Spatial Analysis Datasets (#5)

- added dataconfigs for Fiber Seg, LDA Preprocessing + Training / Inference (9ed93a8dfef9d45e5fb55d45b0c26687b5b189d0)
- add configs to _info (5b0b1187d2703bad6e4a2e73bba41a9efe10ded5)
- remove type hints (2b603f506bf3780cdea2cc6ffcc5d53bc0d5f759)
- added other spatial configs (56f4643c924c481f58689df612887f753bad93fb)
- added post-clustering files (3d4387e8acbcc0863bee5231be80527bf10992d8)
- put in folder (8f872c6b8caf28ca04fb220bac672e3eddd27ae3)
- put in folder (27560f4f4131d66aa0cb1beeb680ab47f9a6cbfa)

ark_example.py

@@ -57,8 +57,6 @@ _LICENSE = "https://github.com/angelolab/ark-analysis/blob/main/LICENSE"
 
 # The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
 # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
-# _URL_REPO = "https://huggingface.co/datasets/angelolab/ark_example"
-
 
 _URL_DATA = {
     "image_data": "./data/image_data.zip",
@@ -66,6 +64,8 @@ _URL_DATA = {
     "deepcell_output": "./data/segmentation/deepcell_output.zip",
     "example_pixel_output_dir": "./data/pixie/example_pixel_output_dir.zip",
     "example_cell_output_dir": "./data/pixie/example_cell_output_dir.zip",
+    "spatial_lda": "./data/spatial_analysis/spatial_lda.zip",
+    "post_clustering": "./data/post_clustering.zip"
 }
 
 _URL_DATASET_CONFIGS = {
@@ -87,6 +87,29 @@ _URL_DATASET_CONFIGS = {
         "deepcell_output": _URL_DATA["deepcell_output"],
         "example_cell_output_dir": _URL_DATA["example_cell_output_dir"],
     },
+    "fiber_segmentation": {
+        "image_data": _URL_DATA["image_data"],
+    },
+    "LDA_preprocessing": {
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+    },
+    "LDA_training_inference": {
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+        "spatial_lda": _URL_DATA["spatial_lda"],
+    },
+    "neighborhood_analysis": {
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+        "deepcell_output": _URL_DATA["deepcell_output"],
+    },
+    "pairwise_spatial_enrichment": {
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+        "deepcell_output": _URL_DATA["deepcell_output"],
+        "post_clustering": _URL_DATA["post_clustering"],
+    }
 }
 
 
@@ -94,15 +117,7 @@ _URL_DATASET_CONFIGS = {
 class ArkExample(datasets.GeneratorBasedBuilder):
     """The Dataset consists of 11 FOVs"""
 
-    VERSION = datasets.Version("0.0.3")
-
-    # This is an example of a dataset with multiple configurations.
-    # If you don't want/need to define several sub-sets in your dataset,
-    # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
-
-    # If you need to make complex sub-parts in the datasets with configurable options
-    # You can create your own builder configuration class to store attribute, inheriting from datasets.BuilderConfig
-    # BUILDER_CONFIG_CLASS = MyBuilderConfig
+    VERSION = datasets.Version("0.0.4")
 
     # You will be able to load one or the other configurations in the following list with
     BUILDER_CONFIGS = [
@@ -126,6 +141,31 @@ class ArkExample(datasets.GeneratorBasedBuilder):
             version=VERSION,
             description="This configuration contains data used by notebook 4 - Post Clustering.",
         ),
+        datasets.BuilderConfig(
+            name="fiber_segmentation",
+            version=VERSION,
+            description="This configuration contains data used by the Fiber Segmentation Notebook.",
+        ),
+        datasets.BuilderConfig(
+            name="LDA_preprocessing",
+            version=VERSION,
+            description="This configuration contains data used by the Spatial LDA - Preprocessing Notebook."
+        ),
+        datasets.BuilderConfig(
+            name="LDA_training_inference",
+            version=VERSION,
+            description="This configuration contains data used by the Spatial LDA - Training and Inference Notebook."
+        ),
+        datasets.BuilderConfig(
+            name="neighborhood_analysis",
+            version=VERSION,
+            description="This configuration contains data used by the Neighborhood Analysis Notebook."
+        ),
+        datasets.BuilderConfig(
+            name="pairwise_spatial_enrichment",
+            version=VERSION,
+            description="This configuration contains data used by the Pairwise Spatial Enrichment Notebook."
+        )
     ]
 
     def _info(self):
@@ -135,6 +175,11 @@ class ArkExample(datasets.GeneratorBasedBuilder):
             "cluster_pixels",
             "cluster_cells",
             "post_clustering",
+            "fiber_segmentation",
+            "LDA_preprocessing",
+            "LDA_training_inference",
+            "neighborhood_analysis",
+            "pairwise_spatial_enrichment",
         ]:
             features = datasets.Features(
                 {f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()}

data/post_clustering.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:639326276833f53e4e831b72c835ea9b2376a964b04504f5d6629f4439a46883
+size 9719468

data/spatial_analysis/spatial_lda.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7028b6b132fa51eee9ebb99f9f79106e9a6f1505cd92604cc1a6dce6f99aee7a
+size 3486371