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Merge pull request #5 from NFDI4BIOIMAGE/dev
Adds molecules, status and description panels
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| Original file line number | Diff line number | Diff line change |
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| import json | ||
| from pathlib import Path | ||
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| from omero.util.temp_files import create_path | ||
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| from . import omero_vitessce_settings | ||
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| from vitessce import VitessceConfig, OmeZarrWrapper, MultiImageWrapper | ||
| from vitessce import ViewType as Vt, FileType as Ft, CoordinationType as Ct | ||
| from vitessce import hconcat, vconcat | ||
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| # Get the address of omeroweb from the config | ||
| SERVER = omero_vitessce_settings.SERVER_ADDRESS[1:-1] | ||
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| def get_files_images(obj_type, obj_id, conn): | ||
| """ Gets all the non config files attached to an object, | ||
| and images if the object is a dataset, | ||
| and returns a list of file names and a list of urls | ||
| for the files and eventually the images | ||
| """ | ||
| obj = conn.getObject(obj_type, obj_id) | ||
| file_names = [ | ||
| i for i in obj.listAnnotations() | ||
| if i.OMERO_TYPE().NAME == | ||
| "ome.model.annotations.FileAnnotation_name"] | ||
| file_names = [i for i in file_names | ||
| if i.getFileName().endswith(".csv")] | ||
| file_urls = [i.getId() for i in file_names] | ||
| file_names = [i.getFileName() for i in file_names] | ||
| file_urls = [SERVER + "/webclient/annotation/" + str(i) for i in file_urls] | ||
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| if obj_type == "dataset": | ||
| imgs = list(obj.listChildren()) | ||
| img_urls = [build_zarr_image_url(i.getId()) for i in imgs] | ||
| img_names = [i.getName() for i in imgs] | ||
| else: | ||
| img_urls = [build_zarr_image_url(obj_id)] | ||
| img_names = [obj.getName()] | ||
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| return file_names, file_urls, img_names, img_urls | ||
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| def build_viewer_url(config_id): | ||
| """ Generates urls like: | ||
| http://localhost:4080/omero_vitessce/?config=http://localhost:4080/webclient/annotation/999 | ||
| """ | ||
| return SERVER + "/omero_vitessce/?config=" + SERVER + \ | ||
| "/webclient/annotation/" + str(config_id) | ||
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| def build_zarr_image_url(image_id): | ||
| """ Generates urls like: | ||
| http://localhost:4080/zarr/v0.4/image/99999.zarr/ | ||
| """ | ||
| return SERVER + "/zarr/v0.4/image/" + str(image_id) + ".zarr" | ||
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| def get_attached_configs(obj_type, obj_id, conn): | ||
| """ Gets all the ".json" files attached to an object | ||
| and returns a list of file names and a list of urls | ||
| generated with build_viewer_url | ||
| """ | ||
| obj = conn.getObject(obj_type, obj_id) | ||
| config_files = [i for i in obj.listAnnotations() | ||
| if i.OMERO_TYPE().NAME == | ||
| "ome.model.annotations.FileAnnotation_name"] | ||
| config_urls = [i.getId() for i in config_files | ||
| if i.getFileName().endswith(".json")] | ||
| config_files = [i.getFileName() for i in config_files | ||
| if i.getFileName().endswith(".json")] | ||
| config_urls = [build_viewer_url(i) for i in config_urls] | ||
| return config_files, config_urls | ||
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| def get_details(obj_type, obj_id, conn): | ||
| """ Gets all the ".json" files attached to an object | ||
| and returns a list of file names and a list of urls | ||
| generated with build_viewer_url | ||
| """ | ||
| obj = conn.getObject(obj_type, obj_id) | ||
| name = obj.getName() | ||
| description = obj.getDescription() | ||
| if not description: | ||
| description = "Generated with omero-vitessce" | ||
| return description, name | ||
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| def add_molecules(config_args, vc_dataset): | ||
| """ | ||
| Adds a file with molecule labels and locations to a vitessce dataset | ||
| """ | ||
| vc_dataset = vc_dataset.add_file( | ||
| url=config_args.get("molecules"), | ||
| file_type=Ft.OBS_LOCATIONS_CSV, | ||
| coordination_values={ | ||
| "obsType": "molecule"}, | ||
| options={ | ||
| "obsIndex": config_args.get("molecule id"), | ||
| "obsLocations": [config_args.get("molecule x"), | ||
| config_args.get("molecule y")]}) | ||
| vc_dataset = vc_dataset.add_file( | ||
| url=config_args.get("molecules"), | ||
| file_type=Ft.OBS_LABELS_CSV, | ||
| coordination_values={ | ||
| "obsType": "molecule"}, | ||
| options={ | ||
| "obsIndex": config_args.get("molecule id"), | ||
| "obsLabels": config_args.get("molecule label")}) | ||
| return vc_dataset | ||
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| def add_embeddings(config_args, vc_dataset): | ||
| """ | ||
| Adds a file with cell embeddings to a vitessce dataset | ||
| """ | ||
| vc_dataset = vc_dataset.add_file( | ||
| url=config_args.get("embeddings"), | ||
| file_type=Ft.OBS_EMBEDDING_CSV, | ||
| coordination_values={ | ||
| "obsType": "cell", | ||
| "embeddingType": "cell"}, | ||
| options={ | ||
| "obsIndex": config_args.get("cell id column"), | ||
| "obsEmbedding": [config_args.get("embedding x"), | ||
| config_args.get("embedding y")]}) | ||
| return vc_dataset | ||
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| def add_cell_identities(config_args, vc_dataset): | ||
| """ | ||
| Adds a file with cell identities to a vitessce dataset | ||
| """ | ||
| vc_dataset = vc_dataset.add_file( | ||
| url=config_args.get("cell identities"), | ||
| file_type=Ft.OBS_SETS_CSV, | ||
| coordination_values={"obsType": "cell"}, | ||
| options={ | ||
| "obsIndex": config_args.get("cell id column"), | ||
| "obsSets": [ | ||
| {"name": "Clustering", | ||
| "column": config_args.get("label column")}]}) | ||
| return vc_dataset | ||
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| def create_config(config_args, obj_type, obj_id, conn): | ||
| """ | ||
| Generates a Vitessce config and returns it, | ||
| the results from the form are used as args. | ||
| """ | ||
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| description, name = get_details(obj_type, obj_id, conn) | ||
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| vc = VitessceConfig(schema_version="1.0.16", | ||
| name=name, description=description) | ||
| vc_dataset = vc.add_dataset() | ||
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| img_url = config_args.get("image") | ||
| images = [OmeZarrWrapper(img_url=img_url, name="Image")] | ||
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| sp = vc.add_view(Vt.SPATIAL, dataset=vc_dataset) | ||
| lc = vc.add_view(Vt.LAYER_CONTROLLER, dataset=vc_dataset) | ||
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| displays = [sp] # Heatmap, scatterplot and image | ||
| controllers = [lc] # Spatial layer, gene and cell set selectors | ||
| hists = [] # Histograms and violin plots | ||
| texts = [] # Status and description | ||
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| if config_args.get("cell identities"): | ||
| vc_dataset = add_cell_identities(config_args, vc_dataset) | ||
| os = vc.add_view(Vt.OBS_SETS, dataset=vc_dataset) | ||
| controllers.append(os) | ||
| if config_args.get("expression"): | ||
| vc_dataset = vc_dataset.add_file( | ||
| url=config_args.get("expression"), | ||
| file_type=Ft.OBS_FEATURE_MATRIX_CSV) | ||
| fl = vc.add_view(Vt.FEATURE_LIST, dataset=vc_dataset) | ||
| controllers.append(fl) | ||
| if config_args.get("embeddings"): | ||
| vc_dataset = add_embeddings(config_args, vc_dataset) | ||
| e_type = vc.add_coordination(Ct.EMBEDDING_TYPE)[0] | ||
| e_type.set_value("cell") | ||
| sc = vc.add_view(Vt.SCATTERPLOT, dataset=vc_dataset) | ||
| sc.use_coordination(e_type) | ||
| displays.append(sc) | ||
| if config_args.get("expression") and config_args.get("cell identities"): | ||
| if config_args.get("histograms"): | ||
| fh = vc.add_view(Vt.FEATURE_VALUE_HISTOGRAM, dataset=vc_dataset) | ||
| oh = vc.add_view(Vt.OBS_SET_SIZES, dataset=vc_dataset) | ||
| fd = vc.add_view(Vt.OBS_SET_FEATURE_VALUE_DISTRIBUTION, | ||
| dataset=vc_dataset) | ||
| hists.extend([fh, oh, fd]) | ||
| if config_args.get("heatmap"): | ||
| hm = vc.add_view(Vt.HEATMAP, dataset=vc_dataset) | ||
| displays.append(hm) | ||
| if config_args.get("segmentation"): | ||
| segmentation = OmeZarrWrapper( | ||
| img_url=config_args.get("segmentation"), | ||
| name="Segmentation", is_bitmask=True) | ||
| images.append(segmentation) | ||
| if config_args.get("molecules"): | ||
| vc_dataset = add_molecules(config_args, vc_dataset) | ||
| vc.link_views([sp, lc], c_types=[Ct.SPATIAL_POINT_LAYER], | ||
| c_values=[{"opacity": 1, "radius": 2, "visible": True}]) | ||
| if config_args.get("description"): | ||
| de = vc.add_view(Vt.DESCRIPTION, dataset=vc_dataset) | ||
| texts.append(de) | ||
| if config_args.get("status"): | ||
| st = vc.add_view(Vt.STATUS, dataset=vc_dataset) | ||
| texts.append(st) | ||
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| vc_dataset.add_object(MultiImageWrapper(image_wrappers=images, | ||
| use_physical_size_scaling=True)) | ||
| vc.add_coordination_by_dict({ | ||
| Ct.SPATIAL_ZOOM: 2, | ||
| Ct.SPATIAL_TARGET_X: 0, | ||
| Ct.SPATIAL_TARGET_Y: 0 | ||
| }) | ||
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| displays = hconcat(*displays) | ||
| controllers = hconcat(*controllers) | ||
| if texts: | ||
| texts = vconcat(*texts) | ||
| controllers = hconcat(texts, controllers) | ||
| if hists: | ||
| hists = hconcat(*hists) | ||
| controllers = hconcat(controllers, hists) | ||
| vc.layout(vconcat(displays, controllers)) | ||
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| return vc | ||
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| def attach_config(vc, obj_type, obj_id, filename, conn): | ||
| """ | ||
| Generates a Vitessce config for an OMERO image and returns it. | ||
| Assumes the images is an OME NGFF v0.4 file | ||
| which can be served with omero-web-zarr. | ||
| """ | ||
| config_path = create_path("omero-vitessce", ".tmp", folder=True) | ||
| if not filename.endswith(".json"): | ||
| filename = filename + ".json" | ||
| filename = Path(filename).name # Sanitize filename | ||
|
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| config_path = Path(config_path).joinpath(filename) | ||
| with open(config_path, "w") as outfile: | ||
| json.dump(vc.to_dict(), outfile, indent=4, sort_keys=False) | ||
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| file_ann = conn.createFileAnnfromLocalFile( | ||
| config_path, mimetype="text/plain") | ||
| obj = conn.getObject(obj_type, obj_id) | ||
| obj.linkAnnotation(file_ann) | ||
| return file_ann.getId() |
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