| Next changeset 1:1a91e551f3a9 (2021-08-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba" |
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added:
README.md macros.xml test-data/Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab test-data/Test1.tabular test-data/Test2.tabular test-data/all.netcdf test-data/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc 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/depth.tabular test-data/info_file.txt test-data/latitude.tabular test-data/longitude.tabular test-data/small.netcdf test-data/time.tabular test-data/var_tab_dataset-ibi test-data/version.tabular xarray_mapplot.py xarray_netcdf2netcdf.py xarray_netcdf2netcdf.xml xarray_tool.py |
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| diff -r 000000000000 -r b0780241f916 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sun Jun 06 08:50:11 2021 +0000 |
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| @@ -0,0 +1,8 @@ +# 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(). |
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| diff -r 000000000000 -r b0780241f916 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jun 06 08:50:11 2021 +0000 |
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| b'@@ -0,0 +1,185 @@\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 value'..b'="Blues">Blues</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="CMRmap">CMRmap</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Greys">Greys</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="PuBuGn">PuBuGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="Purples">Purples</option>\n+ <option value="RdBu">RdBu</option>\n+ <option 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' |
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| diff -r 000000000000 -r b0780241f916 test-data/Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Metadata_infos_from_dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc.Variables.tab Sun Jun 06 08:50:11 2021 +0000 |
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| @@ -0,0 +1,8 @@ +VariableName NumberOfDimensions Dim0Name Dim0Size Dim1Name Dim1Size Dim2Name Dim2Size Dim3Name Dim3Size +phy 4 time 145 depth 1 latitude 97 longitude 103 +chl 4 time 145 depth 1 latitude 97 longitude 103 +nh4 4 time 145 depth 1 latitude 97 longitude 103 +time 1 time 145 +longitude 1 longitude 103 +latitude 1 latitude 97 +depth 1 depth 1 |
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| diff -r 000000000000 -r b0780241f916 test-data/Test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test1.tabular Sun Jun 06 08:50:11 2021 +0000 |
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| b'@@ -0,0 +1,146 @@\n+\ttime\tdepth\tlongitude\tlatitude\tphy\n+0\t2002-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.0500183\n+1\t2003-01-15\t0.5057600140571594\t-2.0000007\t44.0\t1.25\n+2\t2003-02-15\t0.5057600140571594\t-2.0000007\t44.0\t1.3000183\n+3\t2003-03-15\t0.5057600140571594\t-2.0000007\t44.0\t6.0599976\n+4\t2003-04-15\t0.5057600140571594\t-2.0000007\t44.0\t2.25\n+5\t2003-05-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6499939\n+6\t2003-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.42999268\n+7\t2003-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.42999268\n+8\t2003-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+9\t2003-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+10\t2003-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+11\t2003-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.9299927\n+12\t2003-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.3900146\n+13\t2004-01-15\t0.5057600140571594\t-2.0000007\t44.0\t1.7400208\n+14\t2004-02-15\t0.5057600140571594\t-2.0000007\t44.0\t4.5\n+15\t2004-03-15\t0.5057600140571594\t-2.0000007\t44.0\t5.5500183\n+16\t2004-04-15\t0.5057600140571594\t-2.0000007\t44.0\t5.3099976\n+17\t2004-05-15\t0.5057600140571594\t-2.0000007\t44.0\t3.75\n+18\t2004-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.77001953\n+19\t2004-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+20\t2004-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+21\t2004-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.4500122\n+22\t2004-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+23\t2004-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.83999634\n+24\t2004-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.7400208\n+25\t2005-01-15\t0.5057600140571594\t-2.0000007\t44.0\t1.7700195\n+26\t2005-02-15\t0.5057600140571594\t-2.0000007\t44.0\t1.5500183\n+27\t2005-03-15\t0.5057600140571594\t-2.0000007\t44.0\t7.149994\n+28\t2005-04-15\t0.5057600140571594\t-2.0000007\t44.0\t3.649994\n+29\t2005-05-15\t0.5057600140571594\t-2.0000007\t44.0\t2.5200195\n+30\t2005-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+31\t2005-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6700134\n+32\t2005-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.4500122\n+33\t2005-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+34\t2005-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+35\t2005-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6199951\n+36\t2005-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.1499939\n+37\t2006-01-15\t0.5057600140571594\t-2.0000007\t44.0\t3.5299988\n+38\t2006-02-15\t0.5057600140571594\t-2.0000007\t44.0\t7.1799927\n+39\t2006-03-15\t0.5057600140571594\t-2.0000007\t44.0\t6.5599976\n+40\t2006-04-15\t0.5057600140571594\t-2.0000007\t44.0\t3.8000183\n+41\t2006-05-15\t0.5057600140571594\t-2.0000007\t44.0\t0.95999146\n+42\t2006-06-15\t0.5057600140571594\t-2.0000007\t44.0\t1.5\n+43\t2006-07-15\t0.5057600140571594\t-2.0000007\t44.0\t1.0299988\n+44\t2006-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+45\t2006-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.49002075\n+46\t2006-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+47\t2006-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.9299927\n+48\t2006-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.2099915\n+49\t2007-01-15\t0.5057600140571594\t-2.0000007\t44.0\t1.1499939\n+50\t2007-02-15\t0.5057600140571594\t-2.0000007\t44.0\t1.7000122\n+51\t2007-03-15\t0.5057600140571594\t-2.0000007\t44.0\t5.230011\n+52\t2007-04-15\t0.5057600140571594\t-2.0000007\t44.0\t3.8600159\n+53\t2007-05-15\t0.5057600140571594\t-2.0000007\t44.0\t0.83999634\n+54\t2007-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6799927\n+55\t2007-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+56\t2007-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+57\t2007-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+58\t2007-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.89001465\n+59\t2007-11-15\t0.5057600140571594\t-2.0000007\t44.0\t2.0299988\n+60\t2007-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.8399963\n+61\t2008-01-15\t0.5057600140571594\t-2.0000007\t44.0\t1.3399963\n+62\t2008-02-15\t0.5057600140571594\t-2.0000007\t44.0\t3.149994\n+63\t2008-03-15\t0.5057600140571594\t-2.0000007\t44.0\t4.5899963\n+64\t2008-04-15\t0.5057600140571594\t-2.0000007\t44.0\t5.080017\n+65\t2008-05-15\t0.5057600140571594\t-2.0000007\t44.0\t1.0\n+66\t2008-06-15\t0.5057600140571594\t-2.000'..b'2.0000007\t44.0\t1.4900208\n+79\t2009-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+80\t2009-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+81\t2009-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5800171\n+82\t2009-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6499939\n+83\t2009-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.8999939\n+84\t2009-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.3099976\n+85\t2010-01-15\t0.5057600140571594\t-2.0000007\t44.0\t1.5299988\n+86\t2010-02-15\t0.5057600140571594\t-2.0000007\t44.0\t2.9599915\n+87\t2010-03-15\t0.5057600140571594\t-2.0000007\t44.0\t5.450012\n+88\t2010-04-15\t0.5057600140571594\t-2.0000007\t44.0\t7.5899963\n+89\t2010-05-15\t0.5057600140571594\t-2.0000007\t44.0\t1.8000183\n+90\t2010-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+91\t2010-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+92\t2010-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+93\t2010-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.49002075\n+94\t2010-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+95\t2010-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.9299927\n+96\t2010-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.1499939\n+97\t2011-01-15\t0.5057600140571594\t-2.0000007\t44.0\t2.4900208\n+98\t2011-02-15\t0.5057600140571594\t-2.0000007\t44.0\t5.1799927\n+99\t2011-03-15\t0.5057600140571594\t-2.0000007\t44.0\t7.029999\n+100\t2011-04-15\t0.5057600140571594\t-2.0000007\t44.0\t2.4900208\n+101\t2011-05-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6499939\n+102\t2011-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.52001953\n+103\t2011-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+104\t2011-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.75\n+105\t2011-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+106\t2011-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+107\t2011-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.730011\n+108\t2011-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.0299988\n+109\t2012-01-15\t0.5057600140571594\t-2.0000007\t44.0\t3.149994\n+110\t2012-02-15\t0.5057600140571594\t-2.0000007\t44.0\t2.3099976\n+111\t2012-03-15\t0.5057600140571594\t-2.0000007\t44.0\t5.5200195\n+112\t2012-04-15\t0.5057600140571594\t-2.0000007\t44.0\t3.399994\n+113\t2012-05-15\t0.5057600140571594\t-2.0000007\t44.0\t3.7000122\n+114\t2012-06-15\t0.5057600140571594\t-2.0000007\t44.0\t2.5899963\n+115\t2012-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+116\t2012-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.4500122\n+117\t2012-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+118\t2012-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.61001587\n+119\t2012-11-15\t0.5057600140571594\t-2.0000007\t44.0\t2.0299988\n+120\t2012-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.4200134\n+121\t2013-01-15\t0.5057600140571594\t-2.0000007\t44.0\t2.2700195\n+122\t2013-02-15\t0.5057600140571594\t-2.0000007\t44.0\t7.0\n+123\t2013-03-15\t0.5057600140571594\t-2.0000007\t44.0\t10.550018\n+124\t2013-04-15\t0.5057600140571594\t-2.0000007\t44.0\t5.8399963\n+125\t2013-05-15\t0.5057600140571594\t-2.0000007\t44.0\t1.2400208\n+126\t2013-06-15\t0.5057600140571594\t-2.0000007\t44.0\t4.1700134\n+127\t2013-07-15\t0.5057600140571594\t-2.0000007\t44.0\t3.2099915\n+128\t2013-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+129\t2013-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+130\t2013-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.49002075\n+131\t2013-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.7799988\n+132\t2013-12-15\t0.5057600140571594\t-2.0000007\t44.0\t1.4500122\n+133\t2014-01-15\t0.5057600140571594\t-2.0000007\t44.0\t0.95999146\n+134\t2014-02-15\t0.5057600140571594\t-2.0000007\t44.0\t1.3900146\n+135\t2014-03-15\t0.5057600140571594\t-2.0000007\t44.0\t5.779999\n+136\t2014-04-15\t0.5057600140571594\t-2.0000007\t44.0\t5.4299927\n+137\t2014-05-15\t0.5057600140571594\t-2.0000007\t44.0\t1.1799927\n+138\t2014-06-15\t0.5057600140571594\t-2.0000007\t44.0\t0.730011\n+139\t2014-07-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+140\t2014-08-15\t0.5057600140571594\t-2.0000007\t44.0\t0.45999146\n+141\t2014-09-15\t0.5057600140571594\t-2.0000007\t44.0\t0.5\n+142\t2014-10-15\t0.5057600140571594\t-2.0000007\t44.0\t0.6199951\n+143\t2014-11-15\t0.5057600140571594\t-2.0000007\t44.0\t0.480011\n+144\t2014-12-15\t0.5057600140571594\t-2.0000007\t44.0\t0.55999756\n' 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| diff -r 000000000000 -r b0780241f916 test-data/Test2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Test2.tabular Sun Jun 06 08:50:11 2021 +0000 |
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| @@ -0,0 +1,25 @@ + time depth latitude longitude nh4 +0 2003-12-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 81.27 +1 2003-12-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 78.08 +2 2003-12-15 0.5057600140571594 45.5 -0.9166674017906189 55.149998 +3 2004-01-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 65.2 +4 2004-01-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 64.11 +5 2004-02-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 51.0 +6 2004-02-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 51.32 +7 2004-05-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 54.53 +8 2004-06-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 79.79 +9 2004-06-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 61.52 +10 2004-07-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 99.159996 +11 2004-07-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 77.93 +12 2004-08-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 110.149994 +13 2004-08-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 86.759995 +14 2004-09-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 112.369995 +15 2004-09-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 91.979996 +16 2004-10-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 109.63 +17 2004-10-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 95.509995 +18 2004-11-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 98.45 +19 2004-11-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 93.11 +20 2004-11-15 0.5057600140571594 45.5 -0.9166674017906189 56.78 +21 2004-12-15 0.5057600140571594 45.166664123535156 -0.6666674017906189 84.25 +22 2004-12-15 0.5057600140571594 45.416664123535156 -0.8333340883255005 81.83 +23 2004-12-15 0.5057600140571594 45.5 -0.9166674017906189 57.07 |
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| diff -r 000000000000 -r b0780241f916 test-data/depth.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/depth.tabular Sun Jun 06 08:50:11 2021 +0000 |
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| @@ -0,0 +1,1 @@ +0 0.50576 |
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| diff -r 000000000000 -r b0780241f916 test-data/info_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/info_file.txt Sun Jun 06 08:50:11 2021 +0000 |
| [ |
| @@ -0,0 +1,74 @@ +xarray.Dataset { +dimensions: + depth = 1 ; + latitude = 97 ; + longitude = 103 ; + time = 145 ; + +variables: + float32 phy(time, depth, latitude, longitude) ; + phy:_CoordinateAxes = time depth latitude longitude ; + phy:long_name = Mole Concentration of Phytoplankton expressed as carbon in sea water ; + phy:standard_name = mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water ; + phy:units = mmol.m-3 ; + phy:unit_long = mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water ; + datetime64[ns] time(time) ; + time:standard_name = time ; + time:long_name = time ; + time:_CoordinateAxisType = Time ; + time:axis = T ; + float32 chl(time, depth, latitude, longitude) ; + chl:_CoordinateAxes = time depth latitude longitude ; + chl:long_name = Mass Concentration of Chlorophyll in Sea Water ; + chl:standard_name = mass_concentration_of_chlorophyll_in_sea_water ; + chl:units = mg.m-3 ; + chl:unit_long = milligram of chlorophyll per cubic meter ; + float32 nh4(time, depth, latitude, longitude) ; + nh4:_CoordinateAxes = time depth latitude longitude ; + nh4:long_name = Mole Concentration of Ammonium in Sea Water ; + nh4:standard_name = mole_concentration_of_ammonium_in_sea_water ; + nh4:units = mmol.m-3 ; + nh4:unit_long = millimoles of Ammonium per cubic meter ; + float32 longitude(longitude) ; + longitude:long_name = Longitude ; + longitude:units = degrees_east ; + longitude:standard_name = longitude ; + longitude:axis = X ; + longitude:unit_long = Degrees East ; + longitude:step = 0.08333f ; + longitude:_CoordinateAxisType = Lon ; + float32 latitude(latitude) ; + latitude:long_name = Latitude ; + latitude:units = degrees_north ; + latitude:standard_name = latitude ; + latitude:axis = Y ; + latitude:unit_long = Degrees North ; + latitude:step = 0.08333f ; + latitude:_CoordinateAxisType = Lat ; + float32 depth(depth) ; + depth:long_name = Depth ; + depth:units = m ; + depth:axis = Z ; + depth:positive = down ; + depth:unit_long = Meters ; + depth:standard_name = depth ; + depth:_CoordinateAxisType = Height ; + depth:_CoordinateZisPositive = down ; + +// global attributes: + :title = CMEMS IBI REANALYSIS: MONTHLY BIOGEOCHEMICAL PRODUCTS (REGULAR GRID) ; + :institution = Puertos del Estado (PdE) - Mercator-Ocean (MO) ; + :references = http://marine.copernicus.eu ; + :source = CMEMS IBI-MFC ; + :Conventions = CF-1.0 ; + :history = Data extracted from dataset http://puertos2.cesga.es:8080/thredds/dodsC/dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid ; + :time_min = 7272.0 ; + :time_max = 112464.0 ; + :julian_day_unit = Hours since 2002-02-15 ; + :z_min = 0.5057600140571594 ; + :z_max = 0.5057600140571594 ; + :latitude_min = 43.0 ; + :latitude_max = 51.0 ; + :longitude_min = -6.000000476837158 ; + :longitude_max = 2.4999990463256836 ; +} \ No newline at end of file |
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| diff -r 000000000000 -r b0780241f916 test-data/latitude.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/latitude.tabular Sun Jun 06 08:50:11 2021 +0000 |
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| @@ -0,0 +1,97 @@ +0 43.0 +1 43.083332 +2 43.166664 +3 43.25 +4 43.333332 +5 43.416664 +6 43.5 +7 43.583332 +8 43.666664 +9 43.75 +10 43.833332 +11 43.916664 +12 44.0 +13 44.083332 +14 44.166664 +15 44.25 +16 44.333332 +17 44.416664 +18 44.5 +19 44.583332 +20 44.666664 +21 44.75 +22 44.833332 +23 44.916664 +24 45.0 +25 45.083332 +26 45.166664 +27 45.25 +28 45.333332 +29 45.416664 +30 45.5 +31 45.583332 +32 45.666664 +33 45.75 +34 45.833332 +35 45.916664 +36 46.0 +37 46.083332 +38 46.166664 +39 46.25 +40 46.333332 +41 46.416664 +42 46.5 +43 46.583332 +44 46.666664 +45 46.75 +46 46.833332 +47 46.916664 +48 47.0 +49 47.083332 +50 47.166664 +51 47.25 +52 47.333332 +53 47.416664 +54 47.5 +55 47.583332 +56 47.666664 +57 47.75 +58 47.833332 +59 47.916664 +60 48.0 +61 48.083332 +62 48.166664 +63 48.25 +64 48.333332 +65 48.416664 +66 48.5 +67 48.583332 +68 48.666664 +69 48.75 +70 48.833332 +71 48.916664 +72 49.0 +73 49.083332 +74 49.166664 +75 49.25 +76 49.333332 +77 49.416664 +78 49.5 +79 49.583332 +80 49.666664 +81 49.75 +82 49.833332 +83 49.916664 +84 50.0 +85 50.083332 +86 50.166664 +87 50.25 +88 50.333332 +89 50.416664 +90 50.5 +91 50.583332 +92 50.666664 +93 50.75 +94 50.833332 +95 50.916664 +96 51.0 |
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| diff -r 000000000000 -r b0780241f916 test-data/longitude.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/longitude.tabular Sun Jun 06 08:50:11 2021 +0000 |
| b |
| @@ -0,0 +1,103 @@ +0 -6.0000005 +1 -5.916667 +2 -5.833334 +3 -5.7500005 +4 -5.666667 +5 -5.583334 +6 -5.5000005 +7 -5.416667 +8 -5.333334 +9 -5.2500005 +10 -5.166667 +11 -5.083334 +12 -5.0000005 +13 -4.9166675 +14 -4.833334 +15 -4.7500005 +16 -4.6666675 +17 -4.583334 +18 -4.5000005 +19 -4.4166675 +20 -4.333334 +21 -4.2500005 +22 -4.1666675 +23 -4.083334 +24 -4.0000005 +25 -3.9166672 +26 -3.833334 +27 -3.7500007 +28 -3.6666672 +29 -3.583334 +30 -3.5000007 +31 -3.4166672 +32 -3.333334 +33 -3.2500007 +34 -3.1666672 +35 -3.083334 +36 -3.0000007 +37 -2.9166672 +38 -2.833334 +39 -2.7500007 +40 -2.6666672 +41 -2.583334 +42 -2.5000007 +43 -2.4166672 +44 -2.333334 +45 -2.2500007 +46 -2.1666672 +47 -2.083334 +48 -2.0000007 +49 -1.9166673 +50 -1.833334 +51 -1.7500007 +52 -1.6666673 +53 -1.5833341 +54 -1.5000007 +55 -1.4166673 +56 -1.3333341 +57 -1.2500007 +58 -1.1666673 +59 -1.0833341 +60 -1.0000007 +61 -0.9166674 +62 -0.8333341 +63 -0.7500007 +64 -0.6666674 +65 -0.5833341 +66 -0.5000007 +67 -0.4166674 +68 -0.3333341 +69 -0.25000075 +70 -0.16666742 +71 -0.08333409 +72 -7.6e-07 +73 0.08333257 +74 0.1666659 +75 0.24999923 +76 0.33333257 +77 0.41666588 +78 0.49999923 +79 0.58333254 +80 0.66666585 +81 0.7499992 +82 0.83333254 +83 0.91666585 +84 0.9999992 +85 1.0833325 +86 1.1666659 +87 1.2499992 +88 1.3333325 +89 1.4166658 +90 1.4999992 +91 1.5833325 +92 1.6666658 +93 1.7499992 +94 1.8333325 +95 1.9166658 +96 1.9999992 +97 2.0833325 +98 2.1666658 +99 2.249999 +100 2.3333325 +101 2.4166658 +102 2.499999 |
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| diff -r 000000000000 -r b0780241f916 test-data/small.netcdf |
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| Binary file test-data/small.netcdf has changed |
| b |
| diff -r 000000000000 -r b0780241f916 test-data/time.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/time.tabular Sun Jun 06 08:50:11 2021 +0000 |
| b |
| @@ -0,0 +1,145 @@ +0 2002-12-15 +1 2003-01-15 +2 2003-02-15 +3 2003-03-15 +4 2003-04-15 +5 2003-05-15 +6 2003-06-15 +7 2003-07-15 +8 2003-08-15 +9 2003-09-15 +10 2003-10-15 +11 2003-11-15 +12 2003-12-15 +13 2004-01-15 +14 2004-02-15 +15 2004-03-15 +16 2004-04-15 +17 2004-05-15 +18 2004-06-15 +19 2004-07-15 +20 2004-08-15 +21 2004-09-15 +22 2004-10-15 +23 2004-11-15 +24 2004-12-15 +25 2005-01-15 +26 2005-02-15 +27 2005-03-15 +28 2005-04-15 +29 2005-05-15 +30 2005-06-15 +31 2005-07-15 +32 2005-08-15 +33 2005-09-15 +34 2005-10-15 +35 2005-11-15 +36 2005-12-15 +37 2006-01-15 +38 2006-02-15 +39 2006-03-15 +40 2006-04-15 +41 2006-05-15 +42 2006-06-15 +43 2006-07-15 +44 2006-08-15 +45 2006-09-15 +46 2006-10-15 +47 2006-11-15 +48 2006-12-15 +49 2007-01-15 +50 2007-02-15 +51 2007-03-15 +52 2007-04-15 +53 2007-05-15 +54 2007-06-15 +55 2007-07-15 +56 2007-08-15 +57 2007-09-15 +58 2007-10-15 +59 2007-11-15 +60 2007-12-15 +61 2008-01-15 +62 2008-02-15 +63 2008-03-15 +64 2008-04-15 +65 2008-05-15 +66 2008-06-15 +67 2008-07-15 +68 2008-08-15 +69 2008-09-15 +70 2008-10-15 +71 2008-11-15 +72 2008-12-15 +73 2009-01-15 +74 2009-02-15 +75 2009-03-15 +76 2009-04-15 +77 2009-05-15 +78 2009-06-15 +79 2009-07-15 +80 2009-08-15 +81 2009-09-15 +82 2009-10-15 +83 2009-11-15 +84 2009-12-15 +85 2010-01-15 +86 2010-02-15 +87 2010-03-15 +88 2010-04-15 +89 2010-05-15 +90 2010-06-15 +91 2010-07-15 +92 2010-08-15 +93 2010-09-15 +94 2010-10-15 +95 2010-11-15 +96 2010-12-15 +97 2011-01-15 +98 2011-02-15 +99 2011-03-15 +100 2011-04-15 +101 2011-05-15 +102 2011-06-15 +103 2011-07-15 +104 2011-08-15 +105 2011-09-15 +106 2011-10-15 +107 2011-11-15 +108 2011-12-15 +109 2012-01-15 +110 2012-02-15 +111 2012-03-15 +112 2012-04-15 +113 2012-05-15 +114 2012-06-15 +115 2012-07-15 +116 2012-08-15 +117 2012-09-15 +118 2012-10-15 +119 2012-11-15 +120 2012-12-15 +121 2013-01-15 +122 2013-02-15 +123 2013-03-15 +124 2013-04-15 +125 2013-05-15 +126 2013-06-15 +127 2013-07-15 +128 2013-08-15 +129 2013-09-15 +130 2013-10-15 +131 2013-11-15 +132 2013-12-15 +133 2014-01-15 +134 2014-02-15 +135 2014-03-15 +136 2014-04-15 +137 2014-05-15 +138 2014-06-15 +139 2014-07-15 +140 2014-08-15 +141 2014-09-15 +142 2014-10-15 +143 2014-11-15 +144 2014-12-15 |
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| diff -r 000000000000 -r b0780241f916 test-data/var_tab_dataset-ibi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/var_tab_dataset-ibi Sun Jun 06 08:50:11 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +time 1 time 145 +chl 4 time 145 depth 1 latitude 97 longitude 103 +nh4 4 time 145 depth 1 latitude 97 longitude 103 +longitude 1 longitude 103 +latitude 1 latitude 97 +depth 1 depth 1 +phy 4 time 145 depth 1 latitude 97 longitude 103 |
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| diff -r 000000000000 -r b0780241f916 test-data/version.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/version.tabular Sun Jun 06 08:50:11 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Galaxy xarray version 0.18.2 |
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| diff -r 000000000000 -r b0780241f916 xarray_mapplot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xarray_mapplot.py Sun Jun 06 08:50:11 2021 +0000 |
| [ |
| b'@@ -0,0 +1,457 @@\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 = ve'..b't filename with geographical coordinates (netCDF format)\'\n+ )\n+\n+ parser.add_argument(\n+ \'--proj\',\n+ help=\'Specify the projection on which we draw\'\n+ )\n+ parser.add_argument(\n+ \'varname\',\n+ help=\'Specify which variable to plot (case sensitive)\'\n+ )\n+ parser.add_argument(\n+ \'--cmap\',\n+ help=\'Specify which colormap to use for plotting\'\n+ )\n+ parser.add_argument(\n+ \'--output\',\n+ help=\'output filename to store resulting image (png format)\'\n+ )\n+ parser.add_argument(\n+ \'--time\',\n+ help=\'list of times to plot for multiple plots\'\n+ )\n+ parser.add_argument(\n+ \'--title\',\n+ help=\'plot title\'\n+ )\n+ parser.add_argument(\n+ \'--latitude\',\n+ help=\'variable name for latitude\'\n+ )\n+ parser.add_argument(\n+ \'--longitude\',\n+ help=\'variable name for longitude\'\n+ )\n+ parser.add_argument(\n+ \'--land\',\n+ help=\'add land on plot with alpha value [0-1]\'\n+ )\n+ parser.add_argument(\n+ \'--ocean\',\n+ help=\'add oceans on plot with alpha value [0-1]\'\n+ )\n+ parser.add_argument(\n+ \'--coastline\',\n+ help=\'add coastline with alpha value [0-1]\'\n+ )\n+ parser.add_argument(\n+ \'--borders\',\n+ help=\'add country borders with alpha value [0-1]\'\n+ )\n+ parser.add_argument(\n+ \'--xlim\',\n+ help=\'limited geographical area longitudes "x1,x2"\'\n+ )\n+ parser.add_argument(\n+ \'--ylim\',\n+ help=\'limited geographical area latitudes "y1,y2"\'\n+ )\n+ parser.add_argument(\n+ \'--range\',\n+ help=\'min and max values for plotting "minval,maxval"\'\n+ )\n+ parser.add_argument(\n+ \'--threshold\',\n+ help=\'do not plot values below threshold\'\n+ )\n+ parser.add_argument(\n+ \'--label\',\n+ help=\'set a label for colorbar\'\n+ )\n+ parser.add_argument(\n+ \'--shift\',\n+ help=\'shift longitudes if specified\',\n+ action="store_true"\n+ )\n+ parser.add_argument(\n+ "-v", "--verbose",\n+ help="switch on verbose mode",\n+ action="store_true")\n+ args = parser.parse_args()\n+\n+ if args.time is None:\n+ time = []\n+ else:\n+ time = list(map(int, args.time.split(",")))\n+ if args.xlim is None:\n+ xlim = []\n+ else:\n+ xlim = list(map(float, args.xlim.split(",")))\n+ if args.ylim is None:\n+ ylim = []\n+ else:\n+ ylim = list(map(float, args.ylim.split(",")))\n+ if args.range is None:\n+ range_values = []\n+ else:\n+ range_values = list(map(float, args.range.split(",")))\n+ if args.latitude is None:\n+ latitude = "latitude"\n+ else:\n+ latitude = args.latitude\n+ if args.longitude is None:\n+ longitude = "longitude"\n+ else:\n+ longitude = args.longitude\n+ if args.land is None:\n+ land = 0\n+ else:\n+ land = float(args.land)\n+ if args.ocean is None:\n+ ocean = 0\n+ else:\n+ ocean = float(args.ocean)\n+ if args.coastline is None:\n+ coastline = 0\n+ else:\n+ coastline = float(args.coastline)\n+ if args.borders is None:\n+ borders = 0\n+ else:\n+ borders = float(args.borders)\n+\n+ dset = MapPlotXr(input=args.input, proj=args.proj, varname=args.varname,\n+ cmap=args.cmap, output=args.output, verbose=args.verbose,\n+ time=time, title=args.title,\n+ latitude=latitude, longitude=longitude, land=land,\n+ ocean=ocean, coastline=coastline, borders=borders,\n+ xlim=xlim, ylim=ylim, threshold=args.threshold,\n+ label=args.label, shift=args.shift,\n+ range_values=range_values)\n+\n+ if dset.time == []:\n+ dset.plot()\n+ else:\n+ for t in dset.time:\n+ dset.plot(t)\n+ dset.shift = False # only shift once\n+ dset.colorbar = True\n' |
| b |
| diff -r 000000000000 -r b0780241f916 xarray_netcdf2netcdf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xarray_netcdf2netcdf.py Sun Jun 06 08:50:11 2021 +0000 |
| [ |
| @@ -0,0 +1,133 @@ +#!/usr/bin/env python3 +# +# Apply operations on selected variables +# - scale +# one can also select the range of time (for timeseries) +# to apply these operations over the range only +# when a range of time is selected and when scaling, one +# can choose to save the entire timeseries or +# the selected range only. +# when scaling, one can add additional filters on dimensions +# (typically used to filter over latitudes and longitudes) + + +import argparse +import warnings + +import xarray as xr # noqa: E402 + + +class netCDF2netCDF (): + def __init__(self, infile, varname, scale="", + output="output.netcdf", + write_all=False, + filter_list="", + verbose=False): + self.infile = infile + self.verbose = verbose + self.varname = varname + self.write_all = write_all + self.filter = filter_list + self.selection = {} + if scale == "" or scale is None: + self.scale = 1 + else: + self.scale = float(scale) + if output is None: + self.output = "output.netcdf" + else: + self.output = output + # initialization + self.dset = None + self.subset = None + if self.verbose: + print("infile: ", self.infile) + print("varname: ", self.varname) + print("filter_list: ", self.filter) + print("scale: ", self.scale) + print("write_all: ", self.write_all) + print("output: ", self.output) + + def dimension_selection(self, single_filter): + split_filter = single_filter.split('#') + dimension_varname = split_filter[0] + op = split_filter[1] + ll = int(split_filter[2]) + if (op == 'sl'): + rl = int(split_filter[3]) + self.selection[dimension_varname] = slice(ll, rl) + elif (op == 'to'): + self.selection[dimension_varname] = slice(None, ll) + elif (op == 'from'): + self.selection[dimension_varname] = slice(ll, None) + elif (op == 'is'): + self.selection[dimension_varname] = ll + + def filter_selection(self): + for single_filter in self.filter: + self.dimension_selection(single_filter) + if self.write_all: + self.ds[self.varname] = \ + self.ds[self.varname].isel(self.selection)*self.scale + else: + self.dset = \ + self.ds[self.varname].isel(self.selection)*self.scale + + def compute(self): + if self.dset is None: + self.ds = xr.open_dataset(self.infile) + if self.filter: + self.filter_selection() + if self.verbose: + print(self.selection) + elif self.write_all is not None: + self.dset = self.ds[self.varname] + + def save(self): + if self.write_all: + self.ds.to_netcdf(self.output) + else: + self.dset.to_netcdf(self.output) + + +if __name__ == '__main__': + warnings.filterwarnings("ignore") + parser = argparse.ArgumentParser() + parser.add_argument( + 'input', + help='input filename in netCDF format' + ) + parser.add_argument( + 'varname', + help='Specify which variable to plot (case sensitive)' + ) + parser.add_argument( + '--filter', + nargs="*", + help='Filter list variable#operator#value_s#value_e' + ) + parser.add_argument( + '--output', + help='Output filename to store the resulting netCDF file' + ) + parser.add_argument( + '--scale', + help='scale factor to apply to selection (float)' + ) + parser.add_argument( + "--write_all", + help="write all data to netCDF", + action="store_true") + parser.add_argument( + "-v", "--verbose", + help="switch on verbose mode", + action="store_true") + args = parser.parse_args() + + dset = netCDF2netCDF(infile=args.input, varname=args.varname, + scale=args.scale, output=args.output, + filter_list=args.filter, + write_all=args.write_all, + verbose=args.verbose) + dset.compute() + dset.save() |
| b |
| diff -r 000000000000 -r b0780241f916 xarray_netcdf2netcdf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xarray_netcdf2netcdf.xml Sun Jun 06 08:50:11 2021 +0000 |
| [ |
| b'@@ -0,0 +1,190 @@\n+<tool id="xarray_netcdf2netcdf" name="NetCDF xarray operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>manipulate xarray from netCDF and save back to netCDF</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+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir output_dir &&\n+ python \'$__tool_directory__/xarray_netcdf2netcdf.py\' \'$input\' \'$var\'\n+ --filter\n+ #for $i,$uc in enumerate($user_choice)\n+ #if $uc.condi_between.comparator=="sl"\n+ \'${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+ #if $scale\n+ --scale \'$scale\'\n+ #end if\n+ #if $write_all\n+ --write_all\n+ #end if\n+ --verbose\n+ --output \'$output_netcdf\'\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+ <repeat name="user_choice" title="additional filter" min="0" max="20" help="Use this option to filter on the selected dataset">\n+ <param name="dim" type="select" label="Dimensions">\n+ <options from_dataset="var_tab">\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param type="data" label="Tabular containing values of this dimension" name="dim_tab" format="tabular" help="File containing values for this dimension."/>\n+ <conditional name="condi_between">\n+ <param name="comparator" type="select" label="Comparator">\n+ <option value="is">is</option>\n+ <option value="from">from</option>\n+ <option value="to">to</option>\n+ <option value="sl">slice(threshold1,threshold2)</option>\n+ </param>\n+ <when value="sl">\n+ <param name="t1" type="select" multiple="false" label="Choose the start value for slice">\n+ <options from_dataset="dim_tab">\n+ <column name="name" index="1"/>\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ <param name="t2" type="select" multiple="false" label="Choose the end value for slice">\n+ <options from_dataset="dim_tab">\n+ <column name="name" index="1"/>\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="is">\n+ <param name="value" type="select" multiple="false" label="Choose the value to select">\n+ <options from_dataset="dim_tab">\n+ <column name="name" index="1"/>\n+ <column name="value" index="0"/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="to">\n+ <param name="value" '..b'-monthly-regulargrid_1510914389133.nc"/>\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\n+ <param name="var" value="chl"/>\n+ <repeat name="user_choice">\n+ <param name="dim" value="time"/>\n+ <conditional name="condi_between">\n+ <param name="comparator" value="sl"/>\n+ <param name="t1" value="10"/>\n+ <param name="t2" value="12"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="user_choice">\n+ <param name="dim" value="latitude"/>\n+ <param name="dim_tab" value="latitude.tabular"/>\n+ <conditional name="condi_between">\n+ <param name="comparator" value="sl"/>\n+ <param name="t1" value="5"/>\n+ <param name="t2" value="10"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="user_choice">\n+ <param name="dim" value="longitude"/>\n+ <param name="dim_tab" value="longitude.tabular"/>\n+ <conditional name="condi_between">\n+ <param name="comparator" value="sl"/>\n+ <param name="t1" value="4"/>\n+ <param name="t2" value="10"/>\n+ </conditional>\n+ </repeat>\n+ <param name="scale" value="1000.5"/>\n+ <output name="output_netcdf" file="small.netcdf" compare="sim_size" delat="1000"/>\n+ </test>\n+ <test>\n+ <param name="input" value="dataset-ibi-reanalysis-bio-005-003-monthly-regulargrid_1510914389133.nc"/>\n+ <param name="var_tab" value="var_tab_dataset-ibi"/>\n+ <param name="var" value="chl"/>\n+ <repeat name="user_choice">\n+ <param name="dim" value="time"/>\n+ <conditional name="condi_between">\n+ <param name="comparator" value="sl"/>\n+ <param name="t1" value="10"/>\n+ <param name="t2" value="12"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="user_choice">\n+ <param name="dim" value="latitude"/>\n+ <param name="dim_tab" value="latitude.tabular"/>\n+ <conditional name="condi_between">\n+ <param name="comparator" value="sl"/>\n+ <param name="t1" value="5"/>\n+ <param name="t2" value="10"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="user_choice">\n+ <param name="dim" value="longitude"/>\n+ <param name="dim_tab" value="longitude.tabular"/>\n+ <conditional name="condi_between">\n+ <param name="comparator" value="sl"/>\n+ <param name="t1" value="4"/>\n+ <param name="t2" value="10"/>\n+ </conditional>\n+ </repeat>\n+ <param name="scale" value="1000.5"/>\n+ <param name="write_all" value="Yes"/> \n+ <output name="output_netcdf" file="all.netcdf" compare="sim_size" delat="1000"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+Select a variable ans can restrict over any of its dimension and apply a scaling (1 by default).\n+the result is stored in a new netCDF file.\n+One can also select the range of time (for timeseries) to apply these operations over the range only\n+when a range of time is selected and when scaling, one can choose to save the entire timeseries or\n+the selected range only.\n+when scaling, one can add additional filters on dimensions (typically used to filter \n+over latitudes and longitudes)\n+\n+\n+-------------------------------------------------\n+\n+The xarray select tool can be used after the xarray Info and xarray Coord.\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r b0780241f916 xarray_tool.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xarray_tool.py Sun Jun 06 08:50:11 2021 +0000 |
| [ |
| b'@@ -0,0 +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, s'..b'rds = pd.read_csv(self.coords, sep=\'\\t\')\n+ for row in fcoords.itertuples():\n+ self.latvalN = row[0]\n+ self.lonvalE = row[1]\n+ self.outfile = (os.path.join(self.outputdir,\n+ self.select + \'_\' +\n+ str(row.Index) + \'.tabular\'))\n+ self.selection()\n+\n+ def get_coords_info(self):\n+ ds = xr.open_dataset(self.infile)\n+ for c in ds.coords:\n+ filename = os.path.join(self.coords_info,\n+ c.strip() +\n+ \'.tabular\')\n+ pd = ds.coords[c].to_pandas()\n+ pd.index = range(len(pd))\n+ pd.to_csv(filename, header=False, sep=\'\\t\')\n+\n+\n+if __name__ == \'__main__\':\n+ warnings.filterwarnings("ignore")\n+ parser = argparse.ArgumentParser()\n+\n+ parser.add_argument(\n+ \'infile\',\n+ help=\'netCDF input filename\'\n+ )\n+ parser.add_argument(\n+ \'--info\',\n+ help=\'Output filename where metadata information is stored\'\n+ )\n+ parser.add_argument(\n+ \'--summary\',\n+ help=\'Output filename where data summary information is stored\'\n+ )\n+ parser.add_argument(\n+ \'--select\',\n+ help=\'Variable name to select\'\n+ )\n+ parser.add_argument(\n+ \'--latname\',\n+ help=\'Latitude name\'\n+ )\n+ parser.add_argument(\n+ \'--latvalN\',\n+ help=\'North latitude value\'\n+ )\n+ parser.add_argument(\n+ \'--latvalS\',\n+ help=\'South latitude value\'\n+ )\n+ parser.add_argument(\n+ \'--lonname\',\n+ help=\'Longitude name\'\n+ )\n+ parser.add_argument(\n+ \'--lonvalE\',\n+ help=\'East longitude value\'\n+ )\n+ parser.add_argument(\n+ \'--lonvalW\',\n+ help=\'West longitude value\'\n+ )\n+ parser.add_argument(\n+ \'--tolerance\',\n+ help=\'Maximum distance between original and selected value for \'\n+ \' inexact matches e.g. abs(index[indexer] - target) <= tolerance\'\n+ )\n+ parser.add_argument(\n+ \'--coords\',\n+ help=\'Input file containing Latitude and Longitude\'\n+ \'for geographical selection\'\n+ )\n+ parser.add_argument(\n+ \'--coords_info\',\n+ help=\'output-folder where for each coordinate, coordinate values \'\n+ \' are being printed in the corresponding outputfile\'\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+ \'--time\',\n+ help=\'select timeseries variable#operator#value_s[#value_e]\'\n+ )\n+ parser.add_argument(\n+ \'--outfile\',\n+ help=\'csv outfile for storing results of the selection\'\n+ \'(valid only when --select)\'\n+ )\n+ parser.add_argument(\n+ \'--outputdir\',\n+ help=\'folder name for storing results with multiple selections\'\n+ \'(valid only when --select)\'\n+ )\n+ parser.add_argument(\n+ "-v", "--verbose",\n+ help="switch on verbose mode",\n+ action="store_true"\n+ )\n+ parser.add_argument(\n+ "--no_missing",\n+ help="""Do not take into account possible null/missing values\n+ (only valid for single location)""",\n+ action="store_true"\n+ )\n+ args = parser.parse_args()\n+\n+ p = XarrayTool(args.infile, args.info, args.summary, args.select,\n+ args.outfile, args.outputdir, args.latname,\n+ args.latvalN, args.latvalS, args.lonname,\n+ args.lonvalE, args.lonvalW, args.filter,\n+ args.coords, args.time, args.verbose,\n+ args.no_missing, args.coords_info, args.tolerance)\n+ if args.info:\n+ p.info()\n+ if args.summary:\n+ p.summary()\n+ if args.coords:\n+ p.selection_from_coords()\n+ elif args.select:\n+ p.selection()\n+ elif args.coords_info:\n+ p.get_coords_info()\n' |
