Mercurial > repos > muon-spectroscopy-computational-project > larch_athena
changeset 3:82e9dd980916 draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Fri, 22 Mar 2024 14:23:27 +0000 |
| parents | a1e26990131c |
| children | a0d3b0fe0fa3 |
| files | common.py larch_athena.py larch_athena.xml |
| diffstat | 3 files changed, 86 insertions(+), 114 deletions(-) [+] |
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--- a/common.py Mon Mar 04 11:43:19 2024 +0000 +++ b/common.py Fri Mar 22 14:23:27 2024 +0000 @@ -73,7 +73,11 @@ ) for key, parameters_key, default in keys: extract_attribute( - merged_settings, key, bkg_parameters, parameters_key, default + merged_settings=merged_settings, + key=key, + parameters_group=bkg_parameters, + parameters_key=parameters_key, + default=default, ) if settings: @@ -116,7 +120,11 @@ ) for key, parameters_key, default in keys: extract_attribute( - merged_settings, key, fft_parameters, parameters_key, default + merged_settings=merged_settings, + key=key, + parameters_group=fft_parameters, + parameters_key=parameters_key, + default=default, ) if settings:
--- a/larch_athena.py Mon Mar 04 11:43:19 2024 +0000 +++ b/larch_athena.py Fri Mar 22 14:23:27 2024 +0000 @@ -5,7 +5,10 @@ import sys from common import ( - pre_edge_with_defaults, read_all_groups, read_group, xftf_with_defaults + pre_edge_with_defaults, + read_all_groups, + read_group, + xftf_with_defaults, ) from larch.io import ( @@ -45,12 +48,14 @@ ) -> "dict[str, Group]": if merge_inputs: out_group = self.merge_files( - dat_files=dat_file, is_zipped=is_zipped + dat_files=dat_file, + is_zipped=is_zipped, ) return {"out": out_group} else: return self.load_single_file( - filepath=dat_file, is_zipped=is_zipped + filepath=dat_file, + is_zipped=is_zipped, ) def merge_files( @@ -258,7 +263,7 @@ pre_edge_settings: dict, do_xftf: bool, xftf_settings: dict, - plot_graph: bool, + plot_graph: list, annotation: str, path_key: str = "out", ): @@ -287,9 +292,11 @@ xftf_with_defaults(xas_data, xftf_settings) if plot_graph: - plot_edge_fits(f"edge/{path_key}.png", xas_data) - plot_flattened(f"flat/{path_key}.png", xas_data) - plot_derivative(f"derivative/{path_key}.png", xas_data) + plot_graphs( + plot_path=f"plot/{path_key}.png", + xas_data=xas_data, + plot_keys=plot_graph, + ) xas_project = create_athena(f"prj/{path_key}.prj") xas_project.add_group(xas_data) @@ -302,36 +309,43 @@ gc.collect() -def plot_derivative(plot_path: str, xafs_group: Group): - plt.figure() - plt.plot(xafs_group.energy, xafs_group.dmude) - plt.grid(color="r", linestyle=":", linewidth=1) - plt.xlabel("Energy (eV)") - plt.ylabel("Derivative normalised to x$\mu$(E)") # noqa: W605 - plt.savefig(plot_path, format="png") - plt.close("all") - +def plot_graphs( + plot_path: str, + xas_data: Group, + plot_keys: list, +) -> None: + nrows = len(plot_keys) + index = 1 + plt.figure(figsize=(6.4, nrows * 4.8)) + if "edge" in plot_keys: + plt.subplot(nrows, 1, index) + plt.plot(xas_data.energy, xas_data.pre_edge, "g", label="pre-edge") + plt.plot(xas_data.energy, xas_data.post_edge, "r", label="post-edge") + plt.plot(xas_data.energy, xas_data.mu, "b", label="fit data") + plt.grid(color="r", linestyle=":", linewidth=1) + plt.xlabel("Energy (eV)") + plt.ylabel("x$\mu$(E)") # noqa: W605 + plt.title("Pre-edge and post_edge fitting to $\mu$") # noqa: W605 + plt.legend() + index += 1 -def plot_edge_fits(plot_path: str, xafs_group: Group): - plt.figure() - plt.plot(xafs_group.energy, xafs_group.pre_edge, "g", label="pre-edge") - plt.plot(xafs_group.energy, xafs_group.post_edge, "r", label="post-edge") - plt.plot(xafs_group.energy, xafs_group.mu, "b", label="fit data") - plt.grid(color="r", linestyle=":", linewidth=1) - plt.xlabel("Energy (eV)") - plt.ylabel("x$\mu$(E)") # noqa: W605 - plt.title("pre-edge and post_edge fitting to $\mu$") # noqa: W605 - plt.legend() - plt.savefig(plot_path, format="png") - plt.close("all") + if "flat" in plot_keys: + plt.subplot(nrows, 1, index) + plt.plot(xas_data.energy, xas_data.flat) + plt.grid(color="r", linestyle=":", linewidth=1) + plt.xlabel("Energy (eV)") + plt.ylabel("Flattened x$\mu$(E)") # noqa: W605 + index += 1 + if "dmude" in plot_keys: + plt.subplot(nrows, 1, index) + plt.plot(xas_data.energy, xas_data.dmude) + plt.grid(color="r", linestyle=":", linewidth=1) + plt.xlabel("Energy (eV)") + plt.ylabel("Derivative normalised to x$\mu$(E)") # noqa: W605 + index += 1 -def plot_flattened(plot_path: str, xafs_group: Group): - plt.figure() - plt.plot(xafs_group.energy, xafs_group.flat) - plt.grid(color="r", linestyle=":", linewidth=1) - plt.xlabel("Energy (eV)") - plt.ylabel("normalised x$\mu$(E)") # noqa: W605 + plt.tight_layout(rect=(0, 0, 0.88, 1)) plt.savefig(plot_path, format="png") plt.close("all")
--- a/larch_athena.xml Mon Mar 04 11:43:19 2024 +0000 +++ b/larch_athena.xml Fri Mar 22 14:23:27 2024 +0000 @@ -4,7 +4,7 @@ <!-- version of underlying tool (PEP 440) --> <token name="@TOOL_VERSION@">0.9.74</token> <!-- version of this tool wrapper (integer) --> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> <!-- citation should be updated with every underlying tool version --> <!-- typical fields to update are version, month, year, and doi --> <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> @@ -58,7 +58,7 @@ <include type="literal" path="common.py"/> </required_files> <command detect_errors="exit_code"><![CDATA[ - mkdir prj edge flat derivative + mkdir prj plot #if $merge_inputs.format.format=="plaintext": #if $merge_inputs.format.is_zipped.is_zipped=="true": && echo Unzipping '$merge_inputs.format.is_zipped.dat_file.name' @@ -90,7 +90,7 @@ <conditional name="is_zipped" > <expand macro="is_zipped"/> <when value=""> - <param name="dat_file" type="data" format="h5,txt" label="XAFS data file" help="X-ray Absorption Fine Structure (XAFS) data, either in h5 or plaintext."/> + <param name="dat_file" type="data" format="h5,tabular" label="XAFS data file" help="X-ray Absorption Fine Structure (XAFS) data, either in h5 or plaintext."/> </when> <when value="true"> <param name="dat_file" type="data" format="zip" label="Zipped XAFS data files" help="Zipped X-ray Absorption Fine Structure (XAFS) data, either in h5 or plaintext."/> @@ -180,7 +180,11 @@ </when> </conditional> </section> - <param name="plot_graph" type="boolean" label="Plot graph" help="Whether to plot the pre/post edge fitting and the normalised xμ data."/> + <param name="plot_graph" type="select" multiple="true" display="checkboxes" label="Plot graphs"> + <option value="edge">Pre/post edge fitting</option> + <option value="flat">Flattened xμ</option> + <option value="dmude">Derivative of xμ</option> + </param> <param name="zip_outputs" type="boolean" label="Zip outputs" help="Whether to zip all outputs into one dataset."/> </inputs> <outputs> @@ -193,17 +197,7 @@ <filter>not zip_outputs</filter> <filter>not (merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")))</filter> </data> - <data name="edge_plot" format="png" from_work_dir="edge/out.png" label="Edge fitting ${annotation} ${on_string}"> - <filter>plot_graph</filter> - <filter>not zip_outputs</filter> - <filter>not (merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")))</filter> - </data> - <data name="flat_plot" format="png" from_work_dir="flat/out.png" label="Flattened plot ${annotation} ${on_string}"> - <filter>plot_graph</filter> - <filter>not zip_outputs</filter> - <filter>not (merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")))</filter> - </data> - <data name="derivative_plot" format="png" from_work_dir="derivative/out.png" label="Derivative plot ${annotation} ${on_string}"> + <data name="plot" format="png" from_work_dir="plot/out.png" label="Plot of ${annotation} ${on_string}"> <filter>plot_graph</filter> <filter>not zip_outputs</filter> <filter>not (merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")))</filter> @@ -214,20 +208,8 @@ <filter>not zip_outputs</filter> <filter>merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter> </collection> - <collection name="edge_plot_collection" format="png" type="list" label="Edge fittings ${annotation} ${on_string}"> - <discover_datasets pattern="__name_and_ext__" directory="edge"/> - <filter>plot_graph</filter> - <filter>not zip_outputs</filter> - <filter>merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter> - </collection> - <collection name="flat_plot_collection" format="png" type="list" label="Flattened plots ${annotation} ${on_string}"> - <discover_datasets pattern="__name_and_ext__" directory="flat"/> - <filter>plot_graph</filter> - <filter>not zip_outputs</filter> - <filter>merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter> - </collection> - <collection name="derivative_plot_collection" format="png" type="list" label="Derivative plots ${annotation} ${on_string}"> - <discover_datasets pattern="__name_and_ext__" directory="derivative"/> + <collection name="plot_collection" format="png" type="list" label="Plots of ${annotation} ${on_string}"> + <discover_datasets pattern="__name_and_ext__" directory="plot"/> <filter>plot_graph</filter> <filter>not zip_outputs</filter> <filter>merge_inputs["merge_inputs"] == "" and ((merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter> @@ -262,49 +244,37 @@ </output> </test> <!-- 4 --> - <test expect_num_outputs="4"> + <test expect_num_outputs="2"> <param name="dat_file" value="test.xmu"/> - <param name="plot_graph" value="true"/> + <param name="plot_graph" value="edge,flat,dmude"/> <output name="athena_project_file"> <assert_contents> <has_size value="5400" delta="100"/> </assert_contents> </output> - <output name="edge_plot"> - <assert_contents> - <has_size value="54036" delta="20"/> - </assert_contents> - </output> - <output name="flat_plot"> + <output name="plot"> <assert_contents> - <has_size value="39266" delta="20"/> - </assert_contents> - </output> - <output name="derivative_plot"> - <assert_contents> - <has_size value="42435" delta="20"/> + <has_size value="134972" delta="20"/> </assert_contents> </output> </test> <!-- 5 --> - <test expect_num_outputs="4"> + <test expect_num_outputs="2"> <param name="is_zipped" value="true"/> <param name="dat_file" value="test.zip"/> - <param name="plot_graph" value="true"/> + <param name="plot_graph" value="edge,flat,dmude"/> <output_collection name="athena_project_file_collection" type="list" count="2"/> - <output_collection name="edge_plot_collection" type="list" count="2"/> - <output_collection name="flat_plot_collection" type="list" count="2"/> - <output_collection name="derivative_plot_collection" type="list" count="2"/> + <output_collection name="plot_collection" type="list" count="2"/> </test> <!-- 6 --> <test expect_num_outputs="1"> <param name="is_zipped" value="true"/> <param name="dat_file" value="h5.zip"/> - <param name="plot_graph" value="true"/> + <param name="plot_graph" value="edge,flat,dmude"/> <param name="zip_outputs" value="true"/> <output name="out_zip"> <assert_contents> - <has_size value="312000" delta="500"/> + <has_size value="75500" delta="500"/> </assert_contents> </output> </test> @@ -320,30 +290,20 @@ </output> </test> <!-- 8 --> - <test expect_num_outputs="4"> + <test expect_num_outputs="2"> <param name="dat_file" value="test.xmu"/> <param name="calibrate" value="true"/> <param name="energy_min" value="7000"/> <param name="energy_max" value="7200"/> - <param name="plot_graph" value="true"/> + <param name="plot_graph" value="edge,flat,dmude"/> <output name="athena_project_file"> <assert_contents> <has_size value="3300" delta="50"/> </assert_contents> </output> - <output name="edge_plot"> - <assert_contents> - <has_size value="44900" delta="100"/> - </assert_contents> - </output> - <output name="flat_plot"> + <output name="plot"> <assert_contents> - <has_size value="39400" delta="100"/> - </assert_contents> - </output> - <output name="derivative_plot"> - <assert_contents> - <has_size value="45900" delta="100"/> + <has_size value="134700" delta="100"/> </assert_contents> </output> </test> @@ -392,29 +352,19 @@ </output> </test> <!-- 13: Test merging and plotting multiple prj inputs --> - <test expect_num_outputs="4"> + <test expect_num_outputs="2"> <param name="merge_inputs" value="true"/> <param name="format" value="athena"/> <param name="dat_file" value="test.prj,test.prj"/> - <param name="plot_graph" value="true"/> + <param name="plot_graph" value="edge,flat,dmude"/> <output name="athena_project_file"> <assert_contents> <has_size value="4500" delta="100"/> </assert_contents> </output> - <output name="edge_plot"> - <assert_contents> - <has_size value="54200" delta="100"/> - </assert_contents> - </output> - <output name="flat_plot"> + <output name="plot"> <assert_contents> - <has_size value="39400" delta="100"/> - </assert_contents> - </output> - <output name="derivative_plot"> - <assert_contents> - <has_size value="41800" delta="100"/> + <has_size value="135000" delta="100"/> </assert_contents> </output> </test>