| Previous changeset 2:123a9a629bef (2021-06-06) Next changeset 4:b393815e4cb7 (2022-07-31) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4" |
|
modified:
macros.xml test-data/all.netcdf test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time50.png test-data/info_file.txt test-data/small.netcdf test-data/version.tabular xarray_mapplot.py xarray_netcdf2netcdf.py xarray_select.xml xarray_tool.py |
|
added:
macros_mapplot.xml macros_netcdf2netcdf.xml macros_tests_netcdf2netcdf.xml test-data/chl_alltimes.nc test-data/chl_nh4.netcdf test-data/chl_phy_where.netcdf test-data/chl_where_drop.netcdf test-data/data_from_20040615.nc test-data/data_to_20040615.nc test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0_title.png test-data/select_by_values.netcdf test-data/small_all_variables.netcdf test-data/where_condition.txt test-data/where_condition_simple.txt |
|
removed:
README.md |
| b |
| diff -r 123a9a629bef -r bf595d613af4 README.md --- a/README.md Sun Jun 06 08:51:41 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -# Xarray tools for netCDF -## netCDF metadata information - -The first tool `xarray_metadata_info ` uses xarray to provide users with general information about variable names, dimensions -and attributes. -Variables that can be extracted and dimensions available are printed in a tabular file. - -The tool also print a general information file. It's the result of the xarray method info(). |
| b |
| diff -r 123a9a629bef -r bf595d613af4 macros.xml --- a/macros.xml Sun Jun 06 08:51:41 2021 +0000 +++ b/macros.xml Thu Jan 20 17:07:19 2022 +0000 |
| [ |
| b'@@ -1,185 +1,28 @@\n-<macros>\n- <token name="@TOOL_VERSION@">0.18.2</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n- <xml name="edam_ontology">\n- <edam_topics>\n- <edam_topic>topic_0610</edam_topic>\n- <edam_topic>topic_3050</edam_topic>\n- </edam_topics>\n- </xml>\n- <xml name="citations">\n- <citations>\n- <citation type="bibtex">\n- @article{hoyer2017xarray,\n- title = {xarray: {N-D} labeled arrays and datasets in {Python}},\n- author = {Hoyer, S. and J. Hamman},\n- journal = {Journal of Open Research Software},\n- volume = {5},\n- number = {1},\n- year = {2017},\n- publisher = {Ubiquity Press},\n- doi = {10.5334/jors.148},\n- url = {http://doi.org/10.5334/jors.148}\n- }\n- </citation>\n- </citations>\n- </xml>\n- <xml name="customize_appearance_plots">\n- <param name="borders" type="float" optional="true" label="Add country borders with alpha value [0-1] (optional)" />\n- <param name="coastline" type="float" optional="true" label="Add coastline with alpha value [0-1] (optional)" />\n- <param name="ocean" type="float" optional="true" label="Add ocean with alpha value [0-1] (optional)" />\n- <param name="land" type="float" optional="true" label="Add land with alpha value [0-1] (optional)" />\n- <param name="title" type="text" optional="true" label="Specify plot title (optional)" />\n- <param name="colorbar_label" type="text" optional="true" label="Set a label for colormap (optional)" />\n- <param name="cmap" type="select" optional="true" label="Specify which colormap to use for plotting (optional)">\n- <option value="cm.batlow">batlow</option>\n- <option value="cm.batlowW">batlowW</option>\n- <option value="cm.batlowK">batlowK</option>\n- <option value="cm.devon">devon</option>\n- <option value="cm.davos">davos</option>\n- <option value="cm.oslo">oslo</option>\n- <option value="cm.lapaz">lapaz</option>\n- <option value="cm.acton">acton</option>\n- <option value="cm.lajolla">lajolla</option>\n- <option value="cm.bilbao">bilbao</option>\n- <option value="cm.grayC">grayC</option>\n- <option value="cm.tokyo">tokyo</option>\n- <option value="cm.turku">turku</option>\n- <option value="cm.bamako">bamako</option>\n- <option value="cm.nuuk">nuuk</option>\n- <option value="cm.hawaii">hawaii</option>\n- <option value="cm.buda">buda</option>\n- <option value="cm.imola">imola</option>\n- <option value="cm.broc">broc</option>\n- <option value="cm.lisbon">lisbon</option>\n- <option value="cm.roma">roma</option>\n- <option value="cm.cork">cork</option>\n- <option value="cm.tofino">tofino</option>\n- <option value="cm.bam">bam</option>\n- <option value="cm.vik">vik</option>\n- <option value="cm.berlin">berlin</option>\n- <option value="cm.vanimo">vanimo</option>\n- <option value="cm.oleron">oleron</option>\n- <option value="cm.bukavu">bukavu</option>\n- <option value="cm.fes">fes</option>\n- <option value="cm.romaO">romaO</option>\n- <option value="cm.bamO">bamO</option>\n- <option value="cm.brocO">brocO</option>\n- <option value="cm.corkO">corkO</option>\n- <option value="cm.vikO">vikO</option>\n- <option value="cm.batlow_r">batlow_r</option>\n- <option value="cm.batlowW_r">batlowW_r</option>\n- <option value="cm.batlowK_r">batlowK_r</option>\n- <option value="cm.devon_r">devon_r</option>\n- <option valu'..b'tion value="RdGy">RdGy</option>\n- <option value="RdPu">RdPu</option>\n- <option value="RdBu_r">RdBu_r</option>\n- <option value="RdGy_r">RdGy_r</option>\n- <option value="RdPu_r">RdPu_r</option>\n- <option value="RdYlBu">RdYlBu</option>\n- <option value="RdYlGn">RdYlGn</option>\n- <option value="Reds">Reds</option>\n- <option value="Set1">Set1</option>\n- <option value="Set2">Set2</option>\n- <option value="Set3">Set3</option>\n- <option value="Spectral">Spectral</option>\n- <option value="Wistia">Wistia</option>\n- <option value="YlGn">YlGn</option>\n- <option value="YlGnBu">YlGnBu</option>\n- <option value="YlOrBr">YlOrBr</option>\n- <option value="YlOrRd">YlOrRd</option>\n- <option value="afmhot">afmhot</option>\n- <option value="autumn">autumn</option>\n- <option value="binary">binary</option>\n- <option value="bone">bone</option>\n- <option value="brg">brg</option>\n- <option value="bwr">bwr</option>\n- <option value="cool">cool</option>\n- <option value="coolwarm" selected="true">coolwarm</option>\n- <option value="copper">copper</option>\n- <option value="cubehelix">cubehelix</option>\n- <option value="flag">flag</option>\n- <option value="gist_earth">gist_earth</option>\n- <option value="gist_gray">gist_gray</option>\n- <option value="gist_heat">gist_heat</option>\n- <option value="gist_ncar">gist_ncar</option>\n- <option value="gist_rainbow">gist_rainbow</option>\n- <option value="gist_stern">gist_stern</option>\n- <option value="gist_yarg">gist_yarg</option>\n- <option value="gnuplot">gnuplot</option>\n- <option value="gnuplot2">gnuplot2</option>\n- <option value="gray">gray</option>\n- <option value="hot">hot</option>\n- <option value="hsv">hsv</option>\n- <option value="jet">jet</option>\n- <option value="nipy_spectral">nipy_spectral</option>\n- <option value="ocean">ocean</option>\n- <option value="pink">pink</option>\n- <option value="prism">prism</option>\n- <option value="rainbow">rainbow</option>\n- <option value="seismic">seismic</option>\n- <option value="spring">spring</option>\n- <option value="summer">summer</option>\n- <option value="tab10">tab10</option>\n- <option value="tab20">tab20</option>\n- <option value="tab20b">tab20b</option>\n- <option value="tab20c">tab20c</option>\n- <option value="terrain">terrain</option>\n- <option value="winter">winter</option>\n- </param>\n- </xml>\n-</macros>\n+<macros>\r\n+ <token name="@TOOL_VERSION@">0.20.2</token>\r\n+ <token name="@VERSION_SUFFIX@">0</token>\r\n+ <token name="@PROFILE@">20.05</token>\r\n+ <xml name="edam_ontology">\r\n+ <edam_topics>\r\n+ <edam_topic>topic_0610</edam_topic>\r\n+ <edam_topic>topic_3050</edam_topic>\r\n+ </edam_topics>\r\n+ </xml>\r\n+ <xml name="citations">\r\n+ <citations>\r\n+ <citation type="bibtex">\r\n+ @article{hoyer2017xarray,\r\n+ title = {xarray: {N-D} labeled arrays and datasets in {Python}},\r\n+ author = {Hoyer, S. and J. Hamman},\r\n+ journal = {Journal of Open Research Software},\r\n+ volume = {5},\r\n+ number = {1},\r\n+ year = {2017},\r\n+ publisher = {Ubiquity Press},\r\n+ doi = {10.5334/jors.148},\r\n+ url = {http://doi.org/10.5334/jors.148}\r\n+ }\r\n+ </citation>\r\n+ </citations>\r\n+ </xml>\r\n+</macros>\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 macros_mapplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_mapplot.xml Thu Jan 20 17:07:19 2022 +0000 |
| [ |
| b'@@ -0,0 +1,213 @@\n+<macros>\r\n+ <xml name="config_map">\r\n+ <configfiles>\r\n+ <configfile name="map_customization"><![CDATA[\r\n+{\r\n+#if $condi_datetime.datetime=="yes"\r\n+"time":"$condi_datetime.time_values",\r\n+#end if\r\n+"latitude":\'$lat_dim\',\r\n+"longitude":\'$lon_dim\',\r\n+#if $colorbar_label\r\n+"label":\'$colorbar_label\',\r\n+#end if\r\n+#if $title\r\n+"title":"$title",\r\n+#end if\r\n+#if $cmap\r\n+"cmap":\'$cmap\',\r\n+#end if\r\n+#if $land\r\n+"land":\'$land\',\r\n+#end if\r\n+#if $ocean\r\n+"ocean":\'$ocean\',\r\n+#end if\r\n+#if $coastline\r\n+"coastline":\'$coastline\',\r\n+#end if\r\n+#if $borders\r\n+"borders":\'$borders\',\r\n+#end if\r\n+#if $threshold\r\n+"threshold":\'$threshold\',\r\n+#end if\r\n+#if $range\r\n+"range":\'$range\',\r\n+#end if\r\n+#if $xlim\r\n+"xlim":\'$xlim\',\r\n+#end if\r\n+#if $ylim\r\n+"ylim":\'$ylim\',\r\n+#end if\r\n+}\r\n+ ]]>\r\n+ </configfile>\r\n+ <configfile name="map_projection"><![CDATA[\r\n+#if $proj\r\n+\'$proj\'\r\n+#end if \r\n+ ]]>\r\n+ </configfile>\r\n+ </configfiles>\r\n+ </xml>\r\n+ <xml name="customize_appearance_plots">\r\n+ <param name="borders" type="float" optional="true" label="Add country borders with alpha value [0-1] (optional)" />\r\n+ <param name="coastline" type="float" optional="true" label="Add coastline with alpha value [0-1] (optional)" />\r\n+ <param name="ocean" type="float" optional="true" label="Add ocean with alpha value [0-1] (optional)" />\r\n+ <param name="land" type="float" optional="true" label="Add land with alpha value [0-1] (optional)" />\r\n+ <param name="title" type="text" optional="true" label="Specify plot title (optional)" />\r\n+ <param name="colorbar_label" type="text" optional="true" label="Set a label for colormap (optional)" />\r\n+ <param name="cmap" type="select" optional="true" label="Specify which colormap to use for plotting (optional)">\r\n+ <option value="cm.batlow">batlow</option>\r\n+ <option value="cm.batlowW">batlowW</option>\r\n+ <option value="cm.batlowK">batlowK</option>\r\n+ <option value="cm.devon">devon</option>\r\n+ <option value="cm.davos">davos</option>\r\n+ <option value="cm.oslo">oslo</option>\r\n+ <option value="cm.lapaz">lapaz</option>\r\n+ <option value="cm.acton">acton</option>\r\n+ <option value="cm.lajolla">lajolla</option>\r\n+ <option value="cm.bilbao">bilbao</option>\r\n+ <option value="cm.grayC">grayC</option>\r\n+ <option value="cm.tokyo">tokyo</option>\r\n+ <option value="cm.turku">turku</option>\r\n+ <option value="cm.bamako">bamako</option>\r\n+ <option value="cm.nuuk">nuuk</option>\r\n+ <option value="cm.hawaii">hawaii</option>\r\n+ <option value="cm.buda">buda</option>\r\n+ <option value="cm.imola">imola</option>\r\n+ <option value="cm.broc">broc</option>\r\n+ <option value="cm.lisbon">lisbon</option>\r\n+ <option value="cm.roma">roma</option>\r\n+ <option value="cm.cork">cork</option>\r\n+ <option value="cm.tofino">tofino</option>\r\n+ <option value="cm.bam">bam</option>\r\n+ <option value="cm.vik">vik</option>\r\n+ <option value="cm.berlin">berlin</option>\r\n+ <option value="cm.vanimo">vanimo</option>\r\n+ <option value="cm.oleron">oleron</option>\r\n+ <option value="cm.bukavu">bukavu</option>\r\n+ <option value="cm.fes">fes</option>\r\n+ <option value="cm.romaO">romaO</option>\r\n+ <option value="cm.bamO">bamO</option>\r\n+ <option value="cm.brocO">brocO</option>\r\n+ <option value="cm.corkO">corkO</option>\r\n+ <option value="cm.vikO">vikO</option>\r\n+ <option value="cm.batlow_r">batlow_r</option>\r\n+ <option value="cm.batlowW_r">batlowW_r</option>\r\n+ <option value="cm.batlowK_r">batlowK_r</option>\r\n+ <option value="cm.devon_r">devon'..b' <option value="BuGn">BuGn</option>\r\n+ <option value="BuPu">BuPu</option>\r\n+ <option value="CMRmap">CMRmap</option>\r\n+ <option value="Dark2">Dark2</option>\r\n+ <option value="GnBu">GnBu</option>\r\n+ <option value="Greens">Greens</option>\r\n+ <option value="Greys">Greys</option>\r\n+ <option value="OrRd">OrRd</option>\r\n+ <option value="Oranges">Oranges</option>\r\n+ <option value="PRGn">PRGn</option>\r\n+ <option value="Paired">Paired</option>\r\n+ <option value="Pastel1">Pastel1</option>\r\n+ <option value="Pastel2">Pastel2</option>\r\n+ <option value="PiYG">PiYG</option>\r\n+ <option value="PuBu">PuBu</option>\r\n+ <option value="PuBuGn">PuBuGn</option>\r\n+ <option value="PuOr">PuOr</option>\r\n+ <option value="PuRd">PuRd</option>\r\n+ <option value="Purples">Purples</option>\r\n+ <option value="RdBu">RdBu</option>\r\n+ <option value="RdGy">RdGy</option>\r\n+ <option value="RdPu">RdPu</option>\r\n+ <option value="RdBu_r">RdBu_r</option>\r\n+ <option value="RdGy_r">RdGy_r</option>\r\n+ <option value="RdPu_r">RdPu_r</option>\r\n+ <option value="RdYlBu">RdYlBu</option>\r\n+ <option value="RdYlGn">RdYlGn</option>\r\n+ <option value="Reds">Reds</option>\r\n+ <option value="Set1">Set1</option>\r\n+ <option value="Set2">Set2</option>\r\n+ <option value="Set3">Set3</option>\r\n+ <option value="Spectral">Spectral</option>\r\n+ <option value="Wistia">Wistia</option>\r\n+ <option value="YlGn">YlGn</option>\r\n+ <option value="YlGnBu">YlGnBu</option>\r\n+ <option value="YlOrBr">YlOrBr</option>\r\n+ <option value="YlOrRd">YlOrRd</option>\r\n+ <option value="afmhot">afmhot</option>\r\n+ <option value="autumn">autumn</option>\r\n+ <option value="binary">binary</option>\r\n+ <option value="bone">bone</option>\r\n+ <option value="brg">brg</option>\r\n+ <option value="bwr">bwr</option>\r\n+ <option value="cool">cool</option>\r\n+ <option value="coolwarm" selected="true">coolwarm</option>\r\n+ <option value="copper">copper</option>\r\n+ <option value="cubehelix">cubehelix</option>\r\n+ <option value="flag">flag</option>\r\n+ <option value="gist_earth">gist_earth</option>\r\n+ <option value="gist_gray">gist_gray</option>\r\n+ <option value="gist_heat">gist_heat</option>\r\n+ <option value="gist_ncar">gist_ncar</option>\r\n+ <option value="gist_rainbow">gist_rainbow</option>\r\n+ <option value="gist_stern">gist_stern</option>\r\n+ <option value="gist_yarg">gist_yarg</option>\r\n+ <option value="gnuplot">gnuplot</option>\r\n+ <option value="gnuplot2">gnuplot2</option>\r\n+ <option value="gray">gray</option>\r\n+ <option value="hot">hot</option>\r\n+ <option value="hsv">hsv</option>\r\n+ <option value="jet">jet</option>\r\n+ <option value="nipy_spectral">nipy_spectral</option>\r\n+ <option value="ocean">ocean</option>\r\n+ <option value="pink">pink</option>\r\n+ <option value="prism">prism</option>\r\n+ <option value="rainbow">rainbow</option>\r\n+ <option value="seismic">seismic</option>\r\n+ <option value="spring">spring</option>\r\n+ <option value="summer">summer</option>\r\n+ <option value="tab10">tab10</option>\r\n+ <option value="tab20">tab20</option>\r\n+ <option value="tab20b">tab20b</option>\r\n+ <option value="tab20c">tab20c</option>\r\n+ <option value="terrain">terrain</option>\r\n+ <option value="winter">winter</option>\r\n+ </param>\r\n+ </xml>\r\n+</macros>\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 macros_netcdf2netcdf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_netcdf2netcdf.xml Thu Jan 20 17:07:19 2022 +0000 |
| b |
| b'@@ -0,0 +1,143 @@\n+<macros>\r\n+ <xml name="coord_range">\r\n+ <repeat name="user_choice" title="Filter by coordinate values" min="0" max="20" help="Use this option to filter on the values of the selected coordinate">\r\n+ <param name="dim" type="select" label="Dimensions">\r\n+ <options from_dataset="var_tab">\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" type="select" label="Comparator">\r\n+ <option value="is">is</option>\r\n+ <option value="from">from</option>\r\n+ <option value="to">to</option>\r\n+ <option value="sl">slice(threshold1,threshold2)</option>\r\n+ </param>\r\n+ <when value="sl">\r\n+ <param name="t1" type="text" value="" label="Choose the start value for slice"/>\r\n+ <param name="t2" type="text" value="" label="Choose the end value for slice"/>\r\n+ </when>\r\n+ <when value="to">\r\n+ <param name="value" type="text" value="" label="Choose the end value"/>\r\n+ </when>\r\n+ <when value="from">\r\n+ <param name="value" type="text" value="" label="Choose the start value"/>\r\n+ </when>\r\n+ <when value="is">\r\n+ <param name="value" type="text" value="" label="Choose the value to select"/>\r\n+ <yield />\r\n+ </when>\r\n+ </conditional>\r\n+ </repeat>\r\n+ </xml>\r\n+ <xml name="section_variables">\r\n+ <section name="variable" title="Select variables">\r\n+ <param name="var" type="select" multiple="true" label="Choose variables to extract">\r\n+ <options from_dataset="var_tab">\r\n+ <column name="name" index="0"/>\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ <param type="float" name="scale" optional="true" help="scale factor (float) to apply to the selected variable (optional and only if a variable is selected)"/>\r\n+ <param name="write_all" type="boolean" checked="false" label="Write all variables to new netCDF file (only if a variable is selected)"/>\r\n+ <param name="keep_attributes" type="boolean" checked="true" label="Keep all attributes (only if a variable is selected)"/>\r\n+ </section>\r\n+ </xml>\r\n+ <xml name="section_coords">\r\n+ <section name="subset_coords" title="Subset by coordinates">\r\n+ <conditional name="tsel">\r\n+ <param name="by_click" type="select" optional="true" label="Coordinate values">\r\n+ <option value="sel">Coordinate values (sel)</option>\r\n+ <option value="isel">Coordinate indices (isel)</option>\r\n+ <option value="isel_list" selected="true">Coordinate values from list</option>\r\n+ </param>\r\n+ <when value="sel">\r\n+ <expand macro="coord_range">\r\n+ <param name="method" type="select" multiple="false" label="Choose selection method">\r\n+ <option value="None">only exact matches</option>\r\n+ <option value="nearest">use nearest valid index value</option>\r\n+ <option value="pad">propagate last valid index value forward</option>\r\n+ <option value="backfill">propagate next valid index value backward</option>\r\n+ </param>\r\n+ </expand>\r\n+ </when>\r\n+ <when value="isel">\r\n+ <expand macro="coord_range"/>\r\n+ </when>\r\n+ <when value="isel_list">\r\n+ <repeat name="user_choice" title="Filte'..b'>\r\n+ <option value="is">is</option>\r\n+ <option value="from">from</option>\r\n+ <option value="to">to</option>\r\n+ <option value="sl">slice(threshold1,threshold2)</option>\r\n+ </param>\r\n+ <when value="sl">\r\n+ <param name="t1" type="select" multiple="false" label="Choose the start value for slice">\r\n+ <options from_dataset="dim_tab">\r\n+ <column name="name" index="1"/>\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ <param name="t2" type="select" multiple="false" label="Choose the end value for slice">\r\n+ <options from_dataset="dim_tab">\r\n+ <column name="name" index="1"/>\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ </when>\r\n+ <when value="is">\r\n+ <param name="value" type="select" multiple="false" label="Choose the value to select">\r\n+ <options from_dataset="dim_tab">\r\n+ <column name="name" index="1"/>\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ </when>\r\n+ <when value="to">\r\n+ <param name="value" type="select" multiple="false" label="Choose the end value">\r\n+ <options from_dataset="dim_tab">\r\n+ <column name="name" index="1"/>\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ </when>\r\n+ <when value="from">\r\n+ <param name="value" type="select" multiple="false" label="Choose the start value">\r\n+ <options from_dataset="dim_tab">\r\n+ <column name="name" index="1"/>\r\n+ <column name="value" index="0"/>\r\n+ </options>\r\n+ </param>\r\n+ </when>\r\n+ </conditional>\r\n+ </repeat>\r\n+ </when>\r\n+ </conditional>\r\n+ </section>\r\n+ </xml>\r\n+ <xml name="section_where">\r\n+ <section name="mask_values" title="Advanced options to mask by values">\r\n+ <conditional name="mask_condi">\r\n+ <param name="mask_option" type="select" multiple="false" label="Option for masked values">\r\n+ <option value="keep" selected="true">Fill with NA</option>\r\n+ <option value="drop">Drop values</option>\r\n+ <option value="other">Set constant</option>\r\n+ </param>\r\n+ <when value="keep"/>\r\n+ <when value="drop"/>\r\n+ <when value="other">\r\n+ <param name="set_other" type="float" value="0" label="Value to use for locations in this object where cond is False." />\r\n+ </when>\r\n+ </conditional>\r\n+ <param name="where_condition" type="data" optional="true" format="txt" label="file containing a where expression" />\r\n+ </section>\r\n+ </xml>\r\n+</macros>\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 macros_tests_netcdf2netcdf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_tests_netcdf2netcdf.xml Thu Jan 20 17:07:19 2022 +0000 |
| b |
| b'@@ -0,0 +1,263 @@\n+<macros>\r\n+ <xml name="section_tests">\r\n+ <tests>\r\n+ <test>\r\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\r\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\r\n+ <section name="variable">\r\n+ <param name="var" value="chl"/>\r\n+ <param name="scale" value="1000.5"/>\r\n+ </section>\r\n+ <section name="subset_coords">\r\n+ <conditional name="tsel">\r\n+ <param name="by_click" value="isel_list"/>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="time"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="10"/>\r\n+ <param name="t2" value="12"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="latitude"/>\r\n+ <param name="dim_tab" value="latitude.tabular"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="5"/>\r\n+ <param name="t2" value="10"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="longitude"/>\r\n+ <param name="dim_tab" value="longitude.tabular"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="4"/>\r\n+ <param name="t2" value="10"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ </conditional>\r\n+ </section>\r\n+ <output name="output_netcdf" file="small.netcdf" compare="sim_size" delta="1000"/>\r\n+ </test>\r\n+ <test>\r\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\r\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\r\n+ <section name="variable">\r\n+ <param name="var" value="chl"/>\r\n+ <param name="scale" value="1000.5"/>\r\n+ <param name="write_all" value="true"/>\r\n+ <param name="keep_attribute" value="false"/>\r\n+ </section>\r\n+ <section name="subset_coords">\r\n+ <conditional name="tsel">\r\n+ <param name="by_click" value="isel_list"/>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="time"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="10"/>\r\n+ <param name="t2" value="12"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="latitude"/>\r\n+ <param name="dim_tab" value="latitude.tabular"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="5"/>\r\n+ <param name="t2" value="1'..b'ame="method" value="nearest"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ </conditional>\r\n+ </section>\r\n+ <output name="output_netcdf" file="select_by_values.netcdf" compare="sim_size" delta="500"/>\r\n+ </test>\r\n+ <test>\r\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\r\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\r\n+ <section name="variable">\r\n+ <param name="var" value="chl,phy"/>\r\n+ </section>\r\n+ <section name="mask_values">\r\n+ <conditional name="mask_condi">\r\n+ <param name="mask_option" value="other"/>\r\n+ <param name="set_other" value="1000"/>\r\n+ </conditional>\r\n+ <param name="where_condition" ftype="txt" value="where_condition.txt"/>\r\n+ </section>\r\n+ <output name="output_netcdf" file="chl_phy_where.netcdf" compare="sim_size" delta="500"/>\r\n+ </test>\r\n+ <test>\r\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\r\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\r\n+ <section name="variable">\r\n+ <param name="var" value="chl"/>\r\n+ <param name="scale" value="1000.5"/>\r\n+ <param name="write_all" value="true"/>\r\n+ <param name="keep_attribute" value="true"/>\r\n+ </section>\r\n+ <section name="subset_coords">\r\n+ <conditional name="tsel">\r\n+ <param name="by_click" value="isel_list"/>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="time"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="10"/>\r\n+ <param name="t2" value="12"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="latitude"/>\r\n+ <param name="dim_tab" value="latitude.tabular"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="0"/>\r\n+ <param name="t2" value="10"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="longitude"/>\r\n+ <param name="dim_tab" value="longitude.tabular"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="1"/>\r\n+ <param name="t2" value="20"/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ </conditional>\r\n+ </section>\r\n+ <section name="mask_values">\r\n+ <conditional name="mask_condi">\r\n+ <param name="mask_option" value="drop"/>\r\n+ </conditional>\r\n+ <param name="where_condition" ftype="txt" value="where_condition_simple.txt"/>\r\n+ </section>\r\n+ <output name="output_netcdf" file="chl_where_drop.netcdf" compare="sim_size" delta="500"/>\r\n+ </test>\r\n+ </tests>\r\n+ </xml>\r\n+</macros>\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/all.netcdf |
| b |
| Binary file test-data/all.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/chl_alltimes.nc |
| b |
| Binary file test-data/chl_alltimes.nc has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/chl_nh4.netcdf |
| b |
| Binary file test-data/chl_nh4.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/chl_phy_where.netcdf |
| b |
| Binary file test-data/chl_phy_where.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/chl_where_drop.netcdf |
| b |
| Binary file test-data/chl_where_drop.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/data_from_20040615.nc |
| b |
| Binary file test-data/data_from_20040615.nc has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/data_to_20040615.nc |
| b |
| Binary file test-data/data_to_20040615.nc has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png |
| b |
| Binary file test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0.png has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0_title.png |
| b |
| Binary file test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time0_title.png has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png |
| b |
| Binary file test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time1.png has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time50.png |
| b |
| Binary file test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133_time50.png has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/info_file.txt --- a/test-data/info_file.txt Sun Jun 06 08:51:41 2021 +0000 +++ b/test-data/info_file.txt Thu Jan 20 17:07:19 2022 +0000 |
| b |
| @@ -1,9 +1,9 @@ xarray.Dataset { dimensions: + time = 145 ; depth = 1 ; latitude = 97 ; longitude = 103 ; - time = 145 ; variables: float32 phy(time, depth, latitude, longitude) ; |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/select_by_values.netcdf |
| b |
| Binary file test-data/select_by_values.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/small.netcdf |
| b |
| Binary file test-data/small.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/small_all_variables.netcdf |
| b |
| Binary file test-data/small_all_variables.netcdf has changed |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/version.tabular --- a/test-data/version.tabular Sun Jun 06 08:51:41 2021 +0000 +++ b/test-data/version.tabular Thu Jan 20 17:07:19 2022 +0000 |
| b |
| @@ -1,1 +1,1 @@ -Galaxy xarray version 0.18.2 +Galaxy xarray version 0.20.2 |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/where_condition.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/where_condition.txt Thu Jan 20 17:07:19 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((chl > 1) | (chl < 45)) & (nh4 > 1) |
| b |
| diff -r 123a9a629bef -r bf595d613af4 test-data/where_condition_simple.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/where_condition_simple.txt Thu Jan 20 17:07:19 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +nh4 > 5.15 |
| b |
| diff -r 123a9a629bef -r bf595d613af4 xarray_mapplot.py --- a/xarray_mapplot.py Sun Jun 06 08:51:41 2021 +0000 +++ b/xarray_mapplot.py Thu Jan 20 17:07:19 2022 +0000 |
| [ |
| b'@@ -1,457 +1,411 @@\n-#!/usr/bin/env python3\n-#\n-#\n-# usage: xarray_mapplot.py [-h] [--proj PROJ]\n-# [--cmap CMAP]\n-# [--output OUTPUT]\n-# [--time TIMES]\n-# [--nrow NROW]\n-# [--ncol NCOL]\n-# [--title title]\n-# [--latitude LATITUDE]\n-# [--longitude LONGITUDE]\n-# [--land ALPHA-LAND]\n-# [--ocean ALPHA-OCEAN]\n-# [--coastline ALPHA-COASTLINE]\n-# [--borders ALPHA-BORDERS]\n-# [--xlim "x1,x2"]\n-# [--ylim "y1,y2"]\n-# [--range "valmin,valmax"]\n-# [--threshold VAL]\n-# [--label label-colorbar]\n-# [--shift]\n-# [-v]\n-# input varname\n-#\n-# positional arguments:\n-# input input filename with geographical coordinates (netCDF\n-# format)\n-# varname Specify which variable to plot (case sensitive)\n-#\n-# optional arguments:\n-# -h, --help show this help message and exit\n-# --proj PROJ Specify the projection on which we draw\n-# --cmap CMAP Specify which colormap to use for plotting\n-# --output OUTPUT output filename to store resulting image (png format)\n-# --time TIMES time index from the file for multiple plots ("0 1 2 3")\n-# --title plot or subplot title\n-# --latitude variable name for latitude\n-# --longitude variable name for longitude\n-# --land add land on plot with alpha value [0-1]\n-# --ocean add oceans on plot with alpha value [0-1]\n-# --coastline add coastline with alpha value [0-1]\n-# --borders add country borders with alpha value [0-1]\n-# --xlim limited geographical area longitudes "x1,x2"\n-# --ylim limited geographical area latitudes "y1,y2"\n-# --range "valmin,valmax" for plotting\n-# --threshold do not plot values below threshold\n-# --label set a label for colormap\n-# --shift shift longitudes if specified\n-# -v, --verbose switch on verbose mode\n-#\n-\n-import argparse\n-import ast\n-import warnings\n-from pathlib import Path\n-\n-import cartopy.crs as ccrs\n-import cartopy.feature as feature\n-\n-from cmcrameri import cm\n-\n-import matplotlib as mpl\n-mpl.use(\'Agg\')\n-from matplotlib import pyplot # noqa: I202,E402\n-\n-import xarray as xr # noqa: E402\n-\n-\n-class MapPlotXr ():\n- def __init__(self, input, proj, varname, cmap, output, verbose=False,\n- time=[], title="", latitude="latitude",\n- longitude="longitude", land=0, ocean=0,\n- coastline=0, borders=0, xlim=[], ylim=[],\n- threshold="", label="", shift=False,\n- range_values=[]):\n- self.input = input\n- print("PROJ", proj)\n- if proj != "" and proj is not None:\n- self.proj = proj.replace(\'X\', \':\')\n- else:\n- self.proj = proj\n- self.varname = varname\n- self.get_cmap(cmap)\n- self.time = time\n- self.latitude = latitude\n- self.longitude = longitude\n- self.land = land\n- self.ocean = ocean\n- self.coastline = coastline\n- self.borders = borders\n- self.xlim = xlim\n- self.ylim = ylim\n- self.range = range_values\n- self.threshold = threshold\n- self.shift = shift\n- self.xylim_supported = False\n- self.colorbar = True\n- self.title = title\n- if output is None:\n- self.output = Path(input).stem + \'.png\'\n- else:\n- self.output = output\n- self.verbose = '..b'd)\r\n+\r\n+ if self.range == []:\r\n+ minval = self.dset[self.varname].min()\r\n+ maxval = self.dset[self.varname].max()\r\n+ else:\r\n+ minval = self.range[0]\r\n+ maxval = self.range[1]\r\n+\r\n+ if self.verbose:\r\n+ print("minval: ", minval)\r\n+ print("maxval: ", maxval)\r\n+\r\n+ # pass extent with vmin and vmax parameters\r\n+ proj_t = ccrs.PlateCarree()\r\n+ if ts is None:\r\n+ self.dset.where(\r\n+ self.dset[self.varname] > threshold\r\n+ )[self.varname].plot(ax=ax,\r\n+ vmin=minval,\r\n+ vmax=maxval,\r\n+ transform=proj_t,\r\n+ cmap=self.cmap,\r\n+ cbar_kwargs=self.label\r\n+ )\r\n+ if self.title != "" and self.title is not None:\r\n+ pyplot.title(self.title)\r\n+ pyplot.savefig(self.output)\r\n+ else:\r\n+ if self.colorbar:\r\n+ self.dset.where(\r\n+ self.dset[self.varname] > threshold\r\n+ )[self.varname].isel(time=ts).plot(ax=ax,\r\n+ vmin=minval,\r\n+ vmax=maxval,\r\n+ transform=proj_t,\r\n+ cmap=self.cmap,\r\n+ cbar_kwargs=self.label\r\n+ )\r\n+ else:\r\n+ self.dset.where(\r\n+ self.dset[self.varname] > minval\r\n+ )[self.varname].isel(time=ts).plot(ax=ax,\r\n+ vmin=minval,\r\n+ vmax=maxval,\r\n+ transform=proj_t,\r\n+ cmap=self.cmap,\r\n+ add_colorbar=False)\r\n+ if self.title != "" and self.title is not None:\r\n+ pyplot.title(self.title + "(time = " + str(ts) + \')\')\r\n+ pyplot.savefig(self.output[:-4] + "_time" + str(ts) +\r\n+ self.output[-4:]) # assume png format\r\n+\r\n+\r\n+if __name__ == \'__main__\':\r\n+ warnings.filterwarnings("ignore")\r\n+ parser = argparse.ArgumentParser()\r\n+ parser.add_argument(\r\n+ \'input\',\r\n+ help=\'input filename with geographical coordinates (netCDF format)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--proj\',\r\n+ help=\'Config file with the projection on which we draw\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'varname\',\r\n+ help=\'Specify which variable to plot (case sensitive)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--output\',\r\n+ help=\'output filename to store resulting image (png format)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--config\',\r\n+ help=\'pass plotting parameters via a config file\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--shift\',\r\n+ help=\'shift longitudes if specified\',\r\n+ action="store_true"\r\n+ )\r\n+ parser.add_argument(\r\n+ "-v", "--verbose",\r\n+ help="switch on verbose mode",\r\n+ action="store_true")\r\n+ args = parser.parse_args()\r\n+\r\n+ dset = MapPlotXr(input=args.input, varname=args.varname,\r\n+ output=args.output, verbose=args.verbose,\r\n+ config_file=args.config, proj=args.proj,\r\n+ shift=args.shift)\r\n+\r\n+ if dset.time == []:\r\n+ dset.plot()\r\n+ else:\r\n+ for t in dset.time:\r\n+ dset.plot(t)\r\n+ dset.shift = False # only shift once\r\n+ dset.colorbar = True\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 xarray_netcdf2netcdf.py --- a/xarray_netcdf2netcdf.py Sun Jun 06 08:51:41 2021 +0000 +++ b/xarray_netcdf2netcdf.py Thu Jan 20 17:07:19 2022 +0000 |
| [ |
| b'@@ -1,133 +1,268 @@\n-#!/usr/bin/env python3\n-#\n-# Apply operations on selected variables\n-# - scale\n-# one can also select the range of time (for timeseries)\n-# to apply these operations over the range only\n-# when a range of time is selected and when scaling, one\n-# can choose to save the entire timeseries or\n-# the selected range only.\n-# when scaling, one can add additional filters on dimensions\n-# (typically used to filter over latitudes and longitudes)\n-\n-\n-import argparse\n-import warnings\n-\n-import xarray as xr # noqa: E402\n-\n-\n-class netCDF2netCDF ():\n- def __init__(self, infile, varname, scale="",\n- output="output.netcdf",\n- write_all=False,\n- filter_list="",\n- verbose=False):\n- self.infile = infile\n- self.verbose = verbose\n- self.varname = varname\n- self.write_all = write_all\n- self.filter = filter_list\n- self.selection = {}\n- if scale == "" or scale is None:\n- self.scale = 1\n- else:\n- self.scale = float(scale)\n- if output is None:\n- self.output = "output.netcdf"\n- else:\n- self.output = output\n- # initialization\n- self.dset = None\n- self.subset = None\n- if self.verbose:\n- print("infile: ", self.infile)\n- print("varname: ", self.varname)\n- print("filter_list: ", self.filter)\n- print("scale: ", self.scale)\n- print("write_all: ", self.write_all)\n- print("output: ", self.output)\n-\n- def dimension_selection(self, single_filter):\n- split_filter = single_filter.split(\'#\')\n- dimension_varname = split_filter[0]\n- op = split_filter[1]\n- ll = int(split_filter[2])\n- if (op == \'sl\'):\n- rl = int(split_filter[3])\n- self.selection[dimension_varname] = slice(ll, rl)\n- elif (op == \'to\'):\n- self.selection[dimension_varname] = slice(None, ll)\n- elif (op == \'from\'):\n- self.selection[dimension_varname] = slice(ll, None)\n- elif (op == \'is\'):\n- self.selection[dimension_varname] = ll\n-\n- def filter_selection(self):\n- for single_filter in self.filter:\n- self.dimension_selection(single_filter)\n- if self.write_all:\n- self.ds[self.varname] = \\\n- self.ds[self.varname].isel(self.selection)*self.scale\n- else:\n- self.dset = \\\n- self.ds[self.varname].isel(self.selection)*self.scale\n-\n- def compute(self):\n- if self.dset is None:\n- self.ds = xr.open_dataset(self.infile)\n- if self.filter:\n- self.filter_selection()\n- if self.verbose:\n- print(self.selection)\n- elif self.write_all is not None:\n- self.dset = self.ds[self.varname]\n-\n- def save(self):\n- if self.write_all:\n- self.ds.to_netcdf(self.output)\n- else:\n- self.dset.to_netcdf(self.output)\n-\n-\n-if __name__ == \'__main__\':\n- warnings.filterwarnings("ignore")\n- parser = argparse.ArgumentParser()\n- parser.add_argument(\n- \'input\',\n- help=\'input filename in netCDF format\'\n- )\n- parser.add_argument(\n- \'varname\',\n- help=\'Specify which variable to plot (case sensitive)\'\n- )\n- parser.add_argument(\n- \'--filter\',\n- nargs="*",\n- help=\'Filter list variable#operator#value_s#value_e\'\n- )\n- parser.add_argument(\n- \'--output\',\n- help=\'Output filename to store the resulting netCDF file\'\n- )\n- parser.add_argument(\n- \'--scale\',\n- help=\'scale factor to apply to selection (float)\'\n- )\n- parser.add_argument(\n- "--write_all",\n- help="write all data to netCDF",\n- action="store_true")\n- parser.add_argument(\n- "-v", "--verbose",\n- help="switch on verbose mode",\n- '..b'here(\r\n+ self.eval_where(self.where),\r\n+ other=float(self.other)\r\n+ )\r\n+ else:\r\n+ self.ds = self.ds.where(\r\n+ self.eval_where(self.where)\r\n+ )\r\n+ self.filter_selection()\r\n+ if self.verbose:\r\n+ print(self.selection)\r\n+\r\n+ def save(self):\r\n+ if self.varname != \'None\' and \\\r\n+ self.varname is not None and \\\r\n+ not self.write_all:\r\n+ self.dset[self.varname].to_netcdf(self.output)\r\n+ else:\r\n+ self.dset.to_netcdf(self.output)\r\n+\r\n+ def is_float(self, element) -> bool:\r\n+ try:\r\n+ float(element)\r\n+ return True\r\n+ except ValueError:\r\n+ return False\r\n+\r\n+ def eval_where(self, where_condition):\r\n+ eval_cond = None\r\n+ list_names = list(set(\r\n+ list(self.ds.keys()) +\r\n+ list(self.ds.coords.keys()))\r\n+ )\r\n+ wcond = where_condition\r\n+ check_cond = where_condition\r\n+ for var in list_names:\r\n+ wcond = wcond.replace(var, \' self.ds.\' + var + \' \')\r\n+ check_cond = check_cond.replace(var, \'\')\r\n+ to_remove = "[><=&|()]"\r\n+ check_cond = re.sub(to_remove, "", check_cond).replace("!", "")\r\n+ check_cond = re.sub(\' +\', \' \', check_cond).strip()\r\n+ list_flt = check_cond.split(" ")\r\n+ no_convert = False\r\n+ for num in list_flt:\r\n+ if not self.is_float(num):\r\n+ no_convert = True\r\n+ if not no_convert:\r\n+ eval_cond = eval(wcond)\r\n+ return eval_cond\r\n+\r\n+\r\n+if __name__ == \'__main__\':\r\n+ warnings.filterwarnings("ignore")\r\n+ parser = argparse.ArgumentParser()\r\n+ parser.add_argument(\r\n+ \'input\',\r\n+ help=\'input filename in netCDF format\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'varname\',\r\n+ help=\'Specify which variable to plot (case sensitive)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--filter\',\r\n+ nargs="*",\r\n+ help=\'Filter list variable#operator#value_s#value_e\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--where\',\r\n+ help=\'filename with where condition to be evaluated\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--output\',\r\n+ help=\'Output filename to store the resulting netCDF file\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--scale\',\r\n+ help=\'scale factor to apply to selection (float)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--other\',\r\n+ help=\'Value to use for locations where condition is False (float)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ "--write_all",\r\n+ help="write all data to netCDF",\r\n+ action="store_true")\r\n+ parser.add_argument(\r\n+ "--keep_attributes",\r\n+ help="Keep all attributes",\r\n+ action="store_true")\r\n+ parser.add_argument(\r\n+ "-v", "--verbose",\r\n+ help="switch on verbose mode",\r\n+ action="store_true")\r\n+ parser.add_argument(\r\n+ "--selection",\r\n+ help="select by values",\r\n+ action="store_true")\r\n+ parser.add_argument(\r\n+ "--drop",\r\n+ help="drop values where condition is not met",\r\n+ action="store_true")\r\n+ args = parser.parse_args()\r\n+\r\n+ print("args.selection", args.selection)\r\n+ dset = netCDF2netCDF(infile=args.input, varname=args.varname,\r\n+ scale=args.scale, output=args.output,\r\n+ write_all=args.write_all,\r\n+ sel=args.selection,\r\n+ keep_attributes=args.keep_attributes,\r\n+ filter_list=args.filter,\r\n+ where_config=args.where,\r\n+ drop=args.drop, other=args.other,\r\n+ verbose=args.verbose)\r\n+ dset.compute()\r\n+ dset.save()\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 xarray_select.xml --- a/xarray_select.xml Sun Jun 06 08:51:41 2021 +0000 +++ b/xarray_select.xml Thu Jan 20 17:07:19 2022 +0000 |
| [ |
| b'@@ -1,317 +1,317 @@\n-<tool id="xarray_select" name="NetCDF xarray Selection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n- <description>extracts variable values with custom conditions on dimensions</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="edam_ontology"/>\n- <requirements>\n- <requirement type="package" version="3">python</requirement>\n- <requirement type="package" version="1.5.6">netcdf4</requirement>\n- <requirement type="package" version="@TOOL_VERSION@">xarray</requirement>\n- <requirement type="package" version="0.9.0">geopandas</requirement>\n- <requirement type="package" version="1.7.1">shapely</requirement>\n- </requirements>\n- <command detect_errors="exit_code"><![CDATA[\n- mkdir output_dir &&\n- #if $condi_source_coord.coord_source=="coord_from_file"\n- echo "Galaxy xarray version @TOOL_VERSION@" > output_dir/version.tabular &&\n- #end if\n- python \'$__tool_directory__/xarray_tool.py\' \'$input\' --select \'$var\'\n- --verbose\n- --filter\n- #for $i,$uc in enumerate($user_choice)\n- #if $uc.condi_between.comparator=="bi"\n- \'${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.t1}#${uc.condi_between.t2}\'\n- #else\n- \'${uc.dim}#${uc.condi_between.comparator}#${uc.condi_between.value}\'\n- #end if\n- #end for\n-\n- #if $time.condi_datetime.datetime=="yes"\n- --time\n- #if $time.condi_datetime.condi_between.comparator=="sl"\n- \'${time.condi_datetime.dim}#${time.condi_datetime.condi_between.comparator}#${time.condi_datetime.condi_between.t1}#${time.condi_datetime.condi_between.t2}\'\n- #else\n- \'${time.condi_datetime.dim}#${time.condi_datetime.condi_between.comparator}#${time.condi_datetime.condi_between.t1}\'\n- #end if\n- #end if\n-\n- #if $condi_source_coord.coord_source=="coord_from_file"\n- --coords \'$coord_tabular\'\n- --latname \'$condi_source_coord.lat_dim\' --lonname \'$condi_source_coord.lon_dim\'\n- --outputdir output_dir\n- #if $condi_source_coord.tolerance\n- --tolerance \'$condi_source_coord.tolerance\'\n- #end if\n- #else\n- --outfile \'final.tabular\'\n- #if $condi_source_coord.condi_coord.coord==\'single\'\n- --latname $condi_source_coord.condi_coord.lat_dim\n- --latvalN $condi_source_coord.condi_coord.lat_val\n- --lonname $condi_source_coord.condi_coord.lon_dim\n- --lonvalE $condi_source_coord.condi_coord.lon_val\n-\t #if $condi_source_coord.condi_coord.no_missing\n-\t --no_missing\n-\t #end if\n- #if $condi_source_coord.condi_coord.tolerance\n- --tolerance \'$condi_source_coord.condi_coord.tolerance\'\n- #end if\n- #elif $condi_source_coord.condi_coord.coord==\'subregion\'\n- --latname $condi_source_coord.condi_coord.lat_dim\n- --latvalN $condi_source_coord.condi_coord.lat_valN\n- --latvalS $condi_source_coord.condi_coord.lat_valS\n- --lonname $condi_source_coord.condi_coord.lon_dim\n- --lonvalE $condi_source_coord.condi_coord.lon_valE\n- --lonvalW $condi_source_coord.condi_coord.lon_valW\n- #end if\n- #end if\n- ]]></command>\n- <inputs>\n- <param type="data" name="input" label="Input netcdf file" format="netcdf"/>\n- <param type="data" label="Tabular of variables" name="var_tab" format="tabular" help="Select the tabular file which summarize the available variables and dimensions."/>\n-\n- <param name="var" type="select" label="Choose the variable to extract">\n- <options from_dataset="var_tab">\n- <column name="name" index="0"/>\n- <column name="value" index="0"/>\n- </options>\n- </param>\n-\n- <conditional name="condi_source_coord">\n- <param name="coord_source" type="select" label="Source of coo'..b'] == \'coord_from_stdin\'</filter>\r\n+ </data>\r\n+ </outputs>\r\n+ <tests>\r\n+ <test>\r\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\r\n+ <param name="var" value="phy"/>\r\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\r\n+ <conditional name="condi_source_coord">\r\n+ <param name="coord_source" value="coord_from_stdin"/>\r\n+ <conditional name="condi_coord">\r\n+ <param name="coord" value="single"/>\r\n+ <param name="lat_dim" value="latitude"/>\r\n+ <param name="lat_val" value="44.0"/>\r\n+ <param name="lon_dim" value="longitude"/>\r\n+ <param name="lon_val" value="-2.0"/>\r\n+ </conditional>\r\n+ </conditional>\r\n+ <output name="simpleoutput" value="Test1.tabular">\r\n+ <assert_contents>\r\n+ <has_text_matching expression="0\\t2002-12-15\\t0.5"/>\r\n+ <has_text_matching expression="144\\t2014-12-15\\t0.5"/>\r\n+ </assert_contents>\r\n+ </output>\r\n+ </test>\r\n+ <test>\r\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\r\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\r\n+ <param name="var" value="nh4"/>\r\n+\r\n+ <conditional name="condi_source_coord">\r\n+ <param name="coord_source" value="coord_from_stdin"/>\r\n+ <conditional name="condi_coord">\r\n+ <param name="coord" value="global"/>\r\n+ </conditional>\r\n+ </conditional>\r\n+ <section name="time">\r\n+ <conditional name="condi_datetime">\r\n+ <param name="datetime" value="yes"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="sl"/>\r\n+ <param name="t1" value="2003-12-15" />\r\n+ <param name="t2" value="2004-12-15" />\r\n+ </conditional>\r\n+ </conditional>\r\n+ </section>\r\n+ <repeat name="user_choice">\r\n+ <param name="dim" value="nh4"/>\r\n+ <conditional name="condi_between">\r\n+ <param name="comparator" value="ge"/>\r\n+ <param name="value" value="50."/>\r\n+ </conditional>\r\n+ </repeat>\r\n+ <output name="simpleoutput" value="Test2.tabular">\r\n+ <assert_contents>\r\n+ <has_text_matching expression="0\\t2003-12-15\\t0.5"/>\r\n+ <has_text_matching expression="23\\t2004-12-15\\t0.5"/>\r\n+ </assert_contents>\r\n+ </output>\r\n+ </test>\r\n+ </tests>\r\n+ <help><![CDATA[\r\n+**What it does**\r\n+\r\n+This tool extracts variable values with custom conditions on dimensions.\r\n+\r\n+It can use manualy given coordinates or automaticaly take them from a tabular file to filter informations.\r\n+\r\n+If no values are availables at a coordinate X, the tool will search the closest coordinate with a non NA value.\r\n+\r\n+Filter can be set on every dimension. Available filtering operations are : =, >, <, >=, <=, [interval], ]interval[.\r\n+\r\n+\r\n+\r\n+**Input**\r\n+\r\n+A netcdf file (.nc).\r\n+\r\n+Variable tabular file from \'Netcdf Metadate Info\'.\r\n+\r\n+Tabular file with coordinates (only coordinates, no header!) and the following structure : \'lat\'\t\'lon\'.\r\n+\r\n+\r\n+**Outputs**\r\n+\r\n+A single output with values for the wanted variable if there is only one coordinate.\r\n+\r\n+A data collection where one file is created for every coordinate, if multiple coordinates from tabular file.\r\n+\r\n+\r\n+-------------------------------------------------\r\n+\r\n+The xarray select tool can be used after the xarray Info.\r\n+ ]]> </help>\r\n+ <expand macro="citations"/>\r\n+</tool>\r\n' |
| b |
| diff -r 123a9a629bef -r bf595d613af4 xarray_tool.py --- a/xarray_tool.py Sun Jun 06 08:51:41 2021 +0000 +++ b/xarray_tool.py Thu Jan 20 17:07:19 2022 +0000 |
| [ |
| b'@@ -1,365 +1,365 @@\n-# xarray tool for:\n-# - getting metadata information\n-# - select data and save results in csv file for further post-processing\n-\n-import argparse\n-import csv\n-import os\n-import warnings\n-\n-import geopandas as gdp\n-\n-import pandas as pd\n-\n-from shapely.geometry import Point\n-from shapely.ops import nearest_points\n-\n-import xarray as xr\n-\n-\n-class XarrayTool ():\n- def __init__(self, infile, outfile_info="", outfile_summary="",\n- select="", outfile="", outputdir="", latname="",\n- latvalN="", latvalS="", lonname="", lonvalE="",\n- lonvalW="", filter_list="", coords="", time="",\n- verbose=False, no_missing=False, coords_info=None,\n- tolerance=None):\n- self.infile = infile\n- self.outfile_info = outfile_info\n- self.outfile_summary = outfile_summary\n- self.select = select\n- self.outfile = outfile\n- self.outputdir = outputdir\n- self.latname = latname\n- if tolerance != "" and tolerance is not None:\n- self.tolerance = float(tolerance)\n- else:\n- self.tolerance = -1\n- if latvalN != "" and latvalN is not None:\n- self.latvalN = float(latvalN)\n- else:\n- self.latvalN = ""\n- if latvalS != "" and latvalS is not None:\n- self.latvalS = float(latvalS)\n- else:\n- self.latvalS = ""\n- self.lonname = lonname\n- if lonvalE != "" and lonvalE is not None:\n- self.lonvalE = float(lonvalE)\n- else:\n- self.lonvalE = ""\n- if lonvalW != "" and lonvalW is not None:\n- self.lonvalW = float(lonvalW)\n- else:\n- self.lonvalW = ""\n- self.filter = filter_list\n- self.time = time\n- self.coords = coords\n- self.verbose = verbose\n- self.no_missing = no_missing\n- # initialization\n- self.dset = None\n- self.gset = None\n- self.coords_info = coords_info\n- if self.verbose:\n- print("infile: ", self.infile)\n- print("outfile_info: ", self.outfile_info)\n- print("outfile_summary: ", self.outfile_summary)\n- print("outfile: ", self.outfile)\n- print("select: ", self.select)\n- print("outfile: ", self.outfile)\n- print("outputdir: ", self.outputdir)\n- print("latname: ", self.latname)\n- print("latvalN: ", self.latvalN)\n- print("latvalS: ", self.latvalS)\n- print("lonname: ", self.lonname)\n- print("lonvalE: ", self.lonvalE)\n- print("lonvalW: ", self.lonvalW)\n- print("filter: ", self.filter)\n- print("time: ", self.time)\n- print("coords: ", self.coords)\n- print("coords_info: ", self.coords_info)\n-\n- def info(self):\n- f = open(self.outfile_info, \'w\')\n- ds = xr.open_dataset(self.infile)\n- ds.info(f)\n- f.close()\n-\n- def summary(self):\n- f = open(self.outfile_summary, \'w\')\n- ds = xr.open_dataset(self.infile)\n- writer = csv.writer(f, delimiter=\'\\t\')\n- header = [\'VariableName\', \'NumberOfDimensions\']\n- for idx, val in enumerate(ds.dims.items()):\n- header.append(\'Dim\' + str(idx) + \'Name\')\n- header.append(\'Dim\' + str(idx) + \'Size\')\n- writer.writerow(header)\n- for name, da in ds.data_vars.items():\n- line = [name]\n- line.append(len(ds[name].shape))\n- for d, s in zip(da.shape, da.sizes):\n- line.append(s)\n- line.append(d)\n- writer.writerow(line)\n- for name, da in ds.coords.items():\n- line = [name]\n- line.append(len(ds[name].shape))\n- for d, s in zip(da.shape, da.sizes):\n- line.append(s)\n- line.append(d)\n- writer.writerow(line)\n- f.close()\n-\n- def rowfilter(self,'..b' self.lonvalE = row[1]\r\n+ self.outfile = (os.path.join(self.outputdir,\r\n+ self.select + \'_\' +\r\n+ str(row.Index) + \'.tabular\'))\r\n+ self.selection()\r\n+\r\n+ def get_coords_info(self):\r\n+ ds = xr.open_dataset(self.infile)\r\n+ for c in ds.coords:\r\n+ filename = os.path.join(self.coords_info,\r\n+ c.strip() +\r\n+ \'.tabular\')\r\n+ pd = ds.coords[c].to_pandas()\r\n+ pd.index = range(len(pd))\r\n+ pd.to_csv(filename, header=False, sep=\'\\t\')\r\n+\r\n+\r\n+if __name__ == \'__main__\':\r\n+ warnings.filterwarnings("ignore")\r\n+ parser = argparse.ArgumentParser()\r\n+\r\n+ parser.add_argument(\r\n+ \'infile\',\r\n+ help=\'netCDF input filename\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--info\',\r\n+ help=\'Output filename where metadata information is stored\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--summary\',\r\n+ help=\'Output filename where data summary information is stored\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--select\',\r\n+ help=\'Variable name to select\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--latname\',\r\n+ help=\'Latitude name\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--latvalN\',\r\n+ help=\'North latitude value\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--latvalS\',\r\n+ help=\'South latitude value\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--lonname\',\r\n+ help=\'Longitude name\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--lonvalE\',\r\n+ help=\'East longitude value\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--lonvalW\',\r\n+ help=\'West longitude value\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--tolerance\',\r\n+ help=\'Maximum distance between original and selected value for \'\r\n+ \' inexact matches e.g. abs(index[indexer] - target) <= tolerance\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--coords\',\r\n+ help=\'Input file containing Latitude and Longitude\'\r\n+ \'for geographical selection\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--coords_info\',\r\n+ help=\'output-folder where for each coordinate, coordinate values \'\r\n+ \' are being printed in the corresponding outputfile\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--filter\',\r\n+ nargs="*",\r\n+ help=\'Filter list variable#operator#value_s#value_e\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--time\',\r\n+ help=\'select timeseries variable#operator#value_s[#value_e]\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--outfile\',\r\n+ help=\'csv outfile for storing results of the selection\'\r\n+ \'(valid only when --select)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ \'--outputdir\',\r\n+ help=\'folder name for storing results with multiple selections\'\r\n+ \'(valid only when --select)\'\r\n+ )\r\n+ parser.add_argument(\r\n+ "-v", "--verbose",\r\n+ help="switch on verbose mode",\r\n+ action="store_true"\r\n+ )\r\n+ parser.add_argument(\r\n+ "--no_missing",\r\n+ help="""Do not take into account possible null/missing values\r\n+ (only valid for single location)""",\r\n+ action="store_true"\r\n+ )\r\n+ args = parser.parse_args()\r\n+\r\n+ p = XarrayTool(args.infile, args.info, args.summary, args.select,\r\n+ args.outfile, args.outputdir, args.latname,\r\n+ args.latvalN, args.latvalS, args.lonname,\r\n+ args.lonvalE, args.lonvalW, args.filter,\r\n+ args.coords, args.time, args.verbose,\r\n+ args.no_missing, args.coords_info, args.tolerance)\r\n+ if args.info:\r\n+ p.info()\r\n+ if args.summary:\r\n+ p.summary()\r\n+ if args.coords:\r\n+ p.selection_from_coords()\r\n+ elif args.select:\r\n+ p.selection()\r\n+ elif args.coords_info:\r\n+ p.get_coords_info()\r\n' |
