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changeset 0:89ae4a5724a5 draft

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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
author muon-spectroscopy-computational-project
date Thu, 25 Aug 2022 16:17:15 +0000
parents
children 193ed5c2d443
files 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
diffstat 8 files changed, 1620 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_plot.py	Thu Aug 25 16:17:15 2022 +0000
@@ -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()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muspinsim_plot.xml	Thu Aug 25 16:17:15 2022 +0000
@@ -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 &amp; 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/experiment.dat	Thu Aug 25 16:17:15 2022 +0000
@@ -0,0 +1,100 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting.dat	Thu Aug 25 16:17:15 2022 +0000
@@ -0,0 +1,104 @@
+# MUSPINSIM v.1.0.3
+# Output file written on Fri Apr  1 14:57:50 2022
+# Parameters used:
+#
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Binary file test-data/fitting_example.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/high_T.dat	Thu Aug 25 16:17:15 2022 +0000
@@ -0,0 +1,204 @@
+# MUSPINSIM v.1.0.3
+# Output file written on Fri Apr  1 15:08:23 2022
+# Parameters used:
+# 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/low_T.dat	Thu Aug 25 16:17:15 2022 +0000
@@ -0,0 +1,1004 @@
+# MUSPINSIM v.1.0.3
+# Output file written on Fri Apr  1 15:08:29 2022
+# Parameters used:
+# 
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