Move the scripts, evaluation codes and resources into mimic3benchmark…

… package
YerevaNN · Apr 3, 2018 · eec1d55 · eec1d55
1 parent 31c7a97
commit eec1d55
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Showing 21 changed files with 4 additions and 4 deletions.
diff --git a/evaluation/README.md → mimic3benchmark/evaluation/README.md b/evaluation/README.md → mimic3benchmark/evaluation/README.md
diff --git a/evaluation/__init__.py → mimic3benchmark/evaluation/__init__.py b/evaluation/__init__.py → mimic3benchmark/evaluation/__init__.py
diff --git a/evaluation/evaluate_decomp.py → ...c3benchmark/evaluation/evaluate_decomp.py b/evaluation/evaluate_decomp.py → ...c3benchmark/evaluation/evaluate_decomp.py
@@ -14,7 +14,7 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('prediction', type=str)
     parser.add_argument('--test_listfile', type=str,
-                        default=os.path.join(os.path.dirname(__file__), '../data/decompensation/test/listfile.csv'))
+                        default=os.path.join(os.path.dirname(__file__), '../../data/decompensation/test/listfile.csv'))
     parser.add_argument('--n_iters', type=int, default=1000)
     parser.add_argument('--save_file', type=str, default='decomp_results.json')
     args = parser.parse_args()

diff --git a/evaluation/evaluate_ihm.py → mimic3benchmark/evaluation/evaluate_ihm.py b/evaluation/evaluate_ihm.py → mimic3benchmark/evaluation/evaluate_ihm.py
@@ -15,7 +15,7 @@ def main():
     parser.add_argument('prediction', type=str)
     parser.add_argument('--test_listfile', type=str,
                         default=os.path.join(os.path.dirname(__file__),
-                                             '../data/in-hospital-mortality/test/listfile.csv'))
+                                             '../../data/in-hospital-mortality/test/listfile.csv'))
     parser.add_argument('--n_iters', type=int, default=10000)
     parser.add_argument('--save_file', type=str, default='ihm_results.json')
     args = parser.parse_args()

diff --git a/evaluation/evaluate_los.py → mimic3benchmark/evaluation/evaluate_los.py b/evaluation/evaluate_los.py → mimic3benchmark/evaluation/evaluate_los.py
@@ -14,7 +14,7 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('prediction', type=str)
     parser.add_argument('--test_listfile', type=str,
-                        default=os.path.join(os.path.dirname(__file__), '../data/length-of-stay/test/listfile.csv'))
+                        default=os.path.join(os.path.dirname(__file__), '../../data/length-of-stay/test/listfile.csv'))
     parser.add_argument('--n_iters', type=int, default=1000)
     parser.add_argument('--save_file', type=str, default='los_results.json')
     args = parser.parse_args()

diff --git a/evaluation/evaluate_pheno.py → mimic3benchmark/evaluation/evaluate_pheno.py b/evaluation/evaluate_pheno.py → mimic3benchmark/evaluation/evaluate_pheno.py
@@ -14,7 +14,7 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('prediction', type=str)
     parser.add_argument('--test_listfile', type=str,
-                        default=os.path.join(os.path.dirname(__file__), '../data/phenotyping/test/listfile.csv'))
+                        default=os.path.join(os.path.dirname(__file__), '../../data/phenotyping/test/listfile.csv'))
     parser.add_argument('--n_iters', type=int, default=10000)
     parser.add_argument('--save_file', type=str, default='pheno_results.json')
     args = parser.parse_args()

diff --git a/resources/hcup_ccs_2015_definitions.yaml → .../resources/hcup_ccs_2015_definitions.yaml b/resources/hcup_ccs_2015_definitions.yaml → .../resources/hcup_ccs_2015_definitions.yaml
diff --git a/resources/itemid_to_variable_map.csv → ...mark/resources/itemid_to_variable_map.csv b/resources/itemid_to_variable_map.csv → ...mark/resources/itemid_to_variable_map.csv
diff --git a/resources/testset.csv → mimic3benchmark/resources/testset.csv b/resources/testset.csv → mimic3benchmark/resources/testset.csv
diff --git a/resources/variable_ranges.csv → ...c3benchmark/resources/variable_ranges.csv b/resources/variable_ranges.csv → ...c3benchmark/resources/variable_ranges.csv
diff --git a/scripts/__init__.py → mimic3benchmark/scripts/__init__.py b/scripts/__init__.py → mimic3benchmark/scripts/__init__.py
diff --git a/scripts/create_decompensation.py → ...enchmark/scripts/create_decompensation.py b/scripts/create_decompensation.py → ...enchmark/scripts/create_decompensation.py
diff --git a/scripts/create_in_hospital_mortality.py → ...k/scripts/create_in_hospital_mortality.py b/scripts/create_in_hospital_mortality.py → ...k/scripts/create_in_hospital_mortality.py
diff --git a/scripts/create_length_of_stay.py → ...enchmark/scripts/create_length_of_stay.py b/scripts/create_length_of_stay.py → ...enchmark/scripts/create_length_of_stay.py
diff --git a/scripts/create_multitask.py → mimic3benchmark/scripts/create_multitask.py b/scripts/create_multitask.py → mimic3benchmark/scripts/create_multitask.py
diff --git a/scripts/create_phenotyping.py → ...c3benchmark/scripts/create_phenotyping.py b/scripts/create_phenotyping.py → ...c3benchmark/scripts/create_phenotyping.py
diff --git a/scripts/extract_episodes_from_subjects.py → ...scripts/extract_episodes_from_subjects.py b/scripts/extract_episodes_from_subjects.py → ...scripts/extract_episodes_from_subjects.py
diff --git a/scripts/extract_subjects.py → mimic3benchmark/scripts/extract_subjects.py b/scripts/extract_subjects.py → mimic3benchmark/scripts/extract_subjects.py
diff --git a/scripts/more_on_validating_events.md → ...mark/scripts/more_on_validating_events.md b/scripts/more_on_validating_events.md → ...mark/scripts/more_on_validating_events.md
diff --git a/scripts/split_train_and_test.py → ...benchmark/scripts/split_train_and_test.py b/scripts/split_train_and_test.py → ...benchmark/scripts/split_train_and_test.py
diff --git a/scripts/validate_events.py → mimic3benchmark/scripts/validate_events.py b/scripts/validate_events.py → mimic3benchmark/scripts/validate_events.py