srivarra commited on
Commit
56f4643
1 Parent(s): 2b603f5

added other spatial configs

Browse files
Files changed (1) hide show
  1. ark_example.py +23 -3
ark_example.py CHANGED
@@ -33,6 +33,7 @@ TMA24_R9C1 -> fov10
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  """
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  import datasets
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  import pathlib
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@@ -57,8 +58,6 @@ _LICENSE = "https://github.com/angelolab/ark-analysis/blob/main/LICENSE"
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  # The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
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  # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
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- # _URL_REPO = "https://huggingface.co/datasets/angelolab/ark_example"
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-
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  _URL_DATA = {
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  "image_data": "./data/image_data.zip",
@@ -99,6 +98,16 @@ _URL_DATASET_CONFIGS = {
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  "image_data": _URL_DATA["image_data"],
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  "cell_table": _URL_DATA["cell_table"],
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  "spatial_lda": _URL_DATA["spatial_lda"],
 
 
 
 
 
 
 
 
 
 
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  }
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  }
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@@ -154,7 +163,16 @@ class ArkExample(datasets.GeneratorBasedBuilder):
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  version=VERSION,
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  description="This configuration contains data used by the Spatial LDA - Training and Inference Notebook."
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  ),
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-
 
 
 
 
 
 
 
 
 
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  ]
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  def _info(self):
@@ -167,6 +185,8 @@ class ArkExample(datasets.GeneratorBasedBuilder):
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  "fiber_segmentation",
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  "LDA_preprocessing",
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  "LDA_training_inference",
 
 
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  ]:
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  features = datasets.Features(
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  {f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()}
 
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  """
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+ from ensurepip import version
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  import datasets
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  import pathlib
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  # The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
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  # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
 
 
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  _URL_DATA = {
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  "image_data": "./data/image_data.zip",
 
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  "image_data": _URL_DATA["image_data"],
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  "cell_table": _URL_DATA["cell_table"],
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  "spatial_lda": _URL_DATA["spatial_lda"],
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+ },
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+ "neighborhood_analysis": {
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+ "image_data": _URL_DATA["image_data"],
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+ "cell_table": _URL_DATA["cell_table"],
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+ "deepcell_output": _URL_DATA["deepcell_output"],
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+ },
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+ "pairwise_spatial_enrichment": {
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+ "image_data": _URL_DATA["image_data"],
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+ "cell_table": _URL_DATA["cell_table"],
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+ "deepcell_output": _URL_DATA["deepcell_output"],
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  }
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  }
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  version=VERSION,
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  description="This configuration contains data used by the Spatial LDA - Training and Inference Notebook."
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  ),
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+ datasets.BuilderConfig(
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+ name="neighborhood_analysis",
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+ version=VERSION,
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+ description="This configuration contains data used by the Neighborhood Analysis Notebook."
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+ ),
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+ datasets.BuilderConfig(
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+ name="pairwise_spatial_enrichment",
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+ version=VERSION,
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+ description="This configuration contains data used by the Pairwise Spatial Enrichment Notebook."
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+ )
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  ]
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  def _info(self):
 
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  "fiber_segmentation",
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  "LDA_preprocessing",
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  "LDA_training_inference",
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+ "neighborhood_analysis",
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+ "pairwise_spatial_enrichment",
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  ]:
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  features = datasets.Features(
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  {f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()}