set_alpha(1.0)
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g.set_facecolor('xkcd:powder blue')
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plt.xlim(0,50000)
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plt.ylim(0,100000)
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plt.tight_layout()
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plt.show()
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plt.close()
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@ -0,0 +1,88 @@
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#!/usr/bin/python3
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#
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# witzit-plot2png
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#
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# Copyright (C) 2022, Jeff Moe
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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# witzit-plot2png
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# Plot a sample from a SciAps LIBS or XRF and save to PNG.
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#
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# Usage:
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# witzit-plot2png [data filename] [PNG output filename]
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#
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# Examples:
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# witzit-plot2png examples/olympus-vanta.csv tmp/spectrum.png
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# witzit-plot2png examples/sciaps-x555.mca tmp/x555.png
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import numpy as np
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import pandas as pd
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import seaborn as sns
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import matplotlib.pyplot as plt
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import locale
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import sys
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import re
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locale.setlocale(locale.LC_ALL, "en_US.utf8")
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plt.rcParams['axes.formatter.use_locale'] = True
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# Determine what type of file to load to dataframe
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datafile=(sys.argv[1])
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with open(datafile) as f:
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firstline = f.readline().rstrip()
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if firstline == 'File Version = 2':
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print('SciAps X-555 XRF MCA')
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template = pd.read_csv('template/sciaps-x555-ev.csv', header=0,
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skiprows=0,
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usecols = [0])
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mca = pd.read_csv(datafile, skiprows=21, header=0,
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usecols = [0])
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df=template.join(mca)
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df.rename(columns = {'2048':'Counts'}, inplace = True)
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elif re.match(re.compile('Date,*'), firstline):
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print('Olympus Vanta-M XRF')
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df = pd.read_csv(datafile, header=0,
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skiprows=39,
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names=('energy (eV)', 'Counts'),
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usecols = [0, 1])
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df['energy (eV)'] = df['energy (eV)'] * 1000
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elif re.match(re.compile('"Date",*'), firstline):
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print('Possibly SciAps X-555 XRF CSV, not processed. Use .mca file instead of .csv.')
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exit()
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else:
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print('Unknown file type.')
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exit()
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# Plot
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sns.set_theme()
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plt.figure(facecolor='xkcd:off white', figsize=(15, 8))
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g=sns.lineplot(x="energy (eV)", y="Counts", data=df, linestyle='-', linewidth=1, color='xkcd:pale orange')
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g.set_title('XRF Spectrum'.format('seaborn'), color='xkcd:cornflower blue', fontsize='large', fontweight='bold')
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g.set_xlabel('energy (eV)', color='xkcd:goldenrod', fontsize='large', fontweight='bold')
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g.set_ylabel('Counts', color='xkcd:cerulean', fontsize='large', fontweight='bold')
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g.patch.set_alpha(1.0)
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g.set_facecolor('xkcd:powder blue')
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plt.xlim(0,50000)
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plt.ylim(0,100000)
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plt.tight_layout()
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plt.savefig(sys.argv[2], dpi=72, transparent=False, facecolor='xkcd:off white', edgecolor=g.get_facecolor())
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plt.show()
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plt.close()
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