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add optional data_path parameter to generate_spectra_splits #1

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add optional data_path parameter to generate_spectra_splits #1

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d106964
add data_path param to generate_spectra_splits
aaronwtr Apr 24, 2024
dea1a9a
add optional data_path to generate_spectra_splits
aaronwtr Apr 24, 2024
49c8de5
improve generate_spectra_splits
aaronwtr Apr 29, 2024
008b2db
update construct_spectra_graph to save at relative path
aaronwtr Apr 29, 2024
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40 changes: 21 additions & 19 deletions spectrae/spectra.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,12 +38,12 @@ def cross_split_overlap(self, train, test):
"""
pass

def construct_spectra_graph(self, force_reconstruct = False):
def construct_spectra_graph(self, save_path, force_reconstruct = False):
if self.SPG is not None:
return self.SPG
elif os.path.exists(f"{self.dataset.name}_spectral_property_graphs/{self.dataset.name}_SPECTRA_property_graph.gexf") and not force_reconstruct:
elif os.path.exists(f"{save_path}_spectral_property_graphs/{self.dataset.name}_SPECTRA_property_graph.gexf") and not force_reconstruct:
print("Loading spectral property graph")
self.SPG = nx.read_gexf(f"{self.dataset.name}_spectral_property_graphs/{self.dataset.name}_SPECTRA_property_graph.gexf")
self.SPG = nx.read_gexf(f"{save_path}_spectral_property_graphs/{self.dataset.name}_SPECTRA_property_graph.gexf")
self.return_spectra_graph_stats()
return self.SPG
else:
Expand Down Expand Up @@ -85,10 +85,10 @@ def construct_spectra_graph(self, force_reconstruct = False):
if all_fully_connected:
raise Exception("All SPG sub components are fully connected, cannot run SPECTRA, all samples are similar to each other")

if not os.path.exists(f"{self.dataset.name}_spectral_property_graphs"):
os.makedirs(f"{self.dataset.name}_spectral_property_graphs")
if not os.path.exists(f"{save_path}_spectral_property_graphs"):
os.makedirs(f"{save_path}_spectral_property_graphs")

nx.write_gexf( self.SPG, f"{self.dataset.name}_spectral_property_graphs/{self.dataset.name}_SPECTRA_property_graph.gexf")
nx.write_gexf( self.SPG, f"{save_path}_spectral_property_graphs/{self.dataset.name}_SPECTRA_property_graph.gexf")

return self.SPG

Expand Down Expand Up @@ -161,34 +161,36 @@ def generate_spectra_splits(self,
number_repeats,
random_seed,
test_size = 0.2,
force_reconstruct = False):
force_reconstruct = False,
data_path = ""):

#Random seed is a list of random seeds for each number
name = self.dataset.name
self.construct_spectra_graph(force_reconstruct = force_reconstruct)
save_path = f"{data_path}{name}"
self.construct_spectra_graph(save_path = save_path, force_reconstruct = force_reconstruct)
if self.binary:
if nx.density(self.SPG) >= 0.4:
raise Exception("Density of SPG is greater than 0.4, SPECTRA will not work as your dataset is too similar to itself. Please check your dataset and SPECTRA properties.")

if not os.path.exists(f"{name}_SPECTRA_splits"):
os.makedirs(f"{name}_SPECTRA_splits")
if not os.path.exists(f"{name}_spectral_property_graphs"):
os.makedirs(f"{name}_spectral_property_graphs")
if not os.path.exists(f"{save_path}_SPECTRA_splits"):
os.makedirs(f"{save_path}_SPECTRA_splits")
if not os.path.exists(f"{save_path}_spectral_property_graphs"):
os.makedirs(f"{save_path}_spectral_property_graphs")

splits = []
for spectral_parameter in spectral_parameters:
for i in range(number_repeats):
if os.path.exists(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}") and not force_reconstruct:
if os.path.exists(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}") and not force_reconstruct:
print(f"Folder SP_{spectral_parameter}_{i} already exists. Skipping")
elif force_reconstruct or not os.path.exists(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}"):
elif force_reconstruct or not os.path.exists(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}"):
train, test, stats = self.generate_spectra_split(float(spectral_parameter), random_seed[i], test_size)
if train is not None:
if not os.path.exists(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}"):
os.makedirs(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}")
if not os.path.exists(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}"):
os.makedirs(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}")

pickle.dump(train, open(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}/train.pkl", "wb"))
pickle.dump(test, open(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}/test.pkl", "wb"))
pickle.dump(stats, open(f"{name}_SPECTRA_splits/SP_{spectral_parameter}_{i}/stats.pkl", "wb"))
pickle.dump(train, open(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}/train.pkl", "wb"))
pickle.dump(test, open(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}/test.pkl", "wb"))
pickle.dump(stats, open(f"{save_path}_SPECTRA_splits/SP_{spectral_parameter}_{i}/stats.pkl", "wb"))
else:
print(f"Split for SP_{spectral_parameter}_{i} could not be generated since independent set only has one sample")

Expand Down