ark_example.py docs

ark_example.py

@@ -14,7 +14,23 @@
 
 """
 This dataset contains example data for running through the multiplexed imaging data pipeline in
-Ark Analysis: https://github.com/angelolab/ark-analysis
+Ark Analysis: https://github.com/angelolab/ark-analysis.
+
+
+Dataset Fov renaming:
+
+TMA2_R8C3 -> fov0
+TMA6_R4C5 -> fov1
+TMA7_R5C4 -> fov2
+TMA10_R7C3 -> fov3
+TMA11_R9C6 -> fov4
+TMA13_R8C5 -> fov5
+TMA17_R9C2 -> fov6
+TMA18_R9C2 -> fov7
+TMA21_R2C5 -> fov8
+TMA21_R12C6 -> fov9
+TMA24_R9C1 -> fov10
+
 """
 
 import datasets
@@ -74,22 +90,6 @@ _URL_DATASET_CONFIGS = {
 }
 
 
-"""
-Dataset Fov renaming:
-
-TMA2_R8C3 -> fov0
-TMA6_R4C5 -> fov1
-TMA7_R5C4 -> fov2
-TMA10_R7C3 -> fov3
-TMA11_R9C6 -> fov4
-TMA13_R8C5 -> fov5
-TMA17_R9C2 -> fov6
-TMA18_R9C2 -> fov7
-TMA21_R2C5 -> fov8
-TMA21_R12C6 -> fov9
-TMA24_R9C1 -> fov10
-"""
-
 # Note: Name of the dataset usually match the script name with CamelCase instead of snake_case
 class ArkExample(datasets.GeneratorBasedBuilder):
     """The Dataset consists of 11 FOVs"""
@@ -109,17 +109,17 @@ class ArkExample(datasets.GeneratorBasedBuilder):
         datasets.BuilderConfig(
             name="segment_image_data",
             version=VERSION,
-            description="This configuration contains data used by notebook 1; contains only the 12 FOVs, and their 22 channels.",
+            description="This configuration contains data used by notebook 1 - Segment Image Data.",
         ),
         datasets.BuilderConfig(
             name="cluster_pixels",
             version=VERSION,
-            description="This configuration contains data used by notebook 2, Pixel Clustering (Pixie Pipeline #1).",
+            description="This configuration contains data used by notebook 2 - Pixel Clustering (Pixie Pipeline #1).",
         ),
         datasets.BuilderConfig(
             name="cluster_cells",
             version=VERSION,
-            description="This configuration contains data used by notebook 3, Cell Clustering (Pixie Pipeline #2).",
+            description="This configuration contains data used by notebook 3 - Cell Clustering (Pixie Pipeline #2).",
         ),
         datasets.BuilderConfig(
             name="post_clustering",
@@ -137,15 +137,10 @@ class ArkExample(datasets.GeneratorBasedBuilder):
             "post_clustering",
         ]:
             features = datasets.Features(
-                {
-                    f: datasets.Value("string")
-                    for f in _URL_DATASET_CONFIGS[self.config.name].keys()
-                }
+                {f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()}
             )
         else:
-            ValueError(
-                f"Dataset name is incorrect, options include {list(_URL_DATASET_CONFIGS.keys())}"
-            )
+            ValueError(f"Dataset name is incorrect, options include {list(_URL_DATASET_CONFIGS.keys())}")
         return datasets.DatasetInfo(
             # This is the description that will appear on the datasets page.
             description=_DESCRIPTION,
@@ -163,12 +158,7 @@ class ArkExample(datasets.GeneratorBasedBuilder):
         )
 
     def _split_generators(self, dl_manager):
-        # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
-        # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name
-
-        # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLS
-        # 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
+        # This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
         urls = _URL_DATASET_CONFIGS[self.config.name]
         data_dirs = {}
         for data_name, url in urls.items():