Update functions to use odc-geo and add additional content to tests
#1039
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erin-telfer
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May 1, 2023
* Readme update (#1019) * test this * permalink to the template notebook * trying to get the link working * Update README.rst * Update README.rst --------- Co-authored-by: Nathan <95725385+treefern@users.noreply.github.com> * upgrade docker-compose postgres image version to 13 * Update bandindices.py (#1022) Added Normalised Difference Turbidity Index to the 'calculate_indices' tool. NB. acronym 'NDTI' is already in use for Tillage Index. Acronym 'TI' used in lieu. * Readme Update (#1025) Updating to include link back to wiki for approving/reviewing pull requests. * Tiny doc update to remote build trigger (#1026) * Update trigger_docs.yaml Add explanation of triggering build in other doc repo * Formatting suggestions from review * Fix `pixel_tides` issues when `ds` has no time dimension (#1028) * Update pixel_tides func to cover edge cases * Sync with develop branch * Hard code dimension order instead of getting dims from ds * Clean code * Update USAGE.rst (#1029) I've added a recently accepted manuscript where I used DEA to calulcate Geomedians and show landscape changes. And the relevant years where we've used DEA sandbox in our remote sensing topics at Flidners university. Additionally added a conference presentation from AEO22 from Earth Observation Australia 2022 in Brisbane, * Update spellcheck_wordlist.txt * Update DEA Notebooks directory structure (#1027) * New interactive apps folder, moved appropriate notebooks inside * Deleted scientific_workflows * rename DEA_datasets folder to DEA_products * updated 17 notebook references from DEA_datasets to DEA_products * Rename frequently used code * Fix incorrect repo folders * Revert to before dir rename * Rename frequently used code * Update readme for DEA_products and How_to_guides * replace notebook references to Frequently_used_code with How_to_guides * replace notebook references to frequently used code with How_to_guides * replaced notebook references to DEA_datasets * Add readme to interactive apps * updated Real_world_examples readme * Remove defunct tests (replaced by nbval --lax) * Update readme to include interactive apps * Use stable branch * Update real world examples format * Update guided tutorial link * Update template to remove mention of scientific workflows and Scripts dir * Fix formatting * Fix formatting * Last attempt to fix template notebook formatting * Final final fix of formatting --------- Co-authored-by: erialC-P <claire.phillips@ga.gov.au> * Fix geocoding func to still work if geocoding service is down (#1030) * Fix geocoding func to still work if geocoding service is down * Fix format * Extract coastline app from product notebook and move to Interctive_apps (#1032) * Update spellcheck_wordlist.txt (#1037) add: Ai Fanson Fickas Ronan * Update USAGE.rst (#1036) Added Wetlands paper!! * Replace conference paper with Wetlands paper (#1034) updated citation list with paper * Update plotting.py Added a tool named 'plot_variable_images' primarily for use in the "Burnt_area_mapping_near_real_time" notebook. * Update plotting.py * Update plotting.py * small correction to new tool in plotting.py Added extra check to handle error when the input xarray dataset has 0 images. * Update plotting.py Actioned suggestion to raise error. * Add Sentinel-2 and Landsat option to animation notebook (#1043) * Add Sentinel-2 and Landsat option to animation notebook * Set default resolutions * Fix bug where choosing combined product didn't trigger data reload * Update functions to use `odc-geo` and add additional content to tests (#1039) * Make geobox adding func more generic * Remove deprecated map_shapefiles func and replace with .explore * Use odc-geo geobox in xr_animation * Add geomedian collection option to calculate_indices * Update animation notebook to use geomedian so we can add it to tests * Update tests to run on animation notebook * Fix collection number in segmentation notebook * Update rgb func to use odc-geo * Fix attributes being dropped by xr.where, update deprecation version * Remove assign_crs from rgb (not needed), and add error handling to xr_animation * Use better error * Re-run affected notebooks * Update collection param in ML notebooks * Add manual reload trigger to layer selection (#1044) --------- Co-authored-by: Bex Dunn <BexDunn@users.noreply.github.com> Co-authored-by: Nathan <95725385+treefern@users.noreply.github.com> Co-authored-by: Pin Jin <pindge.j@gmail.com> Co-authored-by: Pin Jin <pin.jin@ga.gov.au> Co-authored-by: Matt-dea <129345253+Matt-dea@users.noreply.github.com> Co-authored-by: LaurenSchenk1 <125851593+LaurenSchenk1@users.noreply.github.com> Co-authored-by: Robbi Bishop-Taylor <Robbi.BishopTaylor@ga.gov.au> Co-authored-by: mdasi00 <91014391+mdasi00@users.noreply.github.com> Co-authored-by: erialC-P <claire.phillips@ga.gov.au>
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Proposed changes
odc-geois a fantastic package of tools for performing spatial operations on datacube-loaded data, and will soon replacedatacube's existing Geobox functionality: opendatacube/datacube-core#1424This PR addresses #1038 by switching some of our DEA Tools functions (mainly in
dea_tools.plottingacross to usingodc-geofor spatial operations. This will make it much easier for us to transition toodc-geofunctionality once it replacesdatacube's current Geobox functionality, and will simplify some other code updates in the pipeline (e.g. changes to our coastal scripts). The key change is that rather than doing this to access a datacube Geobox:We now do:
As part of this PR, I've also made a few minor additional changes:
How_to_guides/Animated_timeseries.ipynbnotebook to our automated testsmap_shapfilefunc as Geopandas supports interactive plotting natively via.explorecalculate_band_indices, as we no longer have those collections in DEAHave run every notebook on these changes and confirmed they all pass. 🙂
Closes issues (optional)
odc.geo#1038