Human footprint pipeline clean #100
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Co-Authored-By: Jean-Michel Lord <6223744+jmlord@users.noreply.github.com>
Cambio de nombre
Update of studyarea_to_wkt to be used in the workshop of July 31, 2023
Borrador en español de los textos yml del dpc
esto es una pry¿ueba
Changes are made in the description of the .yml arguments for the dPC indicator, some sections are translated and some disclaimers are included.
A part of the routine that was missing for the dPC indicator, is inserted
…biab-2.0 into test_pipeline_IAvH
We have updated the auk_filter step script from the filter request (e.g. bbox- sp ) to the eBird zf table. The inputs and outputs were adjusted and tested in ByB with the documentation revised by Lina and Helena. The next step is to integrate the pipeline with the covars script step. However The inputs, ebd_file=ebd_CO_relDec-2022 and ebd_sampling_file=ebd_samp_Col_relDec-2022-002, should be manually loaded into the repository/00_auk_filter/input directory, as their size is too large to be accommodated in GIT. We could consider downsizing the dataset to a specific region in order to provide a functional pilot without going through that step.
change the way of presenting the final results
…biab-2.0 into test_pipeline_IAvH
add the images of the documentation in Rmd for the protcon pipeline
-included author, name and external link in script of protcon pipe -deleted .DS_Store -deleted scripts/.DS_Store -deleted README.html -deleted protcon_test -correct errors in .gpkg for studyarea_to_WKT and spatial_to_DistanceMatrix
correct corrupt Colombian_protected_areas.gpkg file
delete redundant files for the Protcon calculation
All corrections and comment made by JM
reupload .gpkg corrupt file
+ re-saved pipeline to get latest changes in yml
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Would it be possible to present the pipeline outputs as a time series graph as well as a table ? We would like to showcase it in the viewer (see and example with SHI here: https://biab2.geobon.org/viewer/SHI_pipeline%3E3652d5fd15ab1f7e4fbc5b648cddca30) and just showing a table would be quite boring... |
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Hi, if I'm choosing P1Y for the time interval, I'm getting this error in the log. Otherwise, it was running with the default values and P5Y. |
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In the input form, it is not clear why an espg is required for the study area. Isn't it already supposed to be in the shp given for the study area? Or it is for transforming everything to this epsg? |
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Why is Protcon in there? It has it's own other pull request
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The casing makes it fail. Make sure to do a big find/replace of all to have the same casing. The folder has uppercase L, it should be lowercase.
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All those images are for protcon analysis html file...
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Could you put these collections on an object storage online somewhere? Since it's a stac catalog, if you access it as stack it should work well... and it will avoid everyone downloading these tiffs. Its a lot of example tiffs since it is a time series...
| description: Path to the output directory where the raster results of the metric analysis are saved | ||
| type: text | ||
| dir_info_layer: | ||
| label: info table path out |
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"info table" would be enought. When using mime types, it is always a path.
| type: image/tiff;application=geotiff | ||
| dir_stack: | ||
| label: stack path out | ||
| description: Path to the output directory where the raster results of the metric analysis are saved |
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Can this output be an array of rasters instead?
That way we could show them in the viewer.
| label: collection path | ||
| description: Path where the collection is hosted. The path can be hosted on the BIAB server (subject to approval from administrators) or in a cloud container | ||
| type: text | ||
| example: 'scripts/Load_collection/Collections/Colombia_human_footprint_collection' |
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Is this accessed as a STAC catalog or a bunch of tiffs? If STAC then it could be put on some object storage and receive a path to the stac as an input.
| label: time interval | ||
| description: String refering to the periods or intervals used for analysis. It specifies the length and units of time that will be considered for analyzing the data. For example, time intervals like 10Y (10 years), 5Y (5 years), 4M (4 months) can be used to define the time granularity for conducting the analysis. If no interval (time_interval) is specified, '1Y' is used by default | ||
| type: text | ||
| example: 'P10Y' |
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Why is there a P ? According to the description it should just be 10Y...
| example: 'NA' | ||
| time_end: | ||
| label: End of time interval | ||
| description: "Refering to the ending date of the time interval. If this value is null or not provided, the minimum date from the column_date will be automatically taken as the starting date for the analysis. This argument is ignored if column_date=NULL." |
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The second sentence of the comment refers to the starting date. What happens for end date if column_date=NULL ?
| - name: Maria Alejandra Molina Berbeo (mmolina@humboldt.org.co) | ||
| - name: Victor Julio Rincon (vrincon@humboldt.org.co) | ||
| - name: Luis Fernando Urbina (lurbina@humboldt.org.co) | ||
| external_link: https://github.com/GEO-BON/biab-2.0 |
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Change ot appropriate link. If there is no external link to put, please remove this.
| dir_stack: | ||
| label: stack path in | ||
| description: Path to the input directory where the raster results of the metric analysis are saved | ||
| type: text |
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This should receive an array of tiffs, not a directory.
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This should not be in this PR, this is in Protcon pipeline.
| author: | ||
| - name: Maria Alejandra Molina Berbeo (mmolina@humboldt.org.co) | ||
| - name: Victor Julio Rincon | ||
| external_link: https://github.com/GEO-BON/biab-2.0 |
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Link to a place where we can find the geopackages (and remove the gpkg from the repo)
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Keep only one GPKG for example, put the rest on an object storage and link to it in the metadata.
the protcon pipe is eliminated leaving the HFI as the only pipe in the branch. Some scripts will be respited because are uses in the two pipes
this is the complete Human footprint pipeline