Fix duplicate Key values

scverse · Jul 19, 2023 · 21733f8 · 21733f8
1 parent 4595f5d
commit 21733f8
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Showing 2 changed files with 15 additions and 20 deletions.
diff --git a/src/spatialdata_io/_constants/_constants.py b/src/spatialdata_io/_constants/_constants.py
@@ -162,36 +162,31 @@ class StereoseqKeys(ModeEnum):
     TISSUECUT_GEF = ".tissuecut.gef"
     TISSUE_GEM = ".tissue.gem.gz"
     # transcripts
-    TRANSCRIPTS_X = "x"
-    TRANSCRIPTS_Y = "y"
     FEATURE_KEY = "gene"
     GENE_NAME = "geneName"
-    GENE_OFFSET = "offset"
     CELL_COUNT = "cellCount"
-    EXP_COUNT = "expCount"
     MAX_MID_COUNT = "maxMIDcount"
     GENE_EXP = "geneExp"
     GENE_COUNT = "count"
     EXPRESSION = "expression"
     EXON = "exon"
     # cells
     CELL_ID = "id"
-    CELL_X = "x"
-    CELL_Y = "y"
-    CELL_OFFSET = "offset"
     GENECOUNT = "geneCount"
-    EXPCOUNT = "expCount"
     DNBCOUNT = "dnbCount"
     CELL_AREA = "area"
     CELL_TYPE_ID = "cellTypeID"
     CLUSTER_ID = "clusterID"
     CELL_BIN = "cellBin"
     CELL_EXON = "cellExon"
     CELL_DATASET = "cell"
-    GENE_DATASET = "gene"
     GENE_EXON = "geneExon"
     CELL_BORDER = "cellBorder"
     # metadata
+    EXP_COUNT
+    OFFSET = "offset"
+    COORD_X = "x"
+    COORD_Y = "y"
     SPATIAL_KEY = "spatial"
     REGION = "cells"
     REGION_KEY = "region"

diff --git a/src/spatialdata_io/readers/stereoseq.py b/src/spatialdata_io/readers/stereoseq.py
@@ -90,28 +90,28 @@ def stereoseq(
         cellbin_gef[StereoseqKeys.CELL_BIN][StereoseqKeys.CELL_DATASET][:],
         columns=[
             StereoseqKeys.CELL_ID,
-            StereoseqKeys.CELL_X,
-            StereoseqKeys.CELL_Y,
-            StereoseqKeys.CELL_OFFSET,
+            StereoseqKeys.COORD_X,
+            StereoseqKeys.COORD_Y,
+            StereoseqKeys.OFFSET,
             StereoseqKeys.GENECOUNT,
-            StereoseqKeys.EXPCOUNT,
+            StereoseqKeys.EXP_COUNT,
             StereoseqKeys.DNBCOUNT,
             StereoseqKeys.CELL_AREA,
             StereoseqKeys.CELL_TYPE_ID,
             StereoseqKeys.CLUSTER_ID,
         ],
     )
 
-    obsm_spatial = obs[[StereoseqKeys.CELL_X, StereoseqKeys.CELL_Y]].to_numpy()
-    obs = obs.drop([StereoseqKeys.CELL_X, StereoseqKeys.CELL_Y], axis=1)
+    obsm_spatial = obs[[StereoseqKeys.COORD_X, StereoseqKeys.COORD_Y]].to_numpy()
+    obs = obs.drop([StereoseqKeys.COORD_X, StereoseqKeys.COORD_Y], axis=1)
     obs[StereoseqKeys.CELL_EXON] = cellbin_gef[StereoseqKeys.CELL_BIN][StereoseqKeys.CELL_EXON][:]
 
     # add gene info to var
     var = pd.DataFrame(
-        cellbin_gef[StereoseqKeys.CELL_BIN][StereoseqKeys.GENE_DATASET][:],
+        cellbin_gef[StereoseqKeys.CELL_BIN][StereoseqKeys.FEATURE_KEY][:],
         columns=[
             StereoseqKeys.GENE_NAME,
-            StereoseqKeys.GENE_OFFSET,
+            StereoseqKeys.OFFSET,
             StereoseqKeys.CELL_COUNT,
             StereoseqKeys.EXP_COUNT,
             StereoseqKeys.MAX_MID_COUNT,
@@ -149,15 +149,15 @@ def stereoseq(
         # get gene info
         arr = squarebin_gef[StereoseqKeys.GENE_EXP][i][StereoseqKeys.FEATURE_KEY][:]
         df_gene = pd.DataFrame(
-            arr, columns=[StereoseqKeys.FEATURE_KEY, StereoseqKeys.GENE_OFFSET, StereoseqKeys.GENE_COUNT]
+            arr, columns=[StereoseqKeys.FEATURE_KEY, StereoseqKeys.OFFSET, StereoseqKeys.GENE_COUNT]
         )
         df_gene[StereoseqKeys.FEATURE_KEY] = df_gene[StereoseqKeys.FEATURE_KEY].str.decode("utf-8")
         df_gene = df_gene.rename(columns={"count": "counts"})  # #138 df_gene.count will throw error if not renamed
 
         # create df for points model
         arr = squarebin_gef[StereoseqKeys.GENE_EXP][i][StereoseqKeys.EXPRESSION][:]
         df_points = pd.DataFrame(
-            arr, columns=[StereoseqKeys.TRANSCRIPTS_X, StereoseqKeys.TRANSCRIPTS_Y, StereoseqKeys.GENE_COUNT]
+            arr, columns=[StereoseqKeys.COORD_X, StereoseqKeys.COORD_Y, StereoseqKeys.GENE_COUNT]
         )
         df_points = df_points.astype(np.float32)
         df_points[StereoseqKeys.EXON] = squarebin_gef[StereoseqKeys.GENE_EXP][i][StereoseqKeys.EXON][:]
@@ -189,7 +189,7 @@ def stereoseq(
     points = {
         f"transcripts_{bin}": PointsModel.parse(
             df,
-            coordinates={"x": StereoseqKeys.TRANSCRIPTS_X, "y": StereoseqKeys.TRANSCRIPTS_Y},
+            coordinates={"x": StereoseqKeys.COORD_X, "y": StereoseqKeys.COORD_Y},
             feature_key=StereoseqKeys.FEATURE_KEY,
         )
         for bin, df in df_by_bin.items()