dsa-helpers 0.3.dev0__py3-none-any.whl → 0.3.dev1__py3-none-any.whl

dsa_helpers/__init__.py

@@ -4,4 +4,4 @@ from .imread import imread
 from .imwrite import imwrite
 
 # Modules that should be available.
-from . import girder_utils, image_utils
+from . import girder_utils, image_utils, dash

dsa_helpers/dash/__init__.py

@@ -0,0 +1 @@
+from . import header

dsa_helpers/dash/header.py

@@ -0,0 +1,141 @@
+from dash import html, dcc
+import dash_bootstrap_components as dbc
+from . import header_callbacks
+
+
+def get_header(title: str = "App", config: dict | None = None) -> html.Div:
+    """Get the Dash html component that contains the header of the application
+    with login capabilities.
+
+    Args:
+        title (str): The title of the application.
+        config (dict): The configuration of the component.
+
+            backgroundColor
+            titleColor
+            fontColor
+
+    Returns:
+        html.Div: The header component.
+
+    """
+    login_modal = dbc.Modal(
+        [
+            dbc.ModalHeader("Log in"),
+            dbc.ModalBody(
+                [
+                    html.Div(
+                        "Login or email", style={"margin": 5, "fontWeight": "bold"}
+                    ),
+                    dbc.Input(
+                        id="login",
+                        type="text",
+                        placeholder="Enter login",
+                        style={"margin": 5},
+                    ),
+                    html.Div(
+                        "Password",
+                        style={"margin": 5, "marginTop": 15, "fontWeight": "bold"},
+                    ),
+                    dbc.Input(
+                        id="password",
+                        type="password",
+                        placeholder="Enter password",
+                        style={"margin": 5},
+                    ),
+                    html.Div(
+                        "Login failed.",
+                        hidden=True,
+                        id="login-failed",
+                        style={"color": "red", "fontWeight": "bold", "margin": 10},
+                    ),
+                ],
+            ),
+            dbc.ModalFooter(
+                dbc.Row(
+                    [
+                        dbc.Col(
+                            dbc.Button(
+                                "Close",
+                                id="close-login-modal",
+                                className="me-1",
+                                color="light",
+                            )
+                        ),
+                        dbc.Col(
+                            dbc.Button(
+                                "Login",
+                                id="log-in-btn",
+                                className="me-1",
+                                color="primary",
+                            )
+                        ),
+                    ],
+                )
+            ),
+        ],
+        is_open=False,
+        id="login-modal",
+    )
+
+    logout_modal = dbc.Modal(
+        [
+            dbc.ModalFooter(
+                [
+                    dbc.Button(
+                        "Log out",
+                        id="logout-btn",
+                        color="danger",
+                        className="me-1",
+                    ),
+                ]
+            )
+        ],
+        is_open=False,
+        id="logout-modal",
+    )
+
+    if config is None:
+        config = {}
+
+    return html.Div(
+        [
+            dbc.Row(
+                [
+                    dbc.Col(
+                        html.H1(
+                            title,
+                            style={
+                                "fontWeight": "bold",
+                                "color": config.get("titleColor", "#d9d9d6"),
+                                "marginLeft": 5,
+                            },
+                        ),
+                        width="auto",
+                    ),
+                    dbc.Col(
+                        dbc.Button(
+                            "Log in",
+                            id="login-btn",
+                            color=config.get("backgroundColor", "#012169"),
+                            style={
+                                "color": config.get("fontColor", "#f2a900"),
+                                "fontSize": "1.2rem",
+                            },
+                            className="me-1",
+                        ),
+                        width="auto",
+                    ),
+                ],
+                justify="between",
+                align="center",
+            ),
+            login_modal,
+            logout_modal,
+            dcc.Store(id="user-store", storage_type="local", data={}),
+        ],
+        style={
+            "backgroundColor": config.get("backgroundColor", "#012169"),
+            "padding": 5,
+        },
+    )

dsa_helpers/dash/header_callbacks.py

@@ -0,0 +1,98 @@
+# Callbacks for the header component.
+from dash import callback, Output, Input, State, no_update
+from girder_client import GirderClient
+from os import getenv
+
+
+@callback(Output("login-btn", "children"), Input("user-store", "data"))
+def check_user_store(data):
+    # Check if the user store has user info or if no one is logged in.
+    return data["user"] if len(data) else "Log in"
+
+
+@callback(
+    [
+        Output("login-modal", "is_open", allow_duplicate=True),
+        Output("logout-modal", "is_open", allow_duplicate=True),
+    ],
+    [Input("login-btn", "n_clicks"), State("login-btn", "children")],
+    prevent_initial_call=True,
+)
+def open_login_modal(n_clicks, children):
+    # Open login / logout modal.
+    if n_clicks:
+        if children == "Log in":
+            return True, False
+        else:
+            return False, True
+
+    return False, False
+
+
+@callback(
+    [
+        Output("user-store", "data"),
+        Output("login-failed", "hidden", allow_duplicate=True),
+        Output("login-modal", "is_open", allow_duplicate=True),
+        Output("login", "value", allow_duplicate=True),
+        Output("password", "value", allow_duplicate=True),
+    ],
+    [
+        Input("log-in-btn", "n_clicks"),
+        State("login", "value"),
+        State("password", "value"),
+    ],
+    prevent_initial_call=True,
+)
+def login(n_clicks, login, password):
+    # Try to login.
+    gc = GirderClient(apiUrl=getenv("DSA_API_URL"))
+
+    try:
+        _ = gc.authenticate(username=login, password=password)
+
+        response = gc.get("token/session")
+
+        user = gc.get("user/me")["login"]
+
+        return {"user": user, "token": response["token"]}, True, False, "", ""
+    except:
+        return (
+            {},
+            False,
+            True,
+            no_update,
+            no_update,
+        )
+
+
+@callback(
+    [
+        Output("login-modal", "is_open", allow_duplicate=True),
+        Output("login", "value", allow_duplicate=True),
+        Output("password", "value", allow_duplicate=True),
+        Output("login-failed", "hidden", allow_duplicate=True),
+    ],
+    Input("close-login-modal", "n_clicks"),
+    prevent_initial_call=True,
+)
+def close_login_modal(n_clicks):
+    if n_clicks:
+        return False, "", "", True
+
+    return False, "", "", True
+
+
+@callback(
+    [
+        Output("user-store", "data", allow_duplicate=True),
+        Output("logout-modal", "is_open", allow_duplicate=True),
+    ],
+    Input("logout-btn", "n_clicks"),
+    prevent_initial_call=True,
+)
+def logout(n_clicks):
+    if n_clicks:
+        return {}, False
+
+    return no_update, False

dsa_helpers/girder_utils.py

@@ -2,6 +2,10 @@
 from girder_client import GirderClient
 import pickle
 import numpy as np
+import pandas as pd
+from pathlib import Path
+import cv2 as cv
+from copy import deepcopy
 
 
 def get_item_large_image_metadata(gc: GirderClient, item_id: str) -> dict:
@@ -83,11 +87,7 @@ def get_region(
 ) -> np.ndarray:
     """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 output image will be the maximum size possible.
-
-    Args:
-        gc (girder_client.GirderClient): The authenticated girder client.
-        item_id (str): The item id.
+    the image size. The outpuzerositem id.
         left (int): The left coordinate.
         top (int): The top coordinate.
         width (int): The width of the region.
@@ -114,3 +114,174 @@ def get_region(
     response = gc.get(get_url, jsonResp=False)
 
     return pickle.loads(response.content)
+
+
+def get_element_contours(element: dict) -> np.ndarray:
+    """Get the contours of an element, regardless of the type.
+
+    Args:
+        element (dict): The element dictionary.
+
+    Returns:
+        np.ndarray: The contours of the element.
+
+    """
+    if element["type"] == "rectangle":
+        return get_rectangle_element_coords(element)
+    else:
+        return None
+
+
+def get_roi_images(
+    gc: GirderClient,
+    item_id: str,
+    save_dir: str,
+    roi_groups: str | list,
+    doc_names: str | list | None = None,
+    mag: float | None = None,
+    rgb_pad: tuple[int, int, int] | None = None,
+) -> pd.DataFrame:
+    """Gets regions of interest (ROIs) as images from DSA annotations.
+
+    Args:
+        gc (girder_client.GirderClient): The authenticated girder client.
+        item_id (str): The item id.
+        save_dir (str): The directory to save the roi images.
+        roi_groups (str | list): The roi group name or list of roi group names.
+        doc_names (str | list, optional): List of documents to look for, if None
+            then it looks at all documents. Defaults to None.
+        mag (float, optional): The magnification to get the roi images. Defaults
+            to None which returns the images at scan magnification.
+        rgb_pad (tuple[int, int, int], optional): The RGB values to pad the image with.
+            This only is used when the annotation is a rotated rectangle or a polygon.
+
+    Returns:
+        pd.DataFrame: The roi images metadata.
+
+    """
+    if isinstance(roi_groups, str):
+        roi_groups = [roi_groups]
+
+    if isinstance(doc_names, str):
+        doc_names = [doc_names]
+
+    # Convert to a comma separated string.
+    roi_groups_str = ",".join(roi_groups)
+
+    if doc_names is None:
+        docs = gc.get(
+            f"annotation?itemId={item_id}&text="
+            f"{roi_groups_str}&limit=0&offset=0&sort=lowerName&sortdir=1"
+        )
+    else:
+        docs = []
+
+        for doc_name in doc_names:
+            docs.extend(
+                gc.get(
+                    f"annotation?itemId={item_id}&text={roi_groups_str}&name={doc_name}&limit=0&offset=0&sort=lowerName&sortdir=1"
+                )
+            )
+
+    # Create the location to save the images.
+    save_dir = Path(save_dir)
+    save_dir.mkdir(parents=True, exist_ok=True)
+
+    # Loop through each document.
+    for doc in docs:
+        # Get the full annotations.
+        doc = gc.get(f"annotation/{doc['_id']}")
+
+        # Get the elements.
+        for element in doc.get("annotation", {}).get("elements", []):
+            if element["group"] in roi_groups:
+                # The annotations need to be handled based on type.
+                contour = get_element_contours(element)
+
+                # Get the minimum and maximum coordinates.
+                xmin, ymin = contour.min(axis=0)
+                xmax, ymax = contour.max(axis=0)
+                w, h = xmax - xmin, ymax - ymin
+
+                # Get the region of interest from the image.
+                roi_image = get_region(gc, item_id, xmin, ymin, w, h, mag=mag)[
+                    :, :, :3
+                ]  # for now assuming images are RGB
+
+                # Use pad if needed.
+                if rgb_pad is not None:
+                    roi_mask = np.ones((h, w), dtype=np.uint8)
+
+                    # Draw the contours.
+                    roi_mask = cv.drawContours(
+                        roi_mask, [contour - (xmin, ymin)], -1, 0, cv.FILLED
+                    )
+
+                    roi_image[roi_mask == 1] = rgb_pad
+
+                return roi_image, contour - (xmin, ymin)
+
+
+def _rotate_point_list(point_list, rotation, center=(0, 0)):
+    """Rotate a list of x, y points around a center location.
+    Adapted from: https://github.com/DigitalSlideArchive/HistomicsTK/blob/master/histomicstk/annotations_and_masks/annotation_and_mask_utils.py
+    INPUTS
+    ------
+    point_list : list
+        list of x, y coordinates
+    rotation : int or float
+        rotation in radians
+    center : list
+        x, y location of center of rotation
+    RETURN
+    ------
+    point_list_rotated : list
+        list of x, y coordinates after rotation around center
+    """
+    point_list_rotated = []
+
+    for point in point_list:
+        cos, sin = np.cos(rotation), np.sin(rotation)
+        x = point[0] - center[0]
+        y = point[1] - center[1]
+
+        point_list_rotated.append(
+            (int(x * cos - y * sin + center[0]), int(x * sin + y * cos + center[1]))
+        )
+
+    return point_list_rotated
+
+
+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
+    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)
+
+    # calculate the corner coordinates, assuming no rotation
+    center_x, center_y = element["center"][:2]
+    h, w = element["height"], element["width"]
+    x_min = center_x - w // 2
+    x_max = center_x + w // 2
+    y_min = center_y - h // 2
+    y_max = center_y + h // 2
+    corner_coords = [(x_min, y_min), (x_max, y_min), (x_max, y_max), (x_min, y_max)]
+
+    # if there is rotation rotate
+    if element["rotation"]:
+        corner_coords = _rotate_point_list(
+            corner_coords, rotation=element["rotation"], center=(center_x, center_y)
+        )
+
+    corner_coords = np.array(corner_coords, dtype=np.int32)
+
+    return corner_coords

dsa_helpers/login.py

@@ -24,7 +24,9 @@ def login(
     gc = GirderClient(apiUrl=api_url)
 
     if api_key is None:
-        if password is None:
+        if login_or_email is None:
+            _ = gc.authenticate(interactive=True)
+        elif password is None:
             _ = gc.authenticate(username=login_or_email, interactive=True)
         else:
             _ = gc.authenticate(username=login_or_email, password=password)

dsa_helpers/mongo_utils.py

@@ -0,0 +1,147 @@
+import pymongo
+from os import getenv
+from gridfs import GridFS
+import numpy as np
+from io import BytesIO
+from bson.objectid import ObjectId
+from PIL import Image
+from typing import Union
+
+
+def get_mongo_database(mongo_url: str | None = None, database: str | None = None) -> pymongo.database.Database:
+    """Get a mongo database. By default the Mongo URL will be assumed from local
+    environment variables:
+        "mongodb://$MONGO_INITDB_ROOT_USERNAME:$MONGO_INITDB_ROOT_PASSWORD@mongodb:27017"
+        
+    and the database will be assumed from the environment variable "MONGODB_DB".
+    
+    Args:
+        mongo_url (str): The mongo URL.
+        database (str): The database name.
+        
+    Returns:
+        pymongo.database.Database: The mongo database.
+    
+    """
+    if mongo_url is None:
+        mongo_url = f"mongodb://{getenv('MONGO_INITDB_ROOT_USERNAME')}:" + \
+                    f"{getenv('MONGO_INITDB_ROOT_PASSWORD')}" + \
+                    f"@{getenv('MONGO_HOST_NAME')}:{getenv("MONGO_HOST_PORT")}"
+    
+    mc = pymongo.MongoClient(mongo_url)
+    
+    if database is None:
+        database = getenv("MONGODB_DB")
+
+    # Return the specific database.
+    return mc[database]
+
+
+def chunks(lst: list, n=500):
+    """Helper function for traversting through a list in chunks.
+
+    Args:
+        lst (list): The list to traverse.
+        n (int): The size of the chunks.
+
+    Returns:
+        generator: A generator of the list in chunks.
+
+    """
+    for i in range(0, len(lst), n):
+        yield lst[i : i + n]
+        
+        
+def add_many_to_collection(
+    mongo_collection: pymongo.collection.Collection,
+    items: dict | list, key: str = "_id"
+) -> dict[str | dict]:
+    """Add items to a mongo collection. For this project we always add items with a unique
+    user key.
+    
+    Args:
+        mongo_collection (pymongo.collection.Collection): The mongo collection to add to.
+        items (dict | list): The items to add to the collection.
+        key (str): The key to use to identify the items.
+        
+    Returns:
+        dict[str | dict]: The items added to the collection.
+
+    """
+    # If the items are a list, then use the "key" parameter to nest it as a dict.
+    if isinstance(items, list):
+        items = {item[key]: item for item in items}
+
+    operations = []
+
+    for item in items:
+        operations.append(
+            pymongo.UpdateOne({"_id": item[key]}, {"$set": item}, upsert=True)
+        )
+
+    for chunk in chunks(operations):
+        _ = mongo_collection.bulk_write(chunk)
+
+    return items
+
+
+def get_img_from_db(mongo_db: pymongo.database.Database, img_id: str) -> Union[np.ndarray, None]:
+    """Get an image from the database by its location id.
+
+    Args:
+        mongo_db (pymongo.database.Database): The mongo database.
+        img_loc (str): The image id in mongo.
+
+    Returns:
+        np.array: The image, if None then the image was not found.
+
+    """
+    fs = GridFS(mongo_db)
+
+    grid_out = fs.get(ObjectId(img_id))
+
+    if grid_out:
+        # Read the byte data from the GridOut object
+        byte_data = grid_out.read()
+
+        # Create a BytesIO object from the byte data
+        byte_io = BytesIO(byte_data)
+
+        # Open the image from the BytesIO object
+        src_img = np.array(Image.open(byte_io))
+
+        return src_img
+    
+    
+def add_img_to_db(
+    mongo_db: pymongo.database.Database,
+    img: Image.Image | np.ndarray,
+) -> str:
+    """Add an image to the database.
+
+    Args:
+        mongo_db (pymongo.database.Database): The mongo database.
+        img (np.ndarray or PIL.Image.Image): The image.
+        
+    Returns:
+        str: The image id in the database.
+
+    """
+    fs = GridFS(mongo_db)
+
+    # Convert image to PIL image if needed.
+    if isinstance(img, np.ndarray):
+        img = Image.fromarray(img)
+
+    # Create a BytesIO object and save the image to it
+    byte_io = BytesIO()
+    img.save(byte_io, "PNG")
+
+    # Get the byte data from the BytesIO object
+    byte_io.seek(0)
+    byte_data = byte_io.read()
+
+    # Save the byte data to MongoDB using GridFS
+    file_id = fs.put(byte_data)
+
+    return file_id

{dsa_helpers-0.3.dev0.dist-info → dsa_helpers-0.3.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.3.dev0
+Version: 0.3.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>
@@ -11,11 +11,15 @@ Classifier: License :: OSI Approved :: MIT License
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 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
+Requires-Dist: girder-client
+Requires-Dist: numpy
+Requires-Dist: setuptools
+Requires-Dist: opencv-python
+Requires-Dist: pandas
+Requires-Dist: pymongo
+Requires-Dist: pillow
+Requires-Dist: dash
+Requires-Dist: dash-bootstrap-components
 
 # Digital Slide Archive (DSA) Helpers
 Digital Slide Archive Python utility library.

dsa_helpers-0.3.dev1.dist-info/RECORD

@@ -0,0 +1,15 @@
+dsa_helpers/__init__.py,sha256=KEU-DySliRpFR1J992Vp6-z0oj5_pE19mbXBiVgZCYQ,182
+dsa_helpers/girder_utils.py,sha256=5dkgF5-dQZy7CvK7K7r6Rd2AvMxJglVDKERWJgABKlw,9630
+dsa_helpers/image_utils.py,sha256=6VUteE_0MfFoRNHt4E2v7pb8XoSjbBxwdhNCk9Gzmgs,1757
+dsa_helpers/imread.py,sha256=jPr6hO4TOtGphENJQWLLtTaQ377yAwLe4F9jSAehJXQ,885
+dsa_helpers/imwrite.py,sha256=eQI8VGn7M35_85QMPrNqGgS66iQn9YboCS50tigAE8s,1159
+dsa_helpers/login.py,sha256=-QyVLW9fKywiPUQCPWxF1BIsufAOqMizDM062nUbupA,1147
+dsa_helpers/mongo_utils.py,sha256=U962oIESlOnv2T439OtvQO4scWa81Pnml3jp9Y9kc7Q,4121
+dsa_helpers/dash/__init__.py,sha256=tNGwvi7Rgr_cSYT7qbbB3Y0mlBZ0pFEA5WFPXjQpugE,21
+dsa_helpers/dash/header.py,sha256=rV3VWbo_LJeJHuByek69errOk2m0csztNZeE9h5WmIE,4433
+dsa_helpers/dash/header_callbacks.py,sha256=FKUcfS4F5SBKumDbY66GDkoIVmBq1EbmmvDrCm6imvw,2594
+dsa_helpers-0.3.dev1.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
+dsa_helpers-0.3.dev1.dist-info/METADATA,sha256=5wxYAX0Ui0pPnFrm70SP9KgzN0xp1z5SbNlNuXdGFQU,1056
+dsa_helpers-0.3.dev1.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+dsa_helpers-0.3.dev1.dist-info/top_level.txt,sha256=BmAEDVvDa1MJlSUFHWzx73UKec3o1K6dFUd9tHwgHGo,12
+dsa_helpers-0.3.dev1.dist-info/RECORD,,

{dsa_helpers-0.3.dev0.dist-info → dsa_helpers-0.3.dev1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.0.3)
+Generator: setuptools (73.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

dsa_helpers-0.3.dev0.dist-info/RECORD

@@ -1,11 +0,0 @@
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