Add util script to print info on hdf5

scripts_python/dwiml_print_hdf5_architecture.py

@@ -0,0 +1,49 @@
+# -*- coding: utf-8 -*-
+import argparse
+
+import h5py
+from scilpy.io.utils import assert_inputs_exist
+
+
+def _prepare_argparser():
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    p.add_argument('hdf5_file',
+                   help="Path to the hdf5 file.")
+    return p
+
+
+def main():
+    p = _prepare_argparser()
+    args = p.parse_args()
+
+    assert_inputs_exist(p, args.hdf5_file)
+
+    with h5py.File(args.hdf5_file, 'r') as hdf_handle:
+
+        print("\n\nHere is the architecture of your hdf5:\n"
+              "--------------------------------------\n")
+        print("- Main hdf5 attributes: {}\n"
+              .format(list(hdf_handle.attrs.keys())))
+
+        if 'training_subjs' in hdf_handle.attrs:
+            print("- List of training subjects: {}\n"
+                  .format(hdf_handle.attrs['training_subjs']))
+
+        if 'validation_subjs' in hdf_handle.attrs:
+            print("- List of validation subjects: {}\n"
+                  .format(hdf_handle.attrs['validation_subjs']))
+
+        if 'testing_subjs' in hdf_handle.attrs:
+            print("- List of testing subjects: {}\n"
+                  .format(hdf_handle.attrs['testing_subjs']))
+
+        print("- For each subject, caracteristics are:")
+        first_subj = list(hdf_handle.keys())[0]
+        for key, val in hdf_handle[first_subj].items():
+            print("   - {}, with attributes {}"
+                  .format(key, list(hdf_handle[first_subj][key].attrs.keys())))
+
+
+if __name__ == '__main__':
+    main()