ctheodoris
commited on
Commit
•
428e3b0
1
Parent(s):
99f40b4
define ncells for clearing memory
Browse files
geneformer/in_silico_perturber.py
CHANGED
@@ -964,7 +964,7 @@ class InSilicoPerturber:
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)
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# save dict to disk every 100 cells
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-
if i % clear_mem_ncells/10 == 0:
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pu.write_perturbation_dictionary(
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cos_sims_dict,
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f"{output_path_prefix}_dict_cell_embs_1Kbatch{pickle_batch}",
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@@ -976,7 +976,7 @@ class InSilicoPerturber:
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)
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# reset and clear memory every 1000 cells
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-
if i % clear_mem_ncells == 0:
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pickle_batch += 1
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if self.cell_states_to_model is None:
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cos_sims_dict = defaultdict(list)
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)
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# save dict to disk every 100 cells
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+
if i % self.clear_mem_ncells/10 == 0:
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pu.write_perturbation_dictionary(
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cos_sims_dict,
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f"{output_path_prefix}_dict_cell_embs_1Kbatch{pickle_batch}",
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)
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# reset and clear memory every 1000 cells
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+
if i % self.clear_mem_ncells == 0:
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pickle_batch += 1
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if self.cell_states_to_model is None:
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cos_sims_dict = defaultdict(list)
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