[FIX] Update references to pandas index.get_values()

This function call was deprecated with newer versions of pandas and has been updated to address issue edickie#170
DESm1th · Nov 3, 2022 · c631502 · c631502
1 parent ce1876b
commit c631502
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/ciftify/bin/ciftify_atlas_report.py b/ciftify/bin/ciftify_atlas_report.py
@@ -57,7 +57,7 @@ def report_atlas_overlap(df, label_data, atlas, surf_va_LR, min_percent_overlap
     # write an overlap report to the outputfile
     o_col = '{}_overlap'.format(atlas['name'])
     df[o_col] = ""
-    for pd_idx in df.index.get_values():
+    for pd_idx in df.index.to_numpy():
         df.loc[pd_idx, o_col] = ciftify.report.get_label_overlap_summary(
                         pd_idx, label_data, atlas_data, atlas_dict, surf_va_LR,
                         min_percent_overlap = min_percent_overlap)
@@ -102,7 +102,7 @@ def run_ciftify_dlabel_report(arguments, tmpdir):
 
     # calculate a column of the surface area for row ROIs
     df['area'] = -999
-    for pd_idx in df.index.get_values():
+    for pd_idx in df.index.to_numpy():
         df.loc[pd_idx, 'area']  = ciftify.report.calc_cluster_area(pd_idx,
                                                         label_data, surf_va_LR)
 

diff --git a/ciftify/bin/ciftify_statclust_report.py b/ciftify/bin/ciftify_statclust_report.py
@@ -117,7 +117,7 @@ def report_atlas_overlap(df, label_data, atlas, surf_va_LR, min_percent_overlap
     # write an overlap report to the outputfile
     o_col = '{}_overlap'.format(atlas['name'])
     df[o_col] = ""
-    for pd_idx in df.index.get_values():
+    for pd_idx in df.index.to_numpy():
         df.loc[pd_idx, o_col] = ciftify.report.get_label_overlap_summary(
                         pd_idx, label_data, atlas_data, atlas_dict, surf_va_LR,
                         min_percent_overlap = min_percent_overlap)
@@ -179,7 +179,7 @@ def run_ciftify_dlabel_report(arguments, tmpdir):
 
     # calculate a column of the surface area for row ROIs
     df['area'] = -999
-    for pd_idx in df.index.get_values():
+    for pd_idx in df.index.to_numpy():
         df.loc[pd_idx, 'area']  = ciftify.report.calc_cluster_area(pd_idx,
                                                         label_data, surf_va_LR)
 

diff --git a/ciftify/report.py b/ciftify/report.py
@@ -174,7 +174,7 @@ def calc_label_to_atlas_overlap(clust_id1, clust_atlas1_data,
     o_df = pd.DataFrame.from_dict(clust_atlas2_dict, orient = "index")
     o_df = o_df.rename(index=str, columns={0: "clusterID"})
 
-    for idx_label2 in o_df.index.get_values():
+    for idx_label2 in o_df.index.to_numpy():
         o_df.loc[idx_label2, 'overlap_area'] = calc_overlapping_area(clust_id1, clust_atlas1_data,
                                                         idx_label2, clust_atlas2, surf_va_array)
     return(o_df)
@@ -184,7 +184,7 @@ def overlap_summary_string(overlap_df, min_percent_overlap):
     rdf = overlap_df[overlap_df.overlap_percent > min_percent_overlap]
     rdf = rdf.sort_values(by='overlap_percent', ascending=False)
     result_string = ""
-    for o_label in rdf.index.get_values():
+    for o_label in rdf.index.to_numpy():
         result_string += '{} ({:2.1f}%); '.format(rdf.loc[o_label, 'clusterID'],
                                                   rdf.loc[o_label, 'overlap_percent'])
     return(result_string)