GeoReferenced ROIs from points shapefile

[HaleySchuhl]

Used this code from Keely to make circular ROIs & will brainstorm how to best add this feature flexibly.

import geopandas as gpd

# Try to convert points file to shapefile with circles

gdf = gpd.read_file("./plant_positions.shp")

# Specify the desired diameter (in the same units as the CRS, e.g., meters)
radius = 0.4  # Half the diameter to use as buffer radius

# Generate a circle (buffer) around each point
gdf['geometry'] = gdf.geometry.buffer(radius)

# Save the resulting circles as a GeoJSON file
gdf.to_file('./output_circles.geojson', driver='GeoJSON')


geo_rois = geo.transform_polygons(img=spectral, geojson='./shpfiles/kura_center_circles.geojson')
# now take these contours and make them into a labeled mask? 
all_objs = Objects()
lbl_mask = np.zeros(np.shape(gray)).astype(np.int32)
i = 1
for roi in geo_rois:
    new = [np.array(roi, dtype=np.int32)]
    lbl_mask = cv2.drawContours(lbl_mask.astype(np.int32), new, -1, (i), -1)
    all_objs.append(contour=roi, h=[])
    i += 1

label_mask_where = np.where(plant_mask == 255, lbl_mask, 0)