Repository 'xarray_netcdf2netcdf'
hg clone https://toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf

Changeset 0:b0780241f916 (2021-06-06)
Next changeset 1:1a91e551f3a9 (2021-08-29)
Commit message:
"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"
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
b
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
b
@@ -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().
b
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
[
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'
b
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
b
@@ -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
b
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
b
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'
b
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
b
@@ -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
b
@@ -0,0 +1,1 @@
+0 0.50576
b
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
b
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
b
@@ -0,0 +1,97 @@
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+95 50.916664
+96 51.0
b
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
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+72 -7.6e-07
+73 0.08333257
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b
diff -r 000000000000 -r b0780241f916 test-data/small.netcdf
b
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
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+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
b
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
b
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
b
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'