dsa-helpers 0.9__tar.gz → 0.9.dev1__tar.gz

{dsa_helpers-0.9/dsa_helpers.egg-info → dsa_helpers-0.9.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.9
+Version: 0.9.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-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/__init__.py

@@ -16,6 +16,8 @@ __all__ = [
     "girder_utils",
     "dash",
     "ml",
+    "imread",
+    "imwrite",
     "mongo_utils",
     "tiling",
     "utils",

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/dash/header.py

@@ -15,8 +15,13 @@ def get_header(
     Args:
         dsa_api_url (str): The URL of the DSA API.
         title (str, optional): The title of the application. Defaults to "App".
-        config (dict, optional): The configuration of the component.
-            Defaults to None which uses default settings.
+        config (dict, optional): The configuration of the component. Defaults to None.
+            If None the default configuration is:
+            {
+                "backgroundColor": "#012169",
+                "titleColor": "#d9d9d6",
+                "fontColor": "#f2a900",
+            }
 
     Returns:
         html.Div: The header component.
@@ -33,8 +38,7 @@ def get_header(
             dbc.ModalBody(
                 [
                     html.Div(
-                        "Login or email",
-                        style={"margin": 5, "fontWeight": "bold"},
+                        "Login or email", style={"margin": 5, "fontWeight": "bold"}
                     ),
                     dbc.Input(
                         id=f"{store_id}=login",
@@ -44,11 +48,7 @@ def get_header(
                     ),
                     html.Div(
                         "Password",
-                        style={
-                            "margin": 5,
-                            "marginTop": 15,
-                            "fontWeight": "bold",
-                        },
+                        style={"margin": 5, "marginTop": 15, "fontWeight": "bold"},
                     ),
                     dbc.Input(
                         id=f"{store_id}=password",
@@ -60,11 +60,7 @@ def get_header(
                         "Login failed.",
                         hidden=True,
                         id=f"{store_id}=login-failed",
-                        style={
-                            "color": "red",
-                            "fontWeight": "bold",
-                            "margin": 10,
-                        },
+                        style={"color": "red", "fontWeight": "bold", "margin": 10},
                     ),
                 ],
             ),

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/girder_utils.py

@@ -88,19 +88,19 @@ def get_region(
     height: int,
     mag: float | None = None,
 ) -> np.ndarray:
-    """Get image region from DSA. Note that the output image might not
-    be in the shape (width, height) if left + width or top + height
-    exceeds the image size.
-
-    Args:
-        gc (girder_client.GirderClient): The authenticated girder client.
-        item_id (str): The item id.
+    """Get a region of the image for an item. Note that the output image might
+    not be in the shape (width, height) if left + width or top + height exceeds
+    the image size. The outpuzerositem id.
         left (int): The left coordinate.
         top (int): The top coordinate.
         width (int): The width of the region.
         height (int): The height of the region.
-        mag (float, optional): The magnification. Defaults to None which
-            returns the image at the scan magnification.
+        mag (float, optional): The magnification. Defaults to None which returns
+            the image at scan magnification. Using a mag lower than the scan
+            magnification will result in an ouptut image smaller than the
+            width and height. Similarly, using a mag higher than the scan
+            magnification will result in an output image larger than the width
+            and height.
 
     Returns:
         np.ndarray: The region of the image.
@@ -258,16 +258,17 @@ def _rotate_point_list(point_list, rotation, center=(0, 0)):
     return point_list_rotated
 
 
-def get_rectangle_element_coords(element: dict) -> np.ndarray:
+def get_rectangle_element_coords(element):
     """Get the corner coordinate from a rectangle HistomicsUI element, can handle rotated elements.
     Adapted from: https://github.com/DigitalSlideArchive/HistomicsTK/blob/master/histomicstk/annotations_and_masks/annotation_and_mask_utils.py
-
-    Args:
-        element (dict): rectangle element from HistomicsUI annotation.
-
-    Returns:
-    corner_coords (np.ndarray): 4x2 array of corner coordinates of rectangle.
-
+    INPUTS
+    ------
+    element : dict
+        rectangle element, in HistomicsUI format
+    RETURN
+    ------
+    corner_coords : array
+        array of shape [4, 2] for the four corners of the rectangle in (x, y) format
     """
     # element is a dict so prevent referencing
     element = deepcopy(element)
@@ -400,9 +401,7 @@ def get_roi_with_yolo_labels_from_single_doc(
         if element.get("group") == roi_element_group:
             # Append the ROI element, there can't more than one.
             if roi_element is not None:
-                raise ValueError(
-                    "Multiple ROI elements found in the document."
-                )
+                raise ValueError("Multiple ROI elements found in the document.")
 
             roi_element = element
         elif element.get("group") in group_map:
@@ -461,9 +460,7 @@ def get_roi_with_yolo_labels_from_single_doc(
     for element in box_elements:
         if element.get("group") in group_map:
             if element.get("type") != "rectangle":
-                print(
-                    f"Skipping element: {element.get('type')} not supported."
-                )
+                print(f"Skipping element: {element.get('type')} not supported.")
                 continue
 
             group_id = group_map[element.get("group")]
@@ -526,9 +523,7 @@ def post_annotations_from_gdf(
     # Process the dataframe.
     for _, row in gdf.iterrows():
         # Flatten multipolygon to list of polygons.
-        list_of_polygons = list(
-            row["geometry"].geoms
-        )  # assuming multipolygons
+        list_of_polygons = list(row["geometry"].geoms)  # assuming multipolygons
         label = row["label"]
 
         for poly in list_of_polygons:

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/ml/datasets/__init__.py

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

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/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__ = ["utils", "get_pearce_roi_images", "tile_image"]

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/ml/segformer_semantic_segmentation/__init__.py

@@ -1,3 +1,3 @@
 from .inference import inference
 
-__all__ = []
+__all__ = ["inference"]

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/ml/segformer_semantic_segmentation/inference.py

@@ -10,7 +10,7 @@ import torch
 import torch.nn as nn
 
 from ... import imread
-from ...tiling import tile_image
+from ...image_utils import tile_image
 
 
 def inference(
@@ -115,9 +115,7 @@ def inference(
     predicted_mask = predicted_mask[:h, :w]
 
     # Extract the contours of the mask.
-    contours = cv.findContours(
-        predicted_mask, cv.RETR_TREE, cv.CHAIN_APPROX_SIMPLE
-    )[0]
+    contours = cv.findContours(predicted_mask, cv.RETR_TREE, cv.CHAIN_APPROX_SIMPLE)[0]
 
     # Return the mask.
     return predicted_mask, contours

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers/ml/tiling/__init__.py

@@ -2,4 +2,4 @@ from .semantic_seg_tile_wsi_with_dsa_annotations import (
     semantic_seg_tile_wsi_with_dsa_annotations,
 )
 
-__all__ = []
+__all__ = ["semantic_seg_tile_wsi_with_dsa_annotations"]

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.9
+Version: 0.9.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-0.9 → dsa_helpers-0.9.dev1}/dsa_helpers.egg-info/SOURCES.txt

@@ -1,12 +1,8 @@
 .gitignore
-.readthedocs.yaml
 LICENSE
 README.md
 app.py
 pyproject.toml
-docs/requirements.txt
-docs/source/conf.py
-docs/source/index.rst
 dsa_helpers/__init__.py
 dsa_helpers/girder_utils.py
 dsa_helpers/imread.py

{dsa_helpers-0.9 → dsa_helpers-0.9.dev1}/pyproject.toml

@@ -35,7 +35,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v0.9"
+version = "v0.9dev1"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"

dsa_helpers-0.9/.readthedocs.yaml

@@ -1,16 +0,0 @@
-version: 2
-
-build:
-  os: "ubuntu-24.04"
-  tools:
-    python: "3.12"
-  jobs:
-    pre_build:
-      - sphinx-apidoc -o docs/source dsa_helpers/
-
-python:
-  install:
-    - requirements: docs/requirements.txt
-
-sphinx:
-  configuration: docs/source/conf.py

dsa_helpers-0.9/docs/requirements.txt

@@ -1,16 +0,0 @@
-girder-client
-numpy
-setuptools
-opencv-python
-pandas
-pymongo
-pillow
-dash
-dash-bootstrap-components
-shapely
-geopandas
-transformers[torch]
-datasets
-torchvision
-large-image
-sphinx_rtd_theme

dsa_helpers-0.9/docs/source/conf.py

@@ -1,42 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath("../.."))
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-
-project = "DSA Helpers"
-copyright = "2024, Juan Carlos Vizcarra"
-author = "Juan Carlos Vizcarra"
-release = "00.00.01"
-
-# -- General configuration ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
-
-extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.napoleon",
-]
-
-templates_path = ["_templates"]
-exclude_patterns = []
-
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = "sphinx_rtd_theme"
-html_static_path = ["_static"]

dsa_helpers-0.9/docs/source/index.rst

@@ -1,18 +0,0 @@
-.. DSA Helpers documentation master file, created by
-   sphinx-quickstart on Fri Dec  6 12:07:31 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-DSA Helpers documentation
-=========================
-
-Add your content using ``reStructuredText`` syntax. See the
-`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
-documentation for details.
-
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-   modules