Merge branch 'main' of https://github.com/uwescience/SciPy2024-GitHubActionsTutorial

Author: gbrencher

.github/workflows/summary_statistics.yml

@@ -32,95 +32,8 @@ jobs:
                   merge-multiple: true
 
             - name: Compute summary statistics
-              shell:  bash -el -c "python -u {0}"
               run: |
-                import xarray as xr
-                import rasterio as rio
-                import rioxarray
-                from glob import glob
-                from datetime import datetime
-                import seaborn as sns
-                import matplotlib.pyplot as plt
-
-                # functions to load tifs to xarray
-                def xr_read_geotif(geotif_file_path, masked=True):
-                    da = rioxarray.open_rasterio(geotif_file_path, masked=True)
-                    # Extract bands and assign as variables in xr.Dataset()
-                    ds = xr.Dataset()
-                    for i, v in enumerate(da.band):
-                        da_tmp = da.sel(band=v)
-                        da_tmp.name = "band" + str(i + 1)
-                        ds[da_tmp.name] = da_tmp
-                    # Delete empty band coordinates.
-                    del ds.coords["band"]
-                
-                    return ds
-                
-                def combine_ds(data_dir, file_type='horizontal_velocity'):
-                    datasets = []
-                    tif_list = glob(f'{data_dir}/S2*{file_type}.tif')
-                    for tif_path in tif_list:
-                        dates = tif_list[0].split('/')[-1][3:20] #parse filename for dates
-                        start_date = datetime.strptime(dates[:8], '%Y%m%d')
-                        end_date = datetime.strptime(dates[-8:], '%Y%m%d')
-                        t_baseline = end_date - start_date
-                        
-                        src = xr_read_geotif(tif_path, masked=False) #read product to xarray ds
-                        src = src.assign_coords({"dates": dates})
-                        src = src.expand_dims("dates")
-                        
-                        src = src.assign_coords(start_date = ('dates', [start_date]))
-                        src = src.assign_coords(end_date = ('dates', [end_date]))
-                        src = src.assign_coords(t_baseline = ('dates', [t_baseline]))
-                
-                        src = src.rename({'band1':file_type})
-                        
-                        datasets.append(src)
-                       
-                    ds = xr.concat(datasets, dim="dates", combine_attrs="no_conflicts") #create dataset
-                    ds = ds.sortby('dates')
-                
-                    return ds 
-
-                # read in tifs
-                veloc_ds = combine_ds(data_dir='glacier_image_correlation', file_type='horizontal_velocity')
-                # calculate and save median velocity
-                veloc_da_median = veloc_ds.horizontal_velocity.median(dim='dates')
-                # veloc_da_median.rio.to_raster('glacier_image_correlation/median_horizontal_velocity.tif')
-                # save standard deviation of velocity
-                veloc_da_stdev = veloc_ds.horizontal_velocity.std(dim='dates')
-                # veloc_da_stdev.rio.to_raster('glacier_image_correlation/stdev_horizontal_velocity.tif')
-                # save valid velocity pixel count
-                veloc_da_count = veloc_ds.horizontal_velocity.count(dim='dates')
-                # veloc_da_count.rio.to_raster('glacier_image_correlation/count_horizontal_velocity.tif')
-
-                # plot summary statistics
-                sns.set_theme()
-                f, ax = plt.subplots(1, 3, figsize=(15, 5), sharex=True, sharey=True)
-                veloc_da_median.plot(ax=ax[0], vmin=0, vmax=600, cmap='inferno', cbar_kwargs= {'shrink':0.7, 'label':'velocity (m/yr)'})
-                veloc_da_stdev.plot(ax=ax[1], vmin=0, vmax=300, cmap='cividis', cbar_kwargs= {'shrink':0.7, 'label':'standard deviation (m/yr)'})
-                veloc_da_count.plot(ax=ax[2], vmin=0, cmap='Blues', cbar_kwargs= {'shrink':0.7, 'label':'pixel count'})
-                ax[0].set_aspect('equal')
-                ax[1].set_aspect('equal')
-                ax[2].set_aspect('equal')
-                ax[0].set_title(f'median velocity')
-                ax[1].set_title(f'velocity standard deviation')
-                ax[2].set_title(f'valid pixel count')
-                ax[0].set_xticks([])
-                ax[0].set_yticks([])
-                ax[1].set_xticks([])
-                ax[1].set_yticks([])
-                ax[2].set_xticks([])
-                ax[2].set_yticks([])
-                ax[0].set_xlabel('')
-                ax[0].set_ylabel('')
-                ax[1].set_xlabel('')
-                ax[1].set_ylabel('')
-                ax[2].set_xlabel('')
-                ax[2].set_ylabel('')
-                f.tight_layout()
-                
-                f.savefig('glacier_image_correlation/velocity_summary_statistics.png', dpi=300)
+                python glacier_image_correlation/summary_statistics.py
 
             - name: Upload summary statistics
               uses: actions/upload-artifact@v4