dsa-helpers 1.1.2.dev0__tar.gz → 1.1.3.dev1__tar.gz

{dsa_helpers-1.1.2.dev0/dsa_helpers.egg-info → dsa_helpers-1.1.3.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.2.dev0
+Version: 1.1.3.dev1
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-1.1.2.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/__init__.py

@@ -3,7 +3,7 @@ from .imread import imread
 from .imwrite import imwrite
 
 # Version of the dsa-helpers package
-__version__ = "1.1.2.dev0"
+__version__ = "1.1.3.dev1"
 
 # To avoid slow downs, do not allow from dsa_helpers import * to import anything.
 __all__ = []

{dsa_helpers-1.1.2.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/girder_utils.py

@@ -21,7 +21,7 @@ from pathlib import Path
 import cv2 as cv
 from copy import deepcopy
 import geopandas as gpd
-from shapely.geometry import Polygon
+from shapely.geometry import Polygon, box
 from .gpd_utils import remove_gdf_overlaps
 
 
@@ -687,7 +687,9 @@ def get_thumbnail_with_mask(
 
 
 def remove_overlapping_annotations(
-    annotation: dict, group_order: list[str]
+    annotation: dict,
+    group_order: list[str],
+    max_coords: tuple[int, int] | None = None,
 ) -> dict:
     """Remove overlapping regions from elements.
 
@@ -697,6 +699,11 @@ def remove_overlapping_annotations(
         earlier in the list will take precedence over those later when
         removing overlapping regions. Groups in the document that are
         not in the list will be kept as is.
+    max_coords (tuple[int, int], optional): The maximum coordinates in
+        the width and height dimension. If annotation element
+        coordinates are larger than this, they will be clipped to the
+        maximum coordinate. If None is passed then no clipping will be
+        performed. Defaults to None.
 
     Returns:
         dict: The modified annotation document.
@@ -772,6 +779,16 @@ def remove_overlapping_annotations(
     if len(elements_to_process):
         gdf = gpd.GeoDataFrame(elements_to_process)
 
+        if max_coords is not None:
+            # Create a bounding box polygon.
+            bbox = box(0, 0, max_coords[0], max_coords[1])
+
+            # Clip the polygons to the bounding box.
+            gdf = gdf.clip(bbox)
+
+            # This could have created multiple polygons, explode them.
+            gdf = gdf.explode(index_parts=False).reset_index(drop=True)
+
         # Map by the groups.
         group_map = {group: i for i, group in enumerate(group_order)}
 

{dsa_helpers-1.1.2.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/tiling.py

@@ -75,7 +75,7 @@ def _proccess_tile_with_masks_from_dsa_annotations(
         )
 
     # Create a blank tile mask.
-    tile_mask = np.zeros(tile_img.shape[:2], dtype=np.uint8)
+    tile_mask = np.zeros((tile_size, tile_size), dtype=np.uint8)
 
     # Loop through contours to draw on tile mask.
     for idx, contour_dict in contours.items():
@@ -106,6 +106,7 @@ def _proccess_tile_with_masks_from_dsa_annotations(
         tile_mask[label_mask == 1] = idx
 
     # Save the image and mask.
+
     imwrite(img_fp, tile_img)
     imwrite(mask_fp, tile_mask, grayscale=True)
 

{dsa_helpers-1.1.2.dev0 → dsa_helpers-1.1.3.dev1/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.2.dev0
+Version: 1.1.3.dev1
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-1.1.2.dev0 → dsa_helpers-1.1.3.dev1}/pyproject.toml

@@ -36,7 +36,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.1.2.dev0"
+version = "v1.1.3.dev1"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"