dsa-helpers 1.1.1.dev0__tar.gz → 1.1.2.dev0__tar.gz

{dsa_helpers-1.1.1.dev0/dsa_helpers.egg-info → dsa_helpers-1.1.2.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.1.dev0
+Version: 1.1.2.dev0
 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/dev.py

@@ -0,0 +1,41 @@
+"""Script to develop functions for the library."""
+
+from argparse import ArgumentParser
+from dsa_helpers.girder_utils import (
+    login,
+    post_annotation,
+    remove_overlapping_annotations,
+)
+
+
+def parse_args():
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--api-token", type=str, default=None, help="Girder API token"
+    )
+    parser.add_argument(
+        "--api-url", type=str, default=None, help="Girder API URL"
+    )
+    return parser.parse_args()
+
+
+def main(args):
+    gc = login(args.api_url, api_key=args.api_token)
+
+    # Get an annotation document.
+    doc = gc.get("annotation/...")
+
+    annotation = remove_overlapping_annotations(
+        doc["annotation"], ["Gray Matter", "White Matter", "Leptomeninges"]
+    )
+
+    # Push the new doc.
+    annotation["name"] = "temp"
+
+    response = post_annotation(gc, "...", annotation)
+
+    print(response)
+
+
+if __name__ == "__main__":
+    main(parse_args())

{dsa_helpers-1.1.1.dev0 → dsa_helpers-1.1.2.dev0}/dsa_helpers/__init__.py

@@ -3,7 +3,7 @@ from .imread import imread
 from .imwrite import imwrite
 
 # Version of the dsa-helpers package
-__version__ = "1.1.1.dev0"
+__version__ = "1.1.2.dev0"
 
 # To avoid slow downs, do not allow from dsa_helpers import * to import anything.
 __all__ = []

{dsa_helpers-1.1.1.dev0 → dsa_helpers-1.1.2.dev0}/dsa_helpers/girder_utils.py

@@ -1,6 +1,16 @@
 """Module for working with the girder client, or related to girder
 documents, such as annotation documents.
 
+Functions:
+- login: Authenticate a girder client with the given credentials or interactively
+- get_item_large_image_metadata: Get large image metadata for an item
+- get_thumbnail: Get the thumbnail image by a specific magnification or shape
+- get_region: Get image region from DSA
+- get_element_contours: Get the contours of an element, regardless of the type
+- get_roi_images: Get regions of interest (ROIs) as images from DSA annotations
+- post_annotation: Post a new annotation to the DSA
+- remove_overlapping_annotations: Remove overlapping regions from elements
+
 """
 
 from girder_client import GirderClient, HttpError

{dsa_helpers-1.1.1.dev0 → dsa_helpers-1.1.2.dev0}/dsa_helpers/image_utils.py

@@ -100,3 +100,31 @@ def label_mask_to_polygons(
                     polygons.append([polygon, int(label)])
 
     return polygons
+
+
+def convert_label_mask_to_rgb(
+    mask: np.ndarray, int2rgb: dict, alpha: bool = False
+) -> np.ndarray:
+    """
+    Convert a label mask to an RGB mask.
+
+    Args:
+        mask: Label mask to convert.
+        int2rgb: Dictionary mapping integer labels to RGB colors. If
+            passing alpha as True, then pass RGBA colors.
+        alpha: Whether to include the alpha channel in the RGB mask.
+
+    Returns:
+        (np.ndarray): RGB(A) mask.
+
+    """
+    # Create a new RGB mask of the same size as the label mask.
+    rgb_mask = np.zeros(
+        (mask.shape[0], mask.shape[1], 4 if alpha else 3), dtype=np.uint8
+    )
+
+    # Loop through the label mask.
+    for label, rgb in int2rgb.items():
+        rgb_mask[mask == label] = rgb
+
+    return rgb_mask

{dsa_helpers-1.1.1.dev0 → dsa_helpers-1.1.2.dev0}/dsa_helpers/tiling.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """Functions for tiling images.
 
-This module contains functions used to tile large images, usually for 
+This module contains functions used to tile large images, usually for
 use in developing deep learning models.
 
 """
@@ -29,12 +29,20 @@ def _proccess_tile_with_masks_from_dsa_annotations(
     mask_dir,
     background_idx,
     edge_thr,
+    ignore_existing,
 ):
     # Calculate the x and y in tile magnification.
     x_mag = int(x * sf)
     y_mag = int(y * sf)
 
+    # Format the filepath to save the tile.
     fn = f"{prepend_name}x{x_mag}y{y_mag}.png"
+    img_fp = img_dir / fn
+    mask_fp = mask_dir / fn
+
+    # Ignore existing tiles.
+    if ignore_existing and img_fp.is_file() and mask_fp.is_file():
+        return str(img_fp), x_mag, y_mag
 
     # Get the tile.
     tile_img = ts.getRegion(
@@ -98,9 +106,8 @@ def _proccess_tile_with_masks_from_dsa_annotations(
         tile_mask[label_mask == 1] = idx
 
     # Save the image and mask.
-    img_fp = img_dir / fn
     imwrite(img_fp, tile_img)
-    imwrite(mask_dir / fn, tile_mask, grayscale=True)
+    imwrite(mask_fp, tile_mask, grayscale=True)
 
     return str(img_fp), x_mag, y_mag
 
@@ -117,6 +124,7 @@ def tile_wsi_with_masks_from_dsa_annotations(
     nproc: int = 1,
     background_idx: int = 0,
     edge_thr: float = 0.25,
+    ignore_existing: bool = False,
 ) -> list[str]:
     """Tile a WSI with semantic segmentation label masks created from
     DSA annotations. DSA annotation class labels for elements are
@@ -146,6 +154,9 @@ def tile_wsi_with_masks_from_dsa_annotations(
             the tile is padded background then it is ignored. If the
             amount of tile in WSI / amount of tile padded is less than
             this threshold, the tile is ignored. Defaults to 0.25.
+        ignore_existing (bool, optional): Whether to ignore existing
+            tiles. If False, tiles will not be created if they already
+            exist. Defaults to False.
 
     Returns:
         list[str]: A list of tuples: (tile file path, x, y coordinates
@@ -256,6 +267,7 @@ def tile_wsi_with_masks_from_dsa_annotations(
                     mask_dir,
                     background_idx,
                     edge_thr,
+                    ignore_existing,
                 ),
             )
             for xy in xys

{dsa_helpers-1.1.1.dev0 → dsa_helpers-1.1.2.dev0/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.1.dev0
+Version: 1.1.2.dev0
 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-1.1.1.dev0 → dsa_helpers-1.1.2.dev0}/dsa_helpers.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@
 LICENSE
 README.md
 app.py
+dev.py
 pyproject.toml
 docs/requirements.txt
 docs/source/conf.py

{dsa_helpers-1.1.1.dev0 → dsa_helpers-1.1.2.dev0}/pyproject.toml

@@ -36,7 +36,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.1.1.dev0"
+version = "v1.1.2.dev0"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"