update user interface

Author: xingzhongyu

examples/atlas/demos/main.py

@@ -0,0 +1,93 @@
+# This script finds the most similar dataset from the atlas for a given user-uploaded dataset
+# It calculates similarity scores and returns the best matching dataset along with its configurations
+
+import argparse
+import json
+
+import pandas as pd
+import scanpy as sc
+
+from dance import logger
+from dance.atlas.sc_similarity.anndata_similarity import AnnDataSimilarity, get_anndata
+from dance.settings import DANCEDIR, SIMILARITYDIR
+
+
+def calculate_similarity(source_data, tissue, atlas_datasets, reduce_error, in_query):
+    """Calculate similarity scores between source data and atlas datasets.
+
+    Args:
+        source_data: User uploaded AnnData object
+        tissue: Target tissue type
+        atlas_datasets: List of candidate datasets from atlas
+        reduce_error: Flag for error reduction mode - when True, applies a significant penalty
+                     to configurations in the atlas that produced errors
+        in_query: Flag for query mode - when True, ranks similarity based on query performance,
+                 when False, ranks based on inter-atlas comparison
+
+    Returns:
+        Dictionary containing similarity scores for each atlas dataset
+
+    """
+    with open(
+            SIMILARITYDIR /
+            f"data/similarity_weights_results/{'reduce_error_' if reduce_error else ''}{'in_query_' if in_query else ''}sim_dict.json",
+            encoding='utf-8') as f:
+        sim_dict = json.load(f)
+    feature_name = sim_dict[tissue]["feature_name"]
+    w1 = sim_dict[tissue]["weight1"]
+    w2 = 1 - w1
+    ans = {}
+    for target_file in atlas_datasets:
+        logger.info(f"calculating similarity for {target_file}")
+        atlas_data = get_anndata(tissue=tissue.capitalize(), species="human", filetype="h5ad",
+                                 train_dataset=[f"{target_file}"], data_dir=str(DANCEDIR / "examples/tuning/temp_data"))
+        similarity_calculator = AnnDataSimilarity(adata1=source_data, adata2=atlas_data, sample_size=10,
+                                                  init_random_state=42, n_runs=1, tissue=tissue)
+        sim_target = similarity_calculator.get_similarity_matrix_A2B(methods=[feature_name, "metadata_sim"])
+        ans[target_file] = sim_target[feature_name] * w1 + sim_target["metadata_sim"] * w2
+    return ans
+
+
+def main(args):
+    """Main function to process user data and find the most similar atlas dataset.
+
+    Args:
+        args: Arguments containing:
+            - tissue: Target tissue type
+            - data_dir: Directory containing the source data
+            - source_file: Name of the source file
+
+    Returns:
+        tuple containing:
+        - ans_file: ID of the most similar dataset
+        - ans_conf: Preprocess configuration dictionary for different cell type annotation methods
+        - ans_value: Similarity score of the best matching dataset
+
+    """
+    reduce_error = False
+    in_query = True
+    tissue = args.tissue
+    tissue = tissue.lower()
+    conf_data = pd.read_excel(SIMILARITYDIR / "data/Cell Type Annotation Atlas.xlsx", sheet_name=tissue)
+    atlas_datasets = list(conf_data[conf_data["queryed"] == False]["dataset_id"])
+    source_data = sc.read_h5ad(f"{args.data_dir}/{args.source_file}.h5ad")
+
+    ans = calculate_similarity(source_data, tissue, atlas_datasets, reduce_error, in_query)
+    ans_file = max(ans, key=ans.get)
+    ans_value = ans[ans_file]
+    ans_conf = {
+        method: conf_data.loc[conf_data["dataset_id"] == ans_file, f"{method}_step2_best_yaml"].iloc[0]
+        for method in ["cta_celltypist", "cta_scdeepsort", "cta_singlecellnet", "cta_actinn"]
+    }
+    return ans_file, ans_conf, ans_value
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--tissue", default="Brain")
+    parser.add_argument("--data_dir", default=str(DANCEDIR / "examples/tuning/temp_data/train/human"))
+    parser.add_argument("--source_file", default="human_Brain364348b4-bc34-4fe1-a851-60d99e36cafa_data")
+
+    args = parser.parse_args()
+    ans_file, ans_conf, ans_value = main(args)
+    print(ans_file, ans_conf, ans_value)

tests/atlas/test_atlas.py

@@ -0,0 +1,74 @@
+"""
+Test suite for the Atlas similarity calculation functionality.
+This test verifies that the main function correctly returns:
+1. The most similar dataset from the atlas
+2. Its corresponding configuration settings
+3. The similarity score
+
+The test ensures:
+- Return value types are correct
+- Similarity score is within valid range (0-1)
+- Configuration dictionary contains all required cell type annotation methods
+"""
+
+import json
+import sys
+
+import pandas as pd
+
+from dance.settings import ATLASDIR, DANCEDIR, SIMILARITYDIR
+
+sys.path.append(str(ATLASDIR))
+from demos.main import main
+
+from dance import logger
+
+
+def test_main():
+    # Construct test parameters with a sample Brain tissue dataset
+    class Args:
+        tissue = "Brain"
+        data_dir = str(DANCEDIR / "examples/tuning/temp_data/train/human")
+        source_file = "human_Brain364348b4-bc34-4fe1-a851-60d99e36cafa_data"
+
+    args = Args()
+    logger.info(f"testing main with args: {args}")
+    source_id = "3643"
+
+    # Execute main function with test parameters
+    ans_file, ans_conf, ans_value = main(args)
+
+    # Verify return value types and ranges
+    assert isinstance(ans_file, str), "ans_file should be a string type"
+    assert isinstance(ans_value, float), "ans_value should be a float type"
+    assert 0 <= ans_value <= 1, "Similarity value should be between 0 and 1"
+
+    # Verify configuration dictionary structure and content
+    expected_methods = ["cta_celltypist", "cta_scdeepsort", "cta_singlecellnet", "cta_actinn"]
+    assert isinstance(ans_conf, dict), "ans_conf should be a dictionary type"
+    assert set(ans_conf.keys()) == set(expected_methods), "ans_conf should contain all expected methods"
+    assert all(isinstance(v, str) for v in ans_conf.values()), "All configuration values should be string type"
+
+    # Verify consistency with Excel spreadsheet results
+    data = pd.read_excel(SIMILARITYDIR / f"data/new_sim/{args.tissue.lower()}_similarity.xlsx", sheet_name=source_id,
+                         index_col=0)
+    reduce_error = False
+    in_query = True
+    # Read weights
+    with open(
+            SIMILARITYDIR /
+            f"data/similarity_weights_results/{'reduce_error_' if reduce_error else ''}{'in_query_' if in_query else ''}sim_dict.json",
+            encoding='utf-8') as f:
+        sim_dict = json.load(f)
+        feature_name = sim_dict[args.tissue.lower()]["feature_name"]
+        w1 = sim_dict[args.tissue.lower()]["weight1"]
+        w2 = 1 - w1
+
+    # Calculate similarity in Excel
+    data.loc["similarity"] = data.loc[feature_name] * w1 + data.loc["metadata_sim"] * w2
+    expected_file = data.loc["similarity"].idxmax()
+    expected_value = data.loc["similarity", expected_file]
+
+    # Verify result consistency with Excel
+    assert abs(ans_value - expected_value) < 1e-4, "Calculated similarity value does not match Excel value"
+    assert ans_file == expected_file, "Selected most similar dataset does not match Excel result"