merged with Joey

tools/SAMTool.py

@@ -4,7 +4,9 @@
 import time
 
 import numpy as np
-import rasterio as rio
+import rasterio
+from rasterio.transform import from_bounds as transform_from_bounds
+from rasterio.features import shapes as get_shapes
 from PyQt5.QtWidgets import QMessageBox
 from qgis.core import QgsRectangle, QgsMessageLog, Qgis
 from torch.utils.data import DataLoader
@@ -94,7 +96,7 @@ def sam_predict(self, canvas_points: Canvas_Points, canvas_rect: Canvas_Rectangl
         bbox = self.sample_bbox  # batch['bbox'][0]
         # Change to sam.img_encoder.img_size
         img_width = img_height = self.predictor.model.image_encoder.img_size  # 1024
-        img_clip_transform = rio.transform.from_bounds(
+        img_clip_transform = transform_from_bounds(
             bbox.minx, bbox.miny, bbox.maxx, bbox.maxy, img_width, img_height)
 
         input_point, input_label = canvas_points.get_points_and_labels(
@@ -129,13 +131,14 @@ def sam_predict(self, canvas_points: Canvas_Points, canvas_rect: Canvas_Rectangl
         # results = ({'properties': {'raster_val': v}, 'geometry': s}
         #            for i, (s, v) in enumerate(rio.features.shapes(mask.astype(np.uint8), mask=mask, transform=img_clip_transform)))
         # geoms = list(results)
-        shape_generator = rio.features.shapes(
+        shape_generator = get_shapes(
             mask.astype(np.uint8),
             mask=mask,
+            connectivity=8,  # change from default:4 to 8
             transform=img_clip_transform
         )
         geojson = [{'properties': {'raster_val': value}, 'geometry': polygon}
-                 for polygon, value in shape_generator]
+                   for polygon, value in shape_generator]
 
         # add to layer
         sam_polygon.rollback_changes()

tools/geoTool.py

@@ -1,12 +1,13 @@
 import os
 import typing
 import numpy as np
-from qgis.core import (QgsProject, QgsCoordinateReferenceSystem, Qgis, QgsMessageLog, 
+from qgis.core import (QgsProject, QgsCoordinateReferenceSystem, Qgis, QgsMessageLog,
                        QgsCoordinateTransform, QgsPointXY,  QgsRectangle, QgsVectorLayer)
 
 
 class ImageCRSManager:
     '''Manage image crs and transform point and extent between image crs and other crs'''
+
     def __init__(self, img_crs) -> None:
         self.img_crs = QgsCoordinateReferenceSystem(
             img_crs)  # from str to QgsCRS
@@ -63,18 +64,19 @@ def extent_to_img_crs(
             dst_crs, self.img_crs, QgsProject.instance())
         extent_transformed = transform.transformBoundingBox(extent)
         return extent_transformed
-    
+
     def img_extent_to_crs(self, extent: QgsRectangle, dst_crs: QgsCoordinateReferenceSystem):
         '''transform extent from this image crs to destination crs
-        
+
         Parameters:
         ----------
         extent: QgsRectangle
             extent in this image crs
         dst_crs: QgsCoordinateReferenceSystem
             destination crs for extent
         '''
-        transform = QgsCoordinateTransform(self.img_crs, dst_crs, QgsProject.instance())
+        transform = QgsCoordinateTransform(
+            self.img_crs, dst_crs, QgsProject.instance())
         extent_transformed = transform.transformBoundingBox(extent)
         return extent_transformed