GTN 'Pangeo 101 for everyone - Xarray'

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Workflow Type: Galaxy

Workflow for GTN Pangeo 101 for everyone - Introduction to Xarray

Associated Tutorial

This workflows is part of the tutorial GTN 'Pangeo 101 for everyone - Xarray', available in the GTN

Thanks to...

Tutorial Author(s): Anne Fouilloux

Workflow Author(s): Anne Fouilloux

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1195?version=1

Inputs

ID Name Description Type
CAMS-PM2_5-20211222.netcdf CAMS-PM2_5-20211222.netcdf netCDF input (4 days forecast) of PM2.5 from Copernicus Atmosphere Monitoring Service https://ads.atmosphere.copernicus.eu/#!/home As an example https://doi.org/10.5281/zenodo.5805953
  • File
plot first time e.g. index=0 plot first time e.g. index=0 Which index to plot. Default is the first one e.g. 0
  • string?
plot forecast time 2 days 12:00 UTC plot forecast time 2 days 12:00 UTC Which index to plot. Default is the first one e.g. 60
  • string?
time=0 time=0 Select time index 9 for plotting
  • string
time=1 time=1 Select time index 1 for plotting
  • string
time=2 time=2 Select time index 2 for plotting
  • string
time=3 time=3 Select time index 3 for plotting
  • string
time=4 time=4 Select time index 4 for plotting
  • string
time=5 time=5 Select time index 5 for plotting
  • string
time=6 time=6 Select time index 6 for plotting
  • string
time=7 time=7 Select time index 7 for plotting
  • string

Steps

ID Name Description
11 NetCDF xarray Coordinate Info toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0
12 NetCDF xarray Metadata Info toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1
13 extract longitude __EXTRACT_DATASET__
14 extract latitude __EXTRACT_DATASET__
15 Extract time from coordinate info This step is used to extract time from all the coordinates. __EXTRACT_DATASET__
16 NetCDF xarray operations toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0
17 NetCDF xarray operations toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0
18 NetCDF xarray operations toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0
19 PM2.5 CAMS Europe 0 days 00:00 UTC (reference time) Map of PM2.5 for the reference date and time. toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
20 PM2.5 CAMS forecast 2 days 12:00 UTC one map plot for the entire region (here Europe) and for day 2 12:00 UTC. toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
21 NetCDF xarray Selection toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1
22 NetCDF xarray Coordinate Info toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0
23 NetCDF xarray Coordinate Info toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0
24 NetCDF xarray Metadata Info toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1
25 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
26 PM2.5 over Naples (4 days forecast) toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2
27 Extract times from coordinates __EXTRACT_DATASET__
28 Extract time __EXTRACT_DATASET__
29 stripes PM2.5 over Naples (4 days forecast) toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1
30 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
31 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
32 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
33 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
34 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
35 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
36 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
37 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
38 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
39 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
40 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
41 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
42 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
43 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
44 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
45 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
46 NetCDF xarray map plotting toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0
47 Merge collections __MERGE_COLLECTION__
48 Merge collections __MERGE_COLLECTION__
49 PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3 We have 8 plots, one for each forecast time for the first forecast day betwwen 100:00 and 17:00 UTC and we applied a mask e.g. only plot values great than 30 um/m3. toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1
50 PM2.5 forecast 10:00 - 17:00 UTC We have 8 plots, one for each forecast time. We take the forecast on day 1 between 10:00 and 17:00 UTC toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
input dataset(s) (extracted element) input dataset(s) (extracted element) n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
PM2.5 reference date Europe PM2.5 reference date Europe n/a
  • File
PM2.5 fc 2 days 12:00 UTC Europe PM2.5 fc 2 days 12:00 UTC Europe n/a
  • File
1D plot PM2.5 over Naples (4 days forecast) 1D plot PM2.5 over Naples (4 days forecast) n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
PM2.5 stripes Naples for 4 days forecast from reference date PM2.5 stripes Naples for 4 days forecast from reference date n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
m3) fc 10:00 - 17:00 UTC over Italy PM2.5 (values > 30 um/m3) fc 10:00 - 17:00 UTC over Italy n/a
  • File
PM2.5 fc 10:00 - 17:00 UTC over Italy PM2.5 fc 10:00 - 17:00 UTC over Italy n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:06 by Helena Rasche

Added/updated 4 files


Open master aaf05c1

2.0 (earliest) Created 25th Jun 2024 at 11:08 by Helena Rasche

Added/updated 4 files


Frozen 2.0 83ae28c
help Creators and Submitter
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Submitter
Discussion Channel
GTN Matrix
Tool
ggplot2
License
MIT License
Activity

Views: 413   Downloads: 141

Created: 25th Jun 2024 at 11:08

Last updated: 25th Jun 2024 at 11:08

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