updates to downloading, dataset updates

ark_example.py

@@ -21,6 +21,8 @@ import os
 import datasets
 import pathlib
 import glob
+import pyarrow
+import pprint
 
 # Find for instance the citation on arxiv or on the dataset repo/website
 _CITATION = """\
@@ -48,17 +50,17 @@ _LICENSE = "https://github.com/angelolab/ark-analysis/blob/main/LICENSE"
 
 
 _URL_DATA = {
-    "input_data": "data/input_data.zip",
-    "segmentation/cell_table": "data/segmentation/cell_table.zip",
-    "segmentation/deepcell_output": "data/segmentation/deepcell_output.zip",
+    "image_data": "./data/image_data.zip",
+    "cell_table": "./data/segmentation/cell_table.zip",
+    "deepcell_output": "./data/segmentation/deepcell_output.zip",
 }
 
 _URL_DATASET_CONFIGS = {
-    "nb1": {"input_data": _URL_DATA["input_data"]},
+    "nb1": {"image_data": _URL_DATA["image_data"]},
     "nb2": {
-        "input_data": _URL_DATA["input_data"],
-        "segmentation/cell_table": _URL_DATA["segmentation/cell_table"],
-        "segmentation/deepcell_output": _URL_DATA["segmentation/deepcell_output"],
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+        "deepcell_output": _URL_DATA["deepcell_output"],
     },
 }
 
@@ -112,12 +114,12 @@ class ArkExample(datasets.GeneratorBasedBuilder):
 
     def _info(self):
         # This is the name of the configuration selected in BUILDER_CONFIGS above
-        if self.config.name == "nb1":
-            features = datasets.Features({"Data Path": datasets.Value("string")})
-        elif self.config.name == "nb2":
-            features = datasets.Features({"Data Path": datasets.Value("string")})
+        if self.config.name in ["nb1", "nb2", "nb3", "nb4"]:
+            features = datasets.Features(
+                {f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()}
+            )
         else:
-            features = datasets.Features({"Data Path": datasets.Value("string")})
+            ValueError("dataset name is incorrect.")
         return datasets.DatasetInfo(
             # This is the description that will appear on the datasets page.
             description=_DESCRIPTION,
@@ -142,29 +144,19 @@ class ArkExample(datasets.GeneratorBasedBuilder):
         # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
         # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
         urls = _URL_DATASET_CONFIGS[self.config.name]
-        data_dir = dl_manager.download_and_extract(urls)
+        data_dirs = {}
+        for data_name, url in urls.items():
+            dl_path = pathlib.Path(dl_manager.download_and_extract(url))
+            data_dirs[data_name] = dl_path
 
         return [
             datasets.SplitGenerator(
                 name=self.config.name,
                 # These kwargs will be passed to _generate_examples
-                gen_kwargs={"filepath": pathlib.Path(data_dir)},
+                gen_kwargs={"dataset_paths": data_dirs},
             ),
         ]
 
     # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
-    def _generate_examples(self, filepath: pathlib.Path):
-
-        # Get all TMA paths
-        file_paths = list(pathlib.Path(filepath / "input_data").glob("*"))
-
-        # Loop over all the TMAs
-        for fp in file_paths:
-
-            # Get the file Name
-            fn = fp.stem
-
-            if self.config.name == "fovs":
-                yield fn, {
-                    "Data Path": filepath.as_posix(),
-                }
+    def _generate_examples(self, dataset_paths: dict[str, pathlib.Path]):
+        yield self.config.name, dataset_paths

data/{input_data.zip → image_data.zip}

@@ -1,3 +1,3 @@
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-oid sha256:37eed9f786570426ee8e7cbd9447ef98c82830b7fee064e56cb79b360887489a
+oid sha256:ed9e347c43a846d4fb795d5c139fbb9dd3b1dc112df39a8ff90a79455b8d1420
 size 400326580

data/segmentation/deepcell_output.zip

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:06d50ac056dd766909c4d66e7de3305e18e7dfa4326692395353fea30cd2a8d0
+oid sha256:1de1fc3a72b500f2862d194b1f2c832af9097cb5139c35d1c5fdda1fc7178473
 size 916593