FIX: Purge nx.read_gpickle

nipy · effigies · Jan 29, 2023 · Jan 28, 2023 · Jan 28, 2023 · Jan 28, 2023
commit f20035c303a88fba3e207ac60388397665bb97be
diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py
@@ -18,6 +18,13 @@
 from .base import CFFBaseInterface, have_cfflib
 
 
+def _read_pickle(fname):
+    import pickle
+
+    with open(fname, 'rb') as f:
+        return pickle.load(f)
+
+
 class CFFConverterInputSpec(BaseInterfaceInputSpec):
     graphml_networks = InputMultiPath(
         File(exists=True), desc="list of graphML networks"
@@ -135,7 +142,7 @@ def _run_interface(self, runtime):
             unpickled = []
             for ntwk in self.inputs.gpickled_networks:
                 _, ntwk_name, _ = split_filename(ntwk)
-                unpickled = nx.read_gpickle(ntwk)
+                unpickled = _read_pickle(ntwk)
                 cnet = cf.CNetwork(name=ntwk_name)
                 cnet.set_with_nxgraph(unpickled)
                 a.add_connectome_network(cnet)

diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py
@@ -24,13 +24,18 @@
 iflogger = logging.getLogger("nipype.interface")
 
 
+def _read_pickle(fname):
+    with open(fname, 'rb') as f:
+        return pickle.load(f)
+
+
 def ntwks_to_matrices(in_files, edge_key):
-    first = nx.read_gpickle(in_files[0])
+    first = _read_pickle(in_files[0])
     files = len(in_files)
     nodes = len(first.nodes())
     matrix = np.zeros((nodes, nodes, files))
     for idx, name in enumerate(in_files):
-        graph = nx.read_gpickle(name)
+        graph = _read_pickle(name)
         for u, v, d in graph.edges(data=True):
             try:
                 graph[u][v]["weight"] = d[
@@ -162,7 +167,7 @@ def _run_interface(self, runtime):
         else:
             node_ntwk_name = self.inputs.in_group1[0]
 
-        node_network = nx.read_gpickle(node_ntwk_name)
+        node_network = _read_pickle(node_ntwk_name)
         iflogger.info(
             "Populating node dictionaries with attributes from %s", node_ntwk_name
         )

diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
@@ -24,11 +24,16 @@
 iflogger = logging.getLogger("nipype.interface")
 
 
+def _read_pickle(fname):
+    with open(fname, 'rb') as f:
+        return pickle.load(f)
+
+
 def read_unknown_ntwk(ntwk):
     if not isinstance(ntwk, nx.classes.graph.Graph):
         _, _, ext = split_filename(ntwk)
         if ext == ".pck":
-            ntwk = nx.read_gpickle(ntwk)
+            ntwk = _read_pickle(ntwk)
         elif ext == ".graphml":
             ntwk = nx.read_graphml(ntwk)
     return ntwk
@@ -121,7 +126,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
         counting_ntwk = ntwk.copy()
         # Sums all the relevant variables
         for index, subject in enumerate(in_files):
-            tmp = nx.read_gpickle(subject)
+            tmp = _read_pickle(subject)
             iflogger.info("File %s has %i edges", subject, tmp.number_of_edges())
             edges = list(tmp.edges())
             for edge in edges:
@@ -461,7 +466,7 @@ def _run_interface(self, runtime):
         edgentwks = list()
         kntwks = list()
         matlab = list()
-        ntwk = nx.read_gpickle(self.inputs.in_file)
+        ntwk = _read_pickle(self.inputs.in_file)
 
         # Each block computes, writes, and saves a measure
         # The names are then added to the output .pck file list