fusion-tools 3.3.2__tar.gz → 3.3.4__tar.gz

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: fusion-tools
-Version: 3.3.2
+Version: 3.3.4
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="fusion-tools",
-    version="3.3.2",
+    version="3.3.4",
     author="Sam Border",
     author_email="sam.border2256@gmail.com",
     description="Modular visualization and analysis dashboard creation for high-resolution microscopy images",

fusion_tools-3.3.4/src/fusion_tools/fusion/data_types.py

@@ -0,0 +1,503 @@
+"""Defining UploadTypes which are accepted in FUSION
+"""
+
+from fusion_tools.handler.dataset_uploader import DSAUploadType, WSI_TYPES, ANN_TYPES
+
+def get_upload_types():
+
+    # Basic Type:
+    kidney_basic_type = DSAUploadType(
+        name = "Kidney Histology Image",
+        description= 'This is a kidney histology image upload with the option to add annotations. Glomeruli, sclerotic glomeruli, tubules, and cortical and medullary interstitium are first segmented using DL and then pathomic features are calculated.',
+        input_files = [
+            {
+                'name': 'Image',
+                'description': 'This is any kidney histology image you would like to upload.',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            },
+            {
+                'name': 'Annotation',
+                'description': 'This is an annotation file that is processed and added to the uploaded image.',
+                'accepted_types': ANN_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'annotation',
+                'parent': 'Image',
+                'required': False
+            }
+        ],
+        processing_plugins=[
+            [
+                {
+                    'name': 'MultiCompartmentSegment',
+                    'image': 'samborder2256/multicomp:latest',
+                    'input_args': [
+                        {
+                            'name': 'files',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'Image'
+                            },
+                            'disabled': True
+                        },
+                        {
+                            'name': 'base_dir',
+                            'default': {
+                                'type': 'upload_folder',
+                                'name': 'Image'
+                            },
+                            'disabled': True
+                        },
+                        {
+                            'name': 'modelfile',
+                            'default': {
+                                'value': '648123761019450486d13dce'
+                            }
+                        }
+                    ]
+                },
+                {
+                    'name': 'FeatureExtraction',
+                    'image': 'fusionplugins/general:latest',
+                    'input_args': [
+                        {
+                            'name': 'input_image',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'Image'
+                            }
+                        },
+                        {
+                            'name': 'extract_sub_compartments',
+                            'default': {
+                                'value': True
+                            },
+                            'disabled': True
+                        },
+                        'hematoxylin_threshold',
+                        'eosinophilic_threshold',
+                        'hematoxylin_min_size',
+                        'eosinophilic_min_size'
+                    ]
+                }
+            ]
+        ],
+        required_metadata=[]
+    )
+
+    # Basic Type:
+    basic_type = DSAUploadType(
+        name = "General Histology Image",
+        description= 'This is a histology image upload with the option to add annotations. Glomeruli, sclerotic glomeruli, tubules, and cortical and medullary interstitium are first segmented using DL and then pathomic features are calculated.',
+        input_files = [
+            {
+                'name': 'Image',
+                'description': 'This is any histology image you would like to upload.',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            },
+            {
+                'name': 'Annotation',
+                'description': 'This is an annotation file that is processed and added to the uploaded image.',
+                'accepted_types': ANN_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'annotation',
+                'parent': 'Image',
+                'required': False
+            }
+        ],
+        processing_plugins=[
+            {
+                'name': 'FeatureExtraction',
+                'image': 'fusionplugins/general:latest',
+                'input_args': [
+                    {
+                        'name': 'input_image',
+                        'default': {
+                            'type': 'upload_file',
+                            'name': 'Image'
+                        }
+                    },
+                    {
+                        'name': 'extract_sub_compartments',
+                        'default': {
+                            'value': True
+                        }
+                    },
+                    {
+                        'name': 'hematoxylin_threshold',
+                        'default': {
+                            'value': 150
+                        }
+                    },
+                    {
+                        'name': 'eosinophilic_threshold',
+                        'default': {
+                            'value': 30
+                        }
+                    },
+                    {
+                        'name': 'hematoxylin_min_size',
+                        'default': {
+                            'value': 40
+                        }
+                    },
+                    {
+                        'name': 'eosinophilic_min_size',
+                        'default': {
+                            'value': 20
+                        }
+                    },
+                ]
+            }
+        ],
+        required_metadata=[
+            {
+                'name': 'Organ',
+                'required': True,
+                'item': 'Image'
+            }
+        ]
+    )
+
+    # 10x Types:
+    visium_type = DSAUploadType(
+        name = '10x Visium',
+        description = 'This upload type is for 10x Visium spatial transcriptomics samples. It includes one histology image and information related to the transcript counts per-"spot".',
+        input_files = [
+            {
+                'name': 'Image',
+                'description': 'This is the full-resolution image associated with this upload. If the full-resolution image is not available, upload the "hires_image" and the "scalefactors_json.json" file to appropriately scale coordinates.',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            },
+            {
+                'name': 'Counts',
+                'description': 'This is the file containing per-spot gene counts',
+                'accepted_types': ['h5','h5ad','csv','rds','RDS'],
+                'preprocessing_plugins': None,
+                'type': 'file',
+                'parent': 'Image',
+                'required': True
+            },
+            {
+                'name': 'Structures',
+                'description': 'If you have annotated any additional structures on the histology image, upload those annotations here.',
+                'accepted_types': ANN_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'annotation',
+                'parent': 'Image',
+                'required': False
+            },
+            {
+                'name': 'Scale Factors',
+                'description': 'If using the "hires" image, upload the "scalefactors_json.json" file here.',
+                'accepted_types': ['json'],
+                'preprocessing_plugins': None,
+                'type': 'file',
+                'parent': 'Image',
+                'required': False
+            },
+            {
+                'name': 'Genes List File',
+                'description': 'If you want to include specific genes which are not included in the "most variable" genes, upload CSV file containing one column with those gene IDs.',
+                'accepted_types': ['csv'],
+                'preprocessing_plugins': None,
+                'type': 'file',
+                'parent': 'Image',
+                'required': False
+            }
+        ],
+        processing_plugins=[
+            [
+                {
+                    'name': 'CellDeconvolution',
+                    'image': 'fusionplugins/visium:latest',
+                    'input_args': [
+                        {
+                            'name': 'counts_file',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'Counts File'
+                            },
+                            'disabled': False
+                        },
+                        'organ'
+                    ]
+                },
+                {
+                    'name': 'SpotAnnotation',
+                    'image': 'fusionplugins/visium:latest',
+                    'input_args': [
+                        {
+                            'name': 'counts_file',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'Counts File',
+                            },
+                            'disabled': True
+                        },
+                        {
+                            'name': 'input_files',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'Image'
+                            },
+                            'disabled': False
+                        },
+                        'use_gene_selection',
+                        'gene_selection_method',
+                        'n'
+                    ]
+                }
+            ]
+        ],
+        required_metadata=[
+            {
+                'name': 'Organ',
+                'required': True,
+                'item': 'Image'
+            }
+        ]
+    )
+
+    xenium_type = DSAUploadType(
+        name = '10x Xenium',
+        description='This is for 10x Xenium samples. It includes a morphology (DAPI) image and, optionally, a histology image as well as cell centroids/boundaries and assigned "group" labels or other information for each segmented cell.',
+        input_files = [
+            {
+                'name': 'Morphology Image',
+                'description': 'This is the morphology image showing the location of nuclei in the sample at different levels.',
+                'accepted_types': ['tif','tiff'],
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            },
+            {
+                'name': 'Histology Image',
+                'description': 'This is a histology image from the same section used for alignment of derived cell segmentations.',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': False
+            },
+            {
+                'name': 'Cell Segmentations',
+                'description': 'This is a file containing either cell centroids and areas or the boundaries of segmented cells.',
+                'accepted_types': ['csv'],
+                'preprocessing_plugins': None,
+                'type': 'annotation',
+                'parent': 'Morphology Image',
+                'required': True
+            },
+            {
+                'name': 'Cell Groups',
+                'description': 'This is a csv file containing one column with "cell_id" and then other columns which are added to per-cell properties (could be cell group labels or any other measurement).',
+                'accepted_types': ['csv'],
+                'preprocessing_plugins': None,
+                'type': 'file',
+                'parent': 'Morphology Image',
+                'required': False
+            }
+        ],
+        processing_plugins=[
+            {
+                'name': '',
+                'image': '',
+                'input_args': [
+                    {
+
+                    }
+                ]
+            }
+        ],
+        required_metadata=[
+            {
+                'name': 'Organ',
+                'required': True,
+                'item': 'Image'
+            }
+        ]
+    )
+
+    hd_type = DSAUploadType(
+        name = "10x Visium HD",
+        description = 'This is for the 10x Visium HD data type.',
+        input_files = [
+            {
+                'name': 'Image',
+                'description': '',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            }
+        ],
+        processing_plugins=[],
+        required_metadata=[
+            {
+                'name': 'Organ',
+                'required': True,
+                'item': 'Image'
+            }
+        ]
+    )
+
+    # MxIF/PhenoCycler
+    mxif_type = DSAUploadType(
+        name = "MxIF / PhenoCycler",
+        description = 'This is for a multiplexed - immunofluorescence (mxIF) type image containing several different fluorescence channels for different markers. If available, you may also choose to align this image with a same-section histology image.',
+        input_files = [
+            {
+                'name': 'IF Image',
+                'description': 'This is a single multi-frame immunofluorescence image containing aligned channels.',
+                'accepted_types': ['tif','tiff'],
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            },
+            {
+                'name': 'Histology Image',
+                'description': 'This is a same-section histology image which the IF image is aligned to during processing.',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': False
+            },
+            {
+                'name': 'IF Annotations',
+                'description': 'If any structures have been segmented from the IF image, upload them here.',
+                'accepted_types': ANN_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'annotation',
+                'parent': 'IF Image',
+                'required': False
+            },
+            {
+                'name': 'Histology Annotations',
+                'description': 'If any structures were segmented from the histology image, upload them here.',
+                'accepted_types': ANN_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'annotation',
+                'parent': 'Histology Image',
+                'required': False
+            }
+        ],
+        processing_plugins = [
+            [
+                {
+                    'image': 'fusionplugins/codex:latest',
+                    'name': 'CellSegmentation',
+                    'input_args': [
+                        {
+                            'name': 'input_image',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'IF Image'
+                            }
+                        }
+                    ]
+                },
+                {
+                    'image': 'fusionplugins/general:latest',
+                    'name': 'FeatureExtraction',
+                    'input_args': [
+                        {
+                            'name': 'input_image',
+                            'default': {
+                                'type': 'upload_file',
+                                'name': 'IF Image'
+                            }
+                        }
+                    ]
+                }
+            ],
+            {
+                'image': 'fusionplugins/general:latest',
+                'name': 'FeatureExtraction',
+                'input_args': [
+                    {
+                        'name': 'input_image',
+                        'default': {
+                            'type': 'upload_file',
+                            'name': 'Histology Image'
+                        }
+                    },
+                    {
+                        'name': 'extract_sub_compartments',
+                        'default': {
+                            'value': True
+                        }
+                    },
+                    'hematoxylin_threshold',
+                    'eosinophilic_threshold',
+                    'hematoxylin_min_size',
+                    'eosinophilic_min_size'
+                ]
+            }
+        ],
+        required_metadata = [
+            {
+                'name': 'Organ',
+                'required': True,
+                'item': 'Image'
+            }
+        ]
+    )
+
+    # HuBMAP Processed Dataset
+    hubmap_type = DSAUploadType(
+        name = "HuBMAP Processed",
+        description='This is for a dataset which has been processed by the Human Biomolecular Atlas Program (HuBMAP).',
+        input_files = [
+            {
+                'name': 'Image',
+                'description': '',
+                'accepted_types': WSI_TYPES,
+                'preprocessing_plugins': None,
+                'type': 'item',
+                'required': True
+            }
+        ],
+        processing_plugins= [
+            {
+                'name': '',
+                'image': '',
+                'input_args': []
+            }
+        ],
+        required_metadata=[
+            {
+                'name': 'Organ',
+                'required': True,
+                'item': 'Image'
+            },
+            {
+                'name': 'Sample ID',
+                'required': True,
+                'item': 'Image'
+            },
+            {
+                'name': 'Assay Type',
+                'required': True,
+                'item': 'Image'
+            }
+        ]
+    )
+
+    return [
+        basic_type,
+        kidney_basic_type,
+        visium_type,
+        xenium_type,
+        hd_type,
+        mxif_type,
+        hubmap_type
+    ]
+

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/src/fusion_tools/fusion/vis.py

@@ -3,16 +3,18 @@
 from fusion_tools.visualization import Visualization
 from fusion_tools.handler.dsa_handler import DSAHandler
 from fusion_tools.components import (
+    SlideMap,
     MultiFrameSlideMap,
     ChannelMixer,
     OverlayOptions,
     PropertyViewer,
     GlobalPropertyPlotter,
     HRAViewer,
-    FeatureAnnotation,
     BulkLabels
 )
 
+from fusion_tools.fusion.data_types import get_upload_types
+
 
 def get_layout(args):
 
@@ -27,12 +29,10 @@ def get_layout(args):
     
     dsa_plugin_progress = dsa_handler.create_plugin_progress()
 
-    dsa_dataset_builder = dsa_handler.create_dataset_builder(
-        include = args['dataset_builder_include']
-    )
+    dsa_dataset_builder = dsa_handler.create_dataset_builder()
 
     dsa_dataset_uploader = dsa_handler.create_uploader(
-        uploader_types = []
+        upload_types = get_upload_types()
     )
 
     user_surveys = []
@@ -51,12 +51,9 @@ def get_layout(args):
         components = {
             "Visualization": [
                 [
-                    MultiFrameSlideMap()
-                ],
-                [
+                    SlideMap(),
                     [
                         OverlayOptions(),
-                        ChannelMixer(),
                         PropertyViewer(ignore_list=['_id','_index']),
                         GlobalPropertyPlotter(ignore_list = ['_id','_index']),
                         HRAViewer(),
@@ -64,6 +61,19 @@ def get_layout(args):
                     ]
                 ]
             ],
+            "MultiFrame Visualization": [
+                [
+                    MultiFrameSlideMap(),
+                    [
+                        ChannelMixer(),
+                        OverlayOptions(),
+                        PropertyViewer(ignore_list = ['_id','_index']),
+                        GlobalPropertyPlotter(ignore_list = ['_id','_index']),
+                        HRAViewer(),
+                        BulkLabels()
+                    ]
+                ]
+            ],
             "Dataset Builder": [
                 dsa_dataset_builder
             ],

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/src/fusion_tools/handler/dataset_builder.py

@@ -82,7 +82,8 @@ class DatasetBuilder(DSATool):
                 'Collection Name': f'User: {session_data["current_user"]["login"]}',
                 'Collection ID': session_data["current_user"]['_id'],
                 'Number of Folder': 2,
-                'Last Updated': '-'
+                'Last Updated': '-',
+                'token': session_data['current_user']['token']
             })
             
         collections_df = pd.DataFrame.from_records(collections_info)
@@ -146,7 +147,10 @@ class DatasetBuilder(DSATool):
                         dcc.Store(
                             id = {'type':'dataset-builder-data-store','index': 0},
                             storage_type='memory',
-                            data = json.dumps({'selected_slides':starting_slides, 'selected_collections': [], 'available_collections': collections_df.to_dict("records")})
+                            data = json.dumps({
+                                'selected_slides':starting_slides, 
+                                'selected_collections': [], 
+                                'available_collections': collections_df.to_dict("records")})
                         )
                     ),
                     dbc.Row([
@@ -238,7 +242,8 @@ class DatasetBuilder(DSATool):
             ],
             [
                 State({'type':'dataset-builder-data-store','index': ALL},'data'),
-                State({'type':'dataset-builder-collection-contents-div','index': ALL},'children')
+                State({'type':'dataset-builder-collection-contents-div','index': ALL},'children'),
+                State('anchor-vis-store','data')
             ],
             [
                 Output({'type':'dataset-builder-collection-contents-div','index': ALL},'children'),
@@ -323,7 +328,7 @@ class DatasetBuilder(DSATool):
         dataframe = pd.json_normalize(dataframe.to_dict('records'))
         selectable_table = dash_table.DataTable(
             id = id,
-            columns = [{'name':i,'id':i,'deletable':False} for i in dataframe.columns],
+            columns = [{'name':i,'id':i,'deletable':False} for i in dataframe.columns if not i=='token'],
             data = dataframe.to_dict('records'),
             editable = False,
             filter_action='native',
@@ -352,13 +357,15 @@ class DatasetBuilder(DSATool):
 
         return selectable_table
 
-    def organize_folder_contents(self, folder_info:dict, show_empty:bool=True, ignore_histoqc:bool=True)->list:
+    def organize_folder_contents(self, folder_info:dict, show_empty:bool=True, ignore_histoqc:bool=True,session_data:dict = {})->list:
         """For a given folder selection, return a list of slides(0th) and folders (1th)
 
         :param folder_info: Folder info dict returned by self.handler.get_path_info(path)
         :type folder_info: dict
         :param show_empty: Whether or not to display folders which contain 0 slides, defaults to False
         :type show_empty: bool, optional
+        :param session_data: Current session information
+        :type session_data: dict
         :return: List of slides within the current folder as well as folders within that folder
         :rtype: list
         """
@@ -371,7 +378,8 @@ class DatasetBuilder(DSATool):
             all_folder_slides = self.handler.get_folder_slides(
                 folder_path = folder_info['_id'],
                 folder_type = folder_info['_modelType'],
-                ignore_histoqc=ignore_histoqc
+                ignore_histoqc=ignore_histoqc,
+                user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
             )
 
             folder_slides_folders = [i['folderId'] for i in all_folder_slides]
@@ -381,8 +389,14 @@ class DatasetBuilder(DSATool):
                 if not u==folder_info['_id'] and not u in folders_in_folder:
                     # This is for all folders in this folder
                     # This grabs parent folders of this folder
-                    u_folder_info = self.handler.get_folder_info(folder_id=u)
-                    u_folder_rootpath = self.handler.get_folder_rootpath(u)
+                    u_folder_info = self.handler.get_folder_info(
+                        folder_id=u,
+                        user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
+                    )
+                    u_folder_rootpath = self.handler.get_folder_rootpath(
+                        u,
+                        user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
+                    )
                     # Folders in order from collection-->child folder-->etc.
                     folder_ids = [i['object']['_id'] for i in u_folder_rootpath]
 
@@ -400,7 +414,8 @@ class DatasetBuilder(DSATool):
 
 
                     child_folder_path_info = self.handler.get_path_info(
-                        path = child_folder_path
+                        path = child_folder_path,
+                        user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
                     )
                     if not child_folder_path_info['_id'] in folders_in_folder:
                         folders_in_folder.append(child_folder_path_info['_id'])
@@ -429,10 +444,13 @@ class DatasetBuilder(DSATool):
 
         else:
             
+            folders_in_folder = []
+            unique_folders = []
             user_folders = ['Private','Public']
             for u_f in user_folders:
                 user_folder_info = self.handler.get_path_info(
-                    path = f'/user/{folder_info["login"]}/{u_f}'
+                    path = f'/user/{folder_info["login"]}/{u_f}',
+                    user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
                 )
 
                 folder_folders.append({
@@ -443,16 +461,23 @@ class DatasetBuilder(DSATool):
                     'Last Updated': user_folder_info['updated']
                 })
 
+                unique_folders.append(user_folder_info['_id'])
+
+
         if show_empty:
             # This is how you get all the empty folders within a folder (does not get child empty folders)
             empty_folders = self.handler.get_folder_folders(
                 folder_id = folder_info['_id'],
-                folder_type = folder_info['_modelType']
+                folder_type = folder_info['_modelType'],
+                user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
             )
             
             for f in empty_folders:
                 if not f['_id'] in folders_in_folder and not f['_id'] in unique_folders:
-                    folder_info = self.handler.gc.get(f'/folder/{f["_id"]}/details')
+                    if not 'current_user' in session_data:
+                        folder_info = self.handler.gc.get(f'/folder/{f["_id"]}/details')
+                    else:
+                        folder_info = self.handler.gc.get(f'/folder/{f["_id"]}/details?token={session_data["current_user"]["token"]}')
                     folder_folders.append(
                         {
                             'Folder Name': f['name'],
@@ -528,20 +553,23 @@ class DatasetBuilder(DSATool):
         
         return slide_card        
 
-    def collection_selection(self, collection_rows, builder_data, collection_div_children):
+    def collection_selection(self, collection_rows, builder_data, collection_div_children,session_data):
         """Callback for when one/multiple collections are selected from the collections table
 
         :param collection_rows: Row indices of selected collections
         :type collection_rows: list
         :param builder_data: Data store on available collections and currently included slides
         :type builder_data: list
-        :param colleciton_div_children: Child cards created by collection_selection
-        :type colleciton_div_children: list
+        :param collection_div_children: Child cards created by collection_selection
+        :type collection_div_children: list
+        :param session_data: Current session information
+        :type session_data: dict
         :return: Children of collection-contents-div (items/folders within selected collections)
         :rtype: list
         """
         selected_collections = get_pattern_matching_value(collection_rows)
         builder_data = json.loads(get_pattern_matching_value(builder_data))
+        session_data = json.loads(session_data)
 
         collection_card_indices = self.get_component_indices(collection_div_children)
 
@@ -559,11 +587,19 @@ class DatasetBuilder(DSATool):
             # For each collection, grab all items and unique folders (as well as those that are not nested in a folder)
             if not 'User: ' in collection_info["Collection Name"]:
                 folder_slides, folder_folders = self.organize_folder_contents(
-                    folder_info = self.handler.get_path_info(f'/collection/{collection_info["Collection Name"]}')
+                    folder_info = self.handler.get_path_info(
+                        f'/collection/{collection_info["Collection Name"]}',
+                        user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
+                    ),
+                    session_data = session_data
                 )
             else:
                 folder_slides, folder_folders = self.organize_folder_contents(
-                    folder_info=self.handler.get_path_info(f'/user/{collection_info["Collection Name"].replace("User: ","")}')
+                    folder_info=self.handler.get_path_info(
+                        f'/user/{collection_info["Collection Name"].replace("User: ","")}',
+                        user_token = session_data['current_user']['token'] if 'current_user' in session_data else None
+                    ),
+                    session_data = session_data
                 )
 
             if len(folder_slides)>0:

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/src/fusion_tools/handler/dataset_uploader.py

@@ -32,12 +32,17 @@ from fusion_tools.handler.resource_selector import DSAResourceSelector
 from girder_job_sequence import Job, Sequence
 from girder_job_sequence.utils import from_list, from_dict
 import threading
+import large_image
+
 
 # Maximum allowed size of uploads (Mb)
 MAX_UPLOAD_SIZE = 1e4
 # Minimum chunk size (Mb)
 MIN_UPLOAD_SIZE = 6
 
+WSI_TYPES = [i for i in list(large_image.listSources()['extensions'].keys()) if not i in ['json','yaml','yml']]
+ANN_TYPES = ['json','geojson','xml','csv']
+
 
 class DSAUploadType:
     """Formatted upload type for a DSAUploader Component.
@@ -305,7 +310,8 @@ class DSAUploadHandler:
                     upload_info
                 )
                 post_response = {
-                    'n_annotations': post_response
+                    'n_annotations': post_response,
+                    '_modelType': 'annotation'
                 }
             else:
                 post_response = r.filename
@@ -1719,7 +1725,7 @@ class DSAUploader(DSATool):
         file_uploads = html.Div([
             dbc.Stack([
                 html.Div([
-                    html.H5(f'{f["name"]}, ({",".join(f["accepted_types"])})',style={'textTransform':'none'}),
+                    html.H5(f'{f["name"]}',style={'textTransform':'none'}),
                     html.Div(
                         self.create_upload_component(
                             file_info = f | {'parentId': folder_info["_id"],'parentType': 'folder', 'fusion_upload_name': f['name'], 'fusion_upload_type': f['type']},
@@ -1730,6 +1736,11 @@ class DSAUploader(DSATool):
                         id = {'type': f'{self.component_prefix}-dsa-uploader-file-upload-div','index': f_idx},
                         style = {'width': '100%'}
                     ),
+                    dbc.Tooltip(
+                        target = {'type': f'{self.component_prefix}-dsa-uploader-file-upload-div','index': f_idx},
+                        placement='top',
+                        children = ','.join(f['accepted_types'])
+                    ),
                     html.Div(
                         id = {'type': f'{self.component_prefix}-dsa-uploader-file-upload-status-div','index': f_idx},
                         children = []

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/src/fusion_tools/utils/shapes.py

@@ -584,7 +584,7 @@ def geojson_to_histomics(geojson_anns: Union[list,dict]):
                     {
                         'type': 'polyline',
                         'user': f['properties'],
-                        'points': [i+[0] for i in f['geometry']['coordinates'][0]]
+                        'points': [list(i)+[0] if type(i)==tuple else i+[0] for i in f['geometry']['coordinates'][0]]
                     }
                     for f in g['features']
                 ]
@@ -841,7 +841,7 @@ def spatially_aggregate(child_geo:dict, parent_geos: list, separate: bool = True
         a_shape = shape(a['geometry'])
         agg_props = {}
         for b_idx,b in enumerate(base_gdf):
-            b_intersect = b.sindex.query(a_shape,predicate='overlaps')
+            b_intersect = b.sindex.query(a_shape,predicate='intersects')
             if len(b_intersect)>0:
                 agg_props[base_names[b_idx]] = []
                 for c in b_intersect:

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/src/fusion_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: fusion-tools
-Version: 3.3.2
+Version: 3.3.4
 Summary: Modular visualization and analysis dashboard creation for high-resolution microscopy images
 Home-page: https://github.com/spborder/fusion-tools
 Author: Sam Border

{fusion_tools-3.3.2 → fusion_tools-3.3.4}/src/fusion_tools.egg-info/SOURCES.txt

@@ -46,6 +46,7 @@ tests/test_extract_recursive.py
 tests/test_feature_annotation.py
 tests/test_feature_extraction.py
 tests/test_file_selector.py
+tests/test_fusion_layout.py
 tests/test_generate_property_dict.py
 tests/test_get_gene_info.py
 tests/test_global_property_plotter.py

fusion_tools-3.3.4/tests/test_fusion_layout.py

@@ -0,0 +1,39 @@
+"""Testing FUSION layout
+"""
+
+import os
+import sys
+sys.path.append('./src/')
+
+from fusion_tools.fusion.vis import get_layout
+
+def main():
+    
+    dsa_url = os.environ.get('DSA_URL')
+    dsa_user = os.environ.get('DSA_USER')
+    dsa_pword = os.environ.get('DSA_PWORD')
+
+    if all([i is None for i in [dsa_url,dsa_user,dsa_pword]]):
+        raise Exception('Need to initialize with at least the environment variable: DSA_URL')
+
+    initial_items = [
+        '6495a4e03e6ae3107da10dc5',
+        '6495a4df3e6ae3107da10dc2'
+    ] 
+
+    args_dict = {
+        'girderApiUrl': dsa_url,
+        'user': dsa_user,
+        'pword': dsa_pword,
+        'initialItems': initial_items,
+        'app_options': {
+            'port': 8050
+        }
+    }
+
+    fusion_vis = get_layout(args_dict)
+
+    fusion_vis.start()
+
+if __name__=='__main__':
+    main()

fusion_tools-3.3.2/src/fusion_tools/fusion/data_types.py

@@ -1,62 +0,0 @@
-"""Defining UploadTypes which are accepted in FUSION
-"""
-
-from fusion_tools.handler.dataset_uploader import DSAUploadType
-
-def get_upload_types(args):
-
-    # Basic Type:
-    basic_type = DSAUploadType(
-        name = "Histology Image",
-        input_files = [],
-        processing_plugins=[],
-        required_metadata=[]
-    )
-
-    # 10x Types:
-    visium_type = DSAUploadType(
-        name = '10x Visium',
-        input_files = [],
-        processing_plugins=[],
-        required_metadata=[]
-    )
-
-    xenium_type = DSAUploadType(
-        name = '10x Xenium',
-        input_files = [],
-        processing_plugins=[],
-        required_metadata=[]
-    )
-
-    hd_type = DSAUploadType(
-        name = "10x Visium HD",
-        input_files = [],
-        processing_plugins=[],
-        required_metadata=[]
-    )
-
-    # MxIF/CODEX
-    mxif_type = DSAUploadType(
-        name = "MxIF / CODEX",
-        input_files = [],
-        processing_plugins = [],
-        required_metadata = []
-    )
-
-    # HuBMAP Processed Dataset
-    hubmap_type = DSAUploadType(
-        name = "HuBMAP Processed",
-        input_files = [],
-        processing_plugins= [],
-        required_metadata=[]
-    )
-
-    return [
-        basic_type,
-        visium_type,
-        xenium_type,
-        hd_type,
-        mxif_type,
-        hubmap_type
-    ]
-