working

Author: seohyonkim

src/metrics/ksim/config.vsh.yaml

@@ -19,10 +19,6 @@ info:
       maximize: true
 
 arguments:
-  - name: "--rep"
-    type: "string"
-    default: "pca"
-    description: The embedding representation to consider.
   - name: "--K"
     type: "integer"
     default: 24

src/metrics/ksim/script.py

@@ -1,25 +1,9 @@
 import anndata as ad
 import sys
 import pegasus as pg
+import pegasusio
+from scipy.sparse import csr_matrix
 
-## VIASH START
-# Note: this section is auto-generated by viash at runtime. To edit it, make changes
-# in config.vsh.yaml and then run `viash config inject config.vsh.yaml`.
-par = {
-  'input_integrated': 'resources_test/task_batch_integration/cxg_immune_cell_atlas/integrated_full.h5ad',
-  'input_solution': 'resources_test/.../solution.h5ad',
-  'output': 'output.h5ad',
-  "rep": "pca",
-  "K": 24,
-  "min_rate": 0.9,
-  "n_jobs": -1,
-  "random_state": 0,
-  "use_cache": True
-}
-meta = {
-  'name': 'ksim'
-}
-## VIASH END
 
 sys.path.append(meta["resources_dir"])
 from read_anndata_partial import read_anndata
@@ -28,20 +12,24 @@
 adata = read_anndata(par['input_integrated'], obs='obs', obsm='obsm', uns='uns')
 adata.obs = read_anndata(par['input_solution'], obs='obs').obs
 adata.uns |= read_anndata(par['input_solution'], uns='uns').uns
+print(adata)
+
+print('Convert to pegasusio.MultimodalData...', flush=True)
+adata.X = csr_matrix(adata.shape)
+mmdata = pegasusio.MultimodalData(adata)
 
 print('Compute metrics', flush=True)
 score = pg.calc_kSIM(
-    adata,
+    mmdata,
     attr='cell_type',
-    rep=par["rep"],
+    rep='emb',
     K=par["K"],
     min_rate=par["min_rate"],
     n_jobs=par["n_jobs"],
     random_state=par["random_state"],
     use_cache=par["use_cache"]
-)[1]
-
-# TODO RETURNS A TOUPLE OF TWO THINGS: kSIM_mean (float) – Mean kSIM rate over all the cells., kSIM_accept_rate (float) – kSIM Acceptance rate of the sample
+)
+print("score:", score)
 
 print('Create output AnnData object', flush=True)
 output = ad.AnnData(