Commit c3a1909

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FIX: Purge nx.read_gpickle

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+23

-7

lines changed

+23

-7

lines changed

Lines changed: 7 additions & 1 deletion

Original file line number	Diff line number	Diff line change
`@@ -18,6 +18,12 @@`
`18`	`18`	`from .base import CFFBaseInterface, have_cfflib`
`19`	`19`
`20`	`20`
	`21`	`+def _read_pickle(fname):`
	`22`	`+ import pickle`
	`23`	`+ with open(fname, 'rb') as f:`
	`24`	`+ return pickle.load(f)`
	`25`	`+`
	`26`	`+`
`21`	`27`	`class CFFConverterInputSpec(BaseInterfaceInputSpec):`
`22`	`28`	`graphml_networks = InputMultiPath(`
`23`	`29`	`File(exists=True), desc="list of graphML networks"`
`@@ -135,7 +141,7 @@ def _run_interface(self, runtime):`
`135`	`141`	`unpickled = []`
`136`	`142`	`for ntwk in self.inputs.gpickled_networks:`
`137`	`143`	`_, ntwk_name, _ = split_filename(ntwk)`
`138`		`- unpickled = nx.read_gpickle(ntwk)`
	`144`	`+ unpickled = _read_pickle(ntwk)`
`139`	`145`	`cnet = cf.CNetwork(name=ntwk_name)`
`140`	`146`	`cnet.set_with_nxgraph(unpickled)`
`141`	`147`	`a.add_connectome_network(cnet)`

Lines changed: 8 additions & 3 deletions

Original file line number	Diff line number	Diff line change
`@@ -24,13 +24,18 @@`
`24`	`24`	`iflogger = logging.getLogger("nipype.interface")`
`25`	`25`
`26`	`26`
	`27`	`+def _read_pickle(fname):`
	`28`	`+ with open(fname, 'rb') as f:`
	`29`	`+ return pickle.load(f)`
	`30`	`+`
	`31`	`+`
`27`	`32`	`def ntwks_to_matrices(in_files, edge_key):`
`28`		`- first = nx.read_gpickle(in_files[0])`
	`33`	`+ first = _read_pickle(in_files[0])`
`29`	`34`	`files = len(in_files)`
`30`	`35`	`nodes = len(first.nodes())`
`31`	`36`	`matrix = np.zeros((nodes, nodes, files))`
`32`	`37`	`for idx, name in enumerate(in_files):`
`33`		`- graph = nx.read_gpickle(name)`
	`38`	`+ graph = _read_pickle(name)`
`34`	`39`	`for u, v, d in graph.edges(data=True):`
`35`	`40`	`try:`
`36`	`41`	`graph[u][v]["weight"] = d[`
`@@ -162,7 +167,7 @@ def _run_interface(self, runtime):`
`162`	`167`	`else:`
`163`	`168`	`node_ntwk_name = self.inputs.in_group1[0]`
`164`	`169`
`165`		`- node_network = nx.read_gpickle(node_ntwk_name)`
	`170`	`+ node_network = _read_pickle(node_ntwk_name)`
`166`	`171`	`iflogger.info(`
`167`	`172`	`"Populating node dictionaries with attributes from %s", node_ntwk_name`
`168`	`173`	`)`

Lines changed: 8 additions & 3 deletions

Original file line number	Diff line number	Diff line change
`@@ -24,11 +24,16 @@`
`24`	`24`	`iflogger = logging.getLogger("nipype.interface")`
`25`	`25`
`26`	`26`
	`27`	`+def _read_pickle(fname):`
	`28`	`+ with open(fname, 'rb') as f:`
	`29`	`+ return pickle.load(f)`
	`30`	`+`
	`31`	`+`
`27`	`32`	`def read_unknown_ntwk(ntwk):`
`28`	`33`	`if not isinstance(ntwk, nx.classes.graph.Graph):`
`29`	`34`	`_, _, ext = split_filename(ntwk)`
`30`	`35`	`if ext == ".pck":`
`31`		`- ntwk = nx.read_gpickle(ntwk)`
	`36`	`+ ntwk = _read_pickle(ntwk)`
`32`	`37`	`elif ext == ".graphml":`
`33`	`38`	`ntwk = nx.read_graphml(ntwk)`
`34`	`39`	`return ntwk`
`@@ -121,7 +126,7 @@ def average_networks(in_files, ntwk_res_file, group_id):`
`121`	`126`	`counting_ntwk = ntwk.copy()`
`122`	`127`	`# Sums all the relevant variables`
`123`	`128`	`for index, subject in enumerate(in_files):`
`124`		`- tmp = nx.read_gpickle(subject)`
	`129`	`+ tmp = _read_pickle(subject)`
`125`	`130`	`iflogger.info("File %s has %i edges", subject, tmp.number_of_edges())`
`126`	`131`	`edges = list(tmp.edges())`
`127`	`132`	`for edge in edges:`
`@@ -461,7 +466,7 @@ def _run_interface(self, runtime):`
`461`	`466`	`edgentwks = list()`
`462`	`467`	`kntwks = list()`
`463`	`468`	`matlab = list()`
`464`		`- ntwk = nx.read_gpickle(self.inputs.in_file)`
	`469`	`+ ntwk = _read_pickle(self.inputs.in_file)`
`465`	`470`
`466`	`471`	`# Each block computes, writes, and saves a measure`
`467`	`472`	`# The names are then added to the output .pck file list`

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