dsa-helpers 1.0.2.dev0__tar.gz → 1.0.3__tar.gz

{dsa_helpers-1.0.2.dev0/dsa_helpers.egg-info → dsa_helpers-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dsa_helpers
-Version: 1.0.2.dev0
+Version: 1.0.3
 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>
@@ -39,15 +39,4 @@ This Python PyPI package is found [here](https://pypi.org/project/dsa-helpers/).
 ## Extra dependencies
 If you are getting a large image error, then install large image using the instructions provided in their [GitHub page](https://github.com/girder/large_image#:~:text=pip%20install%20large%2Dimage%5Ball%5D%20%2D%2Dfind%2Dlinks%20https%3A//girder.github.io/large_image_wheels).
 
-## Instructions for Development
-1. Install requirements for building and distributing package:
-```
-$ python3 -m pip install --upgrade build  # for building package
-$ python3 -m pip install --upgrade twine  # for uploading to PyPI
-```
-2. When ready to build:
-    - Modify "pyproject.toml" file, change the "version" key to a different value than a version already pushed.
-    - Run ```$ python3 -m build```. This will create a dist directory and put your new wheel and tar distribution files there.
-3. To install locally for development: ```$ pip3 install dist/dsa_helpers-*.whl```, choosing the wheel version you want to test.
-4. Upload to PyPI using twine: ```python3 -m twine upload --repository pypi dist/*```
-    * You can specify specific files to upload, the line above pushes everything in dist directory.
+A readthedocs for this library can be found [here](https://david-andrew-gutman-dsa-helpers.readthedocs-hosted.com/en/latest/index.html).

dsa_helpers-1.0.3/README.md

@@ -0,0 +1,13 @@
+# Digital Slide Archive (DSA) Helpers
+Digital Slide Archive Python utility library.
+
+This library is available for installation through [Python Package Index (PyPI)](https://pypi.org/).
+
+This library was tested using Python version 3.11.8 and uses the dependencies described in requirements.txt.
+
+This Python PyPI package is found [here](https://pypi.org/project/dsa-helpers/).
+
+## Extra dependencies
+If you are getting a large image error, then install large image using the instructions provided in their [GitHub page](https://github.com/girder/large_image#:~:text=pip%20install%20large%2Dimage%5Ball%5D%20%2D%2Dfind%2Dlinks%20https%3A//girder.github.io/large_image_wheels).
+
+A readthedocs for this library can be found [here](https://david-andrew-gutman-dsa-helpers.readthedocs-hosted.com/en/latest/index.html).

dsa_helpers-1.0.3/dsa_helpers/__init__.py

@@ -0,0 +1,6 @@
+# Shadow imports.
+from .imread import imread
+from .imwrite import imwrite
+
+# To avoid slow downs, do not allow from dsa_helpers import * to import anything.
+__all__ = []

dsa_helpers-1.0.3/dsa_helpers/dash/__init__.py

@@ -0,0 +1,3 @@
+from . import header
+
+__all__ = []

dsa_helpers-1.0.3/dsa_helpers/ml/__init__.py

@@ -0,0 +1,2 @@
+# Modules that are imported from * notation.
+__all__ = []

{dsa_helpers-1.0.2.dev0 → dsa_helpers-1.0.3}/dsa_helpers/ml/datasets/__init__.py

@@ -1,3 +1,4 @@
+# Shadow import.
 from .SegFormerSegmentationDataset import SegFormerSegmentationDataset
 
-__all__ = ["utils"]
+__all__ = []

{dsa_helpers-1.0.2.dev0 → dsa_helpers-1.0.3}/dsa_helpers/ml/object_detection/__init__.py

@@ -2,4 +2,4 @@
 from .get_pearce_roi_images import get_pearce_roi_images
 from .tile_image import tile_image
 
-__all__ = ["utils"]
+__all__ = []

dsa_helpers-1.0.3/dsa_helpers/ml/transforms/__init__.py

@@ -0,0 +1 @@
+__all__ = []

{dsa_helpers-1.0.2.dev0 → dsa_helpers-1.0.3}/dsa_helpers/tiling.py

@@ -11,7 +11,7 @@ import numpy as np
 from pathlib import Path
 from multiprocessing import Pool
 from tqdm import tqdm
-from . import imwrite
+from . import imwrite, imread
 import pandas as pd
 
 
@@ -338,3 +338,99 @@ def tile_image(
         df_data.append([save_fp, x, y, tile_size])
 
     return pd.DataFrame(df_data, columns=["fp", "x", "y", "tile_size"])
+
+
+def tile_image_with_mask(
+    img: np.ndarray | str,
+    mask: np.ndarray | str,
+    save_dir: str,
+    tile_size: int,
+    stride: int | None = None,
+    fill: tuple[int, int, int] = (255, 255, 255),
+    mask_pad_value: int = 0,
+    prepend_name: str = "",
+) -> pd.DataFrame:
+    """Tile an image and its corresponding mask.
+
+    Args:
+        img (np.ndarray): The image or filepath to tile.
+        mask (np.ndarray): The mask or filepath to mask.
+        save_dir (str): The directory to save the tiles. Images are
+            saved in a "images" subdirectory and masks in a "masks"
+            subdirectory.
+        tile_size (int): The size of the tiles.
+        stride (int, optional): The stride of the tiles. Defaults to
+            None which sets the stride to the tile size
+            (no overlap between tiles).
+        fill (tuple[int, int, int], optional): The fill value for the
+            tiles that go over the edge of image. Defaults to (255,
+            255, 255).
+        mask_pad_value (int, optional): The value to pad the mask with.
+            Defaults to 0.
+        prepend_name (str, optional): A string to prepend to the tile
+            filenames. Default to "". Naming of tiles is:
+            {prepend_name}x{x}y{y}.png.
+
+    Returns:
+        pandas.DataFrame: A pandas dataframe containing the filepath of
+            the image and mask and x, y coordinate.
+
+    """
+    if isinstance(img, str):
+        img = imread(img)
+
+    if isinstance(mask, str):
+        mask = imread(mask, grayscale=True)
+
+    h, w = img.shape[:2]
+
+    # Pad the mask to avoid tiles going over the image boundary.
+    mask = cv.copyMakeBorder(
+        mask.copy(),
+        0,
+        h + tile_size,
+        0,
+        w + tile_size,
+        cv.BORDER_CONSTANT,
+        value=mask_pad_value,
+    )
+
+    # Same for the image.
+    img = cv.copyMakeBorder(
+        img.copy(),
+        0,
+        h + tile_size,
+        0,
+        w + tile_size,
+        cv.BORDER_CONSTANT,
+        value=fill,
+    )
+
+    # Make subdirectories to save images to.
+    img_dir = Path(save_dir).joinpath("images")
+    mask_dir = Path(save_dir).joinpath("masks")
+    img_dir.mkdir(parents=True, exist_ok=True)
+    mask_dir.mkdir(exist_ok=True)
+
+    if stride is None:
+        stride = tile_size
+
+    xys = [(x, y) for x in range(0, w, stride) for y in range(0, h, stride)]
+
+    tile_data = []
+
+    for xy in xys:
+        x, y = xy
+
+        tile_img = img[y : y + tile_size, x : x + tile_size]
+        tile_img_fp = img_dir / f"{prepend_name}x{x}y{y}.png"
+
+        tile_mask = mask[y : y + tile_size, x : x + tile_size]
+        tile_mask_fp = mask_dir / f"{prepend_name}x{x}y{y}.png"
+
+        imwrite(tile_img_fp, tile_img)
+        imwrite(tile_mask_fp, tile_mask, grayscale=True)
+
+        tile_data.append([str(tile_img_fp), str(tile_mask_fp), x, y])
+
+    return pd.DataFrame(tile_data, columns=["fp", "mask_fp", "x", "y"])

{dsa_helpers-1.0.2.dev0 → dsa_helpers-1.0.3/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: dsa_helpers
-Version: 1.0.2.dev0
+Version: 1.0.3
 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>
@@ -39,15 +39,4 @@ This Python PyPI package is found [here](https://pypi.org/project/dsa-helpers/).
 ## Extra dependencies
 If you are getting a large image error, then install large image using the instructions provided in their [GitHub page](https://github.com/girder/large_image#:~:text=pip%20install%20large%2Dimage%5Ball%5D%20%2D%2Dfind%2Dlinks%20https%3A//girder.github.io/large_image_wheels).
 
-## Instructions for Development
-1. Install requirements for building and distributing package:
-```
-$ python3 -m pip install --upgrade build  # for building package
-$ python3 -m pip install --upgrade twine  # for uploading to PyPI
-```
-2. When ready to build:
-    - Modify "pyproject.toml" file, change the "version" key to a different value than a version already pushed.
-    - Run ```$ python3 -m build```. This will create a dist directory and put your new wheel and tar distribution files there.
-3. To install locally for development: ```$ pip3 install dist/dsa_helpers-*.whl```, choosing the wheel version you want to test.
-4. Upload to PyPI using twine: ```python3 -m twine upload --repository pypi dist/*```
-    * You can specify specific files to upload, the line above pushes everything in dist directory.
+A readthedocs for this library can be found [here](https://david-andrew-gutman-dsa-helpers.readthedocs-hosted.com/en/latest/index.html).

{dsa_helpers-1.0.2.dev0 → dsa_helpers-1.0.3}/pyproject.toml

@@ -35,7 +35,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.0.2dev0"
+version = "v1.0.3"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"

dsa_helpers-1.0.2.dev0/README.md

@@ -1,24 +0,0 @@
-# Digital Slide Archive (DSA) Helpers
-Digital Slide Archive Python utility library.
-
-This library is available for installation through [Python Package Index (PyPI)](https://pypi.org/).
-
-This library was tested using Python version 3.11.8 and uses the dependencies described in requirements.txt.
-
-This Python PyPI package is found [here](https://pypi.org/project/dsa-helpers/).
-
-## Extra dependencies
-If you are getting a large image error, then install large image using the instructions provided in their [GitHub page](https://github.com/girder/large_image#:~:text=pip%20install%20large%2Dimage%5Ball%5D%20%2D%2Dfind%2Dlinks%20https%3A//girder.github.io/large_image_wheels).
-
-## Instructions for Development
-1. Install requirements for building and distributing package:
-```
-$ python3 -m pip install --upgrade build  # for building package
-$ python3 -m pip install --upgrade twine  # for uploading to PyPI
-```
-2. When ready to build:
-    - Modify "pyproject.toml" file, change the "version" key to a different value than a version already pushed.
-    - Run ```$ python3 -m build```. This will create a dist directory and put your new wheel and tar distribution files there.
-3. To install locally for development: ```$ pip3 install dist/dsa_helpers-*.whl```, choosing the wheel version you want to test.
-4. Upload to PyPI using twine: ```python3 -m twine upload --repository pypi dist/*```
-    * You can specify specific files to upload, the line above pushes everything in dist directory.

dsa_helpers-1.0.2.dev0/dsa_helpers/__init__.py

@@ -1,23 +0,0 @@
-# Shadow imports.
-from .imread import imread
-from .imwrite import imwrite
-
-# Make modules available.
-from . import girder_utils
-from . import dash
-from . import ml
-from . import mongo_utils
-from . import tiling
-from . import utils
-from . import tile_utils
-
-# Modules that should be available.
-__all__ = [
-    "girder_utils",
-    "dash",
-    "ml",
-    "mongo_utils",
-    "tiling",
-    "utils",
-    "tile_utils",
-]

dsa_helpers-1.0.2.dev0/dsa_helpers/dash/__init__.py

@@ -1,3 +0,0 @@
-from . import header
-
-__all__ = ["dash_paperdragon_utils", "header_callbacks", "header"]

dsa_helpers-1.0.2.dev0/dsa_helpers/ml/__init__.py

@@ -1,20 +0,0 @@
-# Allow modules to be imported.
-from . import (
-    object_detection,
-    datasets,
-    transforms,
-    segformer_semantic_segmentation,
-    callbacks,
-    evaluate,
-)
-
-# Modules that are imported from * notation.
-__all__ = [
-    "object_detection",
-    "datasets",
-    "metrics",
-    "transforms",
-    "segformer_semantic_segmentation",
-    "callbacks",
-    "evaluate",
-]

dsa_helpers-1.0.2.dev0/dsa_helpers/ml/transforms/__init__.py

@@ -1 +0,0 @@
-__all__ = ["segformer_transforms"]