Convert to load_from_config() handling

[unfold-protein.git] / unfold_protein / storage.py

diff --git a/unfold_protein/storage.py b/unfold_protein/storage.py
new file mode 100644 (file)
index 0000000..9b0c64b
--- /dev/null
+++ b/unfold_protein/storage.py
@@ -0,0 +1,71 @@
+# Copyright
+
+import os.path as _os_path
+
+from h5config.storage.hdf5 import HDF5_Storage as _HDF5_Storage
+from h5config.storage.yaml import YAML_Storage as _YAML_Storage
+import pyafm.storage as _pyafm_storage
+
+from . import LOG as _LOG
+from . import config as _config
+from . import scan as _scan
+
+
+DEFAULT_FILENAME = _os_path.expanduser(_os_path.join(
+        '~', '.config', 'unfold-default.yaml'))
+DEFAULT_GROUP = '/'
+
+
+def _get_storage(filename=None, group=None, action=None):
+    if filename is None:
+        filename = DEFAULT_FILENAME
+    if filename.endswith('.h5'):
+        if group is None:
+            group = DEFAULT_GROUP
+        assert group.endswith('/'), group
+        _LOG.info('{} {} {}'.format(action, filename, group))
+        storage = _HDF5_Storage(filename=filename, group=group)
+    elif filename.endswith('.yaml'):
+        assert group is None, group
+        _LOG.info('{} {}'.format(action, filename))
+        storage = _YAML_Storage(filename=filename)
+    else:
+        raise ValueError('unrecognized file extension in {}'.format(filename))
+    return storage
+
+
+def save_scan_config(config, filename=None, group=None):
+    storage = _get_storage(
+        filename=filename, group=group,
+        action='saving unfolding scan config to')
+    storage.save(config=config)
+
+
+def load_scan_config(filename=None, group=None):
+    storage = _get_storage(
+        filename=filename, group=group,
+        action='loading unfolding scan config from')
+    config = _config.ScanConfig(storage=storage)
+    config.load()
+    return config
+
+
+def load_scanner(filename=None, group=None):
+    config = load_scan_config(filename=group, group=group)
+    _LOG.debug(
+        'constructing UnfoldScanner from configuration:\n{}'.format(
+            config.dump()))
+    scanner = _scan.UnfoldScanner(config=config)
+    return scanner
+
+
+def get_default_config():
+    scan_config = _config.ScanConfig()
+    scan_config['velocity'] = _config.VelocityScanConfig()
+    scan_config['position'] = _config.PositionScanConfig()
+    scan_config['unfold'] = _config.UnfoldCycleConfig()
+    scan_config['unfold']['approach'] = _config.ApproachConfig()
+    scan_config['unfold']['unfold'] = _config.UnfoldConfig()
+    scan_config['unfold']['save'] = _config.SaveConfig()
+    scan_config['unfold']['afm'] = _pyafm_storage.load_config()
+    return scan_config