WIP: Slicing and refactoring offline

Closes #37 (closed)

km3io/offline.py

@@ -9,8 +9,9 @@ MAIN_TREE_NAME = "E"
 # 110 MB based on the size of the largest basket found so far in km3net
 BASKET_CACHE_SIZE = 110 * 1024**2
 
-
-BranchMapper = namedtuple("BranchMapper", ['name', 'key', 'extra', 'exclude', 'update', 'attrparser'])
+BranchMapper = namedtuple(
+    "BranchMapper",
+    ['name', 'key', 'extra', 'exclude', 'update', 'attrparser', 'flat'])
 
 
 def _nested_mapper(key):
@@ -19,12 +20,36 @@ def _nested_mapper(key):
 
 
 EXCLUDE_KEYS = set(["AAObject", "t", "fBits", "fUniqueID"])
-BRANCH_MAPS = [
-    BranchMapper("tracks", "trks", {}, ['trks.usr_data', 'trks.usr'], {}, _nested_mapper),
-    BranchMapper("mc_tracks", "mc_trks", {}, ['mc_trks.usr_data', 'mc_trks.usr'], {}, _nested_mapper),
-    BranchMapper("hits", "hits", {}, ['hits.usr'], {}, _nested_mapper),
-    BranchMapper("mc_hits", "mc_hits", {}, ['mc_hits.usr'], {}, _nested_mapper),
-    BranchMapper("events", "Evt", {'t_sec': 't.fSec', 't_ns': 't.fNanoSec'}, [], {'n_hits': 'hits', 'n_mc_hits': 'mc_hits', 'n_tracks': 'trks', 'n_mc_tracks': 'mc_trks'}, lambda a: a),
+
+EVENTS_MAP = BranchMapper("events", "Evt", {
+    't_sec': 't.fSec',
+    't_ns': 't.fNanoSec'
+}, [], {
+    'n_hits': 'hits',
+    'n_mc_hits': 'mc_hits',
+    'n_tracks': 'trks',
+    'n_mc_tracks': 'mc_trks'
+}, lambda a: a, True)
+
+SUBBRANCH_MAPS = [
+    BranchMapper("tracks", "trks", {}, ['trks.usr_data', 'trks.usr'], {},
+                 _nested_mapper, False),
+    BranchMapper("mc_tracks", "mc_trks", {},
+                 ['mc_trks.usr_data', 'mc_trks.usr'], {}, _nested_mapper,
+                 False),
+    BranchMapper("hits", "hits", {}, ['hits.usr'], {}, _nested_mapper, False),
+    BranchMapper("mc_hits", "mc_hits", {},
+                 ['mc_hits.usr', 'mc_hits.dom_id', 'mc_hits.channel_id'], {},
+                 _nested_mapper, False),
+    BranchMapper("events", "Evt", {
+        't_sec': 't.fSec',
+        't_ns': 't.fNanoSec'
+    }, [], {
+        'n_hits': 'hits',
+        'n_mc_hits': 'mc_hits',
+        'n_tracks': 'trks',
+        'n_mc_tracks': 'mc_trks'
+    }, lambda a: a, True),
 ]
 
 
@@ -42,7 +67,7 @@ class cached_property:
 
 class OfflineReader:
     """reader for offline ROOT files"""
-    def __init__(self, file_path=None, fobj=None, data=None, index=slice(None)):
+    def __init__(self, file_path=None, fobj=None, data=None, index=None):
         """ OfflineReader class is an offline ROOT file wrapper
 
         Parameters
@@ -64,8 +89,12 @@ class OfflineReader:
             self._tree = self._fobj[MAIN_TREE_NAME]
             self._data = data
 
-        for mapper in BRANCH_MAPS:
-            setattr(self, mapper.name, BranchElement(self._tree, mapper=mapper, index=self._index))
+    @cached_property
+    def events(self):
+        return Branch(self._tree,
+                      mapper=EVENTS_MAP,
+                      index=self._index,
+                      subbranchmaps=SUBBRANCH_MAPS)
 
     @classmethod
     def from_index(cls, source, index):
@@ -78,7 +107,9 @@ class OfflineReader:
         index: index or slice
             The index or slice to create the subtree.
         """
-        instance = cls(fobj=source._fobj, data=source._data[index], index=index)
+        instance = cls(fobj=source._fobj,
+                       data=source._data[index],
+                       index=index)
         return instance
 
     def __getitem__(self, index):
@@ -86,11 +117,11 @@ class OfflineReader:
 
     def __len__(self):
         tree = self._fobj[MAIN_TREE_NAME]
-        if self._index == slice(None):
+        if self._index is None:
             return len(tree)
         else:
-            return len(tree.lazyarrays(
-                basketcache=uproot.cache.ThreadSafeArrayCache(
+            return len(
+                tree.lazyarrays(basketcache=uproot.cache.ThreadSafeArrayCache(
                     BASKET_CACHE_SIZE))[self.index])
 
     @cached_property
@@ -104,10 +135,6 @@ class OfflineReader:
         else:
             warnings.warn("Your file header has an unsupported format")
 
-    @cached_property
-    def usr(self):
-        return Usr(self._tree)
-
     def get_best_reco(self):
         """returns the best reconstructed track fit data. The best fit is defined
         as the track fit with the maximum reconstruction stages. When "nan" is
@@ -401,10 +428,10 @@ class OfflineReader:
             are not found, None is returned as the stages index.
         """
         if mc is False:
-            stages_data = self.tracks.rec_stages
+            stages_data = self.events.tracks.rec_stages
 
         if mc is True:
-            stages_data = self.mc_tracks.rec_stages
+            stages_data = self.events.mc_tracks.rec_stages
 
         for trk_index, rec_stages in enumerate(stages_data):
             try:
@@ -449,25 +476,37 @@ class OfflineReader:
 
 class Usr:
     """Helper class to access AAObject usr stuff"""
-    def __init__(self, tree):
+    def __init__(self, name, tree, index=None):
         # Here, we assume that every event has the same names in the same order
         # to massively increase the performance. This needs triple check if it's
         # always the case; the usr-format is simply a very bad design.
+        # print("initialising usr for {}".format(name))
+        # print("Setting up usr")
+        self._name = name
         try:
+            tree['usr']  # This will raise a KeyError in old aanet files
+            # which has a different strucuter and key (usr_data)
+            # We do not support those...
             self._usr_names = [
-                n.decode("utf-8") for n in tree['Evt']['usr_names'].array()[0]
+                n.decode("utf-8") for n in tree['usr_names'].lazyarray()[0]
             ]
         except (KeyError, IndexError):  # e.g. old aanet files
             self._usr_names = []
         else:
+            # print(" checking usr data")
             self._usr_idx_lookup = {
                 name: index
                 for index, name in enumerate(self._usr_names)
             }
-            self._usr_data = tree['Evt']['usr'].lazyarray(
+            data = tree['usr'].lazyarray(
                 basketcache=uproot.cache.ThreadSafeArrayCache(
                     BASKET_CACHE_SIZE))
+            if index is not None:
+                data = data[index]
+            self._usr_data = data
+            # print("    adding attributes")
             for name in self._usr_names:
+                # print("  setting {}".format(name))
                 setattr(self, name, self[name])
 
     def __getitem__(self, item):
@@ -482,11 +521,14 @@ class Usr:
             entries.append("{}: {}".format(name, self[name]))
         return '\n'.join(entries)
 
+    def __repr__(self):
+        return "<{}[{}]>".format(self.__class__.__name__, self._name)
+
 
 def _to_num(value):
-    """Convert value to a numerical value if possible"""
+    """Convert a value to a numerical one if possible"""
     if value is None:
-        return None
+        return
     try:
         return int(value)
     except ValueError:
@@ -509,7 +551,9 @@ class Header:
             Constructor = namedtuple(attribute, fields)
             if len(values) < len(fields):
                 values += [None] * (len(fields) - len(values))
-            self._data[attribute] = Constructor(**{f: _to_num(v) for (f, v) in zip(fields, values)})
+            self._data[attribute] = Constructor(
+                **{f: _to_num(v)
+                   for (f, v) in zip(fields, values)})
 
         for attribute, value in self._data.items():
             setattr(self, attribute, value)
@@ -521,56 +565,170 @@ class Header:
         return "\n".join(lines)
 
 
-class BranchElement:
-    """wrapper for offline tracks"""
-    def __init__(self, tree, mapper, index=slice(None)):
+class Branch:
+    """Branch accessor class"""
+    def __init__(self,
+                 tree,
+                 mapper,
+                 index=None,
+                 subbranches=None,
+                 subbranchmaps=None):
         self._tree = tree
         self._mapper = mapper
         self._index = index
         self._keymap = None
-
         self._branch = tree[mapper.key]
+        self._subbranches = []
+
+        self._initialise_keys()  #
 
-        self._initialise_keys()
+        if subbranches is not None:
+            self._subbranches = subbranches
+        if subbranchmaps is not None:
+            for mapper in subbranchmaps:
+                subbranch = Branch(self._tree,
+                                   mapper=mapper,
+                                   index=self._index)
+                self._subbranches.append(subbranch)
+        for subbranch in self._subbranches:
+            setattr(self, subbranch._mapper.name, subbranch)
 
     def _initialise_keys(self):
-        """Create the keymap and instance attributes"""
-        keys = set(k.decode('utf-8') for k in self._branch.keys()) - set(self._mapper.exclude) - EXCLUDE_KEYS
-        self._keymap = {**{self._mapper.attrparser(k): k for k in keys}, **self._mapper.extra}
+        """Create the keymap and instance attributes for branch keys"""
+        keys = set(k.decode('utf-8') for k in self._branch.keys()) - set(
+            self._mapper.exclude) - EXCLUDE_KEYS
+        self._keymap = {
+            **{self._mapper.attrparser(k): k
+               for k in keys},
+            **self._mapper.extra
+        }
         self._keymap.update(self._mapper.update)
         for k in self._mapper.update.values():
             del self._keymap[k]
 
-        # self._EntryType = namedtuple(mapper.name[:-1], self.keys())
-
-        for key in self.keys():
+        for key in self._keymap.keys():
             # print("setting", self._mapper.name, key)
             setattr(self, key, self[key])
 
     def keys(self):
         return self._keymap.keys()
 
+    @cached_property
+    def usr(self):
+        return Usr(self._mapper.name, self._branch, index=self._index)
+
     def __getitem__(self, item):
         """Slicing magic a la numpy"""
+        print("Getting item '{}'".format(item))
         if isinstance(item, slice):
-            return self.__class__(self._tree, self._mapper, index=item)
+            return self.__class__(self._tree,
+                                  self._mapper,
+                                  index=item,
+                                  subbranches=self._subbranches)
         if isinstance(item, int):
-            return {
-                key: self._branch[self._keymap[key]].array()[self._index, item] for key in self.keys()
-                }
-        return self._branch[self._keymap[item]].lazyarray(
+            # A bit ugly, but whatever works
+            if self._mapper.flat:
+                if self._index is None:
+                    dct = {
+                        key: self._branch[self._keymap[key]].lazyarray()
+                        for key in self.keys()
+                    }
+                else:
+                    dct = {
+                        key: self._branch[self._keymap[key]].lazyarray()[
+                            self._index]
+                        for key in self.keys()
+                    }
+                for subbranch in self._subbranches:
+                    dct[subbranch._mapper.name] = subbranch
+                return BranchElement(self._mapper.name, dct)[item]
+            else:
+                if self._index is None:
+                    dct = {
+                        key: self._branch[self._keymap[key]].lazyarray()[item]
+                        for key in self.keys()
+                    }
+                else:
+                    dct = {
+                        key: self._branch[self._keymap[key]].lazyarray()[
+                            self._index, item]
+                        for key in self.keys()
+                    }
+                for subbranch in self._subbranches:
+                    dct[subbranch._mapper.name] = subbranch
+                return BranchElement(self._mapper.name, dct)
+
+        if isinstance(item, tuple):
+            return self[item[0]][item[1]]
+
+        if isinstance(item, str):
+            item = self._keymap[item]
+
+            out = self._branch[item].lazyarray(
                 basketcache=uproot.cache.ThreadSafeArrayCache(
-                    BASKET_CACHE_SIZE))[self._index]
+                    BASKET_CACHE_SIZE))
+            if self._index is not None:
+                out = out[self._index]
+            return out
+
+        return self.__class__(self._tree,
+                              self._mapper,
+                              index=np.array(item),
+                              subbranches=self._subbranches)
 
     def __len__(self):
-        if self._index == slice(None):
+        if self._index is None:
             return len(self._branch)
         else:
-            return len(self._branch[self._keymap['id']].lazyarray()[self._index])
+            return len(
+                self._branch[self._keymap['id']].lazyarray()[self._index])
 
     def __str__(self):
         return "Number of elements: {}".format(len(self._branch))
 
     def __repr__(self):
-        return "<{}[{}]: {} parsed elements>".format(self.__class__.__name__, self._mapper.name,
-                                                 len(self))
+        return "<{}[{}]: {} parsed elements>".format(self.__class__.__name__,
+                                                     self._mapper.name,
+                                                     len(self))
+
+
+class BranchElement:
+    """Represents a single branch element
+
+    Parameters
+    ----------
+    name: str
+        The name of the branch
+    dct: dict (keys=attributes, values=arrays of values)
+        The data
+    index: slice
+        The slice mask to be applied to the sub-arrays
+    """
+    def __init__(self, name, dct, index=None, subbranches=[]):
+        print("Creating branch element '{}'".format(name))
+        self._dct = dct
+        self._name = name
+        self._index = index
+        self.ItemConstructor = namedtuple(self._name[:-1], dct.keys())
+        if index is None:
+            for key, values in dct.items():
+                setattr(self, key, values)
+        else:
+            for key, values in dct.items():
+                setattr(self, key, values[index])
+
+    def __getitem__(self, item):
+        if isinstance(item, slice):
+            return self.__class__(self._name, self._dct, index=item)
+        if isinstance(item, int):
+            if self._index is None:
+                return self.ItemConstructor(
+                    **{k: v[item]
+                       for k, v in self._dct.items()})
+            else:
+                return self.ItemConstructor(
+                    **{k: v[self._index][item]
+                       for k, v in self._dct.items()})
+
+    def __repr__(self):
+        return "<{}[{}]>".format(self.__class__.__name__, self._name)