[single cell ephys] add data overview

single_cell_intracellular_spikes/explore.py

@@ -5,7 +5,19 @@ import os
 from IPython import embed
 
 
-def metadata_overview(nf, sec_type=None, sec_name=None):
+def metadata_overview(nf):
+    assert(nf and isinstance(nf, nix.pycore.file.File) and nf.is_open)
+
+    print("Print some of the stored metadata")
+    print_metadata(nix_file, sec_type="recording", sec_name="recording", max_depth=0)
+    print("\n")
+    print_metadata(nix_file, sec_name="subject")
+    print("\n")
+    print_metadata(nix_file, sec_name="cell")
+    print("\n")
+
+
+def print_metadata(nf, sec_type=None, sec_name=None, max_depth=-1):
     """Display stored metadata using the section's pprint function.
 
     If the desired section name or type are provided, the find_sections
@@ -18,7 +30,10 @@ def metadata_overview(nf, sec_type=None, sec_name=None):
     Keyword arguments:
     sec_type --- string: the section type (default None)
     sec_name --- string, the section name (default None)
+    max_depth --- int, the maximum depth of the metadata tree (default -1, i.e. unlimited)
     """
+    assert(not sec_name or isinstance(sec_name, str))
+    assert(not sec_type or isinstance(sec_type, str))
 
     sec_type = sec_type.lower() if sec_type else None
     sec_name = sec_name.lower() if sec_name else None
@@ -27,7 +42,28 @@ def metadata_overview(nf, sec_type=None, sec_name=None):
                                 and (sec_name and sec_name in s.name.lower() or not sec_name)
                                 or (not sec_name and not sec_type))
     for s in sections:
-        s.pprint()
+        s.pprint(max_depth=max_depth)
+
+
+def data_overview(nf):
+    assert(nf and isinstance(nf, nix.pycore.file.File) and nf.is_open)
+    b = nf.blocks[0]
+
+    print("Regularly sampled data:")
+    regular_sampled_data = [da for da in b.data_arrays if da.dimensions[0].dimension_type == nix.DimensionType.Sample]
+    for rsd in regular_sampled_data:
+        print("\t%s, size: %s" % (rsd.name, str(rsd.shape)))
+
+    print("Event data:")
+    event_data = [da for da in b.data_arrays if da.dimensions[0].dimension_type == nix.DimensionType.Range]
+    for ed in event_data:
+        print("\t%s, size: %s" % (ed.name, str(ed.shape)))
+
+    print("Sets:")
+    set_data = [da for da in b.data_arrays if da.dimensions[0].dimension_type == nix.DimensionType.Set]
+    for sd in set_data:
+        print("\t%s, size: %s" % (sd.name, str(sd.shape)))
+
 
 
 if __name__ == "__main__":
@@ -36,9 +72,9 @@ if __name__ == "__main__":
         print("Example file was not found")
         exit()
     nix_file = nix.File.open(example_file, nix.FileMode.ReadOnly)
-    embed()
-    metadata_overview(nix_file, sec_type="recording", sec_name="recording")
 
-    nix_file.close()
+    metadata_overview(nix_file)
 
+    data_overview(nix_file)
 
+    nix_file.close()