| Previous changeset 2:a1e26990131c (2024-03-04) Next changeset 4:a0d3b0fe0fa3 (2024-04-11) |
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Commit message:
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f |
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modified:
common.py larch_athena.py larch_athena.xml |
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| diff -r a1e26990131c -r 82e9dd980916 common.py --- a/common.py Mon Mar 04 11:43:19 2024 +0000 +++ b/common.py Fri Mar 22 14:23:27 2024 +0000 |
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| @@ -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: |
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| diff -r a1e26990131c -r 82e9dd980916 larch_athena.py --- a/larch_athena.py Mon Mar 04 11:43:19 2024 +0000 +++ b/larch_athena.py Fri Mar 22 14:23:27 2024 +0000 |
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| @@ -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") |
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| diff -r a1e26990131c -r 82e9dd980916 larch_athena.xml --- a/larch_athena.xml Mon Mar 04 11:43:19 2024 +0000 +++ b/larch_athena.xml Fri Mar 22 14:23:27 2024 +0000 |
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| b'@@ -4,7 +4,7 @@\n <!-- version of underlying tool (PEP 440) -->\n <token name="@TOOL_VERSION@">0.9.74</token>\n <!-- version of this tool wrapper (integer) -->\n- <token name="@WRAPPER_VERSION@">0</token>\n+ <token name="@WRAPPER_VERSION@">1</token>\n <!-- citation should be updated with every underlying tool version -->\n <!-- typical fields to update are version, month, year, and doi -->\n <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>\n@@ -58,7 +58,7 @@\n <include type="literal" path="common.py"/>\n </required_files>\n <command detect_errors="exit_code"><![CDATA[\n- mkdir prj edge flat derivative\n+ mkdir prj plot\n #if $merge_inputs.format.format=="plaintext":\n #if $merge_inputs.format.is_zipped.is_zipped=="true":\n && echo Unzipping \'$merge_inputs.format.is_zipped.dat_file.name\'\n@@ -90,7 +90,7 @@\n <conditional name="is_zipped" >\n <expand macro="is_zipped"/>\n <when value="">\n- <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."/>\n+ <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."/>\n </when>\n <when value="true">\n <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."/>\n@@ -180,7 +180,11 @@\n </when>\n </conditional>\n </section>\n- <param name="plot_graph" type="boolean" label="Plot graph" help="Whether to plot the pre/post edge fitting and the normalised x\xce\xbc data."/>\n+ <param name="plot_graph" type="select" multiple="true" display="checkboxes" label="Plot graphs">\n+ <option value="edge">Pre/post edge fitting</option>\n+ <option value="flat">Flattened x\xce\xbc</option>\n+ <option value="dmude">Derivative of x\xce\xbc</option>\n+ </param>\n <param name="zip_outputs" type="boolean" label="Zip outputs" help="Whether to zip all outputs into one dataset."/>\n </inputs>\n <outputs>\n@@ -193,17 +197,7 @@\n <filter>not zip_outputs</filter>\n <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>\n </data>\n- <data name="edge_plot" format="png" from_work_dir="edge/out.png" label="Edge fitting ${annotation} ${on_string}">\n- <filter>plot_graph</filter>\n- <filter>not zip_outputs</filter>\n- <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>\n- </data>\n- <data name="flat_plot" format="png" from_work_dir="flat/out.png" label="Flattened plot ${annotation} ${on_string}">\n- <filter>plot_graph</filter>\n- <filter>not zip_outputs</filter>\n- <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>\n- </data>\n- <data name="derivative_plot" format="png" from_work_dir="derivati'..b'e"/>\n <param name="dat_file" value="test.zip"/>\n- <param name="plot_graph" value="true"/>\n+ <param name="plot_graph" value="edge,flat,dmude"/>\n <output_collection name="athena_project_file_collection" type="list" count="2"/>\n- <output_collection name="edge_plot_collection" type="list" count="2"/>\n- <output_collection name="flat_plot_collection" type="list" count="2"/>\n- <output_collection name="derivative_plot_collection" type="list" count="2"/>\n+ <output_collection name="plot_collection" type="list" count="2"/>\n </test>\n <!-- 6 -->\n <test expect_num_outputs="1">\n <param name="is_zipped" value="true"/>\n <param name="dat_file" value="h5.zip"/>\n- <param name="plot_graph" value="true"/>\n+ <param name="plot_graph" value="edge,flat,dmude"/>\n <param name="zip_outputs" value="true"/>\n <output name="out_zip">\n <assert_contents>\n- <has_size value="312000" delta="500"/>\n+ <has_size value="75500" delta="500"/>\n </assert_contents>\n </output>\n </test>\n@@ -320,30 +290,20 @@\n </output>\n </test>\n <!-- 8 -->\n- <test expect_num_outputs="4">\n+ <test expect_num_outputs="2">\n <param name="dat_file" value="test.xmu"/>\n <param name="calibrate" value="true"/>\n <param name="energy_min" value="7000"/>\n <param name="energy_max" value="7200"/>\n- <param name="plot_graph" value="true"/>\n+ <param name="plot_graph" value="edge,flat,dmude"/>\n <output name="athena_project_file">\n <assert_contents>\n <has_size value="3300" delta="50"/>\n </assert_contents>\n </output>\n- <output name="edge_plot">\n- <assert_contents>\n- <has_size value="44900" delta="100"/>\n- </assert_contents>\n- </output>\n- <output name="flat_plot">\n+ <output name="plot">\n <assert_contents>\n- <has_size value="39400" delta="100"/>\n- </assert_contents>\n- </output>\n- <output name="derivative_plot">\n- <assert_contents>\n- <has_size value="45900" delta="100"/>\n+ <has_size value="134700" delta="100"/>\n </assert_contents>\n </output>\n </test>\n@@ -392,29 +352,19 @@\n </output>\n </test>\n <!-- 13: Test merging and plotting multiple prj inputs -->\n- <test expect_num_outputs="4">\n+ <test expect_num_outputs="2">\n <param name="merge_inputs" value="true"/>\n <param name="format" value="athena"/>\n <param name="dat_file" value="test.prj,test.prj"/>\n- <param name="plot_graph" value="true"/>\n+ <param name="plot_graph" value="edge,flat,dmude"/>\n <output name="athena_project_file">\n <assert_contents>\n <has_size value="4500" delta="100"/>\n </assert_contents>\n </output>\n- <output name="edge_plot">\n- <assert_contents>\n- <has_size value="54200" delta="100"/>\n- </assert_contents>\n- </output>\n- <output name="flat_plot">\n+ <output name="plot">\n <assert_contents>\n- <has_size value="39400" delta="100"/>\n- </assert_contents>\n- </output>\n- <output name="derivative_plot">\n- <assert_contents>\n- <has_size value="41800" delta="100"/>\n+ <has_size value="135000" delta="100"/>\n </assert_contents>\n </output>\n </test>\n' |