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Implement Grid.open_file method support non xarray formats including Shapefile/Geojson #808

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39a16fd
o start on #635
rajeeja Jan 10, 2024
d554571
o Fix conflicts and merge main
rajeeja Jan 11, 2024
6d4e6da
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Jan 23, 2024
6c8ce7a
o Intermittent work
Feb 22, 2024
fc58f4b
Merge branch 'main' into rajeeja/io_shapefile
rajeeja May 5, 2024
04729ec
Merge branch 'rajeeja/io_shapefile' of github.com:UXARRAY/uxarray int…
rajeeja May 6, 2024
efdf46e
Merge branch 'main' into rajeeja/io_shapefile
rajeeja May 8, 2024
bea0e81
o pre-commit changes Ruff
rajeeja May 8, 2024
a627b30
Merge branch 'main' into rajeeja/io_shapefile
rajeeja May 15, 2024
f59f9a6
Merge branch 'main' into rajeeja/io_shapefile
rajeeja May 18, 2024
2a3dba0
Merge branch 'main' into rajeeja/io_shapefile
rajeeja May 20, 2024
2aaabcd
o Read polygon and multipolygon
rajeeja May 31, 2024
7d3875c
Merge branch 'main' into rajeeja/io_shapefile
rajeeja May 31, 2024
939b3b4
o Add a test mesh file
rajeeja May 31, 2024
fb10484
o Add geopandas dependency
rajeeja Jun 3, 2024
fa3b73f
o Fix tests, TODO: Fix API and make open_grid work.
rajeeja Jun 3, 2024
a503c51
Possible that np.intp could have different ranges on 32-bit versus 64…
rajeeja Jun 4, 2024
1353d2b
trying np.int16
rajeeja Jun 4, 2024
66ccc8b
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Jul 9, 2024
a7b8328
Merge branch 'rajeeja/io_shapefile' of github.com:UXARRAY/uxarray int…
rajeeja Jul 9, 2024
9664430
o Make a small example, fix bug with max size for connectivity arrray…
rajeeja Jul 10, 2024
1f12543
o Fix setting the datatype for empty connectivity array to a np.int16…
rajeeja Jul 11, 2024
b5fe8ed
o Setting the dtype to int32 as leaving empty defaults to float
rajeeja Jul 11, 2024
65901dd
o Use np.intp for connectivity init
rajeeja Jul 11, 2024
0ec8002
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Jul 17, 2024
00fc5fa
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Jul 18, 2024
07cfae7
o Check to see if np.fulll instead of pad works
rajeeja Jul 19, 2024
c05cfda
o Add test for multipolygon case and also test a file
rajeeja Jul 20, 2024
5ac3e08
o Fix comments
rajeeja Jul 22, 2024
54daaa1
o Fix comments
rajeeja Jul 22, 2024
e97e76f
o Rearrange code
rajeeja Jul 24, 2024
34decd2
Merge branch 'main' into rajeeja/io_shapefile
philipc2 Aug 2, 2024
258948a
Merge branch 'main' into rajeeja/io_shapefile
philipc2 Aug 5, 2024
2deb7fd
Merge branch 'main' into rajeeja/io_shapefile
philipc2 Aug 12, 2024
547405f
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Aug 21, 2024
92de0ec
Merge branch 'rajeeja/io_shapefile' of github.com:UXARRAY/uxarray int…
rajeeja Aug 21, 2024
112dcc7
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Aug 23, 2024
2dd18d0
o Move to geopandas from shapefile
rajeeja Aug 26, 2024
f1534ad
o Add geopandas reader to doc
rajeeja Aug 28, 2024
9387e9d
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Aug 30, 2024
952240b
Update test/test_geopandas.py
rajeeja Sep 3, 2024
1e3a6ac
o Resolve functions as per Orhan's feedback
rajeeja Sep 3, 2024
38d33f0
o Add readme for meshfiles
rajeeja Sep 3, 2024
9845d1b
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Sep 3, 2024
fa4fcba
o Remove commented lines as logic is to read via Grid object
rajeeja Sep 4, 2024
93d5dc7
o Using lists instead of np.append as list is an amortized O(1), np.…
rajeeja Sep 5, 2024
e451aff
o missed precommit
rajeeja Sep 5, 2024
fc7744b
Merge branch 'main' into rajeeja/io_shapefile
erogluorhan Sep 10, 2024
363ec1d
o change grid.py for a making front end more general
rajeeja Sep 10, 2024
6101a63
Merge branch 'main' into rajeeja/io_shapefile
erogluorhan Sep 10, 2024
793d697
Merge branch 'main' into rajeeja/io_shapefile
philipc2 Sep 13, 2024
c439bbe
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Sep 13, 2024
c591083
o Use from_file class method for shapefile/geojson etc. from geopanda…
rajeeja Sep 13, 2024
d7a9778
Merge branch 'rajeeja/io_shapefile' of github.com:UXARRAY/uxarray int…
rajeeja Sep 13, 2024
35ec0b6
o Fix doc
rajeeja Sep 13, 2024
57ea2f5
Merge branch 'main' into rajeeja/io_shapefile
philipc2 Sep 14, 2024
f383a96
o Call backend xarray instead of NetCDF, fix doc
rajeeja Sep 14, 2024
88f1647
Merge branch 'rajeeja/io_shapefile' of github.com:UXARRAY/uxarray int…
rajeeja Sep 14, 2024
a1fc10e
Update uxarray/grid/grid.py
rajeeja Sep 14, 2024
16ca582
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Sep 17, 2024
120e741
Merge branch 'rajeeja/io_shapefile' of github.com:UXARRAY/uxarray int…
rajeeja Sep 17, 2024
a8ba608
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Sep 18, 2024
f4d0ac4
Update uxarray/core/api.py
rajeeja Sep 19, 2024
9f97dfa
Merge branch 'main' into rajeeja/io_shapefile
rajeeja Sep 19, 2024
610e029
undo previous commit and add only precommit fix
rajeeja Sep 19, 2024
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1 change: 1 addition & 0 deletions ci/asv.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ dependencies:
- scipy
- shapely
- spatialpandas
- geopandas
- xarray
- asv
- pip:
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1 change: 1 addition & 0 deletions ci/docs.yml
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Expand Up @@ -33,6 +33,7 @@ dependencies:
- pandas
- geocat-datafiles
- spatialpandas
- geopandas
- pip:
- antimeridian
- git+https://github.com/philipc2/pyfma.git # fix until https://github.com/nschloe/pyfma/pull/17 is merged
1 change: 1 addition & 0 deletions ci/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ dependencies:
- scipy
- shapely
- spatialpandas
- geopandas
- xarray
- asv
- pip:
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1 change: 1 addition & 0 deletions ci/install-upstream.sh
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Expand Up @@ -33,6 +33,7 @@ python -m pip install \
pandas \
scikit-learn \
scipy \
geopandas \
xarray

# install rest from source
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11 changes: 8 additions & 3 deletions docs/internal_api/index.rst
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Expand Up @@ -285,12 +285,17 @@ SCRIP
io._scrip._encode_scrip


Shapefile
---------
GeoDataFrame
------------
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.. autosummary::
:toctree: generated/

io._shapefile._read_shpfile
io._geopandas._read_geodataframe
io._geopandas._read_geopandas
io._geopandas._encode_geopandas
io._geopandas._standardize_geopandas
io._geopandas._is_geopandas
io._geopandas._validate_minimum_geopandas

Vertices
--------
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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -42,6 +42,7 @@ dependencies = [
"scipy",
"shapely",
"spatialpandas",
"geopandas",
"xarray",
]
# minimal dependencies end
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15 changes: 15 additions & 0 deletions test/meshfiles/geojson/README.md
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@@ -0,0 +1,15 @@
GeoJSON is a format for encoding a variety of geographic data structures, including points, lines, and polygons.

This repository contains "sample_chicago_buildings" GeoJSON file featuring a selection of buildings in Chicago. The file includes:

Number of polygons: 10
Polygon 1: 26 sides
Polygon 2: 36 sides
Polygon 3: 29 sides
Polygon 4: 10 sides
Polygon 5: 30 sides
Polygon 6: 8 sides
Polygon 7: 7 sides
Polygon 8: 9 sides
Polygon 9: 7 sides
Polygon 10: 19 sides
17 changes: 17 additions & 0 deletions test/meshfiles/geojson/sample_chicago_buildings.geojson

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1 change: 1 addition & 0 deletions test/meshfiles/shp/5poly/5poly.cpg
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ISO-8859-1
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15 changes: 15 additions & 0 deletions test/meshfiles/shp/README.md
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### There are 3 sub folders each containing different shapefile examples

1. **5poly** : A very simple file containing only 5 polygons with different number of sides
2. **cb_2018_us_national_20m**: Real word shapefile containing the 2018 Census Bureau US map at 20m resolution
3. **multipoly**: Test file containing multipolygons.

### Files Included in the Shapefile Dataset

1. **.shp** - **Shape Format**: Contains the geometric data (polygons) for the features in the dataset. The first 100 bytes contain metadata about the file.

2. **.shx** - **Shape Index Format**: Contains the index data for the .shp file, allowing for quick access to the geometric data.

3. **.dbf** - **Attribute Format**: Contains attribute data for the features in the .shp file. This is a dBase file that stores information in a tabular format, where each row corresponds to a feature in the .shp file.

4. **.cpg** - **Code Page Format**: Contains character encoding information for the .dbf file, ensuring that text data is correctly interpreted. Eg. ISO-8859-1
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GEOGCS["GCS_North_American_1983",DATUM["D_North_American_1983",SPHEROID["GRS_1980",6378137,298.257222101]],PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]
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<?xml version="1.0" encoding="UTF-8"?>
<!--This file contains all the Entity and Attribute Information--><gfc:FC_FeatureCatalogue xmlns:gmx="http://www.isotc211.org/2005/gmx"
xmlns:gco="http://www.isotc211.org/2005/gco"
xmlns:gmd="http://www.isotc211.org/2005/gmd"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:gml="http://www.opengis.net/gml/3.2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:gfc="http://www.isotc211.org/2005/gfc"
xsi:schemaLocation="https://www.ngdc.noaa.gov/metadata/published/xsd/schema/gfc/featureCataloging.xsd http://www.isotc211.org/2005/gfc">
<gmx:name>
<gco:CharacterString>Feature Catalog for the 2018 United States 1:20,000,000 Cartographic Boundary File</gco:CharacterString>
</gmx:name>
<gmx:scope>
<gco:CharacterString>The United States at a scale of 1:20,000,000</gco:CharacterString>
</gmx:scope>
<gmx:versionNumber>
<gco:CharacterString>cb_2018_nation_20m</gco:CharacterString>
</gmx:versionNumber>
<gmx:versionDate>
<gco:Date>2019-05</gco:Date>
</gmx:versionDate>
<gmx:language>
<gco:CharacterString>eng</gco:CharacterString>
</gmx:language>
<gmx:characterSet>
<gmd:MD_CharacterSetCode codeList="http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#MD_CharacterSetCode"
codeListValue="utf8"
codeSpace="004">utf8
</gmd:MD_CharacterSetCode>
</gmx:characterSet>
<gfc:producer xlink:href="https://www.ngdc.noaa.gov/docucomp/1df27e57-4768-42de-909b-52f530601fba"
xlink:title="U.S Department of Commerce, U.S Census Bureau, Geographic Customer Services Branch"/>
<gfc:featureType>
<gfc:FC_FeatureType>
<gfc:typeName>
<gco:LocalName>cb_2018_us_nation_20m.shp</gco:LocalName>
</gfc:typeName>
<gfc:definition>
<gco:CharacterString>Current Nation (national)</gco:CharacterString>
</gfc:definition>
<gfc:isAbstract>
<gco:Boolean>false</gco:Boolean>
</gfc:isAbstract>
<gfc:featureCatalogue uuidref="2018_nation_20m.ea.iso.xml"/>
<gfc:carrierOfCharacteristics>
<gfc:FC_FeatureAttribute>
<gfc:memberName>
<gco:LocalName>AFFGEOID</gco:LocalName>
</gfc:memberName>
<gfc:definition>
<gco:CharacterString>American FactFinder summary level code + geovariant code + '00US'</gco:CharacterString>
</gfc:definition>
<gfc:cardinality gco:nilReason="unknown"/>
<gfc:definitionReference xlink:title="U.S. Census Bureau"
xlink:href="http://www.ngdc.noaa.gov/docucomp/eb139e38-ee29-4d59-b157-5e874d4420c4"/>
<gfc:listedValue>
<gfc:FC_ListedValue>
<gfc:label>
<gco:CharacterString>American FactFinder geographic identifier</gco:CharacterString>
</gfc:label>
<gfc:definitionReference xlink:title="U.S. Census Bureau"
xlink:href="http://www.ngdc.noaa.gov/docucomp/eb139e38-ee29-4d59-b157-5e874d4420c4"/>
</gfc:FC_ListedValue>
</gfc:listedValue>
</gfc:FC_FeatureAttribute>
</gfc:carrierOfCharacteristics>
<gfc:carrierOfCharacteristics>
<gfc:FC_FeatureAttribute>
<gfc:memberName>
<gco:LocalName>GEOID</gco:LocalName>
</gfc:memberName>
<gfc:definition>
<gco:CharacterString>Nation identifier</gco:CharacterString>
</gfc:definition>
<gfc:cardinality gco:nilReason="unknown"/>
<gfc:definitionReference xlink:title="U.S. Census Bureau"
xlink:href="http://www.ngdc.noaa.gov/docucomp/eb139e38-ee29-4d59-b157-5e874d4420c4"/>
<gfc:listedValue>
<gfc:FC_ListedValue>
<gfc:label>
<gco:CharacterString>US</gco:CharacterString>
</gfc:label>
<gfc:definition>
<gco:CharacterString>United States</gco:CharacterString>
</gfc:definition>
<gfc:definitionReference xlink:title="U.S. Census Bureau"
xlink:href="http://www.ngdc.noaa.gov/docucomp/eb139e38-ee29-4d59-b157-5e874d4420c4"/>
</gfc:FC_ListedValue>
</gfc:listedValue>
</gfc:FC_FeatureAttribute>
</gfc:carrierOfCharacteristics>
<gfc:carrierOfCharacteristics>
<gfc:FC_FeatureAttribute>
<gfc:memberName>
<gco:LocalName>NAME</gco:LocalName>
</gfc:memberName>
<gfc:definition>
<gco:CharacterString>Nation name</gco:CharacterString>
</gfc:definition>
<gfc:cardinality gco:nilReason="unknown"/>
<gfc:definitionReference xlink:title="U.S. Census Bureau"
xlink:href="http://www.ngdc.noaa.gov/docucomp/eb139e38-ee29-4d59-b157-5e874d4420c4"/>
<gfc:listedValue>
<gfc:FC_ListedValue>
<gfc:label>
<gco:CharacterString>United States</gco:CharacterString>
</gfc:label>
<gfc:definition>
<gco:CharacterString>Nation</gco:CharacterString>
</gfc:definition>
<gfc:definitionReference xlink:title="U.S. Census Bureau"
xlink:href="http://www.ngdc.noaa.gov/docucomp/eb139e38-ee29-4d59-b157-5e874d4420c4"/>
</gfc:FC_ListedValue>
</gfc:listedValue>
</gfc:FC_FeatureAttribute>
</gfc:carrierOfCharacteristics>
</gfc:FC_FeatureType>
</gfc:featureType>
</gfc:FC_FeatureCatalogue>
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