Merge pull request #28 from francois-drielsma/develop

Finalize upgrade to allow to store to multiple files (one per input file)

spine/build/manager.py

@@ -173,7 +173,8 @@ def build_sources(self, data, entry=None):
                     sources['label_adapt_tensor'][:, VALUE_COL])
 
             if 'depositions_q_label' in sources:
-                update['depositions_q_label'] = sources['depositions_q_label']
+                update['depositions_q_label'] = (
+                        sources['depositions_q_label'][:, VALUE_COL])
 
         if 'label_g4_tensor' in sources:
             update['label_g4_tensor'] = sources['label_g4_tensor']

spine/io/write/hdf5.py

@@ -37,9 +37,8 @@ class HDF5Writer:
     """
     name = 'hdf5'
 
-    def __init__(self, file_name=None, keys=None, skip_keys=None,
-                 dummy_ds=None, overwrite=False, append=False,
-                 prefix=None, split=False):
+    def __init__(self, file_name=None, keys=None, skip_keys=None, dummy_ds=None,
+                 overwrite=False, append=False, prefix=None, split=False):
         """Initializes the basics of the output file.
 
         Parameters
@@ -74,7 +73,14 @@ def __init__(self, file_name=None, keys=None, skip_keys=None,
                 file_name = [f'{pre}_spine.h5' for pre in prefix]
 
         elif split:
-            file_name = [f'{file_name}_{i}' for i in range(len(prefix))]
+            dir_name = os.path.dirname(file_name)
+            if dir_name:
+                dir_name += '/'
+            base_name = os.path.splitext(os.path.basename(file_name))[0]
+            if not prefix:
+                file_name = [f'{dir_name}{base_name}_{i}.h5' for i in range(len(prefix))]
+            else:
+                file_name = [f'{dir_name}{pre}_{base_name}.h5' for pre in prefix]
 
         # Check that the output file(s) do(es) not already exist, if requested
         if not overwrite:
@@ -154,11 +160,11 @@ def create(self, data, cfg=None):
         for file_name in file_names:
             with h5py.File(file_name, 'w') as out_file:
                 # Initialize the info dataset that stores environment parameters
+                out_file.create_dataset(
+                        'info', (0,), maxshape=(None,), dtype=None)
+                out_file['info'].attrs['version'] = __version__
                 if cfg is not None:
-                    out_file.create_dataset(
-                            'info', (0,), maxshape=(None,), dtype=None)
                     out_file['info'].attrs['cfg'] = yaml.dump(cfg)
-                    out_file['info'].attrs['version'] = __version__
 
                 # Initialize the event dataset and their reference array datasets
                 self.initialize_datasets(out_file)

spine/post/base.py

@@ -41,16 +41,28 @@ class PostBase(ABC):
     # List of recognized run modes
     _run_modes = ('reco', 'truth', 'both', 'all')
 
-    # List of known point modes for true particles
+    # List of known point modes for true particles and their corresponding keys
     _point_modes = {
             'points': 'points_label',
             'points_adapt': 'points',
             'points_g4': 'points_g4'
     }
 
-    # List of known deposition modes
-    _dep_modes = ('depositions', 'depositions_q', 'depositions_adapt',
-                  'depositions_adapt_q', 'depositions_g4')
+    # List of known source modes for true particles and their corresponding keys
+    _source_modes = {
+            'sources': 'sources_label',
+            'sources_adapt': 'sources',
+            'sources_g4': 'sources_g4'
+    }
+
+    # List of known deposition modes for true particles and their corresponding keys
+    _dep_modes = {
+            'depositions': 'depositions_label',
+            'depositions_q': 'depositions_q_label',
+            'depositions_adapt': 'depositions_label_adapt',
+            'depositions_adapt_q': 'depositions',
+            'depositions_g4': 'depositions_g4'
+    }
 
     def __init__(self, obj_type=None, run_mode=None, truth_point_mode=None,
                  truth_dep_mode=None, parent_path=None):
@@ -120,18 +132,25 @@ def __init__(self, obj_type=None, run_mode=None, truth_point_mode=None,
         if truth_point_mode is not None:
             assert truth_point_mode in self._point_modes, (
                      "The `truth_point_mode` argument must be one of "
-                    f"{self._point_modes}. Got `{truth_point_mode}` instead.")
+                    f"{self._point_modes.keys()}. Got `{truth_point_mode}` instead.")
             self.truth_point_mode = truth_point_mode
-            self.truth_point_key = self._point_modes[truth_point_mode]
-            self.truth_index_mode = truth_point_mode.replace('points', 'index')
+            self.truth_point_key = self._point_modes[self.truth_point_mode]
             self.truth_source_mode = truth_point_mode.replace('points', 'sources')
+            self.truth_source_key = self._source_modes[self.truth_source_mode]
+            self.truth_index_mode = truth_point_mode.replace('points', 'index')
 
         # If a truth deposition mode is specified, store it
         if truth_dep_mode is not None:
             assert truth_dep_mode in self._dep_modes, (
                      "The `truth_dep_mode` argument must be one of "
-                    f"{self._dep_modes}. Got `{truth_dep_mode}` instead.")
+                    f"{self._dep_modes.keys()}. Got `{truth_dep_mode}` instead.")
+            if truth_point_mode is not None:
+                prefix = truth_point_mode.replace('points', 'depositions')
+                assert truth_dep_mode.startswith(prefix), (
+                        "Points mode {truth_point_mode} and deposition mode "
+                        "{truth_dep_mode} are incompatible.")
             self.truth_dep_mode = truth_dep_mode
+            self.truth_dep_key = self._dep_modes[truth_dep_mode]
 
         # Store the parent path
         self.parent_path = parent_path

spine/post/reco/calo.py

@@ -69,44 +69,37 @@ class CalibrationProcessor(PostBase):
     aliases = ['apply_calibrations']
     keys = {'run_info': False}
 
-    # Map between point attribute and underlying deposition objects
-    _dep_attr_map = {
-            'points': 'depositions_q',
-            'points_adapt': 'depositions_adapt_q'
-    }
-    _dep_map = {
-            'points': 'depositions_label_q',
-            'points_adapt': 'depositions'
-    }
-
     def __init__(self, dedx=2.2, do_tracking=False, obj_type='particle',
                  run_mode='reco', truth_point_mode='points', **cfg):
         """Initialize the calibration manager.
 
         Parameters
         ----------
         dedx : float, default 2.2
-            Static value of dE/dx used to compute the recombination factor
+            Static value of dE/dx in MeV/cm used to compute the recombination factor
         do_tracking : bool, default False
             Segment track to get a proper local dQ/dx estimate
         **cfg : dict
             Calibration manager configuration
         """
+        # Figure out which truth deposition attribute to use
+        truth_dep_mode = truth_point_mode.replace('points', 'depositions') + '_q'
+
         # Initialize the parent class
-        super().__init__(obj_type, run_mode, truth_point_mode)
+        super().__init__(obj_type, run_mode, truth_point_mode, truth_dep_mode)
 
         # Initialize the calibrator
         self.calibrator = CalibrationManager(**cfg)
         self.dedx = dedx
         self.do_tracking = do_tracking
 
-        # Set the truth attributes to set
-        self.truth_dep_attr = self._dep_attr_map[self.truth_point_mode]
-        self.truth_dep_key = self._dep_map[self.truth_point_mode]
-
         # Add necessary keys
+        self.keys['points'] = run_mode != 'truth'
+        self.keys[self.truth_point_key] = run_mode != 'reco'
         self.keys['depositions'] = run_mode != 'truth'
         self.keys[self.truth_dep_key] = run_mode != 'reco'
+        self.keys['sources'] = run_mode != 'truth'
+        self.keys[self.truth_source_key] = run_mode != 'reco'
 
     def process(self, data):
         """Apply calibrations to each particle in one entry.
@@ -124,29 +117,41 @@ def process(self, data):
 
         # Loop over particle objects
         for k in self.obj_keys:
+            points_key = 'points' if not 'truth' in k else self.truth_point_key
+            source_key = 'sources' if not 'truth' in k else self.truth_source_key
+            dep_key = 'depositions' if not 'truth' in k else self.truth_dep_key
+            unass_mask = np.ones(len(data[dep_key]), dtype=bool)
             for part in data[k]:
                 # Make sure the particle coordinates are expressed in cm
                 self.check_units(part)
 
-                # Get point coordinates
+                # Get point coordinates, sources and depositions
                 points = self.get_points(part)
                 if not len(points):
                     continue
 
+                sources = self.get_sources(part)
+                deps = self.get_depositions(part)
+
                 # Apply calibration
                 if not self.do_tracking or part.shape != TRACK_SHP:
                     depositions = self.calibrator(
-                            points, part.depositions, part.sources,
-                            run_id, self.dedx)
+                            points, deps, sources, run_id, self.dedx)
                 else:
                     depositions = self.calibrator.process(
-                            points, part.depositions, part.sources,
-                            run_id, track=True)
+                            points, deps, sources, run_id, track=True)
 
                 # Update the particle *and* the reference tensor
                 if not part.is_truth:
                     part.depositions = depositions
-                    data['depositions'][part.index] = depositions
                 else:
-                    setattr(part, self.truth_dep_attr, depositions)
-                    data[self.truth_dep_key] = depositions
+                    setattr(part, self.truth_dep_mode, depositions)
+
+                data[dep_key][part.index] = depositions
+                unass_mask[part.index] = False
+
+            # Apply calibration corrections to unassociated depositions
+            unass_index = np.where(unass_mask)[0]
+            data[dep_key][unass_index] = self.calibrator(
+                    data[points_key][unass_index], data[dep_key][unass_index],
+                    data[source_key][unass_index], run_id, self.dedx)