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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| from __future__ import annotations | ||
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| from functools import partial | ||
| from typing import Optional | ||
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| import numpy as np | ||
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| def gen_obs_embedding_schema(options: dict, paths: Optional[list[str]] = None, names: Optional[list[str]] = None, dims: Optional[list[list[int]]] = None): | ||
| if paths is not None: | ||
| if "obsEmbedding" not in options: | ||
| options["obsEmbedding"] = [] | ||
| if names is not None: | ||
| for key, mapping in zip(paths, names): | ||
| options["obsEmbedding"].append({ | ||
| "path": key, | ||
| "dims": [0, 1], | ||
| "embeddingType": mapping | ||
| }) | ||
| else: | ||
| for mapping in paths: | ||
| mapping_key = mapping.split('/')[-1] | ||
| options["obsEmbedding"].append({ | ||
| "path": mapping, | ||
| "dims": [0, 1], | ||
| "embeddingType": mapping_key | ||
| }) | ||
| if dims is not None: | ||
| if "obsEmbedding" not in options: | ||
| options["obsEmbedding"] = [] | ||
| for dim_i, dim in enumerate(dims): | ||
| options["obsEmbedding"][dim_i]['dims'] = dim | ||
| return options | ||
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| def gen_obs_sets_schema(options: dict, paths: Optional[list[str]] = None, names: Optional[list[str]] = None): | ||
| if paths is not None: | ||
| options["obsSets"] = [] | ||
| if names is not None: | ||
| names = names | ||
| else: | ||
| names = [] | ||
| for obs in paths: | ||
| obs_end_path = obs.split('/')[-1] | ||
| names += [obs_end_path] | ||
| for obs, name in zip(paths, names): | ||
| options["obsSets"].append({ | ||
| "name": name, | ||
| "path": obs | ||
| }) | ||
| return options | ||
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| def gen_obs_feature_matrix_schema(options: dict, matrix_path: Optional[str] = None, var_filter_path: Optional[str] = None, init_var_filter_path: Optional[str] = None): | ||
| if matrix_path is not None: | ||
| options["obsFeatureMatrix"] = { | ||
| "path": matrix_path | ||
| } | ||
| if var_filter_path is not None: | ||
| options["obsFeatureMatrix"]["featureFilterPath"] = var_filter_path | ||
| if init_var_filter_path is not None: | ||
| options["obsFeatureMatrix"]["initialFeatureFilterPath"] = init_var_filter_path | ||
| return options | ||
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| def gen_obs_labels_schema(options: dict, paths: Optional[list[str]] = None, names: Optional[list[str]] = None): | ||
| if paths is not None: | ||
| if names is not None and len(paths) == len(names): | ||
| # A name was provided for each path element, so use those values. | ||
| names = names | ||
| else: | ||
| # Names were not provided for each path element, | ||
| # so fall back to using the final part of each path for the names. | ||
| names = [labels_path.split('/')[-1] for labels_path in paths] | ||
| obs_labels = [] | ||
| for path, name in zip(paths, names): | ||
| obs_labels.append({"path": path, "obsLabelsType": name}) | ||
| options["obsLabels"] = obs_labels | ||
| return options | ||
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| def gen_path_schema(key: str, path: Optional[str], options: dict): | ||
| if path is not None: | ||
| options[key] = { | ||
| "path": path | ||
| } | ||
| return options | ||
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| gen_obs_locations_schema = partial(gen_path_schema, "obsLocations") | ||
| gen_obs_segmentations_schema = partial(gen_path_schema, "obsSegmentations") | ||
| gen_obs_spots_schema = partial(gen_path_schema, "obsSpots") | ||
| gen_obs_points_schema = partial(gen_path_schema, "obsPoints") | ||
| gen_feature_labels_schema = partial(gen_path_schema, "featureLabels") | ||
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| def gen_sdata_image_schema(options, path: str, coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict: | ||
| if path is not None: | ||
| options["image"] = { | ||
| "path": path | ||
| } | ||
| if affine_transformation is not None: | ||
| options["image"]['coordinateTransformations'] = affine_transformation | ||
| if coordinate_system is not None: | ||
| options["image"]['coordinateSystem'] = coordinate_system | ||
| return options | ||
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| def gen_sdata_labels_schema(options, path: str, table_path: str = "tables/table", coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None) -> dict: | ||
| if path is not None: | ||
| options["labels"] = { | ||
| "path": path | ||
| } | ||
| if table_path is not None: | ||
| options["labels"]['tablePath'] = table_path | ||
| if affine_transformation is not None: | ||
| options["labels"]['coordinateTransformations'] = affine_transformation | ||
| if coordinate_system is not None: | ||
| options["labels"]['coordinateSystem'] = coordinate_system | ||
| return options | ||
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| def gen_sdata_obs_spots_schema(options: dict, shapes_path: Optional[str] = None, table_path: str = "tables/table", region: Optional[str] = None, coordinate_system: Optional[str] = None) -> dict: | ||
| if shapes_path is not None: | ||
| options['obsSpots'] = { | ||
| "path": shapes_path, | ||
| "tablePath": table_path, | ||
| "region": region | ||
| } | ||
| if coordinate_system is not None: | ||
| options['obsSpots']['coordinateSystem'] = coordinate_system | ||
| return options |
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