dsa-helpers 0.2__tar.gz → 0.3.dev0__tar.gz

{dsa_helpers-0.2/dsa_helpers.egg-info → dsa_helpers-0.3.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.2
+Version: 0.3.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>
@@ -14,6 +14,8 @@ License-File: LICENSE
 Requires-Dist: girder-client==3.2.3
 Requires-Dist: numpy==2.0.0
 Requires-Dist: setuptools==71.0.3
+Requires-Dist: opencv-python==4.10.0.84
+Requires-Dist: pandas==2.2.2
 
 # Digital Slide Archive (DSA) Helpers
 Digital Slide Archive Python utility library.

dsa_helpers-0.3.dev0/dsa_helpers/__init__.py

@@ -0,0 +1,7 @@
+# Shadow imports.
+from .login import login
+from .imread import imread
+from .imwrite import imwrite
+
+# Modules that should be available.
+from . import girder_utils, image_utils

{dsa_helpers-0.2 → dsa_helpers-0.3.dev0}/dsa_helpers/girder_utils.py

@@ -43,18 +43,14 @@ def get_thumbnail(
     Returns:
         np.ndarray: The thumbnail image.
 
-    Raises:
-        ValueError: If neither mag, width, nor height is provided.
-
     """
-    if all([mag is None, width is None, height is None]):
-        raise ValueError("Either mag, width, or height must be provided.")
+    get_url = f"item/{item_id}/tiles/"
 
     if mag is not None:
-        get_url = f"item/{item_id}/tiles/region?magnification{mag}"
+        get_url += f"region?magnification={mag}&encoding=pickle"
     else:
         # Instead use width and height.
-        get_url = f"item/{item_id}/tiles/thumbnail?"
+        params = ["encoding=pickle"]
 
         if width is not None and height is not None:
             if isinstance(fill, (tuple, list)):
@@ -63,13 +59,13 @@ def get_thumbnail(
                 elif len(fill) == 4:
                     fill = f"rgba({fill[0]},{fill[1]},{fill[2]},{fill[3]})"
 
-            get_url += f"width={width}&height={height}&fill={fill}"
+            params.extend([f"width={width}", f"height={height}", f"fill={fill}"])
         elif width is not None:
-            get_url += f"width={width}"
-        else:
-            get_url += f"height={height}"
+            params.append(f"width={width}")
+        elif height is not None:
+            params.append(f"height={height}")
 
-    get_url += "&encoding=pickle"
+        get_url += "thumbnail?" + "&".join(params)
 
     response = gc.get(get_url, jsonResp=False)
 

dsa_helpers-0.3.dev0/dsa_helpers/image_utils.py

@@ -0,0 +1,65 @@
+# Functions for working images.
+import numpy as np
+import pandas as pd
+from pathlib import Path
+import cv2 as cv
+from . import imwrite
+
+
+def tile_image(
+    img: np.ndarray,
+    save_loc: str,
+    tile_size: int,
+    stride: int | None = None,
+    fill: int | tuple = (255, 255, 255),
+    prepend_name: str = "",
+) -> pd.DataFrame:
+    """Tile an image into smaller images.
+
+    Args:
+        img (np.ndarray): The image to tile.
+        save_loc (str): The location to save the tiles.
+        tile_size (int): The size of the tiles.
+        stride (int | None, optional): The stride for the tiles. Defaults to None,
+            in which case it is set  equal to tile_size.
+        fill (int | tuple, optional): The fill value for tiles over the edges.
+            Defaults to (255, 255, 255).
+        prepend_name (str, optional): A string to prepend to the tile names.
+
+    Returns:
+        pandas.DataFrame: A DataFrame with the tile locations.
+
+    """
+    h, w = img.shape[:2]
+
+    img = cv.copyMakeBorder(
+        img, 0, tile_size, 0, tile_size, cv.BORDER_CONSTANT, value=fill
+    )
+
+    # Pad the image to avoid tiles not of the right size.
+    save_loc = Path(save_loc)
+
+    if not save_loc.exists():
+        save_loc.mkdir(parents=True)
+
+    if stride is None:
+        stride = tile_size
+
+    df_data = []
+
+    xys = [(x, y) for x in range(0, w, stride) for y in range(0, h, stride)]
+
+    for xy in xys:
+        x, y = xy
+        # Get the tile from the image.
+        tile_img = img[x : x + tile_size, y : y + tile_size]
+
+        save_fp = str(save_loc.joinpath(f"{prepend_name}x-{x}y-{y}.png"))
+
+        imwrite(save_fp, tile_img)
+
+        df_data.append([save_fp, x, y])
+
+    df = pd.DataFrame(df_data, columns=["fp", "x", "y"])
+
+    return df

dsa_helpers-0.3.dev0/dsa_helpers/imread.py

@@ -0,0 +1,32 @@
+# Function to read image from disk.
+import cv2 as cv
+import numpy as np
+
+
+def imread(fp: str, grayscale: bool = False) -> np.ndarray:
+    """Read image from disk. Currently does not support reading RGBA images.
+
+    Args:
+        fp (str): The file path to save the image.
+        grayscale (bool, optional): If True, the image will be read as grayscale.
+            Defaults to False.
+
+    Returns:
+        np.ndarray: The image read from disk.
+
+    """
+    if grayscale:
+        img = cv.imread(fp, cv.IMREAD_GRAYSCALE)
+    else:
+        img = cv.imread(fp, cv.IMREAD_UNCHANGED)
+
+        # Convert the image from OpenCV's BGR to RGB.
+        shape = img.shape
+
+        if len(shape) == 3:
+            if shape[2] == 3:
+                img = cv.cvtColor(img, cv.COLOR_BGR2RGB)
+            elif shape[2] == 4:
+                img = cv.cvtColor(img, cv.COLOR_RGBA2BGRA)
+
+    return img

dsa_helpers-0.3.dev0/dsa_helpers/imwrite.py

@@ -0,0 +1,37 @@
+# Function to save image to disk.
+import cv2 as cv
+import numpy as np
+
+
+def imwrite(fp: str, img: np.ndarray, grayscale: bool = False) -> None:
+    """Save an image to disk.
+
+    Args:
+        img (np.ndarray): The image to save.
+        fp (str): The file path to save the image.
+        grayscale (bool, optional): Whether to save the image as grayscale.
+            Defaults to False.
+
+    Raises:
+        ValueError: The image must be grayscale, RGB, or RGBA.
+
+    """
+    if grayscale:
+        if len(img.shape) == 2:
+            _ = cv.imwrite(fp, img)
+        else:
+            _ = cv.imwrite(fp, cv.cvtColor(img, cv.COLOR_RGB2GRAY))
+    else:
+        shape = img.shape
+
+        if len(shape) == 2:
+            _ = cv.imwrite(fp)
+        elif len(shape) == 3:
+            if shape[2] == 3:
+                _ = cv.imwrite(fp, cv.cvtColor(img, cv.COLOR_RGB2BGR))
+            elif shape[2] == 4:
+                _ = cv.imwrite(fp, cv.cvtColor(img, cv.COLOR_RGBA2BGRA))
+            else:
+                raise ValueError("The image must be grayscale, RGB, or RGBA.")
+        else:
+            raise ValueError("The image must be grayscale, RGB, or RGBA.")

{dsa_helpers-0.2 → dsa_helpers-0.3.dev0}/dsa_helpers/login.py

@@ -20,13 +20,7 @@ def login(
     Returns:
         girder_client.GirderClient: The authenticated girder client.
 
-    Raises:
-        ValueError: If neither login_or_email nor api_key is provided.
-
     """
-    if login_or_email is None and api_key is None:
-        raise ValueError("Either login_or_email or api_key must be provided.")
-
     gc = GirderClient(apiUrl=api_url)
 
     if api_key is None:

{dsa_helpers-0.2 → dsa_helpers-0.3.dev0/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.2
+Version: 0.3.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>
@@ -14,6 +14,8 @@ License-File: LICENSE
 Requires-Dist: girder-client==3.2.3
 Requires-Dist: numpy==2.0.0
 Requires-Dist: setuptools==71.0.3
+Requires-Dist: opencv-python==4.10.0.84
+Requires-Dist: pandas==2.2.2
 
 # Digital Slide Archive (DSA) Helpers
 Digital Slide Archive Python utility library.

{dsa_helpers-0.2 → dsa_helpers-0.3.dev0}/dsa_helpers.egg-info/SOURCES.txt

@@ -5,10 +5,12 @@ pyproject.toml
 requirements.txt
 dsa_helpers/__init__.py
 dsa_helpers/girder_utils.py
+dsa_helpers/image_utils.py
+dsa_helpers/imread.py
+dsa_helpers/imwrite.py
 dsa_helpers/login.py
 dsa_helpers.egg-info/PKG-INFO
 dsa_helpers.egg-info/SOURCES.txt
 dsa_helpers.egg-info/dependency_links.txt
 dsa_helpers.egg-info/requires.txt
-dsa_helpers.egg-info/top_level.txt
-tests/general-tests.py
+dsa_helpers.egg-info/top_level.txt

dsa_helpers-0.3.dev0/dsa_helpers.egg-info/requires.txt

@@ -0,0 +1,5 @@
+girder-client==3.2.3
+numpy==2.0.0
+setuptools==71.0.3
+opencv-python==4.10.0.84
+pandas==2.2.2

{dsa_helpers-0.2 → dsa_helpers-0.3.dev0}/pyproject.toml

@@ -6,7 +6,9 @@ build-backend = "setuptools.build_meta"
 dependencies = [
     'girder-client==3.2.3',
     'numpy==2.0.0',
-    'setuptools==71.0.3'
+    'setuptools==71.0.3',
+    'opencv-python==4.10.0.84',
+    'pandas==2.2.2'
 ]
 name = "dsa_helpers"
 authors = [
@@ -23,7 +25,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v0.2"
+version = "v0.3dev"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"

dsa_helpers-0.2/dsa_helpers.egg-info/requires.txt → dsa_helpers-0.3.dev0/requirements.txt

@@ -1,3 +1,5 @@
+setuptools==71.0.3
 girder-client==3.2.3
 numpy==2.0.0
-setuptools==71.0.3
+opencv-python==4.10.0.84
+pandas==2.2.2

dsa_helpers-0.2/dsa_helpers/__init__.py

@@ -1,5 +0,0 @@
-# Shadow imports.
-from .login import login
-
-# Modules that should be available.
-from . import girder_utils

dsa_helpers-0.2/requirements.txt

@@ -1,3 +0,0 @@
-setuptools==71.0.3
-girder-client==3.2.3
-numpy==2.0.0

dsa_helpers-0.2/tests/general-tests.py

@@ -1,11 +0,0 @@
-# Run various tests on the dash_utils module.
-import dsa_utils as du
-
-
-def main():
-    # Use this script to test out various development functions.
-    pass
-
-
-if __name__ == "__main__":
-    main()