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

{dsa_helpers-0.3 → dsa_helpers-0.3.dev0}/.gitignore

@@ -5,6 +5,4 @@ pyenv/
 # Do not push the version file.
 dsa_utils/_version.py
 
-*.pyc
-*.egg-info
-dist/
+*.pyc

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.3
+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>
@@ -11,17 +11,11 @@ Classifier: License :: OSI Approved :: MIT License
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-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
-Requires-Dist: shapely
-Requires-Dist: geopandas
+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 → dsa_helpers-0.3.dev0}/dsa_helpers/__init__.py

@@ -1,8 +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, dash
-
-__all__ = ["girder_utils", "image_utils", "dash"]
+from . import girder_utils, image_utils

dsa_helpers-0.3.dev0/dsa_helpers/girder_utils.py

@@ -0,0 +1,116 @@
+# Functions using the girder client.
+from girder_client import GirderClient
+import pickle
+import numpy as np
+
+
+def get_item_large_image_metadata(gc: GirderClient, item_id: str) -> dict:
+    """Get large image metadata for an item.
+
+    Args:
+        gc (girder_client.GirderClient): The authenticated girder client.
+        item_id (str): The item id.
+
+    Returns:
+        dict: The metadata of the large image item.
+
+    """
+    return gc.get(f"item/{item_id}/tiles")
+
+
+def get_thumbnail(
+    gc: GirderClient,
+    item_id: str,
+    mag: float | None = None,
+    width: int | None = None,
+    height: int | None = None,
+    fill: int | tuple = (255, 255, 255),
+) -> np.ndarray:
+    """Get the thumbnail image by a specific magnification or shape. If mag is
+    not None, then width and height are ignored. Fill is only used when both
+    width and height are provided, to return the thumbnail at the exact shape.
+    DSA convention will fill the height of the image, centering the image and
+    filling the top and bottom of the image equally.
+
+    Args:
+        gc (girder_client.GirderClient): The authenticated girder client.
+        item_id (str): The item id.
+        mag (float, optional): The magnification. Defaults to None.
+        width (int, optional): The width of the thumbnail. Defaults to None.
+        height (int, optional): The height of the thumbnail. Defaults to None.
+        fill (int | tuple, optional): The fill color. Defaults to (255, 255, 255).
+
+    Returns:
+        np.ndarray: The thumbnail image.
+
+    """
+    get_url = f"item/{item_id}/tiles/"
+
+    if mag is not None:
+        get_url += f"region?magnification={mag}&encoding=pickle"
+    else:
+        # Instead use width and height.
+        params = ["encoding=pickle"]
+
+        if width is not None and height is not None:
+            if isinstance(fill, (tuple, list)):
+                if len(fill) == 3:
+                    fill = f"rgb({fill[0]},{fill[1]},{fill[2]})"
+                elif len(fill) == 4:
+                    fill = f"rgba({fill[0]},{fill[1]},{fill[2]},{fill[3]})"
+
+            params.extend([f"width={width}", f"height={height}", f"fill={fill}"])
+        elif width is not None:
+            params.append(f"width={width}")
+        elif height is not None:
+            params.append(f"height={height}")
+
+        get_url += "thumbnail?" + "&".join(params)
+
+    response = gc.get(get_url, jsonResp=False)
+
+    return pickle.loads(response.content)
+
+
+def get_region(
+    gc: GirderClient,
+    item_id: str,
+    left: int,
+    top: int,
+    width: int,
+    height: int,
+    mag: float | None = None,
+) -> 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.
+        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 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.
+
+    """
+    get_url = (
+        f"item/{item_id}/tiles/region?left={left}&top={top}&regionWidth="
+        f"{width}&regionHeight={height}&encoding=pickle"
+    )
+
+    if mag is not None:
+        get_url += f"&magnification={mag}"
+
+    response = gc.get(get_url, jsonResp=False)
+
+    return pickle.loads(response.content)

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

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

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.3
+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>
@@ -11,17 +11,11 @@ Classifier: License :: OSI Approved :: MIT License
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-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
-Requires-Dist: shapely
-Requires-Dist: geopandas
+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.egg-info/SOURCES.txt

@@ -0,0 +1,16 @@
+.gitignore
+LICENSE
+README.md
+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

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

@@ -4,17 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 dependencies = [
-    'girder-client',
-    'numpy',
-    'setuptools',
-    'opencv-python',
-    'pandas',
-    'pymongo',
-    'pillow',
-    'dash',
-    'dash_bootstrap_components',
-    'shapely',
-    'geopandas'
+    'girder-client==3.2.3',
+    'numpy==2.0.0',
+    'setuptools==71.0.3',
+    'opencv-python==4.10.0.84',
+    'pandas==2.2.2'
 ]
 name = "dsa_helpers"
 authors = [
@@ -31,7 +25,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v0.3"
+version = "v0.3dev"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"

dsa_helpers-0.3.dev0/requirements.txt

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

dsa_helpers-0.3/app.py

@@ -1,14 +0,0 @@
-# A test application.
-from dash import Dash, html
-import dash_bootstrap_components as dbc
-from dsa_helpers.dash.header import get_header
-import os
-
-os.environ["DSA_API_URL"] = "https://megabrain.neurology.emory.edu/api/v1"
-
-app = Dash(__name__, external_stylesheets=[dbc.themes.BOOTSTRAP])
-
-app.layout = html.Div([get_header("Test")])
-
-if __name__ == "__main__":
-    app.run_server(debug=True)

dsa_helpers-0.3/dsa_helpers/dash/__init__.py

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

dsa_helpers-0.3/dsa_helpers/dash/header.py

@@ -1,141 +0,0 @@
-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-0.3/dsa_helpers/dash/header_callbacks.py

@@ -1,98 +0,0 @@
-# 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