| Next changeset 1:193ed5c2d443 (2022-09-15) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4 |
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added:
generate_plot.py muspinsim_plot.xml test-data/experiment.dat test-data/fitting.dat test-data/fitting_example.pdf test-data/high_T.dat test-data/low_T.dat test-data/temp_example.png |
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| diff -r 000000000000 -r 89ae4a5724a5 generate_plot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_plot.py Thu Aug 25 16:17:15 2022 +0000 |
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| @@ -0,0 +1,46 @@ +import json +import sys + +import matplotlib.pyplot as plt + +import numpy as np + + +def main(): + input_json_path = sys.argv[1] + + plot_params = json.load(open(input_json_path, "r")) + + for series in plot_params["mu_out_series"]: + mu_data = np.loadtxt(series['mu_data'], usecols=(0, 1)) + x, y = mu_data.T + { + 'line': lambda x, y, label, c, args: + plt.plot(x, y, + label=label, + c=c, + ls=args['linestyle'], + lw=args['linewidth'] + ), + 'points': lambda x, y, label, c, args: + plt.scatter(x, y, + label=label, + c=c, + s=args['pointscale'], + marker=args['pointstyle'], + ) + }.get(series['series_type']['type'])( + x, y, series['mu_label'], series['colour'], series['series_type'] + ) + + plt.xlabel(plot_params['xlab']) + plt.ylabel(plot_params['ylab']) + plt.title(plot_params['title']) + plt.legend(loc="upper right") + + outfile = "outfile.{}".format(plot_params['out_file_type']) + plt.savefig(outfile, format=plot_params['out_file_type']) + + +if __name__ == '__main__': + main() |
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| diff -r 000000000000 -r 89ae4a5724a5 muspinsim_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muspinsim_plot.xml Thu Aug 25 16:17:15 2022 +0000 |
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| @@ -0,0 +1,162 @@ +<tool id="muspinsim_plot" name="MuSpinSim Plot" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> + <macros> + <!-- version of underlying tool (PEP 440) --> + <token name="@TOOL_VERSION@">3.5.1</token> + <!-- version of this tool wrapper (integer) --> + <token name="@WRAPPER_VERSION@">0</token> + <!-- citation should be updated with every underlying tool version --> + <!-- typical fields to update are version, month, year, and doi --> + <token name="@TOOL_CITATION@"> + @article{Hunter:2007, + author = {Hunter, J. D.}, + title = {Matplotlib: A 2D graphics environment}, + journal = {Computing in Science & Engineering}, + volume = {9}, + number = {3}, + pages = {90--95}, + abstract = {Matplotlib is a 2D graphics package used for Python for + application development, interactive scripting, and publication-quality + image generation across user interfaces and operating systems.}, + publisher = {IEEE COMPUTER SOC}, + doi = {10.1109/MCSE.2007.55}, + year = {2007} + } + </token> + </macros> + <creator> + <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> + <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> + <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> + </creator> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">matplotlib</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python ${__tool_directory__}/generate_plot.py inputs.json + ]]></command> + <configfiles> + <inputs name="inputs" data_style="paths" filename="inputs.json"/> + </configfiles> + <inputs> + <param type="text" name="title" label="Plot Title" value=""/> + <param type="text" name="xlab" label="Label for x axis" value=""/> + <param type="text" name="ylab" label="Label for y axis" value=""/> + <param name="out_file_type" type="select" label="Output File Type"> + <option value="pdf">PDF</option> + <option value="png">PNG</option> + </param> + <repeat name="mu_out_series" title="Muspinsim File Series"> + <param type="data" name="mu_data" format="txt" label="Muspinsim Experiment Data (.dat)"/> + <param type="text" name="mu_label" optional="true" label="Muspinsim Experiment Label" value="" help="Label to use for this series in the plot legend."/> + <param type="select" name="colour" label="Line/Point Color"> + <option value="k">Black</option> + <option value="r">Red</option> + <option value="g">Green</option> + <option value="b">Blue</option> + </param> + <conditional name="series_type"> + <param type="select" name="type" label="Series Type"> + <option value="line">Line</option> + <option value="points">Points</option> + </param> + <when value="line"> + <param type="select" name="linestyle" label="Line type"> + <option value="solid">Solid</option> + <option value="dashed">Dashed</option> + <option value="dotted">Dotted</option> + </param> + <param type="float" name="linewidth" label="Line width" value="1.0"/> + </when> + <when value="points"> + <param type="select" name="pointstyle" label="Point Type"> + <option value="s">Square</option> + <option value="o">Circle</option> + </param> + <param type="float" name="pointscale" label="Point Scale" value="1.0"/> + </when> + </conditional> + </repeat> + </inputs> + <outputs> + <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf"> + <filter>(out_file_type == 'pdf')</filter> + </data> + <data format="png" name="out_file_png" from_work_dir="outfile.png"> + <filter>(out_file_type == 'png')</filter> + </data> + </outputs> + <tests> + <test> + <param name="title" value="Temperature Example"/> + <param name="xlab" value="Time"/> + <param name="ylab" value="Asymmetry"/> + <param name="out_file_type" value="png"/> + <param name="mu_data" value="high_T.dat" ftype="txt"/> + <param name="mu_label" value="High T limit"/> + <param name="type" value="points"/> + <param name="pointstyle" value="s"/> + <param name="colour" value="r"/> + <param name="pointscale" value="2.0"/> + <param name="mu_data" value="low_T.dat" ftype="txt"/> + <param name="mu_label" value="T=1 K"/> + <param name="type" value="line"/> + <param name="linestyle" value="solid"/> + <param name="colour" value="k"/> + <param name="linewidth" value="1.0"/> + <output name="out_file_png" ftype="png"> + <assert_contents> + <has_size value="52486" delta="20"/> + </assert_contents> + </output> + </test> + <test> + <param name="title" value="Fitting Example"/> + <param name="xlab" value="Time"/> + <param name="ylab" value="Asymmetry"/> + <param name="out_file_type" value="pdf"/> + <param name="mu_data" value="experiment.dat" ftype="txt"/> + <param name="mu_label" value="Data"/> + <param name="type" value="points"/> + <param name="pointstyle" value="o"/> + <param name="pointscale" value="3.0"/> + <param name="colour" value="b"/> + <param name="mu_data" value="fitting.dat" ftype="txt"/> + <param name="mu_label" value="Fitting"/> + <param name="type" value="line"/> + <param name="linestyle" value="solid"/> + <param name="colour" value="b"/> + <param name="linewidth" value="1.0"/> + <output name="out_file_pdf" ftype="pdf"> + <assert_contents> + <has_size value="14785" delta="20"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + This tool allows you to plot values generated from muspinsim using Matplotlib. + + + You can plot them as points or as lines. + + + You can overlay multiple plots on top of each other by providing more than one data file. + ]]></help> + <citations> + <citation type="bibtex"> + @TOOL_CITATION@ + </citation> + <citation type="bibtex"> + @software{muspinsim, + author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}}, + license = {MIT}, + title = {{muspinsim}}, + url = {https://github.com/muon-spectroscopy-computational-project/muspinsim}, + version = {v1.1.0}, + month = {5}, + year = {2022}, + doi = {10.5281/zenodo.6563074} + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 89ae4a5724a5 test-data/experiment.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/experiment.dat Thu Aug 25 16:17:15 2022 +0000 |
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| @@ -0,0 +1,100 @@ +0.000000000000000000e+00 5.005778399056657335e-01 +1.010101010101010187e-02 4.913142788391854365e-01 +2.020202020202020374e-02 4.625960774510225471e-01 +3.030303030303030387e-02 4.529727926470791810e-01 +4.040404040404040747e-02 4.201084135897126814e-01 +5.050505050505051108e-02 4.102951709644535039e-01 +6.060606060606060774e-02 3.943894674205472572e-01 +7.070707070707071829e-02 3.614924122022374342e-01 +8.080808080808081495e-02 3.335847485026482429e-01 +9.090909090909091161e-02 3.242904460614065565e-01 +1.010101010101010222e-01 2.947929241310389692e-01 +1.111111111111111188e-01 2.682338522764465272e-01 +1.212121212121212155e-01 2.499741447755643442e-01 +1.313131313131313260e-01 2.246842301024072619e-01 +1.414141414141414366e-01 2.054104137278633946e-01 +1.515151515151515194e-01 1.768606299542749838e-01 +1.616161616161616299e-01 1.571509466787300857e-01 +1.717171717171717404e-01 1.394992240477620771e-01 +1.818181818181818232e-01 1.208113647730562346e-01 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| diff -r 000000000000 -r 89ae4a5724a5 test-data/fitting.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fitting.dat Thu Aug 25 16:17:15 2022 +0000 |
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| @@ -0,0 +1,104 @@ +# MUSPINSIM v.1.0.3 +# Output file written on Fri Apr 1 14:57:50 2022 +# Parameters used: +# +0.000000000000000000e+00 5.000000000000000000e-01 +1.010101010101010187e-02 4.839188562974035546e-01 +2.020202020202020374e-02 4.664633082870883185e-01 +3.030303030303030387e-02 4.477992370076759321e-01 +4.040404040404040747e-02 4.280884746475391855e-01 +5.050505050505051108e-02 4.074882658312278805e-01 +6.060606060606060774e-02 3.861507830642957884e-01 +7.070707070707071829e-02 3.642226954481366796e-01 +8.080808080808081495e-02 3.418447895726685060e-01 +9.090909090909091161e-02 3.191516413083217985e-01 +1.010101010101010222e-01 2.962713370496566911e-01 +1.111111111111111188e-01 2.733252428108397525e-01 +1.212121212121212155e-01 2.504278194378757871e-01 +1.313131313131313260e-01 2.276864820835683423e-01 +1.414141414141414366e-01 2.052015019882667823e-01 +1.515151515151515194e-01 1.830659485220967053e-01 +1.616161616161616299e-01 1.613656693720554314e-01 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2.677474208198871858e-02 +9.494949494949496138e-01 2.657290764758631768e-02 +9.595959595959596689e-01 2.625506521748296324e-02 +9.696969696969697239e-01 2.582964932112596923e-02 +9.797979797979798899e-01 2.530511082451557259e-02 +9.898989898989899450e-01 2.468987524488667346e-02 +1.000000000000000000e+00 2.399230366807731177e-02 |
| b |
| diff -r 000000000000 -r 89ae4a5724a5 test-data/fitting_example.pdf |
| b |
| Binary file test-data/fitting_example.pdf has changed |
| b |
| diff -r 000000000000 -r 89ae4a5724a5 test-data/high_T.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/high_T.dat Thu Aug 25 16:17:15 2022 +0000 |
| b |
| b'@@ -0,0 +1,204 @@\n+# MUSPINSIM v.1.0.3\n+# Output file written on Fri Apr 1 15:08:23 2022\n+# Parameters used:\n+# \n+0.000000000000000000e+00 5.000000000000000000e-01\n+5.025125628140704025e-04 4.548524693297328336e-01\n+1.005025125628140805e-03 3.276059962899626754e-01\n+1.507537688442211208e-03 1.413532974885093607e-01\n+2.010050251256281610e-03 -7.012892919953786497e-02\n+2.512562814070352230e-03 -2.685372365807210393e-01\n+3.015075376884422415e-03 -4.180151586530714836e-01\n+3.517587939698492601e-03 -4.916672722768279935e-01\n+4.020100502512563220e-03 -4.764240631303121587e-01\n+4.522613065326633840e-03 -3.753730198257079209e-01\n+5.025125628140704459e-03 -2.071380005853223905e-01\n+5.527638190954774211e-03 -2.430871430766215480e-03\n+6.030150753768844830e-03 2.015832825524755956e-01\n+6.532663316582915450e-03 3.680685254804669793e-01\n+7.035175879396985202e-03 4.672040376039552356e-01\n+7.537688442211055821e-03 4.815538403458245464e-01\n+8.040201005025126441e-03 4.091482613100387300e-01\n+8.542713567839196193e-03 2.637298174699946873e-01\n+9.045226130653267679e-03 7.213860675815035595e-02\n+9.547738693467337431e-03 -1.306642695149698163e-01\n+1.005025125628140892e-02 -3.080085344380294465e-01\n+1.055276381909547867e-02 -4.281801648443375186e-01\n+1.105527638190954842e-02 -4.701226252809459494e-01\n+1.155778894472361991e-02 -4.271435716169332819e-01\n+1.206030150753768966e-02 -3.079713335521952478e-01\n+1.256281407035175941e-02 -1.349967024951781447e-01\n+1.306532663316583090e-02 5.994810039257951473e-02\n+1.356783919597990065e-02 2.414751047346597734e-01\n+1.407035175879397040e-02 3.770978010877490405e-01\n+1.457286432160804189e-02 4.430756889761133799e-01\n+1.507537688442211164e-02 4.285891259334860814e-01\n+1.557788944723618313e-02 3.375067727319158162e-01\n+1.608040201005025288e-02 1.874582697066057846e-01\n+1.658291457286432263e-02 6.421571523474459142e-03\n+1.708542713567839239e-02 -1.725143974382218892e-01\n+1.758793969849246561e-02 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2.000057310720851078e-01\n+3.718592964824121022e-02 1.896839135390429587e-01\n+3.768844221105527997e-'..b'658607e-02 6.347377206405235839e-02\n+6.180904522613066276e-02 1.302376421674228957e-01\n+6.231155778894473252e-02 1.777287270455245594e-01\n+6.281407035175880227e-02 1.951542741049450691e-01\n+6.331658291457287202e-02 1.768148920230087351e-01\n+6.381909547738694177e-02 1.235977542459716638e-01\n+6.432160804020101152e-02 4.325111938040765436e-02\n+6.482412060301508128e-02 -5.068776376192626887e-02\n+6.532663316582915103e-02 -1.411755090553940550e-01\n+6.582914572864322078e-02 -2.107708458891604519e-01\n+6.633165829145729053e-02 -2.449985387618227595e-01\n+6.683417085427136028e-02 -2.353198064957194857e-01\n+6.733668341708543004e-02 -1.811059770177198824e-01\n+6.783919597989949979e-02 -9.017954011348530696e-02\n+6.834170854271356954e-02 2.225242459671394890e-02\n+6.884422110552763929e-02 1.361409899607548546e-01\n+6.934673366834170904e-02 2.301892401128996513e-01\n+6.984924623115579267e-02 2.858496244240414930e-01\n+7.035175879396986243e-02 2.909719368661195515e-01\n+7.085427135678393218e-02 2.423860458148995034e-01\n+7.135678391959800193e-02 1.468807094625041443e-01\n+7.185929648241207168e-02 2.032779063549158827e-02\n+7.236180904522614143e-02 -1.149520475140755338e-01\n+7.286432160804021119e-02 -2.341456070921206778e-01\n+7.336683417085428094e-02 -3.145205644044935522e-01\n+7.386934673366835069e-02 -3.397691649449845475e-01\n+7.437185929648242044e-02 -3.032908093968177399e-01\n+7.487437185929649019e-02 -2.097569670752049142e-01\n+7.537688442211055995e-02 -7.460733176011935530e-02\n+7.587939698492462970e-02 7.849234915475722385e-02\n+7.638190954773869945e-02 2.218134710828332246e-01\n+7.688442211055276920e-02 3.286128730133611731e-01\n+7.738693467336683895e-02 3.781424427997103765e-01\n+7.788944723618090871e-02 3.596782343063738008e-01\n+7.839195979899497846e-02 2.747869506738540579e-01\n+7.889447236180904821e-02 1.373590814399697768e-01\n+7.939698492462311796e-02 -2.865410052872488511e-02\n+7.989949748743718771e-02 -1.934329531665233692e-01\n+8.040201005025127134e-02 -3.266740790855787724e-01\n+8.090452261306534110e-02 -4.031897053028388189e-01\n+8.140703517587941085e-02 -4.076825193038747797e-01\n+8.190954773869348060e-02 -3.377885042887722733e-01\n+8.241206030150755035e-02 -2.047850234200215280e-01\n+8.291457286432162010e-02 -3.178509837039474040e-02\n+8.341708542713568986e-02 1.502957770739300203e-01\n+8.391959798994975961e-02 3.082933931618698220e-01\n+8.442211055276382936e-02 4.128661759858053282e-01\n+8.492462311557789911e-02 4.439671663763212761e-01\n+8.542713567839196886e-02 3.946921284211223346e-01\n+8.592964824120603862e-02 2.727642724331449386e-01\n+8.643216080402010837e-02 9.934332084033507815e-02\n+8.693467336683417812e-02 -9.466149063795656349e-02\n+8.743718592964824787e-02 -2.741292502614064985e-01\n+8.793969849246231762e-02 -4.061186184654671516e-01\n+8.844221105527638738e-02 -4.659434557396006649e-01\n+8.894472361809045713e-02 -4.418070870248382298e-01\n+8.944723618090452688e-02 -3.371222436321156257e-01\n+8.994974874371859663e-02 -1.700614627125307809e-01\n+9.045226130653266639e-02 2.961038168832489520e-02\n+9.095477386934673614e-02 2.258669260562105596e-01\n+9.145728643216081977e-02 3.829547520763129653e-01\n+9.195979899497488952e-02 4.719400350307773606e-01\n+9.246231155778895927e-02 4.760627664039074336e-01\n+9.296482412060302902e-02 3.939033566252438945e-01\n+9.346733668341709877e-02 2.397616168514637158e-01\n+9.396984924623116853e-02 4.115729210020925566e-02\n+9.447236180904523828e-02 -1.661089979581054088e-01\n+9.497487437185930803e-02 -3.444432909981581803e-01\n+9.547738693467337778e-02 -4.613125302448755072e-01\n+9.597989949748744753e-02 -4.952094996705523333e-01\n+9.648241206030151729e-02 -4.396294378621908860e-01\n+9.698492462311558704e-02 -3.043197741150853730e-01\n+9.748743718592965679e-02 -1.135626284234362293e-01\n+9.798994974874372654e-02 9.820581498687230848e-02\n+9.849246231155779630e-02 2.926446037515830767e-01\n+9.899497487437186605e-02 4.344860087996524900e-01\n+9.949748743718593580e-02 4.979657214762875372e-01\n+1.000000000000000056e-01 4.715269204165091210e-01\n' |
| b |
| diff -r 000000000000 -r 89ae4a5724a5 test-data/low_T.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/low_T.dat Thu Aug 25 16:17:15 2022 +0000 |
| b |
| b'@@ -0,0 +1,1004 @@\n+# MUSPINSIM v.1.0.3\n+# Output file written on Fri Apr 1 15:08:29 2022\n+# Parameters used:\n+# \n+0.000000000000000000e+00 5.000000000000000000e-01\n+1.001001001001001047e-04 4.981033135329970274e-01\n+2.002002002002002093e-04 4.924277044580595009e-01\n+3.003003003003003411e-04 4.830163953152626366e-01\n+4.004004004004004186e-04 4.699410204948861192e-01\n+5.005005005005004962e-04 4.533010769114754757e-01\n+6.006006006006006821e-04 4.332231931920127455e-01\n+7.007007007007007597e-04 4.098601849845365797e-01\n+8.008008008008008372e-04 3.833898746108277966e-01\n+9.009009009009009148e-04 3.540137024310235359e-01\n+1.001001001001000992e-03 3.219551819737365150e-01\n+1.101101101101101178e-03 2.874582203870960639e-01\n+1.201201201201201364e-03 2.507852822354347810e-01\n+1.301301301301301333e-03 2.122153773667754262e-01\n+1.401401401401401519e-03 1.720419004949797492e-01\n+1.501501501501501488e-03 1.305703806449169391e-01\n+1.601601601601601674e-03 8.811617362706007650e-02\n+1.701701701701701860e-03 4.500208438560602403e-02\n+1.801801801801801830e-03 1.555900590454642463e-03\n+1.901901901901902016e-03 -4.189213780194039893e-02\n+2.002002002002001985e-03 -8.501187288878778170e-02\n+2.102102102102102171e-03 -1.274757259209254590e-01\n+2.202202202202202357e-03 -1.689611641010432819e-01\n+2.302302302302302543e-03 -2.091531576169390338e-01\n+2.402402402402402729e-03 -2.477466087969406316e-01\n+2.502502502502502481e-03 -2.844486958982454516e-01\n+2.602602602602602667e-03 -3.189810865937854345e-01\n+2.702702702702702853e-03 -3.510820248661400966e-01\n+2.802802802802803039e-03 -3.805083163671193480e-01\n+2.902902902902903225e-03 -4.070372042584569638e-01\n+3.003003003003002977e-03 -4.304680851090599836e-01\n+3.103103103103103163e-03 -4.506240201477559326e-01\n+3.203203203203203349e-03 -4.673530450527574320e-01\n+3.303303303303303535e-03 -4.805293098801032281e-01\n+3.403403403403403721e-03 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