Merge branch 'develop' into feature/metadata_class

.gitignore

@@ -2,3 +2,4 @@
 *~
 pylot/RELEASE-VERSION
 *.idea
+autopylot.sh*

PyLoT.py

@@ -110,21 +110,8 @@ class MainWindow(QMainWindow):
     def __init__(self, parent=None, infile=None):
         super(MainWindow, self).__init__(parent)
 
-        # check for default pylot.in-file
+        self.init_config_files(infile)
-        if not infile:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-        if os.path.isfile(infile) == False:
-            infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')
 
-            if not os.path.exists(infile[0]):
-                QMessageBox.warning(self, "PyLoT Warning",
-                                    "No PyLoT-input file declared!")
-                sys.exit(0)
-            self.infile = infile[0]
-        else:
-            self.infile = infile
-        self._inputs = PylotParameter(infile)
         self._props = None
 
         self.dirty = False
@@ -208,6 +195,22 @@ class MainWindow(QMainWindow):
 
         self.loc = False
 
+
+    def init_config_files(self, infile):
+        pylot_config_dir = os.path.join(os.path.expanduser('~'), '.pylot')
+        if not os.path.exists(pylot_config_dir):
+            os.mkdir(pylot_config_dir)
+
+        self._inputs = PylotParameter(infile)
+        if not infile:
+            self._inputs.reset_defaults()
+            # check for default pylot.in-file
+            infile = os.path.join(pylot_config_dir, '.pylot.in')
+            print('Using default input file {}'.format(infile))
+            self._inputs.export2File(infile)
+        self.infile = infile
+
+
     def setupUi(self):
         try:
             self.startTime = min(
@@ -1058,9 +1061,12 @@ class MainWindow(QMainWindow):
             eventlist = ed.selectedFiles()
             basepath = eventlist[0].split(os.path.basename(eventlist[0]))[0]
             if check_obspydmt_structure(basepath):
-                print('Recognized obspyDMT structure in selected files.')
+                print('Recognized obspyDMT structure in selected files. Settings Datastructure to ObspyDMT')
+                self.dataStructure = DATASTRUCTURE['obspyDMT']()
                 eventlist = check_all_obspy(eventlist)
             else:
+                print('Settings Datastructure to PILOT')
+                self.dataStructure = DATASTRUCTURE['PILOT']()
                 eventlist = check_all_pylot(eventlist)
             if not eventlist:
                 print('No events found! Expected structure for event folders: [eEVID.DOY.YR],\n'

pylot/core/io/data.py

@@ -733,6 +733,22 @@ class PilotDataStructure(GenericDataStructure):
         self.setExpandFields(['root', 'database'])
 
 
+class ObspyDMTdataStructure(GenericDataStructure):
+    """
+    Object containing the data access information for the old PILOT data
+    structure.
+    """
+
+    def __init__(self, **fields):
+        if not fields:
+            fields = {'database': '',
+                      'root': ''}
+
+        GenericDataStructure.__init__(self, **fields)
+
+        self.setExpandFields(['root', 'database'])
+
+
 class SeiscompDataStructure(GenericDataStructure):
     """
     Dictionary containing the data access information for an SDS data archive:

pylot/core/io/default_parameters.py

@@ -63,7 +63,7 @@ defaults = {'rootpath': {'type': str,
 
             'ctrfile': {'type': str,
                         'tooltip': 'name of autoPyLoT-output control file for NLLoc',
-                        'value': 'Insheim_min1d2015_auto.in',
+                        'value': '',
                         'namestring': 'Control filename'},
 
             'ttpatter': {'type': str,

pylot/core/io/inputs.py

@@ -48,6 +48,7 @@ class PylotParameter(object):
         self.__init_default_paras()
         self.__init_subsettings()
         self.__filename = fnin
+        self.__parameter = {}
         self._verbosity = verbosity
         self._parFileCont = {}
         # io from parsed arguments alternatively
@@ -273,8 +274,8 @@ class PylotParameter(object):
         :rtype: None
         """
         defaults = self.get_defaults()
-        for param in defaults:
+        for param_name, param in defaults.items():
-            self.setParamKV(param, defaults[param]['value'])
+            self.setParamKV(param_name, param['value'])
 
     def from_file(self, fnin=None):
         """

pylot/core/pick/autopick.py

@@ -93,7 +93,9 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
     #result = serial_picking(input_tuples)
 
     for pick in result:
-        if pick:
+        if type(pick) == BaseException:
+            print(pick)
+        elif pick:
             station = pick['station']
             pick.pop('station')
             all_onsets[station] = pick
@@ -130,7 +132,10 @@ def call_autopickstation(input_tuple):
     """
     wfstream, pickparam, verbose, metadata, origin = input_tuple
     # multiprocessing not possible with interactive plotting
-    return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin)
+    try:
+        return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin)
+    except Exception as e:
+        return e
 
 
 def get_source_coords(parser, station_id):

pylot/core/util/structure.py

@@ -6,7 +6,7 @@ Created on Wed Jan 26 17:47:25 2015
 @author: sebastianw
 """
 
-from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure
+from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure, ObspyDMTdataStructure
 
 DATASTRUCTURE = {'PILOT': PilotDataStructure, 'SeisComP': SeiscompDataStructure,
-                 'obspyDMT': None, None: None}
+                 'obspyDMT': ObspyDMTdataStructure, None: PilotDataStructure}

tests/test_Metadata/test_Metadata.py

@@ -0,0 +1,104 @@
+import unittest
+import os
+
+from pylot.core.util.dataprocessing import Metadata
+
+class TestMetadata(unittest.TestCase):
+
+    def setUp(self):
+        self.station_id = 'BW.WETR..HH'
+        metadata_folder = 'metadata1'
+        self.m = Metadata(metadata_folder)
+
+    def test_get_coordinates_sucess(self):
+        expected = {'Z': {u'elevation': 607.0, u'longitude': 12.87571, u'local_depth': 0.0, u'azimuth': 0.0, u'latitude': 49.14502, u'dip': -90.0},
+                    'E': {u'azimuth': 90.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0, u'longitude': 12.87571},
+                    'N': {u'azimuth': 0.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0, u'longitude': 12.87571}
+                    }
+        result = {}
+        for channel in ('Z', 'N', 'E'):
+            coords = self.m.get_coordinates(self.station_id+channel)
+            result[channel] = coords
+            self.assertDictEqual(result[channel], expected[channel])
+
+class TestMetadataAdding(unittest.TestCase):
+    """Tests if adding files and directories to a metadata object works."""
+
+    def setUp(self):
+        self.station_id = 'BW.WETR..HH'
+        self.metadata_folders = ('metadata1', 'metadata2')
+        self.m = Metadata()
+
+    def test_add_inventory_folder(self):
+        """Test if add_inventory adds the folder to the list of inventories"""
+        self.m.add_inventory(self.metadata_folders[0])
+        # adding an inventory folder should append it to the list of inventories
+        self.assertDictEqual({}, self.m.inventory_files)
+        self.assertDictEqual({}, self.m.seed_ids)
+        self.assertEqual([self.metadata_folders[0]], self.m.inventories)
+
+    def test_add_inventory_file(self):
+        """Test if add_inventory_file adds the folder containing the file to the list of inventories and
+        if the files is added to inventory_files"""
+        fpath = os.path.join(self.metadata_folders[0], 'DATALESS.BW.WETR..HHZ')
+        self.m.add_inventory_file(fpath)
+        # adding an inventory file should append its folder to the list of inventories and the file to the
+        self.assertEqual(['metadata1/DATALESS.BW.WETR..HHZ'], self.m.inventory_files.keys())  # does the filename exist in inventory files?
+        self.assertEqual(['data', 'invtype'], self.m.inventory_files['metadata1/DATALESS.BW.WETR..HHZ'].keys())  # is the required information attacht to the filename?
+        self.assertDictEqual({}, self.m.seed_ids)
+        self.assertEqual([self.metadata_folders[0]], self.m.inventories)
+
+    def test_add_inventory_invalid_path(self):
+        """Test if adding an inventory that is not an existing directory fails with an exception"""
+        with self.assertRaises(Exception):
+            self.m.add_inventory('InvalidDirName')
+        self.assertEqual([], self.m.inventories)  # inventory list should still be empty
+
+    def test_add_inventory_file_invalid_path(self):
+        """Test if adding a inventory file with an invalid path fails with an exception"""
+        with self.assertRaises(Exception):
+            self.m.add_inventory_file('/invalid/file/name')
+        self.assertEqual([], self.m.inventories)  # inventory list should still be empty
+
+
+class TestMetadataRemoval(unittest.TestCase):
+    """Tests if removing files and directories to a metadata object works."""
+
+    def setUp(self):
+        self.station_id = 'BW.WETR..HH'
+        self.metadata_folders = ('metadata1', 'metadata2')
+        self.m = Metadata()
+
+    def test_remove_all_inventories(self):
+        """Test if function remove_inventory cleans the Metadata object """
+        # add multiple inventories
+        for folder in self.metadata_folders:
+            self.m.add_inventory(folder)
+        self.m.remove_all_inventories()
+        self.isEmpty(self.m)
+
+    def test_remove_inventory(self):
+        """Test if remove_inventory removes single inventories"""
+        # add multiple inventories
+        for folder in self.metadata_folders:
+            self.m.add_inventory(folder)
+        self.m.remove_inventory(self.metadata_folders[0])
+        self.assertNotIn(self.metadata_folders[0], self.m.inventories)
+        self.m.remove_inventory(self.metadata_folders[1])
+        self.assertNotIn(self.metadata_folders[1], self.m.inventories)
+        self.isEmpty(self.m)
+
+    def test_remove_inventory_not_in_inventory_list(self):
+        """Test if remove_inventory does not modify the metadata instance if the given inventory to remove does not
+        exist in the instance."""
+        # add multiple inventories
+        self.m.add_inventory(self.metadata_folders[0])
+        self.m.remove_inventory('metadata_not_existing')
+        self.assertIn(self.metadata_folders[0], self.m.inventories)
+
+    def isEmpty(self, metadata):
+        """Asserts if the given metadata object is empty"""
+        self.assertDictEqual({}, metadata.inventory_files)
+        self.assertDictEqual({}, metadata.seed_ids)
+        self.assertEqual([], metadata.inventories)
+