fusion-tools 0.0.1__tar.gz

fusion_tools-0.0.1/LICENSE

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fusion_tools-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: fusion-tools
+Version: 0.0.1
+Summary: Utility functions for generating, saving, and converting annotation files
+Home-page: https://github.com/spborder/fusion-tools
+Author: Sam Border
+Author-email: sam.border2256@gmail.com
+Project-URL: Homepage, https://github.com/spborder/fusion-tools
+Project-URL: Issues, https://github.com/spborder/fusion-tools/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: dynamic
+
+# fusion-tools
+Some utilities, accession, and visualization tools for data derived from FUSION (Functional Unit State Identification in WSIs).

fusion_tools-0.0.1/README.md

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+# fusion-tools
+Some utilities, accession, and visualization tools for data derived from FUSION (Functional Unit State Identification in WSIs).

fusion_tools-0.0.1/fusion_tools.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: fusion-tools
+Version: 0.0.1
+Summary: Utility functions for generating, saving, and converting annotation files
+Home-page: https://github.com/spborder/fusion-tools
+Author: Sam Border
+Author-email: sam.border2256@gmail.com
+Project-URL: Homepage, https://github.com/spborder/fusion-tools
+Project-URL: Issues, https://github.com/spborder/fusion-tools/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: dynamic
+
+# fusion-tools
+Some utilities, accession, and visualization tools for data derived from FUSION (Functional Unit State Identification in WSIs).

fusion_tools-0.0.1/fusion_tools.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+fusion_tools.egg-info/PKG-INFO
+fusion_tools.egg-info/SOURCES.txt
+fusion_tools.egg-info/dependency_links.txt
+fusion_tools.egg-info/requires.txt
+fusion_tools.egg-info/top_level.txt
+src/__init__.py
+src/fusion_tools/__init__.py
+src/fusion_tools/access.py
+src/fusion_tools/handler.py
+src/fusion_tools/utils.py
+src/fusion_tools/visualization.py
+tests/test_feature_visualization.py
+tests/test_tile_server.py

fusion_tools-0.0.1/fusion_tools.egg-info/dependency_links.txt

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+

fusion_tools-0.0.1/fusion_tools.egg-info/requires.txt

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+dynamic

fusion_tools-0.0.1/fusion_tools.egg-info/top_level.txt

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+src

fusion_tools-0.0.1/pyproject.toml

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+[project]
+name = "fusion-tools"
+dynamic = ["version","authors","readme","description","classifiers"]
+dependencies = ["dynamic"]
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project.urls]
+Homepage = "https://github.com/spborder/fusion-tools"
+Issues = "https://github.com/spborder/fusion-tools/issues"

fusion_tools-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

fusion_tools-0.0.1/setup.py

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+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="fusion-tools",
+    version="0.0.1",
+    author="Sam Border",
+    author_email="sam.border2256@gmail.com",
+    description="Utility functions for generating, saving, and converting annotation files",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/spborder/fusion-tools",
+    install_requires=[
+        "lxml>=4.9.2",
+        "geojson>=3.0.1",
+        "shapely>=2.0.1",
+        "tqdm",
+        "numpy>=1.20.0",
+        "large-image[common]",
+        "wsi-annotations-kit",
+        "uuid",
+        "scikit-image",
+        "fastapi",
+        "uvicorn",
+        "threading"
+    ],
+    packages=setuptools.find_packages(),
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: Apache Software License",
+        "Operating System :: OS Independent",
+    ],
+)

fusion_tools-0.0.1/src/fusion_tools/access.py

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+"""
+Functions related to access of data derived from FUSION
+
+- Query available data in FUSION instance
+    - Count of slides, names of annotations, annotation names per slide, slide metadata
+- Extract
+    - annotations (various formats, regions, full), images (regions, full, thumbnails), files
+
+"""
+
+import os
+import sys
+import json
+import requests
+
+import girder_client
+
+import pandas as pd
+import anndata as ad
+import geojson
+
+import geopandas as gpd
+
+from typing_extensions import Union
+
+
+class Accessor:
+    def __init__(self,
+                 fusion_handler):
+        
+        self.fusion_handler = fusion_handler
+
+    def query_annotation_count(self, item:Union[str,list]) -> dict:
+        """
+        Get count of annotations for a given item
+        """
+
+        if type(item)==str:
+            item = [item]
+
+        ann_counts = []
+        for it in item:
+            item_dict = {}
+            if '/' in it:
+                item_info = self.get_path_info(it)
+            else:
+                item_info = self.fusion_handler.gc.get(f'/item/{it}')
+
+            item_dict['name'] = item_info['name']
+            item_dict['id'] = item_info['_id']
+            item_anns = self.fusion_handler.gc.get(f'/annotation',parameters={'itemId':it})
+
+            if len(item_anns)>0:
+                for ann in item_anns:
+                    # Only grabbing centroids to make it a little more lightweight
+                    ann_centroids = self.fusion_handler.gc.get(f'/annotation/{ann["_id"]}',parameters={'centroids': True})
+                    ann_count = len(ann_centroids['annotation']['elements'])
+
+                    item_dict[ann['annotation']['name']] = ann_count
+
+            ann_counts.append(item_dict)
+
+        ann_counts_df = pd.DataFrame.from_records(ann_counts).fillna(0)
+
+        return ann_counts_df
+    
+    def get_path_info(self, item_path: str) -> dict:
+        """
+        Get item information from path
+        """
+
+        # First searching for the "resource"
+        assert any([i in item_path for i in ['collection','user']])
+
+        resource_find = self.fusion_handler.gc.get('/resource/lookup',parameters={'path': item_path})
+
+        return resource_find
+    
+    def get_folder_slide_count(self, folder_path: str, ignore_histoqc = True) -> list:
+        """
+        Get number of slide items in a folder
+        """
+
+        if '/' in folder_path:
+            folder_info = self.get_path_info(folder_path)
+        else:
+            folder_info = self.fusion_handler.gc.get(f'/folder/{folder_path}')
+
+        folder_items = self.fusion_handler.gc.get(f'/resource/{folder_info["_id"]}',
+                                                  parameters = {
+                                                      'type': folder_info["type"],
+                                                      'limit': 0 
+                                                  })
+
+        if len(folder_items)>0:
+            if ignore_histoqc:
+                folders_in_folder = list(set([i['folderId'] for i in folder_items]))
+                folder_names = [
+                    self.fusion_handler.gc.get(f'/folder/{i}')['name']
+                    for i in folders_in_folder
+                ]
+
+                if 'histoqc_outputs' not in folder_names:
+                    ignore_folders = []
+                else:
+                    ignore_folders = [folders_in_folder[i] for i in range(len(folder_names)) if folder_names[i]=='histoqc_outputs']
+
+            else:
+                ignore_folders = []
+
+            folder_image_items = [i for i in folder_items if 'largeImage' in i and not i['folderId'] in ignore_folders]
+
+        else:
+            folder_image_items = []
+
+        return folder_image_items
+
+    

fusion_tools-0.0.1/src/fusion_tools/handler.py

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+"""
+Handler for requests made to a running FUSION instance.
+
+"""
+
+import os
+import sys
+
+import girder_client
+
+import requests
+import json
+import numpy as np
+
+from typing_extensions import Union
+
+from skimage.draw import polygon
+from PIL import Image
+from io import BytesIO
+
+
+class FUSIONHandler:
+    def __init__(self,
+                 girderApiUrl: str,
+                 username: str,
+                 password: str):
+        
+        self.girderApiUrl = girderApiUrl
+        self.username = username
+        self.password = password
+
+        self.gc = girder_client.GirderClient(apiUrl=self.girderApiUrl)
+        self.gc.authenticate(
+            username = self.username,
+            password=self.password
+        )
+
+        # Token used for authenticating requests
+        self.user_token = self.gc.get(f'/token/session')['token']
+
+    def get_image_region(self, item_id: str, coords_list: list, style: Union[dict,None] = None)->np.ndarray:
+        """
+        Grabbing image region from list of bounding box coordinates
+        """
+
+        image_array = np.zeros((256,256))
+
+        if style is None:
+            image_array = np.uint8(
+                np.array(
+                    Image.open(
+                        BytesIO(
+                            requests.get(
+                                self.gc.urlBase+f'/item/{item_id}/tiles/region?token={self.user_token}&left={coords_list[0]}&top={coords_list[1]}&right={coords_list[2]}&bottom={coords_list[3]}'
+                            ).content
+                        )
+                    )
+                )
+            )
+        
+        else:
+            print('Adding style parameters are in progress')
+            raise NotImplementedError
+
+        return image_array
+
+    def make_boundary_mask(self, exterior_coords: list) -> np.ndarray:
+        """
+        Making a binary mask given a set of coordinates, scales coordinates to fit within bounding box.
+        
+        Expects coordinates in x,y format
+        """
+        x_coords = [i[0] for i in exterior_coords]
+        y_coords = [i[1] for i in exterior_coords]
+
+        min_x = min(x_coords)
+        max_x = max(x_coords)
+        min_y = min(y_coords)
+        max_y = max(y_coords)
+        
+        scaled_coords = [[int(i[0]-min_x), int(i[1]-min_y)] for i in exterior_coords]
+
+        boundary_mask = np.zeros((int(max_y-min_y),int(max_x-min_x)))
+
+        row,col = polygon(
+            [i[1] for i in scaled_coords],
+            [i[0] for i in scaled_coords],
+            (int(max_y-min_y), int(max_x-min_x))
+        )
+
+        boundary_mask[row,col] = 1
+
+        return boundary_mask
+
+
+

fusion_tools-0.0.1/src/fusion_tools/utils.py

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+"""
+Utility functions for data derived from FUSION
+
+"""
+
+import os
+import sys
+
+import numpy as np
+
+import geopandas as gpd
+import pandas as pd
+
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fusion_tools-0.0.1/src/fusion_tools/visualization.py

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+"""
+Functions related to visualization for data derived from FUSION.
+
+- Interactive feature charts
+    - View images at points
+- Local slide viewers
+
+"""
+
+import large_image.exceptions
+from fastapi import FastAPI, APIRouter, Response
+
+import large_image
+import pandas as pd
+import dash_leaflet as dl
+from dash import dcc, callback, ctx, ALL, exceptions
+import dash_bootstrap_components as dbc
+from dash_extensions.enrich import DashProxy, html, Input, Output, State
+
+import plotly.express as px
+import plotly.graph_objects as go
+
+import numpy as np
+
+from typing_extensions import Union
+from PIL import Image
+from io import BytesIO
+import json
+import uvicorn
+import requests
+
+class TileServer:
+    def __init__(self,
+                 local_image_path: str
+                 ):
+
+        self.local_image_path = local_image_path
+
+        self.tile_source = large_image.open(self.local_image_path,encoding='PNG')
+        self.tile_metadata = self.tile_source.getMetadata()
+
+        self.router = APIRouter()
+        self.router.add_api_route('/',self.root,methods=["GET"])
+        self.router.add_api_route('/tiles/{z}/{x}/{y}',self.get_tile,methods=["GET"])
+        self.router.add_api_route('/metadata',self.get_metadata,methods=["GET"])
+
+    def root(self):
+        return {'message': "Oh yeah, now we're cooking"}
+
+    def get_tile(self,z:int, x:int, y:int):
+        try:
+            raw_tile = self.tile_source.getTile(
+                        x = x,
+                        y = y,
+                        z = z
+                    )
+            
+        except large_image.exceptions.TileSourceXYZRangeError:
+            # This error appears for any negative tile coordinates
+            raw_tile = np.zeros((self.tile_metadata['tileHeight'],self.tile_metadata['tileWidth']),dtype=np.uint8).tobytes()
+
+        return Response(content = raw_tile, media_type='image/png')
+    
+    def get_metadata(self):
+        large_image_metadata = self.tile_source.getMetadata()
+        return Response(content = json.dumps(large_image_metadata),media_type = 'application/json')
+    
+    def start(self, port = 8050):
+        app = FastAPI()
+        app.include_router(self.router)
+
+        uvicorn.run(app,host='0.0.0.0',port=port)
+
+
+class LocalSlideViewer:
+    def __init__(self,
+                 tile_server_port: str,
+                 app_port: str):
+        
+        self.app_port = app_port
+        self.tile_server_port = tile_server_port
+
+        image_metadata = requests.get(
+            f'http://localhost:{self.tile_server_port}/metadata'
+        ).json()
+        
+        self.viewer_app = DashProxy(__name__)
+        self.viewer_app.layout = self.gen_layout(
+            tile_size = image_metadata['tileWidth'],
+            zoom_levels = image_metadata['levels'],
+            tile_server_port = self.tile_server_port
+        )
+        self.viewer_app.title = 'FUSION'
+
+        # Add callback functions here
+        self.get_callbacks()
+
+        # Running using default Flask server
+        self.viewer_app.run(
+            host = '0.0.0.0',
+            port = self.app_port,
+            debug = False
+        )
+
+    def gen_layout(self, tile_size:int, zoom_levels: int, tile_server_port:str):
+        """
+        Generate simple slide viewer layout
+        """
+        layout = html.Div(
+            dbc.Container(
+                id = 'container',
+                fluid = True,
+                children = [
+                    dbc.Row(
+                        html.Div(
+                            dl.Map(
+                                id = 'slide-map',
+                                crs = 'Simple',
+                                center = [120,-120],
+                                zoom = 0,
+                                style = {'height': '100vh','width': '100vw','margin': 'auto','display': 'inline-block'},
+                                children = [
+                                    dl.TileLayer(
+                                        id = 'slide-tile-layer',
+                                        url = f'http://localhost:{tile_server_port}/tiles'+'/{z}/{x}/{y}',
+                                        tileSize=tile_size,
+                                        maxNativeZoom=zoom_levels-1,
+                                        minZoom = 0,
+                                        #bounds = [[0,0],[tile_size,-tile_size]]
+                                    ),
+                                    dl.FullScreenControl(
+                                        position = 'upper-left'
+                                    ),
+                                    dl.LayersControl(
+                                        id = 'slid-layers-control',
+                                        children = []
+                                    )
+                                ]
+                            )
+                        )
+                    )
+                ]
+            )
+        )
+
+        return layout
+
+    def get_callbacks(self):
+        # Add callbacks to self.viewer_app
+        # Maybe add something so users can point the app to some zarr storage or add polygons either through uploads or on initialization
+
+
+        pass
+
+
+class FeatureViewer:
+    def __init__(self,
+                 feature_df: pd.DataFrame,
+                 item_id: str,
+                 ann_name: str,
+                 mode: str,
+                 mode_col: Union[str,list],
+                 fusion_handler,
+                 viewer_title = 'Feature Viewer'
+                 ):
+        
+        self.feature_df = feature_df
+        self.viewer_title = viewer_title
+        self.item_id = item_id
+        self.mode = mode
+        self.mode_col = mode_col
+        self.ann_name = ann_name
+        
+        assert mode in ['bbox','index','column_index','element_id']
+
+        if self.mode=='bbox' and not type(self.mode_col)==list:
+            print('If using "bbox" mode, provide a list of column names containing bounding box coordinates in minx, miny, maxx, maxy format.')
+            raise TypeError
+        elif not self.mode=='bbox' and type(self.mode_col)==list:
+            print('Provide a single column name (type: str) to identify samples in the target slide.')
+            raise TypeError
+
+        self.fusion_handler = fusion_handler
+
+        self.feature_viewer = DashProxy(
+            __name__
+        )
+
+        self.feature_viewer.title = self.viewer_title
+        self.feature_viewer.layout = self.get_layout()
+        self.get_callbacks()
+
+    
+    def get_callbacks(self):
+        """
+        Put all callbacks in here
+        """
+        # First callback is selecting features to view and plotting them when "Plot" button is pressed
+        self.feature_viewer.callback(
+            [
+                Output('feature-graph','figure'),
+                Output('image-graph','figure')
+            ],
+            [
+                Input('feature-drop','value'),
+                Input('label-drop','value')
+            ],
+            prevent_initial_call = True
+        )(self.update_plot)
+
+        # Second callback is grabbing images associated with selected points
+        self.feature_viewer.callback(
+            [
+                Output('image-graph','figure')
+            ],
+            [
+                Input('feature-graph','selectedData')
+            ],
+            prevent_initial_call = True
+        )(self.graph_image)
+
+    def get_layout(self):
+        """
+        Assembling a layout based on the provided feature dataframe
+        """
+
+        main_layout = html.Div([
+            dbc.Container(
+                id = 'feature-viewer-container',
+                fluid = True,
+                children = [
+                    html.H1(self.viewer_title),
+                    dbc.Row([
+                        dbc.Col([
+                            dbc.Row([
+                                dbc.Col(
+                                    dbc.Label('Select feature(s) for plotting:',html_for='feature-drop'),
+                                    md = 3
+                                ),
+                                dbc.Col(
+                                    dcc.Dropdown(
+                                        options = [
+                                            {'label': i, 'value': i, 'disabled': False}
+                                            if not i in self.mode_col else
+                                            {'label': i, 'value': i, 'disabled': True}
+                                            for i in self.feature_df.columns.tolist() 
+                                        ],
+                                        value = [],
+                                        multi = True,
+                                        id = 'feature-drop'
+                                    ),
+                                    md = 9
+                                )
+                            ]),
+                            dbc.Row([
+                                dbc.Col(
+                                    dbc.Label('(Optional) Select a label for the plot:',html_for='label-drop'),
+                                    md = 3
+                                ),
+                                dbc.Col(
+                                    dcc.Dropdown(
+                                        options = [
+                                            {'label': i,'value': i,'disabled': False}
+                                            if not i in self.mode_col else
+                                            {'label': i, 'value': i, 'disabled': True}
+                                            for i in self.feature_df.columns.tolist()
+                                        ],
+                                        value = [],
+                                        multi = False,
+                                        id = 'label-drop'
+                                    )
+                                )
+                            ]),
+                            dbc.Row([
+                                dcc.Graph(
+                                    id = 'feature-graph',
+                                    figure = go.Figure()
+                                )
+                            ])
+                        ], md = 6),
+                        dbc.Col([
+                            dbc.Row(
+                                html.H3('Select points to see the image at that point')
+                            ),
+                            dbc.Row(
+                                dcc.Graph(
+                                    id = 'image-graph',
+                                    figure = go.Figure()
+                                )
+                            )
+                        ])
+                    ])
+                ]
+            )
+        ])
+
+
+        return main_layout
+
+    def update_plot(self, features_selected, labels_selected, plot_button):
+        """
+        Plotting selected data with label
+        """
+
+        print(ctx.triggered)
+
+        if not ctx.triggered:
+            raise exceptions.PreventUpdate
+
+        return_plot = go.Figure()
+
+
+
+        return return_plot
+
+    def grab_image(self, selected_points):
+        """
+        Grabbing image region based on selected points
+        """
+
+        return_image = go.Figure()
+
+
+
+        return return_image
+
+

fusion_tools-0.0.1/tests/test_feature_visualization.py

@@ -0,0 +1,44 @@
+"""
+
+Testing visualization functionality
+
+"""
+
+import os
+import sys
+
+import pandas as pd
+
+from src.fusion_tools.handler import FUSIONHandler
+from src.fusion_tools.visualization import FeatureViewer
+
+
+def main():
+
+
+    feature_path = ''
+    feature_df = pd.read_csv(feature_path)
+
+    fusion_handler = FUSIONHandler(
+        girderApiUrl = os.environ.get('DSA_URL'),
+        username = os.environ.get('DSA_USER'),
+        password = os.environ.get('DSA_PWORD')
+    )
+
+    feature_viewer = FeatureViewer(
+        feature_df = feature_df,
+        item_id = '',
+        mode = '',
+        mode_col = '',
+        fusion_handler=fusion_handler,
+        viewer_title = 'Test Feature Viewer'
+    )
+
+
+
+
+
+if __name__=='__main__':
+    main()
+
+

fusion_tools-0.0.1/tests/test_tile_server.py

@@ -0,0 +1,36 @@
+"""
+
+Testing tile server with local tile source
+
+"""
+
+import os
+import sys
+sys.path.append('./src/')
+from fusion_tools.visualization import TileServer, LocalSlideViewer
+import threading
+
+
+def main():
+
+    path_to_slide = 'C:\\Users\\samuelborder\\Desktop\\HIVE_Stuff\\FUSION\\Test Upload\\XY01_IU-21-015F.svs'
+
+    tile_server = TileServer(
+        local_image_path = path_to_slide
+    )
+
+    #TODO: Should this be included in the tile_server.start method?
+    new_thread = threading.Thread(target = tile_server.start, name = 'local_tile_server', args = ['8050'])
+    new_thread.daemon = True
+    new_thread.start()
+
+    slide_viewer = LocalSlideViewer(
+        tile_server_port='8050',
+        app_port = '8080'
+    )
+
+
+if __name__=='__main__':
+    main()
+
+