Olympus Vanta XRF plotting
Jeff Moe
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README.md
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README.md
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@ -3,14 +3,6 @@
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AI categorization of spectra from LIBS/XRF analyzers.
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# Status
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Alpha software under development.
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Need to check:
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* *API: 501 Not Implemented*
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https://spacecruft.org/spacecruft/pysalx/issues/2
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# Install
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## Install Dependencies
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Get system dependency and upgrade Python pip.
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@ -35,7 +27,6 @@ cd pysalx/
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..
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```
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## Clone Git Repo
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Get source code with `git`.
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@ -43,21 +34,23 @@ The default `requirements.txt` installs a Tensorflow without
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GPU support. You can edit the `requirements.txt` file to change
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which is supported. The "generic" version supports both.
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```
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git clone https://spacecruft.org/spacecruft/witzit
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cd witzit/
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pip install --user --upgrade -r requirements.txt
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```
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# witzit scripts
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* `witzit-load.py` --- Load and text display an example MCA.
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* `witzit-load-x555` --- Load and text display data from SciAps X-555 XRF.
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* `witzit-load-vanta` --- Load and text display data from Olympus Vanta XRF.
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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.ipynb` --- witzit Jupyter notebook, plotting application.
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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-predict.ipynb` --- witzit Jupyter notebook, prediction application.
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* `witzit-train.ipynb` --- witzit Jupyter notebook, training application.
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@ -95,7 +88,7 @@ HOWTO USE. Getting closer...
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```
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# Example:
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debian@workstation:~/spacecruft/witzit$ ./witzit-load.py
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debian@workstation:~/spacecruft/witzit$ ./witzit-load-x555
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energy (eV) 2048
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0 20.590676 0
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1 45.021816 0
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@ -111,9 +104,12 @@ debian@workstation:~/spacecruft/witzit$ ./witzit-load.py
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```
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## Jupyter Notebooks
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Example plot:
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Example plot from SciAps X-555 XRF:
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Example plot from Olympus Vanta XRF:
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Run jupyter thusly:
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@ -129,6 +125,8 @@ jupyter-lab
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* SciAps XRF Analyzer
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* Olympus XRF Analyzer
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# Deep Learning Algorithm
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Can use lots from `wut`.
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@ -187,15 +185,6 @@ same as in `wut`, so makes a good reference.
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*Feature selection of infrared spectra analysis with convolutional neural network*
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# Misc
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Will likely work best with binary categorizations. E.g. like this:
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Is it element A or not element A?
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Is it element B or not element B?
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Is it element C or not element C?
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Not "is it element A, B, or C?"
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# See Also
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* `pysalx` --- Unofficial scripts for interacting with the SciAps LIBS
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@ -208,6 +197,14 @@ https://spacecruft.org/spacecruft/pysalx/
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https://spacecruft.org/spacecruft/satnogs-wut/
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# Status
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Alpha software under development.
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Need to check:
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* *API: 501 Not Implemented*
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https://spacecruft.org/spacecruft/pysalx/issues/2
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# Unofficial
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Unofficial, unaffiliated with SciAps.
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@ -61,7 +61,11 @@
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"outputs": [],
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"source": [
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"df = pd.read_csv('examples/olympus-vanta.csv', header = 0,\n",
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" skiprows=[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40], usecols = [0, 1])"
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" skiprows=40,\n",
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" names=('eV', 'Counts'),\n",
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" usecols = [0, 1])\n",
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"\n",
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"df['eV'] = df['eV'] * 1000"
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]
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},
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{
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@ -82,14 +86,14 @@
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"sns.set_theme()\n",
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"plt.figure(facecolor='xkcd:off white', figsize=(15, 8))\n",
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"# XXX y=\n",
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"g=sns.lineplot(x=\"Date\", y=\"2022-04-08\", data=df, linestyle='-', linewidth=1, color='xkcd:pale orange')\n",
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"g=sns.lineplot(x=\"eV\", y=\"Counts\", data=df, linestyle='-', linewidth=1, color='xkcd:pale orange')\n",
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"g.set_title('XRF Spectrum'.format('seaborn'), color='xkcd:cornflower blue', fontsize='large', fontweight='bold')\n",
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"g.set_xlabel('energy (keV)', color='xkcd:goldenrod', fontsize='large', fontweight='bold')\n",
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"g.set_xlabel('energy (eV)', color='xkcd:goldenrod', fontsize='large', fontweight='bold')\n",
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"g.set_ylabel('Counts', color='xkcd:cerulean', fontsize='large', fontweight='bold')\n",
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"g.patch.set_alpha(1.0)\n",
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"g.set_facecolor('xkcd:powder blue')\n",
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"plt.tight_layout()\n",
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"plt.savefig(\"xrf-spectrum.png\", dpi=72, transparent=False, facecolor='xkcd:off white', edgecolor=g.get_facecolor())\n",
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"plt.savefig(\"xrf-spectrum-vanta.png\", dpi=72, transparent=False, facecolor='xkcd:off white', edgecolor=g.get_facecolor())\n",
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"plt.show()\n",
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"plt.close()"
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]
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