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tables.table
_g_col
Like `self._f_col()` but it does not check arguments.
def _g_col(self, colname): """Like `self._f_col()` but it does not check arguments.""" # Get the Column or Description object inames = colname.split('/') cols = self for iname in inames: cols = cols.__dict__[iname] return cols
(self, colname)
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728,166
tables.table
_g_update_table_location
Updates the location information about the associated `table`.
def _g_update_table_location(self, table): """Updates the location information about the associated `table`.""" myDict = self.__dict__ myDict['_v__tableFile'] = table._v_file myDict['_v__tablePath'] = table._v_pathname # Update the locations in individual columns. for colname in self._v_colnames: myDict[colname]._g_update_table_location(table)
(self, table)
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728,167
tables.table
Column
Accessor for a non-nested column in a table. Each instance of this class is associated with one *non-nested* column of a table. These instances are mainly used to read and write data from the table columns using item access (like the Cols class - see :ref:`ColsClassDescr`), but there are a few other associated methods to deal with indexes. .. rubric:: Column attributes .. attribute:: descr The Description (see :ref:`DescriptionClassDescr`) instance of the parent table or nested column. .. attribute:: name The name of the associated column. .. attribute:: pathname The complete pathname of the associated column (the same as Column.name if the column is not inside a nested column). .. attribute:: attrs Column attributes (see :ref:`ColClassDescr`). Parameters ---------- table The parent table instance name The name of the column that is associated with this object descr The parent description object
class Column: """Accessor for a non-nested column in a table. Each instance of this class is associated with one *non-nested* column of a table. These instances are mainly used to read and write data from the table columns using item access (like the Cols class - see :ref:`ColsClassDescr`), but there are a few other associated methods to deal with indexes. .. rubric:: Column attributes .. attribute:: descr The Description (see :ref:`DescriptionClassDescr`) instance of the parent table or nested column. .. attribute:: name The name of the associated column. .. attribute:: pathname The complete pathname of the associated column (the same as Column.name if the column is not inside a nested column). .. attribute:: attrs Column attributes (see :ref:`ColClassDescr`). Parameters ---------- table The parent table instance name The name of the column that is associated with this object descr The parent description object """ @lazyattr def dtype(self): """The NumPy dtype that most closely matches this column.""" return self.descr._v_dtypes[self.name].base # Get rid of shape info @lazyattr def type(self): """The PyTables type of the column (a string).""" return self.descr._v_types[self.name] @property def table(self): """The parent Table instance (see :ref:`TableClassDescr`).""" return self._table_file._get_node(self._table_path) @property def index(self): """The Index instance (see :ref:`IndexClassDescr`) associated with this column (None if the column is not indexed).""" indexPath = _index_pathname_of_column_(self._table_path, self.pathname) try: index = self._table_file._get_node(indexPath) except NodeError: index = None # The column is not indexed return index @lazyattr def _itemtype(self): return self.descr._v_dtypes[self.name] @property def shape(self): """The shape of this column.""" return (self.table.nrows,) + self.descr._v_dtypes[self.name].shape @property def is_indexed(self): """True if the column is indexed, false otherwise.""" if self.index is None: return False else: return True @property def maindim(self): """"The dimension along which iterators work. Its value is 0 (i.e. the first dimension).""" return 0 def __init__(self, table, name, descr): self._table_file = table._v_file self._table_path = table._v_pathname self.name = name """The name of the associated column.""" self.pathname = descr._v_colobjects[name]._v_pathname """The complete pathname of the associated column (the same as Column.name if the column is not inside a nested column).""" self.descr = descr """The Description (see :ref:`DescriptionClassDescr`) instance of the parent table or nested column.""" self._v_attrs = ColumnAttributeSet(self) def _g_update_table_location(self, table): """Updates the location information about the associated `table`.""" self._table_file = table._v_file self._table_path = table._v_pathname def __len__(self): """Get the number of elements in the column. This matches the length in rows of the parent table. """ return self.table.nrows def __getitem__(self, key): """Get a row or a range of rows from a column. If key argument is an integer, the corresponding element in the column is returned as an object of the current flavor. If key is a slice, the range of elements determined by it is returned as an array of the current flavor. Examples -------- :: print("Column handlers:") for name in table.colnames: print(table.cols._f_col(name)) print("Select table.cols.name[1]-->", table.cols.name[1]) print("Select table.cols.name[1:2]-->", table.cols.name[1:2]) print("Select table.cols.name[:]-->", table.cols.name[:]) print("Select table.cols._f_col('name')[:]-->", table.cols._f_col('name')[:]) The output of this for a certain arbitrary table is:: Column handlers: /table.cols.name (Column(), string, idx=None) /table.cols.lati (Column(), int32, idx=None) /table.cols.longi (Column(), int32, idx=None) /table.cols.vector (Column(2,), int32, idx=None) /table.cols.matrix2D (Column(2, 2), float64, idx=None) Select table.cols.name[1]--> Particle: 11 Select table.cols.name[1:2]--> ['Particle: 11'] Select table.cols.name[:]--> ['Particle: 10' 'Particle: 11' 'Particle: 12' 'Particle: 13' 'Particle: 14'] Select table.cols._f_col('name')[:]--> ['Particle: 10' 'Particle: 11' 'Particle: 12' 'Particle: 13' 'Particle: 14'] See the :file:`examples/table2.py` file for a more complete example. """ table = self.table # Generalized key support not there yet, but at least allow # for a tuple with one single element (the main dimension). # (key,) --> key if isinstance(key, tuple) and len(key) == 1: key = key[0] if is_idx(key): key = operator.index(key) # Index out of range protection if key >= table.nrows: raise IndexError("Index out of range") if key < 0: # To support negative values key += table.nrows (start, stop, step) = table._process_range(key, key + 1, 1) return table.read(start, stop, step, self.pathname)[0] elif isinstance(key, slice): (start, stop, step) = table._process_range( key.start, key.stop, key.step) return table.read(start, stop, step, self.pathname) else: raise TypeError( "'%s' key type is not valid in this context" % key) def __iter__(self): """Iterate through all items in the column.""" table = self.table itemsize = self.dtype.itemsize nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE'] // itemsize buf = np.empty((nrowsinbuf, ), self._itemtype) max_row = len(self) for start_row in range(0, len(self), nrowsinbuf): end_row = min(start_row + nrowsinbuf, max_row) buf_slice = buf[0:end_row - start_row] table.read(start_row, end_row, 1, field=self.pathname, out=buf_slice) yield from buf_slice def __setitem__(self, key, value): """Set a row or a range of rows in a column. If key argument is an integer, the corresponding element is set to value. If key is a slice, the range of elements determined by it is set to value. Examples -------- :: # Modify row 1 table.cols.col1[1] = -1 # Modify rows 1 and 3 table.cols.col1[1::2] = [2,3] Which is equivalent to:: # Modify row 1 table.modify_columns(start=1, columns=[[-1]], names=['col1']) # Modify rows 1 and 3 columns = np.rec.fromarrays([[2,3]], formats='i4') table.modify_columns(start=1, step=2, columns=columns, names=['col1']) """ table = self.table table._v_file._check_writable() # Generalized key support not there yet, but at least allow # for a tuple with one single element (the main dimension). # (key,) --> key if isinstance(key, tuple) and len(key) == 1: key = key[0]
(table, name, descr)
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728,168
tables.table
__getitem__
Get a row or a range of rows from a column. If key argument is an integer, the corresponding element in the column is returned as an object of the current flavor. If key is a slice, the range of elements determined by it is returned as an array of the current flavor. Examples -------- :: print("Column handlers:") for name in table.colnames: print(table.cols._f_col(name)) print("Select table.cols.name[1]-->", table.cols.name[1]) print("Select table.cols.name[1:2]-->", table.cols.name[1:2]) print("Select table.cols.name[:]-->", table.cols.name[:]) print("Select table.cols._f_col('name')[:]-->", table.cols._f_col('name')[:]) The output of this for a certain arbitrary table is:: Column handlers: /table.cols.name (Column(), string, idx=None) /table.cols.lati (Column(), int32, idx=None) /table.cols.longi (Column(), int32, idx=None) /table.cols.vector (Column(2,), int32, idx=None) /table.cols.matrix2D (Column(2, 2), float64, idx=None) Select table.cols.name[1]--> Particle: 11 Select table.cols.name[1:2]--> ['Particle: 11'] Select table.cols.name[:]--> ['Particle: 10' 'Particle: 11' 'Particle: 12' 'Particle: 13' 'Particle: 14'] Select table.cols._f_col('name')[:]--> ['Particle: 10' 'Particle: 11' 'Particle: 12' 'Particle: 13' 'Particle: 14'] See the :file:`examples/table2.py` file for a more complete example.
def __getitem__(self, key): """Get a row or a range of rows from a column. If key argument is an integer, the corresponding element in the column is returned as an object of the current flavor. If key is a slice, the range of elements determined by it is returned as an array of the current flavor. Examples -------- :: print("Column handlers:") for name in table.colnames: print(table.cols._f_col(name)) print("Select table.cols.name[1]-->", table.cols.name[1]) print("Select table.cols.name[1:2]-->", table.cols.name[1:2]) print("Select table.cols.name[:]-->", table.cols.name[:]) print("Select table.cols._f_col('name')[:]-->", table.cols._f_col('name')[:]) The output of this for a certain arbitrary table is:: Column handlers: /table.cols.name (Column(), string, idx=None) /table.cols.lati (Column(), int32, idx=None) /table.cols.longi (Column(), int32, idx=None) /table.cols.vector (Column(2,), int32, idx=None) /table.cols.matrix2D (Column(2, 2), float64, idx=None) Select table.cols.name[1]--> Particle: 11 Select table.cols.name[1:2]--> ['Particle: 11'] Select table.cols.name[:]--> ['Particle: 10' 'Particle: 11' 'Particle: 12' 'Particle: 13' 'Particle: 14'] Select table.cols._f_col('name')[:]--> ['Particle: 10' 'Particle: 11' 'Particle: 12' 'Particle: 13' 'Particle: 14'] See the :file:`examples/table2.py` file for a more complete example. """ table = self.table # Generalized key support not there yet, but at least allow # for a tuple with one single element (the main dimension). # (key,) --> key if isinstance(key, tuple) and len(key) == 1: key = key[0] if is_idx(key): key = operator.index(key) # Index out of range protection if key >= table.nrows: raise IndexError("Index out of range") if key < 0: # To support negative values key += table.nrows (start, stop, step) = table._process_range(key, key + 1, 1) return table.read(start, stop, step, self.pathname)[0] elif isinstance(key, slice): (start, stop, step) = table._process_range( key.start, key.stop, key.step) return table.read(start, stop, step, self.pathname) else: raise TypeError( "'%s' key type is not valid in this context" % key)
(self, key)
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728,169
tables.table
__init__
null
def __init__(self, table, name, descr): self._table_file = table._v_file self._table_path = table._v_pathname self.name = name """The name of the associated column.""" self.pathname = descr._v_colobjects[name]._v_pathname """The complete pathname of the associated column (the same as Column.name if the column is not inside a nested column).""" self.descr = descr """The Description (see :ref:`DescriptionClassDescr`) instance of the parent table or nested column.""" self._v_attrs = ColumnAttributeSet(self)
(self, table, name, descr)
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728,170
tables.table
__iter__
Iterate through all items in the column.
def __iter__(self): """Iterate through all items in the column.""" table = self.table itemsize = self.dtype.itemsize nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE'] // itemsize buf = np.empty((nrowsinbuf, ), self._itemtype) max_row = len(self) for start_row in range(0, len(self), nrowsinbuf): end_row = min(start_row + nrowsinbuf, max_row) buf_slice = buf[0:end_row - start_row] table.read(start_row, end_row, 1, field=self.pathname, out=buf_slice) yield from buf_slice
(self)
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728,171
tables.table
__len__
Get the number of elements in the column. This matches the length in rows of the parent table.
def __len__(self): """Get the number of elements in the column. This matches the length in rows of the parent table. """ return self.table.nrows
(self)
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728,172
tables.table
__repr__
A detailed string representation for this object.
def __repr__(self): """A detailed string representation for this object.""" return str(self)
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728,173
tables.table
__setitem__
Set a row or a range of rows in a column. If key argument is an integer, the corresponding element is set to value. If key is a slice, the range of elements determined by it is set to value. Examples -------- :: # Modify row 1 table.cols.col1[1] = -1 # Modify rows 1 and 3 table.cols.col1[1::2] = [2,3] Which is equivalent to:: # Modify row 1 table.modify_columns(start=1, columns=[[-1]], names=['col1']) # Modify rows 1 and 3 columns = np.rec.fromarrays([[2,3]], formats='i4') table.modify_columns(start=1, step=2, columns=columns, names=['col1'])
def __setitem__(self, key, value): """Set a row or a range of rows in a column. If key argument is an integer, the corresponding element is set to value. If key is a slice, the range of elements determined by it is set to value. Examples -------- :: # Modify row 1 table.cols.col1[1] = -1 # Modify rows 1 and 3 table.cols.col1[1::2] = [2,3] Which is equivalent to:: # Modify row 1 table.modify_columns(start=1, columns=[[-1]], names=['col1']) # Modify rows 1 and 3 columns = np.rec.fromarrays([[2,3]], formats='i4') table.modify_columns(start=1, step=2, columns=columns, names=['col1']) """ table = self.table table._v_file._check_writable() # Generalized key support not there yet, but at least allow # for a tuple with one single element (the main dimension). # (key,) --> key if isinstance(key, tuple) and len(key) == 1: key = key[0] if is_idx(key): key = operator.index(key) # Index out of range protection if key >= table.nrows: raise IndexError("Index out of range") if key < 0: # To support negative values key += table.nrows return table.modify_column(key, key + 1, 1, [[value]], self.pathname) elif isinstance(key, slice): (start, stop, step) = table._process_range( key.start, key.stop, key.step) return table.modify_column(start, stop, step, value, self.pathname) else: raise ValueError("Non-valid index or slice: %s" % key)
(self, key, value)
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728,174
tables.table
__str__
The string representation for this object.
def __str__(self): """The string representation for this object.""" return (f"{self._table_path}.cols.{self.pathname.replace('/', '.')} " f"({self.__class__.__name__}{self.shape}, " f"{self.descr._v_types[self.name]}, idx={self.index})")
(self)
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728,175
tables.table
_do_reindex
Common code for reindex() and reindex_dirty() codes.
def _do_reindex(self, dirty): """Common code for reindex() and reindex_dirty() codes.""" index = self.index dodirty = True if dirty and not index.dirty: dodirty = False if index is not None and dodirty: self._table_file._check_writable() # Get the old index parameters kind = index.kind optlevel = index.optlevel filters = index.filters # We *need* to tell the index that it is going to be undirty. # This is needed here so as to unnail() the condition cache. index.dirty = False # Delete the existing Index index._f_remove() # Create a new Index with the previous parameters return SizeType(self.create_index( kind=kind, optlevel=optlevel, filters=filters)) else: return SizeType(0) # The column is not intended for indexing
(self, dirty)
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728,176
tables.table
_g_update_table_location
Updates the location information about the associated `table`.
def _g_update_table_location(self, table): """Updates the location information about the associated `table`.""" self._table_file = table._v_file self._table_path = table._v_pathname
(self, table)
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728,177
tables.table
close
Close this column.
def close(self): """Close this column.""" self.__dict__.clear()
(self)
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728,178
tables.table
create_csindex
Create a completely sorted index (CSI) for this column. This method guarantees the creation of an index with zero entropy, that is, a completely sorted index (CSI) -- provided that the number of rows in the table does not exceed the 2**48 figure (that is more than 100 trillions of rows). A CSI index is needed for some table methods (like :meth:`Table.itersorted` or :meth:`Table.read_sorted`) in order to ensure completely sorted results. For the meaning of filters and tmp_dir arguments see :meth:`Column.create_index`. Notes ----- This method is equivalent to Column.create_index(optlevel=9, kind='full', ...).
def create_csindex(self, filters=None, tmp_dir=None, _blocksizes=None, _testmode=False, _verbose=False): """Create a completely sorted index (CSI) for this column. This method guarantees the creation of an index with zero entropy, that is, a completely sorted index (CSI) -- provided that the number of rows in the table does not exceed the 2**48 figure (that is more than 100 trillions of rows). A CSI index is needed for some table methods (like :meth:`Table.itersorted` or :meth:`Table.read_sorted`) in order to ensure completely sorted results. For the meaning of filters and tmp_dir arguments see :meth:`Column.create_index`. Notes ----- This method is equivalent to Column.create_index(optlevel=9, kind='full', ...). """ return self.create_index( kind='full', optlevel=9, filters=filters, tmp_dir=tmp_dir, _blocksizes=_blocksizes, _testmode=_testmode, _verbose=_verbose)
(self, filters=None, tmp_dir=None, _blocksizes=None, _testmode=False, _verbose=False)
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728,179
tables.table
create_index
Create an index for this column. .. warning:: In some situations it is useful to get a completely sorted index (CSI). For those cases, it is best to use the :meth:`Column.create_csindex` method instead. Parameters ---------- optlevel : int The optimization level for building the index. The levels ranges from 0 (no optimization) up to 9 (maximum optimization). Higher levels of optimization mean better chances for reducing the entropy of the index at the price of using more CPU, memory and I/O resources for creating the index. kind : str The kind of the index to be built. It can take the 'ultralight', 'light', 'medium' or 'full' values. Lighter kinds ('ultralight' and 'light') mean that the index takes less space on disk, but will perform queries slower. Heavier kinds ('medium' and 'full') mean better chances for reducing the entropy of the index (increasing the query speed) at the price of using more disk space as well as more CPU, memory and I/O resources for creating the index. Note that selecting a full kind with an optlevel of 9 (the maximum) guarantees the creation of an index with zero entropy, that is, a completely sorted index (CSI) - provided that the number of rows in the table does not exceed the 2**48 figure (that is more than 100 trillions of rows). See :meth:`Column.create_csindex` method for a more direct way to create a CSI index. filters : Filters Specify the Filters instance used to compress the index. If None, default index filters will be used (currently, zlib level 1 with shuffling). tmp_dir When kind is other than 'ultralight', a temporary file is created during the index build process. You can use the tmp_dir argument to specify the directory for this temporary file. The default is to create it in the same directory as the file containing the original table.
def create_index(self, optlevel=6, kind="medium", filters=None, tmp_dir=None, _blocksizes=None, _testmode=False, _verbose=False): """Create an index for this column. .. warning:: In some situations it is useful to get a completely sorted index (CSI). For those cases, it is best to use the :meth:`Column.create_csindex` method instead. Parameters ---------- optlevel : int The optimization level for building the index. The levels ranges from 0 (no optimization) up to 9 (maximum optimization). Higher levels of optimization mean better chances for reducing the entropy of the index at the price of using more CPU, memory and I/O resources for creating the index. kind : str The kind of the index to be built. It can take the 'ultralight', 'light', 'medium' or 'full' values. Lighter kinds ('ultralight' and 'light') mean that the index takes less space on disk, but will perform queries slower. Heavier kinds ('medium' and 'full') mean better chances for reducing the entropy of the index (increasing the query speed) at the price of using more disk space as well as more CPU, memory and I/O resources for creating the index. Note that selecting a full kind with an optlevel of 9 (the maximum) guarantees the creation of an index with zero entropy, that is, a completely sorted index (CSI) - provided that the number of rows in the table does not exceed the 2**48 figure (that is more than 100 trillions of rows). See :meth:`Column.create_csindex` method for a more direct way to create a CSI index. filters : Filters Specify the Filters instance used to compress the index. If None, default index filters will be used (currently, zlib level 1 with shuffling). tmp_dir When kind is other than 'ultralight', a temporary file is created during the index build process. You can use the tmp_dir argument to specify the directory for this temporary file. The default is to create it in the same directory as the file containing the original table. """ kinds = ['ultralight', 'light', 'medium', 'full'] if kind not in kinds: raise ValueError("Kind must have any of these values: %s" % kinds) if (not isinstance(optlevel, int) or (optlevel < 0 or optlevel > 9)): raise ValueError("Optimization level must be an integer in the " "range 0-9") if filters is None: filters = default_index_filters if tmp_dir is None: tmp_dir = str(Path(self._table_file.filename).parent) else: if not Path(tmp_dir).is_dir(): raise ValueError( f"Temporary directory '{tmp_dir}' does not exist" ) if (_blocksizes is not None and (not isinstance(_blocksizes, tuple) or len(_blocksizes) != 4)): raise ValueError("_blocksizes must be a tuple with exactly 4 " "elements") idxrows = _column__create_index(self, optlevel, kind, filters, tmp_dir, _blocksizes, _verbose) return SizeType(idxrows)
(self, optlevel=6, kind='medium', filters=None, tmp_dir=None, _blocksizes=None, _testmode=False, _verbose=False)
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728,180
tables.table
reindex
Recompute the index associated with this column. This can be useful when you suspect that, for any reason, the index information is no longer valid and you want to rebuild it. This method does nothing if the column is not indexed.
def reindex(self): """Recompute the index associated with this column. This can be useful when you suspect that, for any reason, the index information is no longer valid and you want to rebuild it. This method does nothing if the column is not indexed. """ self._do_reindex(dirty=False)
(self)
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728,181
tables.table
reindex_dirty
Recompute the associated index only if it is dirty. This can be useful when you have set :attr:`Table.autoindex` to false for the table and you want to update the column's index after an invalidating index operation (like :meth:`Table.remove_rows`). This method does nothing if the column is not indexed.
def reindex_dirty(self): """Recompute the associated index only if it is dirty. This can be useful when you have set :attr:`Table.autoindex` to false for the table and you want to update the column's index after an invalidating index operation (like :meth:`Table.remove_rows`). This method does nothing if the column is not indexed. """ self._do_reindex(dirty=True)
(self)
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728,182
tables.table
remove_index
Remove the index associated with this column. This method does nothing if the column is not indexed. The removed index can be created again by calling the :meth:`Column.create_index` method.
def remove_index(self): """Remove the index associated with this column. This method does nothing if the column is not indexed. The removed index can be created again by calling the :meth:`Column.create_index` method. """ self._table_file._check_writable() # Remove the index if existing. if self.is_indexed: index = self.index index._f_remove() self.table._set_column_indexing(self.pathname, False)
(self)
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728,183
tables.atom
_ComplexErrorAtom
Reminds the user to stop using the old complex atom names.
class _ComplexErrorAtom(ComplexAtom, metaclass=type): """Reminds the user to stop using the old complex atom names.""" def __init__(self, shape=(), dflt=ComplexAtom._defvalue): raise TypeError( "to avoid confusions with PyTables 1.X complex atom names, " "please use ``ComplexAtom(itemsize=N)``, " "where N=8 for single precision complex atoms, " "and N=16 for double precision complex atoms")
(shape=(), dflt=0j)
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728,185
tables.atom
__init__
null
def __init__(self, shape=(), dflt=ComplexAtom._defvalue): raise TypeError( "to avoid confusions with PyTables 1.X complex atom names, " "please use ``ComplexAtom(itemsize=N)``, " "where N=8 for single precision complex atoms, " "and N=16 for double precision complex atoms")
(self, shape=(), dflt=0j)
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728,191
tables.description
Complex128Col
Defines a non-nested column of a particular type. The constructor accepts the same arguments as the equivalent `Atom` class, plus an additional ``pos`` argument for position information, which is assigned to the `_v_pos` attribute and an ``attrs`` argument for storing additional metadata similar to `table.attrs`, which is assigned to the `_v_col_attrs` attribute.
from tables.description import Complex128Col
(*args, **kwargs)
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728,207
tables.description
Complex256Col
Defines a non-nested column of a particular type. The constructor accepts the same arguments as the equivalent `Atom` class, plus an additional ``pos`` argument for position information, which is assigned to the `_v_pos` attribute and an ``attrs`` argument for storing additional metadata similar to `table.attrs`, which is assigned to the `_v_col_attrs` attribute.
from tables.description import Complex256Col
(*args, **kwargs)
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728,223
tables.description
Complex32Col
Defines a non-nested column of a particular type. The constructor accepts the same arguments as the equivalent `Atom` class, plus an additional ``pos`` argument for position information, which is assigned to the `_v_pos` attribute and an ``attrs`` argument for storing additional metadata similar to `table.attrs`, which is assigned to the `_v_col_attrs` attribute.
from tables.description import Complex32Col
(*args, **kwargs)
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728,239
tables.description
Complex64Col
Defines a non-nested column of a particular type. The constructor accepts the same arguments as the equivalent `Atom` class, plus an additional ``pos`` argument for position information, which is assigned to the `_v_pos` attribute and an ``attrs`` argument for storing additional metadata similar to `table.attrs`, which is assigned to the `_v_col_attrs` attribute.
from tables.description import Complex64Col
(*args, **kwargs)
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728,247
tables.atom
ComplexAtom
Defines an atom of kind complex. Allowed item sizes are 8 (single precision) and 16 (double precision). This class must be used instead of more concrete ones to avoid confusions with numarray-like precision specifications used in PyTables 1.X.
class ComplexAtom(Atom): """Defines an atom of kind complex. Allowed item sizes are 8 (single precision) and 16 (double precision). This class must be used instead of more concrete ones to avoid confusions with numarray-like precision specifications used in PyTables 1.X. """ # This definition is a little more complex (no pun intended) # because, although the complex kind is a normal numerical one, # the usage of bottom-level classes is artificially forbidden. # Everything will be back to normality when people has stopped # using the old bottom-level complex classes. kind = 'complex' _deftype = 'complex128' _defvalue = 0j _isizes = [8, 16] @property def itemsize(self): """Size in bytes of a sigle item in the atom.""" return self.dtype.base.itemsize # Only instances have a `type` attribute, so complex types must be # registered by hand. all_types.add('complex64') all_types.add('complex128') if hasattr(np, 'complex192'): all_types.add('complex192') _isizes.append(24) if hasattr(np, 'complex256'): all_types.add('complex256') _isizes.append(32) def __init__(self, itemsize, shape=(), dflt=_defvalue): if itemsize not in self._isizes: raise _invalid_itemsize_error('complex', itemsize, self._isizes) self.type = '%s%d' % (self.kind, itemsize * 8) Atom.__init__(self, self.type, shape, dflt)
(itemsize, shape=(), dflt=0j)
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728,249
tables.atom
__init__
null
def __init__(self, itemsize, shape=(), dflt=_defvalue): if itemsize not in self._isizes: raise _invalid_itemsize_error('complex', itemsize, self._isizes) self.type = '%s%d' % (self.kind, itemsize * 8) Atom.__init__(self, self.type, shape, dflt)
(self, itemsize, shape=(), dflt=0j)
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728,255
tables.description
ComplexCol
Defines a non-nested column of a particular type. The constructor accepts the same arguments as the equivalent `Atom` class, plus an additional ``pos`` argument for position information, which is assigned to the `_v_pos` attribute and an ``attrs`` argument for storing additional metadata similar to `table.attrs`, which is assigned to the `_v_col_attrs` attribute.
from tables.description import ComplexCol
(*args, **kwargs)
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728,263
tables.exceptions
DataTypeWarning
Unsupported data type. This warning is issued when an unsupported HDF5 data type is found (normally in a file created with other tool than PyTables).
class DataTypeWarning(Warning): """Unsupported data type. This warning is issued when an unsupported HDF5 data type is found (normally in a file created with other tool than PyTables). """ pass
null
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728,264
tables.description
Description
This class represents descriptions of the structure of tables. An instance of this class is automatically bound to Table (see :ref:`TableClassDescr`) objects when they are created. It provides a browseable representation of the structure of the table, made of non-nested (Col - see :ref:`ColClassDescr`) and nested (Description) columns. Column definitions under a description can be accessed as attributes of it (*natural naming*). For instance, if table.description is a Description instance with a column named col1 under it, the later can be accessed as table.description.col1. If col1 is nested and contains a col2 column, this can be accessed as table.description.col1.col2. Because of natural naming, the names of members start with special prefixes, like in the Group class (see :ref:`GroupClassDescr`). .. rubric:: Description attributes .. attribute:: _v_colobjects A dictionary mapping the names of the columns hanging directly from the associated table or nested column to their respective descriptions (Col - see :ref:`ColClassDescr` or Description - see :ref:`DescriptionClassDescr` instances). .. versionchanged:: 3.0 The *_v_colObjects* attribute has been renamed into *_v_colobjects*. .. attribute:: _v_dflts A dictionary mapping the names of non-nested columns hanging directly from the associated table or nested column to their respective default values. .. attribute:: _v_dtype The NumPy type which reflects the structure of this table or nested column. You can use this as the dtype argument of NumPy array factories. .. attribute:: _v_dtypes A dictionary mapping the names of non-nested columns hanging directly from the associated table or nested column to their respective NumPy types. .. attribute:: _v_is_nested Whether the associated table or nested column contains further nested columns or not. .. attribute:: _v_itemsize The size in bytes of an item in this table or nested column. .. attribute:: _v_name The name of this description group. The name of the root group is '/'. .. attribute:: _v_names A list of the names of the columns hanging directly from the associated table or nested column. The order of the names matches the order of their respective columns in the containing table. .. attribute:: _v_nested_descr A nested list of pairs of (name, format) tuples for all the columns under this table or nested column. You can use this as the dtype and descr arguments of NumPy array factories. .. versionchanged:: 3.0 The *_v_nestedDescr* attribute has been renamed into *_v_nested_descr*. .. attribute:: _v_nested_formats A nested list of the NumPy string formats (and shapes) of all the columns under this table or nested column. You can use this as the formats argument of NumPy array factories. .. versionchanged:: 3.0 The *_v_nestedFormats* attribute has been renamed into *_v_nested_formats*. .. attribute:: _v_nestedlvl The level of the associated table or nested column in the nested datatype. .. attribute:: _v_nested_names A nested list of the names of all the columns under this table or nested column. You can use this as the names argument of NumPy array factories. .. versionchanged:: 3.0 The *_v_nestedNames* attribute has been renamed into *_v_nested_names*. .. attribute:: _v_pathname Pathname of the table or nested column. .. attribute:: _v_pathnames A list of the pathnames of all the columns under this table or nested column (in preorder). If it does not contain nested columns, this is exactly the same as the :attr:`Description._v_names` attribute. .. attribute:: _v_types A dictionary mapping the names of non-nested columns hanging directly from the associated table or nested column to their respective PyTables types. .. attribute:: _v_offsets A list of offsets for all the columns. If the list is empty, means that there are no padding in the data structure. However, the support for offsets is currently limited to flat tables; for nested tables, the potential padding is always removed (exactly the same as in pre-3.5 versions), and this variable is set to empty. .. versionadded:: 3.5 Previous to this version all the compound types were converted internally to 'packed' types, i.e. with no padding between the component types. Starting with 3.5, the holes in native HDF5 types (non-nested) are honored and replicated during dataset and attribute copies.
class Description: """This class represents descriptions of the structure of tables. An instance of this class is automatically bound to Table (see :ref:`TableClassDescr`) objects when they are created. It provides a browseable representation of the structure of the table, made of non-nested (Col - see :ref:`ColClassDescr`) and nested (Description) columns. Column definitions under a description can be accessed as attributes of it (*natural naming*). For instance, if table.description is a Description instance with a column named col1 under it, the later can be accessed as table.description.col1. If col1 is nested and contains a col2 column, this can be accessed as table.description.col1.col2. Because of natural naming, the names of members start with special prefixes, like in the Group class (see :ref:`GroupClassDescr`). .. rubric:: Description attributes .. attribute:: _v_colobjects A dictionary mapping the names of the columns hanging directly from the associated table or nested column to their respective descriptions (Col - see :ref:`ColClassDescr` or Description - see :ref:`DescriptionClassDescr` instances). .. versionchanged:: 3.0 The *_v_colObjects* attribute has been renamed into *_v_colobjects*. .. attribute:: _v_dflts A dictionary mapping the names of non-nested columns hanging directly from the associated table or nested column to their respective default values. .. attribute:: _v_dtype The NumPy type which reflects the structure of this table or nested column. You can use this as the dtype argument of NumPy array factories. .. attribute:: _v_dtypes A dictionary mapping the names of non-nested columns hanging directly from the associated table or nested column to their respective NumPy types. .. attribute:: _v_is_nested Whether the associated table or nested column contains further nested columns or not. .. attribute:: _v_itemsize The size in bytes of an item in this table or nested column. .. attribute:: _v_name The name of this description group. The name of the root group is '/'. .. attribute:: _v_names A list of the names of the columns hanging directly from the associated table or nested column. The order of the names matches the order of their respective columns in the containing table. .. attribute:: _v_nested_descr A nested list of pairs of (name, format) tuples for all the columns under this table or nested column. You can use this as the dtype and descr arguments of NumPy array factories. .. versionchanged:: 3.0 The *_v_nestedDescr* attribute has been renamed into *_v_nested_descr*. .. attribute:: _v_nested_formats A nested list of the NumPy string formats (and shapes) of all the columns under this table or nested column. You can use this as the formats argument of NumPy array factories. .. versionchanged:: 3.0 The *_v_nestedFormats* attribute has been renamed into *_v_nested_formats*. .. attribute:: _v_nestedlvl The level of the associated table or nested column in the nested datatype. .. attribute:: _v_nested_names A nested list of the names of all the columns under this table or nested column. You can use this as the names argument of NumPy array factories. .. versionchanged:: 3.0 The *_v_nestedNames* attribute has been renamed into *_v_nested_names*. .. attribute:: _v_pathname Pathname of the table or nested column. .. attribute:: _v_pathnames A list of the pathnames of all the columns under this table or nested column (in preorder). If it does not contain nested columns, this is exactly the same as the :attr:`Description._v_names` attribute. .. attribute:: _v_types A dictionary mapping the names of non-nested columns hanging directly from the associated table or nested column to their respective PyTables types. .. attribute:: _v_offsets A list of offsets for all the columns. If the list is empty, means that there are no padding in the data structure. However, the support for offsets is currently limited to flat tables; for nested tables, the potential padding is always removed (exactly the same as in pre-3.5 versions), and this variable is set to empty. .. versionadded:: 3.5 Previous to this version all the compound types were converted internally to 'packed' types, i.e. with no padding between the component types. Starting with 3.5, the holes in native HDF5 types (non-nested) are honored and replicated during dataset and attribute copies. """ def __init__(self, classdict, nestedlvl=-1, validate=True, ptparams=None): if not classdict: raise ValueError("cannot create an empty data type") # Do a shallow copy of classdict just in case this is going to # be shared by other instances newdict = self.__dict__ newdict["_v_name"] = "/" # The name for root descriptor newdict["_v_names"] = [] newdict["_v_dtypes"] = {} newdict["_v_types"] = {} newdict["_v_dflts"] = {} newdict["_v_colobjects"] = {} newdict["_v_is_nested"] = False nestedFormats = [] nestedDType = [] if not hasattr(newdict, "_v_nestedlvl"): newdict["_v_nestedlvl"] = nestedlvl + 1 cols_with_pos = [] # colum (position, name) pairs cols_no_pos = [] # just column names cols_offsets = [] # the offsets of the columns valid_offsets = False # by default there a no valid offsets # Check for special variables and convert column descriptions for (name, descr) in classdict.items(): if name.startswith('_v_'): if name in newdict: # print("Warning!") # special methods &c: copy to newdict, warn about conflicts warnings.warn("Can't set attr %r in description class %r" % (name, self)) else: # print("Special variable!-->", name, classdict[name]) newdict[name] = descr continue # This variable is not needed anymore columns = None if (type(descr) == type(IsDescription) and issubclass(descr, IsDescription)): # print("Nested object (type I)-->", name) columns = descr().columns elif (type(descr.__class__) == type(IsDescription) and issubclass(descr.__class__, IsDescription)): # print("Nested object (type II)-->", name) columns = descr.columns elif isinstance(descr, dict): # print("Nested object (type III)-->", name) columns = descr else: # print("Nested object (type IV)-->", name) descr = copy.copy(descr) # The copies above and below ensure that the structures # provided by the user will remain unchanged even if we # tamper with the values of ``_v_pos`` here. if columns is not None: descr = Description(copy.copy(columns), self._v_nestedlvl, ptparams=ptparams) classdict[name] = descr pos = getattr(descr, '_v_pos', None) if pos is None: cols_no_pos.append(name) else: cols_with_pos.append((pos, name)) offset = getattr(descr, '_v_offset', None) if offset is not None: cols_offsets.append(offset) # Sort field names: # # 1. Fields with explici
(classdict, nestedlvl=-1, validate=True, ptparams=None)
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728,265
tables.description
__init__
null
def __init__(self, classdict, nestedlvl=-1, validate=True, ptparams=None): if not classdict: raise ValueError("cannot create an empty data type") # Do a shallow copy of classdict just in case this is going to # be shared by other instances newdict = self.__dict__ newdict["_v_name"] = "/" # The name for root descriptor newdict["_v_names"] = [] newdict["_v_dtypes"] = {} newdict["_v_types"] = {} newdict["_v_dflts"] = {} newdict["_v_colobjects"] = {} newdict["_v_is_nested"] = False nestedFormats = [] nestedDType = [] if not hasattr(newdict, "_v_nestedlvl"): newdict["_v_nestedlvl"] = nestedlvl + 1 cols_with_pos = [] # colum (position, name) pairs cols_no_pos = [] # just column names cols_offsets = [] # the offsets of the columns valid_offsets = False # by default there a no valid offsets # Check for special variables and convert column descriptions for (name, descr) in classdict.items(): if name.startswith('_v_'): if name in newdict: # print("Warning!") # special methods &c: copy to newdict, warn about conflicts warnings.warn("Can't set attr %r in description class %r" % (name, self)) else: # print("Special variable!-->", name, classdict[name]) newdict[name] = descr continue # This variable is not needed anymore columns = None if (type(descr) == type(IsDescription) and issubclass(descr, IsDescription)): # print("Nested object (type I)-->", name) columns = descr().columns elif (type(descr.__class__) == type(IsDescription) and issubclass(descr.__class__, IsDescription)): # print("Nested object (type II)-->", name) columns = descr.columns elif isinstance(descr, dict): # print("Nested object (type III)-->", name) columns = descr else: # print("Nested object (type IV)-->", name) descr = copy.copy(descr) # The copies above and below ensure that the structures # provided by the user will remain unchanged even if we # tamper with the values of ``_v_pos`` here. if columns is not None: descr = Description(copy.copy(columns), self._v_nestedlvl, ptparams=ptparams) classdict[name] = descr pos = getattr(descr, '_v_pos', None) if pos is None: cols_no_pos.append(name) else: cols_with_pos.append((pos, name)) offset = getattr(descr, '_v_offset', None) if offset is not None: cols_offsets.append(offset) # Sort field names: # # 1. Fields with explicit positions, according to their # positions (and their names if coincident). # 2. Fields with no position, in alphabetical order. cols_with_pos.sort() cols_no_pos.sort() keys = [name for (pos, name) in cols_with_pos] + cols_no_pos pos = 0 nested = False # Get properties for compound types for k in keys: if validate: # Check for key name validity check_name_validity(k) # Class variables object = classdict[k] newdict[k] = object # To allow natural naming if not isinstance(object, (Col, Description)): raise TypeError('Passing an incorrect value to a table column.' ' Expected a Col (or subclass) instance and ' 'got: "%s". Please make use of the Col(), or ' 'descendant, constructor to properly ' 'initialize columns.' % object) object._v_pos = pos # Set the position of this object object._v_parent = self # The parent description pos += 1 newdict['_v_colobjects'][k] = object newdict['_v_names'].append(k) object.__dict__['_v_name'] = k if not isinstance(k, str): # numpy only accepts "str" for field names # Python 3.x: bytes --> str (unicode) kk = k.decode() else: kk = k if isinstance(object, Col): dtype = object.dtype newdict['_v_dtypes'][k] = dtype newdict['_v_types'][k] = object.type newdict['_v_dflts'][k] = object.dflt nestedFormats.append(object.recarrtype) baserecarrtype = dtype.base.str[1:] nestedDType.append((kk, baserecarrtype, dtype.shape)) else: # A description nestedFormats.append(object._v_nested_formats) nestedDType.append((kk, object._v_dtype)) nested = True # Useful for debugging purposes # import traceback # if ptparams is None: # print("*** print_stack:") # traceback.print_stack() # Check whether we are gonna use padding or not. Two possibilities: # 1) Make padding True by default (except if ALLOW_PADDING is set # to False) # 2) Make padding False by default (except if ALLOW_PADDING is set # to True) # Currently we choose 1) because it favours honoring padding even on # unhandled situations (should be very few). # However, for development, option 2) is recommended as it catches # most of the unhandled situations. allow_padding = ptparams is None or ptparams['ALLOW_PADDING'] # allow_padding = ptparams is not None and ptparams['ALLOW_PADDING'] if (allow_padding and len(cols_offsets) > 1 and len(keys) == len(cols_with_pos) and len(keys) == len(cols_offsets) and not nested): # TODO: support offsets with nested types # We have to sort the offsets too, as they must follow the column # order. As the offsets and the pos should be place in the same # order, a single sort is enough here. cols_offsets.sort() valid_offsets = True else: newdict['_v_offsets'] = [] # Assign the format list to _v_nested_formats newdict['_v_nested_formats'] = nestedFormats if self._v_nestedlvl == 0: # Get recursively nested _v_nested_names and _v_nested_descr attrs self._g_set_nested_names_descr() # Get pathnames for nested groups self._g_set_path_names() # Check the _v_byteorder has been used an issue an Error if hasattr(self, "_v_byteorder"): raise ValueError( "Using a ``_v_byteorder`` in the description is obsolete. " "Use the byteorder parameter in the constructor instead.") # Compute the dtype with offsets or without # print("offsets ->", cols_offsets, nestedDType, nested, valid_offsets) if valid_offsets: # TODO: support offsets within nested types dtype_fields = { 'names': newdict['_v_names'], 'formats': nestedFormats, 'offsets': cols_offsets} itemsize = newdict.get('_v_itemsize', None) if itemsize is not None: dtype_fields['itemsize'] = itemsize dtype = np.dtype(dtype_fields) else: dtype = np.dtype(nestedDType) newdict['_v_dtype'] = dtype newdict['_v_itemsize'] = dtype.itemsize newdict['_v_offsets'] = [dtype.fields[name][1] for name in dtype.names]
(self, classdict, nestedlvl=-1, validate=True, ptparams=None)
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728,266
tables.description
__repr__
Gives a detailed Description column representation.
def __repr__(self): """Gives a detailed Description column representation.""" rep = ['%s\"%s\": %r' % (" " * self._v_nestedlvl, k, self._v_colobjects[k]) for k in self._v_names] return '{\n %s}' % (',\n '.join(rep))
(self)
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728,267
tables.description
__str__
Gives a brief Description representation.
def __str__(self): """Gives a brief Description representation.""" return f'Description({self._v_nested_descr})'
(self)
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728,268
tables.description
_f_walk
Iterate over nested columns. If type is 'All' (the default), all column description objects (Col and Description instances) are yielded in top-to-bottom order (preorder). If type is 'Col' or 'Description', only column descriptions of that type are yielded.
def _f_walk(self, type='All'): """Iterate over nested columns. If type is 'All' (the default), all column description objects (Col and Description instances) are yielded in top-to-bottom order (preorder). If type is 'Col' or 'Description', only column descriptions of that type are yielded. """ if type not in ["All", "Col", "Description"]: raise ValueError("""\ type can only take the parameters 'All', 'Col' or 'Description'.""") stack = [self] while stack: object = stack.pop(0) # pop at the front so as to ensure the order if type in ["All", "Description"]: yield object # yield description for name in object._v_names: new_object = object._v_colobjects[name] if isinstance(new_object, Description): stack.append(new_object) else: if type in ["All", "Col"]: yield new_object # yield column
(self, type='All')
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728,269
tables.description
_g_set_nested_names_descr
Computes the nested names and descriptions for nested datatypes.
def _g_set_nested_names_descr(self): """Computes the nested names and descriptions for nested datatypes.""" names = self._v_names fmts = self._v_nested_formats self._v_nested_names = names[:] # Important to do a copy! self._v_nested_descr = list(zip(names, fmts)) for i, name in enumerate(names): new_object = self._v_colobjects[name] if isinstance(new_object, Description): new_object._g_set_nested_names_descr() # replace the column nested name by a correct tuple self._v_nested_names[i] = (name, new_object._v_nested_names) self._v_nested_descr[i] = (name, new_object._v_nested_descr) # set the _v_is_nested flag self._v_is_nested = True
(self)
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728,270
tables.description
_g_set_path_names
Compute the pathnames for arbitrary nested descriptions. This method sets the ``_v_pathname`` and ``_v_pathnames`` attributes of all the elements (both descriptions and columns) in this nested description.
def _g_set_path_names(self): """Compute the pathnames for arbitrary nested descriptions. This method sets the ``_v_pathname`` and ``_v_pathnames`` attributes of all the elements (both descriptions and columns) in this nested description. """ def get_cols_in_order(description): return [description._v_colobjects[colname] for colname in description._v_names] def join_paths(path1, path2): if not path1: return path2 return f'{path1}/{path2}' # The top of the stack always has a nested description # and a list of its child columns # (be they nested ``Description`` or non-nested ``Col`` objects). # In the end, the list contains only a list of column paths # under this one. # # For instance, given this top of the stack:: # # (<Description X>, [<Column A>, <Column B>]) # # After computing the rest of the stack, the top is:: # # (<Description X>, ['a', 'a/m', 'a/n', ... , 'b', ...]) stack = [] # We start by pushing the top-level description # and its child columns. self._v_pathname = '' stack.append((self, get_cols_in_order(self))) while stack: desc, cols = stack.pop() head = cols[0] # What's the first child in the list? if isinstance(head, Description): # A nested description. We remove it from the list and # push it with its child columns. This will be the next # handled description. head._v_pathname = join_paths(desc._v_pathname, head._v_name) stack.append((desc, cols[1:])) # alter the top stack.append((head, get_cols_in_order(head))) # new top elif isinstance(head, Col): # A non-nested column. We simply remove it from the # list and append its name to it. head._v_pathname = join_paths(desc._v_pathname, head._v_name) cols.append(head._v_name) # alter the top stack.append((desc, cols[1:])) # alter the top else: # Since paths and names are appended *to the end* of # children lists, a string signals that no more children # remain to be processed, so we are done with the # description at the top of the stack. assert isinstance(head, str) # Assign the computed set of descendent column paths. desc._v_pathnames = cols if len(stack) > 0: # Compute the paths with respect to the parent node # (including the path of the current description) # and append them to its list. descName = desc._v_name colPaths = [join_paths(descName, path) for path in cols] colPaths.insert(0, descName) parentCols = stack[-1][1] parentCols.extend(colPaths) # (Nothing is pushed, we are done with this description.)
(self)
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728,271
tables.earray
EArray
This class represents extendable, homogeneous datasets in an HDF5 file. The main difference between an EArray and a CArray (see :ref:`CArrayClassDescr`), from which it inherits, is that the former can be enlarged along one of its dimensions, the *enlargeable dimension*. That means that the :attr:`Leaf.extdim` attribute (see :class:`Leaf`) of any EArray instance will always be non-negative. Multiple enlargeable dimensions might be supported in the future. New rows can be added to the end of an enlargeable array by using the :meth:`EArray.append` method. Parameters ---------- parentnode The parent :class:`Group` object. .. versionchanged:: 3.0 Renamed from *parentNode* to *parentnode*. name : str The name of this node in its parent group. atom An `Atom` instance representing the *type* and *shape* of the atomic objects to be saved. shape The shape of the new array. One (and only one) of the shape dimensions *must* be 0. The dimension being 0 means that the resulting `EArray` object can be extended along it. Multiple enlargeable dimensions are not supported right now. title A description for this node (it sets the ``TITLE`` HDF5 attribute on disk). filters An instance of the `Filters` class that provides information about the desired I/O filters to be applied during the life of this object. expectedrows A user estimate about the number of row elements that will be added to the growable dimension in the `EArray` node. If not provided, the default value is ``EXPECTED_ROWS_EARRAY`` (see ``tables/parameters.py``). If you plan to create either a much smaller or a much bigger `EArray` try providing a guess; this will optimize the HDF5 B-Tree creation and management process time and the amount of memory used. chunkshape The shape of the data chunk to be read or written in a single HDF5 I/O operation. Filters are applied to those chunks of data. The dimensionality of `chunkshape` must be the same as that of `shape` (beware: no dimension should be 0 this time!). If ``None``, a sensible value is calculated based on the `expectedrows` parameter (which is recommended). byteorder The byteorder of the data *on disk*, specified as 'little' or 'big'. If this is not specified, the byteorder is that of the platform. track_times Whether time data associated with the leaf are recorded (object access time, raw data modification time, metadata change time, object birth time); default True. Semantics of these times depend on their implementation in the HDF5 library: refer to documentation of the H5O_info_t data structure. As of HDF5 1.8.15, only ctime (metadata change time) is implemented. .. versionadded:: 3.4.3 Examples -------- See below a small example of the use of the `EArray` class. The code is available in ``examples/earray1.py``:: import numpy as np import tables as tb fileh = tb.open_file('earray1.h5', mode='w') a = tb.StringAtom(itemsize=8) # Use ``a`` as the object type for the enlargeable array. array_c = fileh.create_earray(fileh.root, 'array_c', a, (0,), "Chars") array_c.append(np.array(['a'*2, 'b'*4], dtype='S8')) array_c.append(np.array(['a'*6, 'b'*8, 'c'*10], dtype='S8')) # Read the string ``EArray`` we have created on disk. for s in array_c: print('array_c[%s] => %r' % (array_c.nrow, s)) # Close the file. fileh.close() The output for the previous script is something like:: array_c[0] => 'aa' array_c[1] => 'bbbb' array_c[2] => 'aaaaaa' array_c[3] => 'bbbbbbbb' array_c[4] => 'cccccccc'
class EArray(CArray): """This class represents extendable, homogeneous datasets in an HDF5 file. The main difference between an EArray and a CArray (see :ref:`CArrayClassDescr`), from which it inherits, is that the former can be enlarged along one of its dimensions, the *enlargeable dimension*. That means that the :attr:`Leaf.extdim` attribute (see :class:`Leaf`) of any EArray instance will always be non-negative. Multiple enlargeable dimensions might be supported in the future. New rows can be added to the end of an enlargeable array by using the :meth:`EArray.append` method. Parameters ---------- parentnode The parent :class:`Group` object. .. versionchanged:: 3.0 Renamed from *parentNode* to *parentnode*. name : str The name of this node in its parent group. atom An `Atom` instance representing the *type* and *shape* of the atomic objects to be saved. shape The shape of the new array. One (and only one) of the shape dimensions *must* be 0. The dimension being 0 means that the resulting `EArray` object can be extended along it. Multiple enlargeable dimensions are not supported right now. title A description for this node (it sets the ``TITLE`` HDF5 attribute on disk). filters An instance of the `Filters` class that provides information about the desired I/O filters to be applied during the life of this object. expectedrows A user estimate about the number of row elements that will be added to the growable dimension in the `EArray` node. If not provided, the default value is ``EXPECTED_ROWS_EARRAY`` (see ``tables/parameters.py``). If you plan to create either a much smaller or a much bigger `EArray` try providing a guess; this will optimize the HDF5 B-Tree creation and management process time and the amount of memory used. chunkshape The shape of the data chunk to be read or written in a single HDF5 I/O operation. Filters are applied to those chunks of data. The dimensionality of `chunkshape` must be the same as that of `shape` (beware: no dimension should be 0 this time!). If ``None``, a sensible value is calculated based on the `expectedrows` parameter (which is recommended). byteorder The byteorder of the data *on disk*, specified as 'little' or 'big'. If this is not specified, the byteorder is that of the platform. track_times Whether time data associated with the leaf are recorded (object access time, raw data modification time, metadata change time, object birth time); default True. Semantics of these times depend on their implementation in the HDF5 library: refer to documentation of the H5O_info_t data structure. As of HDF5 1.8.15, only ctime (metadata change time) is implemented. .. versionadded:: 3.4.3 Examples -------- See below a small example of the use of the `EArray` class. The code is available in ``examples/earray1.py``:: import numpy as np import tables as tb fileh = tb.open_file('earray1.h5', mode='w') a = tb.StringAtom(itemsize=8) # Use ``a`` as the object type for the enlargeable array. array_c = fileh.create_earray(fileh.root, 'array_c', a, (0,), \"Chars\") array_c.append(np.array(['a'*2, 'b'*4], dtype='S8')) array_c.append(np.array(['a'*6, 'b'*8, 'c'*10], dtype='S8')) # Read the string ``EArray`` we have created on disk. for s in array_c: print('array_c[%s] => %r' % (array_c.nrow, s)) # Close the file. fileh.close() The output for the previous script is something like:: array_c[0] => 'aa' array_c[1] => 'bbbb' array_c[2] => 'aaaaaa' array_c[3] => 'bbbbbbbb' array_c[4] => 'cccccccc' """ # Class identifier. _c_classid = 'EARRAY' def __init__(self, parentnode, name, atom=None, shape=None, title="", filters=None, expectedrows=None, chunkshape=None, byteorder=None, _log=True, track_times=True): # Specific of EArray if expectedrows is None: expectedrows = parentnode._v_file.params['EXPECTED_ROWS_EARRAY'] self._v_expectedrows = expectedrows """The expected number of rows to be stored in the array.""" # Call the parent (CArray) init code super().__init__(parentnode, name, atom, shape, title, filters, chunkshape, byteorder, _log, track_times) def _g_create(self): """Create a new array in file (specific part).""" # Pre-conditions and extdim computation zerodims = np.sum(np.array(self.shape) == 0) if zerodims > 0: if zerodims == 1: self.extdim = list(self.shape).index(0) else: raise NotImplementedError( "Multiple enlargeable (0-)dimensions are not " "supported.") else: raise ValueError( "When creating EArrays, you need to set one of " "the dimensions of the Atom instance to zero.") # Finish the common part of the creation process return self._g_create_common(self._v_expectedrows) def _check_shape_append(self, nparr): """Test that nparr shape is consistent with underlying EArray.""" # Does the array conform to self expandibility? myrank = len(self.shape) narank = len(nparr.shape) - len(self.atom.shape) if myrank != narank: raise ValueError(("the ranks of the appended object (%d) and the " "``%s`` EArray (%d) differ") % (narank, self._v_pathname, myrank)) for i in range(myrank): if i != self.extdim and self.shape[i] != nparr.shape[i]: raise ValueError(("the shapes of the appended object and the " "``%s`` EArray differ in non-enlargeable " "dimension %d") % (self._v_pathname, i)) def append(self, sequence): """Add a sequence of data to the end of the dataset. The sequence must have the same type as the array; otherwise a TypeError is raised. In the same way, the dimensions of the sequence must conform to the shape of the array, that is, all dimensions must match, with the exception of the enlargeable dimension, which can be of any length (even 0!). If the shape of the sequence is invalid, a ValueError is raised. """ self._g_check_open() self._v_file._check_writable() # Convert the sequence into a NumPy object nparr = convert_to_np_atom2(sequence, self.atom) # Check if it has a consistent shape with underlying EArray self._check_shape_append(nparr) # If the size of the nparr is zero, don't do anything else if nparr.size > 0: self._append(nparr) def _g_copy_with_stats(self, group, name, start, stop, step, title, filters, chunkshape, _log, **kwargs): """Private part of Leaf.copy() for each kind of leaf.""" (start, stop, step) = self._process_range_read(start, stop, step) # Build the new EArray object maindim = self.maindim shape = list(self.shape) shape[maindim] = 0 # The number of final rows nrows = len(range(start, stop, step)) # Build the new EArray object object = EArray( group, name, atom=self.atom, shape=shape, title=title, filters=filters, expectedrows=nrows, chunkshape=chunkshape, _log=_log) # Now, fill the new earray with values from source nrowsinbuf = self.nrowsinbuf # The slices parameter for
(parentnode, name, atom=None, shape=None, title='', filters=None, expectedrows=None, chunkshape=None, byteorder=None, _log=True, track_times=True)
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728,274
tables.earray
__init__
null
def __init__(self, parentnode, name, atom=None, shape=None, title="", filters=None, expectedrows=None, chunkshape=None, byteorder=None, _log=True, track_times=True): # Specific of EArray if expectedrows is None: expectedrows = parentnode._v_file.params['EXPECTED_ROWS_EARRAY'] self._v_expectedrows = expectedrows """The expected number of rows to be stored in the array.""" # Call the parent (CArray) init code super().__init__(parentnode, name, atom, shape, title, filters, chunkshape, byteorder, _log, track_times)
(self, parentnode, name, atom=None, shape=None, title='', filters=None, expectedrows=None, chunkshape=None, byteorder=None, _log=True, track_times=True)
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728,284
tables.earray
_check_shape_append
Test that nparr shape is consistent with underlying EArray.
def _check_shape_append(self, nparr): """Test that nparr shape is consistent with underlying EArray.""" # Does the array conform to self expandibility? myrank = len(self.shape) narank = len(nparr.shape) - len(self.atom.shape) if myrank != narank: raise ValueError(("the ranks of the appended object (%d) and the " "``%s`` EArray (%d) differ") % (narank, self._v_pathname, myrank)) for i in range(myrank): if i != self.extdim and self.shape[i] != nparr.shape[i]: raise ValueError(("the shapes of the appended object and the " "``%s`` EArray differ in non-enlargeable " "dimension %d") % (self._v_pathname, i))
(self, nparr)
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728,301
tables.earray
_g_copy_with_stats
Private part of Leaf.copy() for each kind of leaf.
def _g_copy_with_stats(self, group, name, start, stop, step, title, filters, chunkshape, _log, **kwargs): """Private part of Leaf.copy() for each kind of leaf.""" (start, stop, step) = self._process_range_read(start, stop, step) # Build the new EArray object maindim = self.maindim shape = list(self.shape) shape[maindim] = 0 # The number of final rows nrows = len(range(start, stop, step)) # Build the new EArray object object = EArray( group, name, atom=self.atom, shape=shape, title=title, filters=filters, expectedrows=nrows, chunkshape=chunkshape, _log=_log) # Now, fill the new earray with values from source nrowsinbuf = self.nrowsinbuf # The slices parameter for self.__getitem__ slices = [slice(0, dim, 1) for dim in self.shape] # This is a hack to prevent doing unnecessary conversions # when copying buffers self._v_convert = False # Start the copy itself for start2 in range(start, stop, step * nrowsinbuf): # Save the records on disk stop2 = start2 + step * nrowsinbuf if stop2 > stop: stop2 = stop # Set the proper slice in the extensible dimension slices[maindim] = slice(start2, stop2, step) object._append(self.__getitem__(tuple(slices))) # Active the conversion again (default) self._v_convert = True nbytes = np.prod(self.shape, dtype=SizeType) * self.atom.itemsize return (object, nbytes)
(self, group, name, start, stop, step, title, filters, chunkshape, _log, **kwargs)
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728,302
tables.earray
_g_create
Create a new array in file (specific part).
def _g_create(self): """Create a new array in file (specific part).""" # Pre-conditions and extdim computation zerodims = np.sum(np.array(self.shape) == 0) if zerodims > 0: if zerodims == 1: self.extdim = list(self.shape).index(0) else: raise NotImplementedError( "Multiple enlargeable (0-)dimensions are not " "supported.") else: raise ValueError( "When creating EArrays, you need to set one of " "the dimensions of the Atom instance to zero.") # Finish the common part of the creation process return self._g_create_common(self._v_expectedrows)
(self)
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728,333
tables.earray
append
Add a sequence of data to the end of the dataset. The sequence must have the same type as the array; otherwise a TypeError is raised. In the same way, the dimensions of the sequence must conform to the shape of the array, that is, all dimensions must match, with the exception of the enlargeable dimension, which can be of any length (even 0!). If the shape of the sequence is invalid, a ValueError is raised.
def append(self, sequence): """Add a sequence of data to the end of the dataset. The sequence must have the same type as the array; otherwise a TypeError is raised. In the same way, the dimensions of the sequence must conform to the shape of the array, that is, all dimensions must match, with the exception of the enlargeable dimension, which can be of any length (even 0!). If the shape of the sequence is invalid, a ValueError is raised. """ self._g_check_open() self._v_file._check_writable() # Convert the sequence into a NumPy object nparr = convert_to_np_atom2(sequence, self.atom) # Check if it has a consistent shape with underlying EArray self._check_shape_append(nparr) # If the size of the nparr is zero, don't do anything else if nparr.size > 0: self._append(nparr)
(self, sequence)
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728,348
tables.misc.enum
Enum
Enumerated type. Each instance of this class represents an enumerated type. The values of the type must be declared *exhaustively* and named with *strings*, and they might be given explicit concrete values, though this is not compulsory. Once the type is defined, it can not be modified. There are three ways of defining an enumerated type. Each one of them corresponds to the type of the only argument in the constructor of Enum: - *Sequence of names*: each enumerated value is named using a string, and its order is determined by its position in the sequence; the concrete value is assigned automatically:: >>> boolEnum = Enum(['True', 'False']) - *Mapping of names*: each enumerated value is named by a string and given an explicit concrete value. All of the concrete values must be different, or a ValueError will be raised:: >>> priority = Enum({'red': 20, 'orange': 10, 'green': 0}) >>> colors = Enum({'red': 1, 'blue': 1}) Traceback (most recent call last): ... ValueError: enumerated values contain duplicate concrete values: 1 - *Enumerated type*: in that case, a copy of the original enumerated type is created. Both enumerated types are considered equal:: >>> prio2 = Enum(priority) >>> priority == prio2 True Please note that names starting with _ are not allowed, since they are reserved for internal usage:: >>> prio2 = Enum(['_xx']) Traceback (most recent call last): ... ValueError: name of enumerated value can not start with ``_``: '_xx' The concrete value of an enumerated value is obtained by getting its name as an attribute of the Enum instance (see __getattr__()) or as an item (see __getitem__()). This allows comparisons between enumerated values and assigning them to ordinary Python variables:: >>> redv = priority.red >>> redv == priority['red'] True >>> redv > priority.green True >>> priority.red == priority.orange False The name of the enumerated value corresponding to a concrete value can also be obtained by using the __call__() method of the enumerated type. In this way you get the symbolic name to use it later with __getitem__():: >>> priority(redv) 'red' >>> priority.red == priority[priority(priority.red)] True (If you ask, the __getitem__() method is not used for this purpose to avoid ambiguity in the case of using strings as concrete values.)
class Enum: """Enumerated type. Each instance of this class represents an enumerated type. The values of the type must be declared *exhaustively* and named with *strings*, and they might be given explicit concrete values, though this is not compulsory. Once the type is defined, it can not be modified. There are three ways of defining an enumerated type. Each one of them corresponds to the type of the only argument in the constructor of Enum: - *Sequence of names*: each enumerated value is named using a string, and its order is determined by its position in the sequence; the concrete value is assigned automatically:: >>> boolEnum = Enum(['True', 'False']) - *Mapping of names*: each enumerated value is named by a string and given an explicit concrete value. All of the concrete values must be different, or a ValueError will be raised:: >>> priority = Enum({'red': 20, 'orange': 10, 'green': 0}) >>> colors = Enum({'red': 1, 'blue': 1}) Traceback (most recent call last): ... ValueError: enumerated values contain duplicate concrete values: 1 - *Enumerated type*: in that case, a copy of the original enumerated type is created. Both enumerated types are considered equal:: >>> prio2 = Enum(priority) >>> priority == prio2 True Please note that names starting with _ are not allowed, since they are reserved for internal usage:: >>> prio2 = Enum(['_xx']) Traceback (most recent call last): ... ValueError: name of enumerated value can not start with ``_``: '_xx' The concrete value of an enumerated value is obtained by getting its name as an attribute of the Enum instance (see __getattr__()) or as an item (see __getitem__()). This allows comparisons between enumerated values and assigning them to ordinary Python variables:: >>> redv = priority.red >>> redv == priority['red'] True >>> redv > priority.green True >>> priority.red == priority.orange False The name of the enumerated value corresponding to a concrete value can also be obtained by using the __call__() method of the enumerated type. In this way you get the symbolic name to use it later with __getitem__():: >>> priority(redv) 'red' >>> priority.red == priority[priority(priority.red)] True (If you ask, the __getitem__() method is not used for this purpose to avoid ambiguity in the case of using strings as concrete values.) """ def __init__(self, enum): mydict = self.__dict__ mydict['_names'] = {} mydict['_values'] = {} if isinstance(enum, list) or isinstance(enum, tuple): for (value, name) in enumerate(enum): # values become 0, 1, 2... self._check_and_set_pair(name, value) elif isinstance(enum, dict): for (name, value) in enum.items(): self._check_and_set_pair(name, value) elif isinstance(enum, Enum): for (name, value) in enum._names.items(): self._check_and_set_pair(name, value) else: raise TypeError("""\ enumerations can only be created from \ sequences, mappings and other enumerations""") def _check_and_set_pair(self, name, value): """Check validity of enumerated value and insert it into type.""" names = self._names values = self._values if not isinstance(name, str): raise TypeError( f"name of enumerated value is not a string: {name!r}") if name.startswith('_'): raise ValueError( "name of enumerated value can not start with ``_``: %r" % name) # This check is only necessary with a sequence base object. if name in names: raise ValueError( "enumerated values contain duplicate names: %r" % name) # This check is only necessary with a mapping base object. if value in values: raise ValueError( "enumerated values contain duplicate concrete values: %r" % value) names[name] = value values[value] = name self.__dict__[name] = value def __getitem__(self, name): """Get the concrete value of the enumerated value with that name. The name of the enumerated value must be a string. If there is no value with that name in the enumeration, a KeyError is raised. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum['T1'] 2 >>> enum['foo'] Traceback (most recent call last): ... KeyError: "no enumerated value with that name: 'foo'" """ try: return self._names[name] except KeyError: raise KeyError(f"no enumerated value with that name: {name!r}") def __setitem__(self, name, value): """This operation is forbidden.""" raise IndexError("operation not allowed") def __delitem__(self, name): """This operation is forbidden.""" raise IndexError("operation not allowed") def __getattr__(self, name): """Get the concrete value of the enumerated value with that name. The name of the enumerated value must be a string. If there is no value with that name in the enumeration, an AttributeError is raised. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum.T1 2 >>> enum.foo Traceback (most recent call last): ... AttributeError: no enumerated value with that name: 'foo' """ try: return self[name] except KeyError as ke: raise AttributeError(*ke.args) def __setattr__(self, name, value): """This operation is forbidden.""" raise AttributeError("operation not allowed") def __delattr__(self, name): """This operation is forbidden.""" raise AttributeError("operation not allowed") def __contains__(self, name): """Is there an enumerated value with that name in the type? If the enumerated type has an enumerated value with that name, True is returned. Otherwise, False is returned. The name must be a string. This method does *not* check for concrete values matching a value in an enumerated type. For that, please use the :meth:`Enum.__call__` method. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> 'T1' in enum True >>> 'foo' in enum False >>> 0 in enum Traceback (most recent call last): ... TypeError: name of enumerated value is not a string: 0 >>> enum.T1 in enum # Be careful with this! Traceback (most recent call last): ... TypeError: name of enumerated value is not a string: 2 """ if not isinstance(name, str): raise TypeError( f"name of enumerated value is not a string: {name!r}") return name in self._names def __call__(self, value, *default): """Get the name of the enumerated value with that concrete value. If there is no value with that concrete value in the enumeration and a second argument is given as a default, this is returned. Else, a ValueError is raised. This method can be used for checking that a concrete value belongs to the set of concrete values in an enumerated type. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5})
(enum)
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728,349
tables.misc.enum
__call__
Get the name of the enumerated value with that concrete value. If there is no value with that concrete value in the enumeration and a second argument is given as a default, this is returned. Else, a ValueError is raised. This method can be used for checking that a concrete value belongs to the set of concrete values in an enumerated type. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum(5) 'T2' >>> enum(42, None) is None True >>> enum(42) Traceback (most recent call last): ... ValueError: no enumerated value with that concrete value: 42
def __call__(self, value, *default): """Get the name of the enumerated value with that concrete value. If there is no value with that concrete value in the enumeration and a second argument is given as a default, this is returned. Else, a ValueError is raised. This method can be used for checking that a concrete value belongs to the set of concrete values in an enumerated type. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum(5) 'T2' >>> enum(42, None) is None True >>> enum(42) Traceback (most recent call last): ... ValueError: no enumerated value with that concrete value: 42 """ try: return self._values[value] except KeyError: if len(default) > 0: return default[0] raise ValueError( f"no enumerated value with that concrete value: {value!r}")
(self, value, *default)
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728,350
tables.misc.enum
__contains__
Is there an enumerated value with that name in the type? If the enumerated type has an enumerated value with that name, True is returned. Otherwise, False is returned. The name must be a string. This method does *not* check for concrete values matching a value in an enumerated type. For that, please use the :meth:`Enum.__call__` method. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> 'T1' in enum True >>> 'foo' in enum False >>> 0 in enum Traceback (most recent call last): ... TypeError: name of enumerated value is not a string: 0 >>> enum.T1 in enum # Be careful with this! Traceback (most recent call last): ... TypeError: name of enumerated value is not a string: 2
def __contains__(self, name): """Is there an enumerated value with that name in the type? If the enumerated type has an enumerated value with that name, True is returned. Otherwise, False is returned. The name must be a string. This method does *not* check for concrete values matching a value in an enumerated type. For that, please use the :meth:`Enum.__call__` method. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> 'T1' in enum True >>> 'foo' in enum False >>> 0 in enum Traceback (most recent call last): ... TypeError: name of enumerated value is not a string: 0 >>> enum.T1 in enum # Be careful with this! Traceback (most recent call last): ... TypeError: name of enumerated value is not a string: 2 """ if not isinstance(name, str): raise TypeError( f"name of enumerated value is not a string: {name!r}") return name in self._names
(self, name)
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728,351
tables.misc.enum
__delattr__
This operation is forbidden.
def __delattr__(self, name): """This operation is forbidden.""" raise AttributeError("operation not allowed")
(self, name)
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728,352
tables.misc.enum
__delitem__
This operation is forbidden.
def __delitem__(self, name): """This operation is forbidden.""" raise IndexError("operation not allowed")
(self, name)
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728,353
tables.misc.enum
__eq__
Is the other enumerated type equivalent to this one? Two enumerated types are equivalent if they have exactly the same enumerated values (i.e. with the same names and concrete values). Examples -------- Let ``enum*`` be enumerated types defined as: >>> enum1 = Enum({'T0': 0, 'T1': 2}) >>> enum2 = Enum(enum1) >>> enum3 = Enum({'T1': 2, 'T0': 0}) >>> enum4 = Enum({'T0': 0, 'T1': 2, 'T2': 5}) >>> enum5 = Enum({'T0': 0}) >>> enum6 = Enum({'T0': 10, 'T1': 20}) then: >>> enum1 == enum1 True >>> enum1 == enum2 == enum3 True >>> enum1 == enum4 False >>> enum5 == enum1 False >>> enum1 == enum6 False Comparing enumerated types with other kinds of objects produces a false result: >>> enum1 == {'T0': 0, 'T1': 2} False >>> enum1 == ['T0', 'T1'] False >>> enum1 == 2 False
def __eq__(self, other): """Is the other enumerated type equivalent to this one? Two enumerated types are equivalent if they have exactly the same enumerated values (i.e. with the same names and concrete values). Examples -------- Let ``enum*`` be enumerated types defined as: >>> enum1 = Enum({'T0': 0, 'T1': 2}) >>> enum2 = Enum(enum1) >>> enum3 = Enum({'T1': 2, 'T0': 0}) >>> enum4 = Enum({'T0': 0, 'T1': 2, 'T2': 5}) >>> enum5 = Enum({'T0': 0}) >>> enum6 = Enum({'T0': 10, 'T1': 20}) then: >>> enum1 == enum1 True >>> enum1 == enum2 == enum3 True >>> enum1 == enum4 False >>> enum5 == enum1 False >>> enum1 == enum6 False Comparing enumerated types with other kinds of objects produces a false result: >>> enum1 == {'T0': 0, 'T1': 2} False >>> enum1 == ['T0', 'T1'] False >>> enum1 == 2 False """ if not isinstance(other, Enum): return False return self._names == other._names
(self, other)
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728,354
tables.misc.enum
__getattr__
Get the concrete value of the enumerated value with that name. The name of the enumerated value must be a string. If there is no value with that name in the enumeration, an AttributeError is raised. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum.T1 2 >>> enum.foo Traceback (most recent call last): ... AttributeError: no enumerated value with that name: 'foo'
def __getattr__(self, name): """Get the concrete value of the enumerated value with that name. The name of the enumerated value must be a string. If there is no value with that name in the enumeration, an AttributeError is raised. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum.T1 2 >>> enum.foo Traceback (most recent call last): ... AttributeError: no enumerated value with that name: 'foo' """ try: return self[name] except KeyError as ke: raise AttributeError(*ke.args)
(self, name)
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728,355
tables.misc.enum
__getitem__
Get the concrete value of the enumerated value with that name. The name of the enumerated value must be a string. If there is no value with that name in the enumeration, a KeyError is raised. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum['T1'] 2 >>> enum['foo'] Traceback (most recent call last): ... KeyError: "no enumerated value with that name: 'foo'"
def __getitem__(self, name): """Get the concrete value of the enumerated value with that name. The name of the enumerated value must be a string. If there is no value with that name in the enumeration, a KeyError is raised. Examples -------- Let ``enum`` be an enumerated type defined as: >>> enum = Enum({'T0': 0, 'T1': 2, 'T2': 5}) then: >>> enum['T1'] 2 >>> enum['foo'] Traceback (most recent call last): ... KeyError: "no enumerated value with that name: 'foo'" """ try: return self._names[name] except KeyError: raise KeyError(f"no enumerated value with that name: {name!r}")
(self, name)
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728,356
tables.misc.enum
__init__
null
def __init__(self, enum): mydict = self.__dict__ mydict['_names'] = {} mydict['_values'] = {} if isinstance(enum, list) or isinstance(enum, tuple): for (value, name) in enumerate(enum): # values become 0, 1, 2... self._check_and_set_pair(name, value) elif isinstance(enum, dict): for (name, value) in enum.items(): self._check_and_set_pair(name, value) elif isinstance(enum, Enum): for (name, value) in enum._names.items(): self._check_and_set_pair(name, value) else: raise TypeError("""\ enumerations can only be created from \ sequences, mappings and other enumerations""")
(self, enum)
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728,357
tables.misc.enum
__iter__
Iterate over the enumerated values. Enumerated values are returned as (name, value) pairs *in no particular order*. Examples -------- >>> enumvals = {'red': 4, 'green': 2, 'blue': 1} >>> enum = Enum(enumvals) >>> enumdict = dict([(name, value) for (name, value) in enum]) >>> enumvals == enumdict True
def __iter__(self): """Iterate over the enumerated values. Enumerated values are returned as (name, value) pairs *in no particular order*. Examples -------- >>> enumvals = {'red': 4, 'green': 2, 'blue': 1} >>> enum = Enum(enumvals) >>> enumdict = dict([(name, value) for (name, value) in enum]) >>> enumvals == enumdict True """ yield from self._names.items()
(self)
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728,358
tables.misc.enum
__len__
Return the number of enumerated values in the enumerated type. Examples -------- >>> len(Enum(['e%d' % i for i in range(10)])) 10
def __len__(self): """Return the number of enumerated values in the enumerated type. Examples -------- >>> len(Enum(['e%d' % i for i in range(10)])) 10 """ return len(self._names)
(self)
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728,359
tables.misc.enum
__ne__
Is the `other` enumerated type different from this one? Two enumerated types are different if they don't have exactly the same enumerated values (i.e. with the same names and concrete values). Examples -------- Let ``enum*`` be enumerated types defined as: >>> enum1 = Enum({'T0': 0, 'T1': 2}) >>> enum2 = Enum(enum1) >>> enum3 = Enum({'T1': 2, 'T0': 0}) >>> enum4 = Enum({'T0': 0, 'T1': 2, 'T2': 5}) >>> enum5 = Enum({'T0': 0}) >>> enum6 = Enum({'T0': 10, 'T1': 20}) then: >>> enum1 != enum1 False >>> enum1 != enum2 != enum3 False >>> enum1 != enum4 True >>> enum5 != enum1 True >>> enum1 != enum6 True
def __ne__(self, other): """Is the `other` enumerated type different from this one? Two enumerated types are different if they don't have exactly the same enumerated values (i.e. with the same names and concrete values). Examples -------- Let ``enum*`` be enumerated types defined as: >>> enum1 = Enum({'T0': 0, 'T1': 2}) >>> enum2 = Enum(enum1) >>> enum3 = Enum({'T1': 2, 'T0': 0}) >>> enum4 = Enum({'T0': 0, 'T1': 2, 'T2': 5}) >>> enum5 = Enum({'T0': 0}) >>> enum6 = Enum({'T0': 10, 'T1': 20}) then: >>> enum1 != enum1 False >>> enum1 != enum2 != enum3 False >>> enum1 != enum4 True >>> enum5 != enum1 True >>> enum1 != enum6 True """ return not self.__eq__(other)
(self, other)
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728,360
tables.misc.enum
__repr__
Return the canonical string representation of the enumeration. The output of this method can be evaluated to give a new enumeration object that will compare equal to this one. Examples -------- >>> repr(Enum({'name': 10})) "Enum({'name': 10})"
def __repr__(self): """Return the canonical string representation of the enumeration. The output of this method can be evaluated to give a new enumeration object that will compare equal to this one. Examples -------- >>> repr(Enum({'name': 10})) "Enum({'name': 10})" """ return 'Enum(%s)' % self._names
(self)
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728,361
tables.misc.enum
__setattr__
This operation is forbidden.
def __setattr__(self, name, value): """This operation is forbidden.""" raise AttributeError("operation not allowed")
(self, name, value)
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728,362
tables.misc.enum
__setitem__
This operation is forbidden.
def __setitem__(self, name, value): """This operation is forbidden.""" raise IndexError("operation not allowed")
(self, name, value)
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728,363
tables.misc.enum
_check_and_set_pair
Check validity of enumerated value and insert it into type.
def _check_and_set_pair(self, name, value): """Check validity of enumerated value and insert it into type.""" names = self._names values = self._values if not isinstance(name, str): raise TypeError( f"name of enumerated value is not a string: {name!r}") if name.startswith('_'): raise ValueError( "name of enumerated value can not start with ``_``: %r" % name) # This check is only necessary with a sequence base object. if name in names: raise ValueError( "enumerated values contain duplicate names: %r" % name) # This check is only necessary with a mapping base object. if value in values: raise ValueError( "enumerated values contain duplicate concrete values: %r" % value) names[name] = value values[value] = name self.__dict__[name] = value
(self, name, value)
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728,364
tables.atom
EnumAtom
Description of an atom of an enumerated type. Instances of this class describe the atom type used to store enumerated values. Those values belong to an enumerated type, defined by the first argument (enum) in the constructor of the atom, which accepts the same kinds of arguments as the Enum class (see :ref:`EnumClassDescr`). The enumerated type is stored in the enum attribute of the atom. A default value must be specified as the second argument (dflt) in the constructor; it must be the *name* (a string) of one of the enumerated values in the enumerated type. When the atom is created, the corresponding concrete value is broadcast and stored in the dflt attribute (setting different default values for items in a multidimensional atom is not supported yet). If the name does not match any value in the enumerated type, a KeyError is raised. Another atom must be specified as the base argument in order to determine the base type used for storing the values of enumerated values in memory and disk. This *storage atom* is kept in the base attribute of the created atom. As a shorthand, you may specify a PyTables type instead of the storage atom, implying that this has a scalar shape. The storage atom should be able to represent each and every concrete value in the enumeration. If it is not, a TypeError is raised. The default value of the storage atom is ignored. The type attribute of enumerated atoms is always enum. Enumerated atoms also support comparisons with other objects:: >>> enum = ['T0', 'T1', 'T2'] >>> atom1 = EnumAtom(enum, 'T0', 'int8') # same as ``atom2`` >>> atom2 = EnumAtom(enum, 'T0', Int8Atom()) # same as ``atom1`` >>> atom3 = EnumAtom(enum, 'T0', 'int16') >>> atom4 = Int8Atom() >>> atom1 == enum False >>> atom1 == atom2 True >>> atom2 != atom1 False >>> atom1 == atom3 False >>> atom1 == atom4 False >>> atom4 != atom1 True Examples -------- The next C enum construction:: enum myEnum { T0, T1, T2 }; would correspond to the following PyTables declaration:: >>> my_enum_atom = EnumAtom(['T0', 'T1', 'T2'], 'T0', 'int32') Please note the dflt argument with a value of 'T0'. Since the concrete value matching T0 is unknown right now (we have not used explicit concrete values), using the name is the only option left for defining a default value for the atom. The chosen representation of values for this enumerated atom uses unsigned 32-bit integers, which surely wastes quite a lot of memory. Another size could be selected by using the base argument (this time with a full-blown storage atom):: >>> my_enum_atom = EnumAtom(['T0', 'T1', 'T2'], 'T0', UInt8Atom()) You can also define multidimensional arrays for data elements:: >>> my_enum_atom = EnumAtom( ... ['T0', 'T1', 'T2'], 'T0', base='uint32', shape=(3,2)) for 3x2 arrays of uint32.
class EnumAtom(Atom): """Description of an atom of an enumerated type. Instances of this class describe the atom type used to store enumerated values. Those values belong to an enumerated type, defined by the first argument (enum) in the constructor of the atom, which accepts the same kinds of arguments as the Enum class (see :ref:`EnumClassDescr`). The enumerated type is stored in the enum attribute of the atom. A default value must be specified as the second argument (dflt) in the constructor; it must be the *name* (a string) of one of the enumerated values in the enumerated type. When the atom is created, the corresponding concrete value is broadcast and stored in the dflt attribute (setting different default values for items in a multidimensional atom is not supported yet). If the name does not match any value in the enumerated type, a KeyError is raised. Another atom must be specified as the base argument in order to determine the base type used for storing the values of enumerated values in memory and disk. This *storage atom* is kept in the base attribute of the created atom. As a shorthand, you may specify a PyTables type instead of the storage atom, implying that this has a scalar shape. The storage atom should be able to represent each and every concrete value in the enumeration. If it is not, a TypeError is raised. The default value of the storage atom is ignored. The type attribute of enumerated atoms is always enum. Enumerated atoms also support comparisons with other objects:: >>> enum = ['T0', 'T1', 'T2'] >>> atom1 = EnumAtom(enum, 'T0', 'int8') # same as ``atom2`` >>> atom2 = EnumAtom(enum, 'T0', Int8Atom()) # same as ``atom1`` >>> atom3 = EnumAtom(enum, 'T0', 'int16') >>> atom4 = Int8Atom() >>> atom1 == enum False >>> atom1 == atom2 True >>> atom2 != atom1 False >>> atom1 == atom3 False >>> atom1 == atom4 False >>> atom4 != atom1 True Examples -------- The next C enum construction:: enum myEnum { T0, T1, T2 }; would correspond to the following PyTables declaration:: >>> my_enum_atom = EnumAtom(['T0', 'T1', 'T2'], 'T0', 'int32') Please note the dflt argument with a value of 'T0'. Since the concrete value matching T0 is unknown right now (we have not used explicit concrete values), using the name is the only option left for defining a default value for the atom. The chosen representation of values for this enumerated atom uses unsigned 32-bit integers, which surely wastes quite a lot of memory. Another size could be selected by using the base argument (this time with a full-blown storage atom):: >>> my_enum_atom = EnumAtom(['T0', 'T1', 'T2'], 'T0', UInt8Atom()) You can also define multidimensional arrays for data elements:: >>> my_enum_atom = EnumAtom( ... ['T0', 'T1', 'T2'], 'T0', base='uint32', shape=(3,2)) for 3x2 arrays of uint32. """ # Registering this class in the class map may be a little wrong, # since the ``Atom.from_kind()`` method fails miserably with # enumerations, as they don't support an ``itemsize`` argument. # However, resetting ``__metaclass__`` to ``type`` doesn't seem to # work and I don't feel like creating a subclass of ``MetaAtom``. kind = 'enum' type = 'enum' @property def itemsize(self): """Size in bytes of a single item in the atom.""" return self.dtype.base.itemsize def _checkbase(self, base): """Check the `base` storage atom.""" if base.kind == 'enum': raise TypeError("can not use an enumerated atom " "as a storage atom: %r" % base) # Check whether the storage atom can represent concrete values # in the enumeration... basedtype = base.dtype pyvalues = [value for (name, value) in self.enum] try: npgenvalues = np.array(pyvalues) except ValueError: raise TypeError("concrete values are not uniformly-shaped") try: npvalues = np.array(npgenvalues, dtype=basedtype.base) except ValueError: raise TypeError("storage atom type is incompatible with " "concrete values in the enumeration") if npvalues.shape[1:] != basedtype.shape: raise TypeError("storage atom shape does not match that of " "concrete values in the enumeration") if npvalues.tolist() != npgenvalues.tolist(): raise TypeError("storage atom type lacks precision for " "concrete values in the enumeration") # ...with some implementation limitations. if npvalues.dtype.kind not in ['i', 'u']: raise NotImplementedError("only integer concrete values " "are supported for the moment, sorry") if len(npvalues.shape) > 1: raise NotImplementedError("only scalar concrete values " "are supported for the moment, sorry") def _get_init_args(self): """Get a dictionary of instance constructor arguments.""" return dict(enum=self.enum, dflt=self._defname, base=self.base, shape=self.shape) def _is_equal_to_atom(self, atom): """Is this object equal to the given `atom`?""" return False def _is_equal_to_enumatom(self, enumatom): """Is this object equal to the given `enumatom`?""" return (self.enum == enumatom.enum and self.shape == enumatom.shape and np.all(self.dflt == enumatom.dflt) and self.base == enumatom.base) def __init__(self, enum, dflt, base, shape=()): if not isinstance(enum, Enum): enum = Enum(enum) self.enum = enum if isinstance(base, str): base = Atom.from_type(base) self._checkbase(base) self.base = base default = enum[dflt] # check default value self._defname = dflt # kept for representation purposes # These are kept to ease dumping this particular # representation of the enumeration to storage. names, values = [], [] for (name, value) in enum: names.append(name) values.append(value) basedtype = self.base.dtype self._names = names self._values = np.array(values, dtype=basedtype.base) Atom.__init__(self, basedtype, shape, default) def __repr__(self): return ('EnumAtom(enum=%r, dflt=%r, base=%r, shape=%r)' % (self.enum, self._defname, self.base, self.shape)) __eq__ = _cmp_dispatcher('_is_equal_to_enumatom') # XXX: API incompatible change for PyTables 3 line # Overriding __eq__ blocks inheritance of __hash__ in 3.x # def __hash__(self): # return hash((self.__class__, self.enum, self.shape, self.dflt, # self.base))
(enum, dflt, base, shape=())
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728,366
tables.atom
__init__
null
def __init__(self, enum, dflt, base, shape=()): if not isinstance(enum, Enum): enum = Enum(enum) self.enum = enum if isinstance(base, str): base = Atom.from_type(base) self._checkbase(base) self.base = base default = enum[dflt] # check default value self._defname = dflt # kept for representation purposes # These are kept to ease dumping this particular # representation of the enumeration to storage. names, values = [], [] for (name, value) in enum: names.append(name) values.append(value) basedtype = self.base.dtype self._names = names self._values = np.array(values, dtype=basedtype.base) Atom.__init__(self, basedtype, shape, default)
(self, enum, dflt, base, shape=())
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728,368
tables.atom
__repr__
null
def __repr__(self): return ('EnumAtom(enum=%r, dflt=%r, base=%r, shape=%r)' % (self.enum, self._defname, self.base, self.shape))
(self)
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0.0020611979998648167, -0.03872370347380638 ]
728,369
tables.atom
_checkbase
Check the `base` storage atom.
def _checkbase(self, base): """Check the `base` storage atom.""" if base.kind == 'enum': raise TypeError("can not use an enumerated atom " "as a storage atom: %r" % base) # Check whether the storage atom can represent concrete values # in the enumeration... basedtype = base.dtype pyvalues = [value for (name, value) in self.enum] try: npgenvalues = np.array(pyvalues) except ValueError: raise TypeError("concrete values are not uniformly-shaped") try: npvalues = np.array(npgenvalues, dtype=basedtype.base) except ValueError: raise TypeError("storage atom type is incompatible with " "concrete values in the enumeration") if npvalues.shape[1:] != basedtype.shape: raise TypeError("storage atom shape does not match that of " "concrete values in the enumeration") if npvalues.tolist() != npgenvalues.tolist(): raise TypeError("storage atom type lacks precision for " "concrete values in the enumeration") # ...with some implementation limitations. if npvalues.dtype.kind not in ['i', 'u']: raise NotImplementedError("only integer concrete values " "are supported for the moment, sorry") if len(npvalues.shape) > 1: raise NotImplementedError("only scalar concrete values " "are supported for the moment, sorry")
(self, base)
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728,370
tables.atom
_get_init_args
Get a dictionary of instance constructor arguments.
def _get_init_args(self): """Get a dictionary of instance constructor arguments.""" return dict(enum=self.enum, dflt=self._defname, base=self.base, shape=self.shape)
(self)
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728,371
tables.atom
_is_equal_to_atom
Is this object equal to the given `atom`?
def _is_equal_to_atom(self, atom): """Is this object equal to the given `atom`?""" return False
(self, atom)
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728,372
tables.atom
_is_equal_to_enumatom
Is this object equal to the given `enumatom`?
def _is_equal_to_enumatom(self, enumatom): """Is this object equal to the given `enumatom`?""" return (self.enum == enumatom.enum and self.shape == enumatom.shape and np.all(self.dflt == enumatom.dflt) and self.base == enumatom.base)
(self, enumatom)
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728,374
tables.description
EnumCol
Defines a non-nested column of a particular type. The constructor accepts the same arguments as the equivalent `Atom` class, plus an additional ``pos`` argument for position information, which is assigned to the `_v_pos` attribute and an ``attrs`` argument for storing additional metadata similar to `table.attrs`, which is assigned to the `_v_col_attrs` attribute.
from tables.description import EnumCol
(*args, **kwargs)
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728,382
tables.description
_is_equal_to_enumatom
Is this object equal to the given `enumatom`?
def same_position(oldmethod): """Decorate `oldmethod` to also compare the `_v_pos` attribute.""" def newmethod(self, other): try: other._v_pos except AttributeError: return False # not a column definition return self._v_pos == other._v_pos and oldmethod(self, other) newmethod.__name__ = oldmethod.__name__ newmethod.__doc__ = oldmethod.__doc__ return newmethod
(self, other)
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728,384
tables.exceptions
ExperimentalFeatureWarning
Generic warning for experimental features. This warning is issued when using a functionality that is still experimental and that users have to use with care.
class ExperimentalFeatureWarning(Warning): """Generic warning for experimental features. This warning is issued when using a functionality that is still experimental and that users have to use with care. """ pass
null
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728,385
tables.expression
Expr
A class for evaluating expressions with arbitrary array-like objects. Expr is a class for evaluating expressions containing array-like objects. With it, you can evaluate expressions (like "3 * a + 4 * b") that operate on arbitrary large arrays while optimizing the resources required to perform them (basically main memory and CPU cache memory). It is similar to the Numexpr package (see :ref:`[NUMEXPR] <NUMEXPR>`), but in addition to NumPy objects, it also accepts disk-based homogeneous arrays, like the Array, CArray, EArray and Column PyTables objects. .. warning:: Expr class only offers a subset of the Numexpr features due to the complexity of implement some of them when dealing with huge amount of data. All the internal computations are performed via the Numexpr package, so all the broadcast and upcasting rules of Numexpr applies here too. These rules are very similar to the NumPy ones, but with some exceptions due to the particularities of having to deal with potentially very large disk-based arrays. Be sure to read the documentation of the Expr constructor and methods as well as that of Numexpr, if you want to fully grasp these particularities. Parameters ---------- expr : str This specifies the expression to be evaluated, such as "2 * a + 3 * b". uservars : dict This can be used to define the variable names appearing in *expr*. This mapping should consist of identifier-like strings pointing to any `Array`, `CArray`, `EArray`, `Column` or NumPy ndarray instances (or even others which will tried to be converted to ndarrays). When `uservars` is not provided or `None`, the current local and global namespace is sought instead of `uservars`. It is also possible to pass just some of the variables in expression via the `uservars` mapping, and the rest will be retrieved from the current local and global namespaces. kwargs : dict This is meant to pass additional parameters to the Numexpr kernel. This is basically the same as the kwargs argument in Numexpr.evaluate(), and is mainly meant for advanced use. Examples -------- The following shows an example of using Expr:: >>> f = tb.open_file('/tmp/test_expr.h5', 'w') >>> a = f.create_array('/', 'a', np.array([1,2,3])) >>> b = f.create_array('/', 'b', np.array([3,4,5])) >>> c = np.array([4,5,6]) >>> expr = tb.Expr("2 * a + b * c") # initialize the expression >>> expr.eval() # evaluate it array([14, 24, 36], dtype=int64) >>> sum(expr) # use as an iterator 74 where you can see that you can mix different containers in the expression (whenever shapes are consistent). You can also work with multidimensional arrays:: >>> a2 = f.create_array('/', 'a2', np.array([[1,2],[3,4]])) >>> b2 = f.create_array('/', 'b2', np.array([[3,4],[5,6]])) >>> c2 = np.array([4,5]) # This will be broadcasted >>> expr = tb.Expr("2 * a2 + b2-c2") >>> expr.eval() array([[1, 3], [7, 9]], dtype=int64) >>> sum(expr) array([ 8, 12], dtype=int64) >>> f.close() .. rubric:: Expr attributes .. attribute:: append_mode The append mode for user-provided output containers. .. attribute:: maindim Common main dimension for inputs in expression. .. attribute:: names The names of variables in expression (list). .. attribute:: out The user-provided container (if any) for the expression outcome. .. attribute:: o_start The start range selection for the user-provided output. .. attribute:: o_stop The stop range selection for the user-provided output. .. attribute:: o_step The step range selection for the user-provided output. .. attribute:: shape Common shape for the arrays in expression. .. attribute:: values The values of variables in expression (list).
class Expr: """A class for evaluating expressions with arbitrary array-like objects. Expr is a class for evaluating expressions containing array-like objects. With it, you can evaluate expressions (like "3 * a + 4 * b") that operate on arbitrary large arrays while optimizing the resources required to perform them (basically main memory and CPU cache memory). It is similar to the Numexpr package (see :ref:`[NUMEXPR] <NUMEXPR>`), but in addition to NumPy objects, it also accepts disk-based homogeneous arrays, like the Array, CArray, EArray and Column PyTables objects. .. warning:: Expr class only offers a subset of the Numexpr features due to the complexity of implement some of them when dealing with huge amount of data. All the internal computations are performed via the Numexpr package, so all the broadcast and upcasting rules of Numexpr applies here too. These rules are very similar to the NumPy ones, but with some exceptions due to the particularities of having to deal with potentially very large disk-based arrays. Be sure to read the documentation of the Expr constructor and methods as well as that of Numexpr, if you want to fully grasp these particularities. Parameters ---------- expr : str This specifies the expression to be evaluated, such as "2 * a + 3 * b". uservars : dict This can be used to define the variable names appearing in *expr*. This mapping should consist of identifier-like strings pointing to any `Array`, `CArray`, `EArray`, `Column` or NumPy ndarray instances (or even others which will tried to be converted to ndarrays). When `uservars` is not provided or `None`, the current local and global namespace is sought instead of `uservars`. It is also possible to pass just some of the variables in expression via the `uservars` mapping, and the rest will be retrieved from the current local and global namespaces. kwargs : dict This is meant to pass additional parameters to the Numexpr kernel. This is basically the same as the kwargs argument in Numexpr.evaluate(), and is mainly meant for advanced use. Examples -------- The following shows an example of using Expr:: >>> f = tb.open_file('/tmp/test_expr.h5', 'w') >>> a = f.create_array('/', 'a', np.array([1,2,3])) >>> b = f.create_array('/', 'b', np.array([3,4,5])) >>> c = np.array([4,5,6]) >>> expr = tb.Expr("2 * a + b * c") # initialize the expression >>> expr.eval() # evaluate it array([14, 24, 36], dtype=int64) >>> sum(expr) # use as an iterator 74 where you can see that you can mix different containers in the expression (whenever shapes are consistent). You can also work with multidimensional arrays:: >>> a2 = f.create_array('/', 'a2', np.array([[1,2],[3,4]])) >>> b2 = f.create_array('/', 'b2', np.array([[3,4],[5,6]])) >>> c2 = np.array([4,5]) # This will be broadcasted >>> expr = tb.Expr("2 * a2 + b2-c2") >>> expr.eval() array([[1, 3], [7, 9]], dtype=int64) >>> sum(expr) array([ 8, 12], dtype=int64) >>> f.close() .. rubric:: Expr attributes .. attribute:: append_mode The append mode for user-provided output containers. .. attribute:: maindim Common main dimension for inputs in expression. .. attribute:: names The names of variables in expression (list). .. attribute:: out The user-provided container (if any) for the expression outcome. .. attribute:: o_start The start range selection for the user-provided output. .. attribute:: o_stop The stop range selection for the user-provided output. .. attribute:: o_step The step range selection for the user-provided output. .. attribute:: shape Common shape for the arrays in expression. .. attribute:: values The values of variables in expression (list). """ _exprvars_cache = {} """Cache of variables participating in expressions. .. versionadded:: 3.0 """ def __init__(self, expr, uservars=None, **kwargs): self.append_mode = False """The append mode for user-provided output containers.""" self.maindim = 0 """Common main dimension for inputs in expression.""" self.names = [] """The names of variables in expression (list).""" self.out = None """The user-provided container (if any) for the expression outcome.""" self.o_start = None """The start range selection for the user-provided output.""" self.o_stop = None """The stop range selection for the user-provided output.""" self.o_step = None """The step range selection for the user-provided output.""" self.shape = None """Common shape for the arrays in expression.""" self.start, self.stop, self.step = (None,) * 3 self.start = None """The start range selection for the input.""" self.stop = None """The stop range selection for the input.""" self.step = None """The step range selection for the input.""" self.values = [] """The values of variables in expression (list).""" self._compiled_expr = None """The compiled expression.""" self._single_row_out = None """A sample of the output with just a single row.""" # First, get the signature for the arrays in expression vars_ = self._required_expr_vars(expr, uservars) context = ne.necompiler.getContext(kwargs) self.names, _ = ne.necompiler.getExprNames(expr, context) # Raise a ValueError in case we have unsupported objects for name, var in vars_.items(): if type(var) in (int, float, str): continue if not isinstance(var, (tb.Leaf, tb.Column)): if hasattr(var, "dtype"): # Quacks like a NumPy object continue raise TypeError("Unsupported variable type: %r" % var) objname = var.__class__.__name__ if objname not in ("Array", "CArray", "EArray", "Column"): raise TypeError("Unsupported variable type: %r" % var) # NumPy arrays to be copied? (we don't need to worry about # PyTables objects, as the reads always return contiguous and # aligned objects, or at least I think so). for name, var in vars_.items(): if isinstance(var, np.ndarray): # See numexpr.necompiler.evaluate for a rational # of the code below if not var.flags.aligned: if var.ndim != 1: # Do a copy of this variable var = var.copy() # Update the vars_ dictionary vars_[name] = var # Get the variables and types values = self.values types_ = [] for name in self.names: value = vars_[name] if hasattr(value, 'atom'): types_.append(value.atom) elif hasattr(value, 'dtype'): types_.append(value) else: # try to convert into a NumPy array value = np.array(value) types_.append(value) values.append(value) # Create a signature for the expression signature = [(name, ne.necompiler.getType(type_)) for (name, type_) in zip(self.names, types_)] # Compile the expression self._compiled_expr = ne.necompiler.NumExpr(expr, signature, **kwargs) # Guess the shape for the outcome and the maindim of inputs self.shape, self.maindim = self._guess_shape() # The next method is similar to their counterpart in `Table`, but # adapted to the `Expr`
(expr, uservars=None, **kwargs)
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728,386
tables.expression
__init__
null
def __init__(self, expr, uservars=None, **kwargs): self.append_mode = False """The append mode for user-provided output containers.""" self.maindim = 0 """Common main dimension for inputs in expression.""" self.names = [] """The names of variables in expression (list).""" self.out = None """The user-provided container (if any) for the expression outcome.""" self.o_start = None """The start range selection for the user-provided output.""" self.o_stop = None """The stop range selection for the user-provided output.""" self.o_step = None """The step range selection for the user-provided output.""" self.shape = None """Common shape for the arrays in expression.""" self.start, self.stop, self.step = (None,) * 3 self.start = None """The start range selection for the input.""" self.stop = None """The stop range selection for the input.""" self.step = None """The step range selection for the input.""" self.values = [] """The values of variables in expression (list).""" self._compiled_expr = None """The compiled expression.""" self._single_row_out = None """A sample of the output with just a single row.""" # First, get the signature for the arrays in expression vars_ = self._required_expr_vars(expr, uservars) context = ne.necompiler.getContext(kwargs) self.names, _ = ne.necompiler.getExprNames(expr, context) # Raise a ValueError in case we have unsupported objects for name, var in vars_.items(): if type(var) in (int, float, str): continue if not isinstance(var, (tb.Leaf, tb.Column)): if hasattr(var, "dtype"): # Quacks like a NumPy object continue raise TypeError("Unsupported variable type: %r" % var) objname = var.__class__.__name__ if objname not in ("Array", "CArray", "EArray", "Column"): raise TypeError("Unsupported variable type: %r" % var) # NumPy arrays to be copied? (we don't need to worry about # PyTables objects, as the reads always return contiguous and # aligned objects, or at least I think so). for name, var in vars_.items(): if isinstance(var, np.ndarray): # See numexpr.necompiler.evaluate for a rational # of the code below if not var.flags.aligned: if var.ndim != 1: # Do a copy of this variable var = var.copy() # Update the vars_ dictionary vars_[name] = var # Get the variables and types values = self.values types_ = [] for name in self.names: value = vars_[name] if hasattr(value, 'atom'): types_.append(value.atom) elif hasattr(value, 'dtype'): types_.append(value) else: # try to convert into a NumPy array value = np.array(value) types_.append(value) values.append(value) # Create a signature for the expression signature = [(name, ne.necompiler.getType(type_)) for (name, type_) in zip(self.names, types_)] # Compile the expression self._compiled_expr = ne.necompiler.NumExpr(expr, signature, **kwargs) # Guess the shape for the outcome and the maindim of inputs self.shape, self.maindim = self._guess_shape()
(self, expr, uservars=None, **kwargs)
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728,387
tables.expression
__iter__
Iterate over the rows of the outcome of the expression. This iterator always returns rows as NumPy objects, so a possible out container specified in :meth:`Expr.set_output` method is ignored here.
def __iter__(self): """Iterate over the rows of the outcome of the expression. This iterator always returns rows as NumPy objects, so a possible out container specified in :meth:`Expr.set_output` method is ignored here. """ values, shape, maindim = self.values, self.shape, self.maindim # Get different info we need for the main computation loop (i_nrows, slice_pos, start, stop, step, nrowsinbuf) = \ self._get_info(shape, maindim, itermode=True) if i_nrows == 0: # No elements to compute return # Create a key that selects every element in inputs # (including the main dimension) i_slices = [slice(None)] * (maindim + 1) # This is a hack to prevent doing unnecessary flavor conversions # while reading buffers for val in values: if hasattr(val, 'maindim'): val._v_convert = False # Start the computation itself for start2 in range(start, stop, step * nrowsinbuf): stop2 = start2 + step * nrowsinbuf if stop2 > stop: stop2 = stop # Set the proper slice in the main dimension i_slices[maindim] = slice(start2, stop2, step) # Get the values for computing the buffer vals = [] for i, val in enumerate(values): if i in slice_pos: vals.append(val.__getitem__(tuple(i_slices))) else: # A read of values is not apparently needed, as PyTables # leaves seems to work just fine inside Numexpr vals.append(val) # Do the actual computation rout = self._compiled_expr(*vals) # Return one row per call yield from rout # Activate the conversion again (default) for val in values: if hasattr(val, 'maindim'): val._v_convert = True
(self)
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728,388
tables.expression
_calc_nrowsinbuf
Calculate the number of rows that will fit in a buffer.
def _calc_nrowsinbuf(self, object_): """Calculate the number of rows that will fit in a buffer.""" # Compute the rowsize for the *leading* dimension shape_ = list(object_.shape) if shape_: shape_[0] = 1 rowsize = np.prod(shape_) * object_.dtype.itemsize # Compute the nrowsinbuf # Multiplying the I/O buffer size by 4 gives optimal results # in my benchmarks with `tables.Expr` (see ``bench/poly.py``) buffersize = IO_BUFFER_SIZE * 4 nrowsinbuf = buffersize // rowsize # Safeguard against row sizes being extremely large if nrowsinbuf == 0: nrowsinbuf = 1 # If rowsize is too large, issue a Performance warning maxrowsize = BUFFER_TIMES * buffersize if rowsize > maxrowsize: warnings.warn("""\ The object ``%s`` is exceeding the maximum recommended rowsize (%d bytes); be ready to see PyTables asking for *lots* of memory and possibly slow I/O. You may want to reduce the rowsize by trimming the value of dimensions that are orthogonal (and preferably close) to the *leading* dimension of this object.""" % (object, maxrowsize), PerformanceWarning) return nrowsinbuf
(self, object_)
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728,389
tables.expression
_get_info
Return various info needed for evaluating the computation loop.
def _get_info(self, shape, maindim, itermode=False): """Return various info needed for evaluating the computation loop.""" # Compute the shape of the resulting container having # in account new possible values of start, stop and step in # the inputs range if maindim is not None: (start, stop, step) = slice( self.start, self.stop, self.step).indices(shape[maindim]) shape[maindim] = min( shape[maindim], len(range(start, stop, step))) i_nrows = shape[maindim] else: start, stop, step = 0, 0, None i_nrows = 0 if not itermode: # Create a container for output if not defined yet o_maindim = 0 # Default maindim if self.out is None: out = np.empty(shape, dtype=self._single_row_out.dtype) # Get the trivial values for start, stop and step if maindim is not None: (o_start, o_stop, o_step) = (0, shape[maindim], 1) else: (o_start, o_stop, o_step) = (0, 0, 1) else: out = self.out # Out container already provided. Do some sanity checks. if hasattr(out, "maindim"): o_maindim = out.maindim # Refine the shape of the resulting container having in # account new possible values of start, stop and step in # the output range o_shape = list(out.shape) s = slice(self.o_start, self.o_stop, self.o_step) o_start, o_stop, o_step = s.indices(o_shape[o_maindim]) o_shape[o_maindim] = min(o_shape[o_maindim], len(range(o_start, o_stop, o_step))) # Check that the shape of output is consistent with inputs tr_oshape = list(o_shape) # this implies a copy olen_ = tr_oshape.pop(o_maindim) tr_shape = list(shape) # do a copy if maindim is not None: len_ = tr_shape.pop(o_maindim) else: len_ = 1 if tr_oshape != tr_shape: raise ValueError( "Shape for out container does not match expression") # Force the input length to fit in `out` if not self.append_mode and olen_ < len_: shape[o_maindim] = olen_ stop = start + olen_ # Get the positions of inputs that should be sliced (the others # will be broadcasted) ndim = len(shape) slice_pos = [i for i, val in enumerate(self.values) if len(val.shape) == ndim] # The size of the I/O buffer nrowsinbuf = 1 for i, val in enumerate(self.values): # Skip scalar values in variables if i in slice_pos: nrows = self._calc_nrowsinbuf(val) if nrows > nrowsinbuf: nrowsinbuf = nrows if not itermode: return (i_nrows, slice_pos, start, stop, step, nrowsinbuf, out, o_maindim, o_start, o_stop, o_step) else: # For itermode, we don't need the out info return (i_nrows, slice_pos, start, stop, step, nrowsinbuf)
(self, shape, maindim, itermode=False)
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728,390
tables.expression
_guess_shape
Guess the shape of the output of the expression.
def _guess_shape(self): """Guess the shape of the output of the expression.""" # First, compute the maximum dimension of inputs and maindim # (if it exists) maxndim = 0 maindims = [] for val in self.values: # Get the minimum of the lengths if len(val.shape) > maxndim: maxndim = len(val.shape) if hasattr(val, "maindim"): maindims.append(val.maindim) if maxndim == 0: self._single_row_out = out = self._compiled_expr(*self.values) return (), None if maindims and [maindims[0]] * len(maindims) == maindims: # If all maindims detected are the same, use this as maindim maindim = maindims[0] else: # If not, the main dimension will be the default one maindim = 0 # The slices parameter for inputs slices = (slice(None),) * maindim + (0,) # Now, collect the values in first row of arrays with maximum dims vals = [] lens = [] for val in self.values: shape = val.shape # Warning: don't use len(val) below or it will raise an # `Overflow` error on 32-bit platforms for large enough arrays. if shape != () and shape[maindim] == 0: vals.append(val[:]) lens.append(0) elif len(shape) < maxndim: vals.append(val) else: vals.append(val.__getitem__(slices)) lens.append(shape[maindim]) minlen = min(lens) self._single_row_out = out = self._compiled_expr(*vals) shape = list(out.shape) if minlen > 0: shape.insert(maindim, minlen) return shape, maindim
(self)
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728,391
tables.expression
_required_expr_vars
Get the variables required by the `expression`. A new dictionary defining the variables used in the `expression` is returned. Required variables are first looked up in the `uservars` mapping, then in the set of top-level columns of the table. Unknown variables cause a `NameError` to be raised. When `uservars` is `None`, the local and global namespace where the API callable which uses this method is called is sought instead. To disable this mechanism, just specify a mapping as `uservars`. Nested columns and variables with an ``uint64`` type are not allowed (`TypeError` and `NotImplementedError` are raised, respectively). `depth` specifies the depth of the frame in order to reach local or global variables.
def _required_expr_vars(self, expression, uservars, depth=2): """Get the variables required by the `expression`. A new dictionary defining the variables used in the `expression` is returned. Required variables are first looked up in the `uservars` mapping, then in the set of top-level columns of the table. Unknown variables cause a `NameError` to be raised. When `uservars` is `None`, the local and global namespace where the API callable which uses this method is called is sought instead. To disable this mechanism, just specify a mapping as `uservars`. Nested columns and variables with an ``uint64`` type are not allowed (`TypeError` and `NotImplementedError` are raised, respectively). `depth` specifies the depth of the frame in order to reach local or global variables. """ # Get the names of variables used in the expression. exprvars_cache = self._exprvars_cache if expression not in exprvars_cache: # Protection against growing the cache too much if len(exprvars_cache) > 256: # Remove 10 (arbitrary) elements from the cache for k in list(exprvars_cache)[:10]: del exprvars_cache[k] cexpr = compile(expression, '<string>', 'eval') exprvars = [var for var in cexpr.co_names if var not in ['None', 'False', 'True'] and var not in ne.expressions.functions] exprvars_cache[expression] = exprvars else: exprvars = exprvars_cache[expression] # Get the local and global variable mappings of the user frame # if no mapping has been explicitly given for user variables. user_locals, user_globals = {}, {} if uservars is None: user_frame = sys._getframe(depth) user_locals = user_frame.f_locals user_globals = user_frame.f_globals # Look for the required variables first among the ones # explicitly provided by the user. reqvars = {} for var in exprvars: # Get the value. if uservars is not None and var in uservars: val = uservars[var] elif uservars is None and var in user_locals: val = user_locals[var] elif uservars is None and var in user_globals: val = user_globals[var] else: raise NameError("name ``%s`` is not defined" % var) # Check the value. if hasattr(val, 'dtype') and val.dtype.str[1:] == 'u8': raise NotImplementedError( "variable ``%s`` refers to " "a 64-bit unsigned integer object, that is " "not yet supported in expressions, sorry; " % var) elif hasattr(val, '_v_colpathnames'): # nested column # This branch is never reached because the compile step # above already raise a ``TypeError`` for nested # columns, but that could change in the future. So it # is best to let this here. raise TypeError( "variable ``%s`` refers to a nested column, " "not allowed in expressions" % var) reqvars[var] = val return reqvars
(self, expression, uservars, depth=2)
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728,392
tables.expression
eval
Evaluate the expression and return the outcome. Because of performance reasons, the computation order tries to go along the common main dimension of all inputs. If not such a common main dimension is found, the iteration will go along the leading dimension instead. For non-consistent shapes in inputs (i.e. shapes having a different number of dimensions), the regular NumPy broadcast rules applies. There is one exception to this rule though: when the dimensions orthogonal to the main dimension of the expression are consistent, but the main dimension itself differs among the inputs, then the shortest one is chosen for doing the computations. This is so because trying to expand very large on-disk arrays could be too expensive or simply not possible. Also, the regular Numexpr casting rules (which are similar to those of NumPy, although you should check the Numexpr manual for the exceptions) are applied to determine the output type. Finally, if the setOuput() method specifying a user container has already been called, the output is sent to this user-provided container. If not, a fresh NumPy container is returned instead. .. warning:: When dealing with large on-disk inputs, failing to specify an on-disk container may consume all your available memory.
def eval(self): """Evaluate the expression and return the outcome. Because of performance reasons, the computation order tries to go along the common main dimension of all inputs. If not such a common main dimension is found, the iteration will go along the leading dimension instead. For non-consistent shapes in inputs (i.e. shapes having a different number of dimensions), the regular NumPy broadcast rules applies. There is one exception to this rule though: when the dimensions orthogonal to the main dimension of the expression are consistent, but the main dimension itself differs among the inputs, then the shortest one is chosen for doing the computations. This is so because trying to expand very large on-disk arrays could be too expensive or simply not possible. Also, the regular Numexpr casting rules (which are similar to those of NumPy, although you should check the Numexpr manual for the exceptions) are applied to determine the output type. Finally, if the setOuput() method specifying a user container has already been called, the output is sent to this user-provided container. If not, a fresh NumPy container is returned instead. .. warning:: When dealing with large on-disk inputs, failing to specify an on-disk container may consume all your available memory. """ values, shape, maindim = self.values, self.shape, self.maindim # Get different info we need for the main computation loop (i_nrows, slice_pos, start, stop, step, nrowsinbuf, out, o_maindim, o_start, o_stop, o_step) = \ self._get_info(shape, maindim) if i_nrows == 0: # No elements to compute if start >= stop and self.start is not None: return out else: return self._single_row_out # Create a key that selects every element in inputs and output # (including the main dimension) i_slices = [slice(None)] * (maindim + 1) o_slices = [slice(None)] * (o_maindim + 1) # This is a hack to prevent doing unnecessary flavor conversions # while reading buffers for val in values: if hasattr(val, 'maindim'): val._v_convert = False # Start the computation itself for start2 in range(start, stop, step * nrowsinbuf): stop2 = start2 + step * nrowsinbuf if stop2 > stop: stop2 = stop # Set the proper slice for inputs i_slices[maindim] = slice(start2, stop2, step) # Get the input values vals = [] for i, val in enumerate(values): if i in slice_pos: vals.append(val.__getitem__(tuple(i_slices))) else: # A read of values is not apparently needed, as PyTables # leaves seems to work just fine inside Numexpr vals.append(val) # Do the actual computation for this slice rout = self._compiled_expr(*vals) # Set the values into the out buffer if self.append_mode: out.append(rout) else: # Compute the slice to be filled in output start3 = o_start + (start2 - start) // step stop3 = start3 + nrowsinbuf * o_step if stop3 > o_stop: stop3 = o_stop o_slices[o_maindim] = slice(start3, stop3, o_step) # Set the slice out[tuple(o_slices)] = rout # Activate the conversion again (default) for val in values: if hasattr(val, 'maindim'): val._v_convert = True return out
(self)
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728,393
tables.expression
set_inputs_range
Define a range for all inputs in expression. The computation will only take place for the range defined by the start, stop and step parameters in the main dimension of inputs (or the leading one, if the object lacks the concept of main dimension, like a NumPy container). If not a common main dimension exists for all inputs, the leading dimension will be used instead.
def set_inputs_range(self, start=None, stop=None, step=None): """Define a range for all inputs in expression. The computation will only take place for the range defined by the start, stop and step parameters in the main dimension of inputs (or the leading one, if the object lacks the concept of main dimension, like a NumPy container). If not a common main dimension exists for all inputs, the leading dimension will be used instead. """ self.start = start self.stop = stop self.step = step
(self, start=None, stop=None, step=None)
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728,394
tables.expression
set_output
Set out as container for output as well as the append_mode. The out must be a container that is meant to keep the outcome of the expression. It should be an homogeneous type container and can typically be an Array, CArray, EArray, Column or a NumPy ndarray. The append_mode specifies the way of which the output is filled. If true, the rows of the outcome are *appended* to the out container. Of course, for doing this it is necessary that out would have an append() method (like an EArray, for example). If append_mode is false, the output is set via the __setitem__() method (see the Expr.set_output_range() for info on how to select the rows to be updated). If out is smaller than what is required by the expression, only the computations that are needed to fill up the container are carried out. If it is larger, the excess elements are unaffected.
def set_output(self, out, append_mode=False): """Set out as container for output as well as the append_mode. The out must be a container that is meant to keep the outcome of the expression. It should be an homogeneous type container and can typically be an Array, CArray, EArray, Column or a NumPy ndarray. The append_mode specifies the way of which the output is filled. If true, the rows of the outcome are *appended* to the out container. Of course, for doing this it is necessary that out would have an append() method (like an EArray, for example). If append_mode is false, the output is set via the __setitem__() method (see the Expr.set_output_range() for info on how to select the rows to be updated). If out is smaller than what is required by the expression, only the computations that are needed to fill up the container are carried out. If it is larger, the excess elements are unaffected. """ if not (hasattr(out, "shape") and hasattr(out, "__setitem__")): raise ValueError( "You need to pass a settable multidimensional container " "as output") self.out = out if append_mode and not hasattr(out, "append"): raise ValueError( "For activating the ``append`` mode, you need a container " "with an `append()` method (like the `EArray`)") self.append_mode = append_mode
(self, out, append_mode=False)
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728,395
tables.expression
set_output_range
Define a range for user-provided output object. The output object will only be modified in the range specified by the start, stop and step parameters in the main dimension of output (or the leading one, if the object does not have the concept of main dimension, like a NumPy container).
def set_output_range(self, start=None, stop=None, step=None): """Define a range for user-provided output object. The output object will only be modified in the range specified by the start, stop and step parameters in the main dimension of output (or the leading one, if the object does not have the concept of main dimension, like a NumPy container). """ if self.out is None: raise IndexError( "You need to pass an output object to `setOut()` first") self.o_start = start self.o_stop = stop self.o_step = step
(self, start=None, stop=None, step=None)
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728,396
tables.file
File
The in-memory representation of a PyTables file. An instance of this class is returned when a PyTables file is opened with the :func:`tables.open_file` function. It offers methods to manipulate (create, rename, delete...) nodes and handle their attributes, as well as methods to traverse the object tree. The *user entry point* to the object tree attached to the HDF5 file is represented in the root_uep attribute. Other attributes are available. File objects support an *Undo/Redo mechanism* which can be enabled with the :meth:`File.enable_undo` method. Once the Undo/Redo mechanism is enabled, explicit *marks* (with an optional unique name) can be set on the state of the database using the :meth:`File.mark` method. There are two implicit marks which are always available: the initial mark (0) and the final mark (-1). Both the identifier of a mark and its name can be used in *undo* and *redo* operations. Hierarchy manipulation operations (node creation, movement and removal) and attribute handling operations (setting and deleting) made after a mark can be undone by using the :meth:`File.undo` method, which returns the database to the state of a past mark. If undo() is not followed by operations that modify the hierarchy or attributes, the :meth:`File.redo` method can be used to return the database to the state of a future mark. Else, future states of the database are forgotten. Note that data handling operations can not be undone nor redone by now. Also, hierarchy manipulation operations on nodes that do not support the Undo/Redo mechanism issue an UndoRedoWarning *before* changing the database. The Undo/Redo mechanism is persistent between sessions and can only be disabled by calling the :meth:`File.disable_undo` method. File objects can also act as context managers when using the with statement introduced in Python 2.5. When exiting a context, the file is automatically closed. Parameters ---------- filename : str The name of the file (supports environment variable expansion). It is suggested that file names have any of the .h5, .hdf or .hdf5 extensions, although this is not mandatory. mode : str The mode to open the file. It can be one of the following: * *'r'*: Read-only; no data can be modified. * *'w'*: Write; a new file is created (an existing file with the same name would be deleted). * *'a'*: Append; an existing file is opened for reading and writing, and if the file does not exist it is created. * *'r+'*: It is similar to 'a', but the file must already exist. title : str If the file is to be created, a TITLE string attribute will be set on the root group with the given value. Otherwise, the title will be read from disk, and this will not have any effect. root_uep : str The root User Entry Point. This is a group in the HDF5 hierarchy which will be taken as the starting point to create the object tree. It can be whatever existing group in the file, named by its HDF5 path. If it does not exist, an HDF5ExtError is issued. Use this if you do not want to build the *entire* object tree, but rather only a *subtree* of it. .. versionchanged:: 3.0 The *rootUEP* parameter has been renamed into *root_uep*. filters : Filters An instance of the Filters (see :ref:`FiltersClassDescr`) class that provides information about the desired I/O filters applicable to the leaves that hang directly from the *root group*, unless other filter properties are specified for these leaves. Besides, if you do not specify filter properties for child groups, they will inherit these ones, which will in turn propagate to child nodes. Notes ----- In addition, it recognizes the (lowercase) names of parameters present in :file:`tables/parameters.py` as additional keyword arguments. See :ref:`parameter_files` for a detailed info on the supported parameters. .. rubric:: File attributes .. attribute:: filename The name of the opened file. .. attribute:: format_version The PyTables version number of this file. .. attribute:: isopen True if the underlying file is open, false otherwise. .. attribute:: mode The mode in which the file was opened. .. attribute:: root The *root* of the object tree hierarchy (a Group instance). .. attribute:: root_uep The UEP (user entry point) group name in the file (see the :func:`open_file` function). .. versionchanged:: 3.0 The *rootUEP* attribute has been renamed into *root_uep*.
class File(hdf5extension.File): """The in-memory representation of a PyTables file. An instance of this class is returned when a PyTables file is opened with the :func:`tables.open_file` function. It offers methods to manipulate (create, rename, delete...) nodes and handle their attributes, as well as methods to traverse the object tree. The *user entry point* to the object tree attached to the HDF5 file is represented in the root_uep attribute. Other attributes are available. File objects support an *Undo/Redo mechanism* which can be enabled with the :meth:`File.enable_undo` method. Once the Undo/Redo mechanism is enabled, explicit *marks* (with an optional unique name) can be set on the state of the database using the :meth:`File.mark` method. There are two implicit marks which are always available: the initial mark (0) and the final mark (-1). Both the identifier of a mark and its name can be used in *undo* and *redo* operations. Hierarchy manipulation operations (node creation, movement and removal) and attribute handling operations (setting and deleting) made after a mark can be undone by using the :meth:`File.undo` method, which returns the database to the state of a past mark. If undo() is not followed by operations that modify the hierarchy or attributes, the :meth:`File.redo` method can be used to return the database to the state of a future mark. Else, future states of the database are forgotten. Note that data handling operations can not be undone nor redone by now. Also, hierarchy manipulation operations on nodes that do not support the Undo/Redo mechanism issue an UndoRedoWarning *before* changing the database. The Undo/Redo mechanism is persistent between sessions and can only be disabled by calling the :meth:`File.disable_undo` method. File objects can also act as context managers when using the with statement introduced in Python 2.5. When exiting a context, the file is automatically closed. Parameters ---------- filename : str The name of the file (supports environment variable expansion). It is suggested that file names have any of the .h5, .hdf or .hdf5 extensions, although this is not mandatory. mode : str The mode to open the file. It can be one of the following: * *'r'*: Read-only; no data can be modified. * *'w'*: Write; a new file is created (an existing file with the same name would be deleted). * *'a'*: Append; an existing file is opened for reading and writing, and if the file does not exist it is created. * *'r+'*: It is similar to 'a', but the file must already exist. title : str If the file is to be created, a TITLE string attribute will be set on the root group with the given value. Otherwise, the title will be read from disk, and this will not have any effect. root_uep : str The root User Entry Point. This is a group in the HDF5 hierarchy which will be taken as the starting point to create the object tree. It can be whatever existing group in the file, named by its HDF5 path. If it does not exist, an HDF5ExtError is issued. Use this if you do not want to build the *entire* object tree, but rather only a *subtree* of it. .. versionchanged:: 3.0 The *rootUEP* parameter has been renamed into *root_uep*. filters : Filters An instance of the Filters (see :ref:`FiltersClassDescr`) class that provides information about the desired I/O filters applicable to the leaves that hang directly from the *root group*, unless other filter properties are specified for these leaves. Besides, if you do not specify filter properties for child groups, they will inherit these ones, which will in turn propagate to child nodes. Notes ----- In addition, it recognizes the (lowercase) names of parameters present in :file:`tables/parameters.py` as additional keyword arguments. See :ref:`parameter_files` for a detailed info on the supported parameters. .. rubric:: File attributes .. attribute:: filename The name of the opened file. .. attribute:: format_version The PyTables version number of this file. .. attribute:: isopen True if the underlying file is open, false otherwise. .. attribute:: mode The mode in which the file was opened. .. attribute:: root The *root* of the object tree hierarchy (a Group instance). .. attribute:: root_uep The UEP (user entry point) group name in the file (see the :func:`open_file` function). .. versionchanged:: 3.0 The *rootUEP* attribute has been renamed into *root_uep*. """ # The top level kinds. Group must go first! _node_kinds = ('Group', 'Leaf', 'Link', 'Unknown') @property def title(self): """The title of the root group in the file.""" return self.root._v_title @title.setter def title(self, title): self.root._v_title = title @title.deleter def title(self): del self.root._v_title @property def filters(self): """Default filter properties for the root group (see :ref:`FiltersClassDescr`).""" return self.root._v_filters @filters.setter def filters(self, filters): self.root._v_filters = filters @filters.deleter def filters(self): del self.root._v_filters def __init__(self, filename, mode="r", title="", root_uep="/", filters=None, **kwargs): self.filename = os.fspath(filename) """The name of the opened file.""" self.mode = mode """The mode in which the file was opened.""" if mode not in ('r', 'r+', 'a', 'w'): raise ValueError("invalid mode string ``%s``. Allowed modes are: " "'r', 'r+', 'a' and 'w'" % mode) # Get all the parameters in parameter file(s) params = {k: v for k, v in parameters.__dict__.items() if k.isupper() and not k.startswith('_')} # Update them with possible keyword arguments if [k for k in kwargs if k.isupper()]: warnings.warn("The use of uppercase keyword parameters is " "deprecated", DeprecationWarning) kwargs = {k.upper(): v for k, v in kwargs.items()} params.update(kwargs) # If MAX_ * _THREADS is not set yet, set it to the number of cores # on this machine. if params['MAX_NUMEXPR_THREADS'] is None: params['MAX_NUMEXPR_THREADS'] = detect_number_of_cores() if params['MAX_BLOSC_THREADS'] is None: params['MAX_BLOSC_THREADS'] = detect_number_of_cores() self.params = params # Now, it is time to initialize the File extension self._g_new(filename, mode, **params) # Check filters and set PyTables format version for new files. new = self._v_new if new: _checkfilters(filters) self.format_version = format_version """The PyTables version number of this file.""" # The node manager must be initialized before the root group # initialization but the node_factory attribute is set onl later # because it is a bount method of the root grop itself. node_cache_slots = params['NODE_CACHE_SLOTS'] self._node_manager = NodeManager(nslots=node_cache_slots) # For the moment Undo/Redo is not enabled. self._undoEnabled = False # Set the flag to indicate that the file has been opened. # It must be set before opening the root group # to allow some basic access to its attributes. self.isopen = 1 """True if the underlying file os open, False otherwise.""" # Append the name of the file to the global dict of files opened. _open_files.add
(filename, mode='r', title='', root_uep='/', filters=None, **kwargs)
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728,397
tables.file
__get_root_group
Returns a Group instance which will act as the root group in the hierarchical tree. If file is opened in "r", "r+" or "a" mode, and the file already exists, this method dynamically builds a python object tree emulating the structure present on file.
def __get_root_group(self, root_uep, title, filters): """Returns a Group instance which will act as the root group in the hierarchical tree. If file is opened in "r", "r+" or "a" mode, and the file already exists, this method dynamically builds a python object tree emulating the structure present on file. """ self._v_objectid = self._get_file_id() if root_uep in [None, ""]: root_uep = "/" # Save the User Entry Point in a variable class self.root_uep = root_uep new = self._v_new # Get format version *before* getting the object tree if not new: # Firstly, get the PyTables format version for this file self.format_version = utilsextension.read_f_attr( self._v_objectid, 'PYTABLES_FORMAT_VERSION') if not self.format_version: # PYTABLES_FORMAT_VERSION attribute is not present self.format_version = "unknown" self._isPTFile = False elif not isinstance(self.format_version, str): # system attributes should always be str self.format_version = self.format_version.decode('utf-8') # Create new attributes for the root Group instance and # create the object tree return RootGroup(self, root_uep, title=title, new=new, filters=filters)
(self, root_uep, title, filters)
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728,398
tables.file
__contains__
Is there a node with that path? Returns True if the file has a node with the given path (a string), False otherwise.
def __contains__(self, path): """Is there a node with that path? Returns True if the file has a node with the given path (a string), False otherwise. """ try: self.get_node(path) except NoSuchNodeError: return False else: return True
(self, path)
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728,399
tables.file
__enter__
Enter a context and return the same file.
def __enter__(self): """Enter a context and return the same file.""" return self
(self)
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728,400
tables.file
__exit__
Exit a context and close the file.
def __exit__(self, *exc_info): """Exit a context and close the file.""" self.close() return False # do not hide exceptions
(self, *exc_info)
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728,401
tables.file
__init__
null
def __init__(self, filename, mode="r", title="", root_uep="/", filters=None, **kwargs): self.filename = os.fspath(filename) """The name of the opened file.""" self.mode = mode """The mode in which the file was opened.""" if mode not in ('r', 'r+', 'a', 'w'): raise ValueError("invalid mode string ``%s``. Allowed modes are: " "'r', 'r+', 'a' and 'w'" % mode) # Get all the parameters in parameter file(s) params = {k: v for k, v in parameters.__dict__.items() if k.isupper() and not k.startswith('_')} # Update them with possible keyword arguments if [k for k in kwargs if k.isupper()]: warnings.warn("The use of uppercase keyword parameters is " "deprecated", DeprecationWarning) kwargs = {k.upper(): v for k, v in kwargs.items()} params.update(kwargs) # If MAX_ * _THREADS is not set yet, set it to the number of cores # on this machine. if params['MAX_NUMEXPR_THREADS'] is None: params['MAX_NUMEXPR_THREADS'] = detect_number_of_cores() if params['MAX_BLOSC_THREADS'] is None: params['MAX_BLOSC_THREADS'] = detect_number_of_cores() self.params = params # Now, it is time to initialize the File extension self._g_new(filename, mode, **params) # Check filters and set PyTables format version for new files. new = self._v_new if new: _checkfilters(filters) self.format_version = format_version """The PyTables version number of this file.""" # The node manager must be initialized before the root group # initialization but the node_factory attribute is set onl later # because it is a bount method of the root grop itself. node_cache_slots = params['NODE_CACHE_SLOTS'] self._node_manager = NodeManager(nslots=node_cache_slots) # For the moment Undo/Redo is not enabled. self._undoEnabled = False # Set the flag to indicate that the file has been opened. # It must be set before opening the root group # to allow some basic access to its attributes. self.isopen = 1 """True if the underlying file os open, False otherwise.""" # Append the name of the file to the global dict of files opened. _open_files.add(self) # Set the number of times this file has been opened to 1 self._open_count = 1 # Get the root group from this file self.root = root = self.__get_root_group(root_uep, title, filters) """The *root* of the object tree hierarchy (a Group instance).""" # Complete the creation of the root node # (see the explanation in ``RootGroup.__init__()``. root._g_post_init_hook() self._node_manager.node_factory = self.root._g_load_child # Save the PyTables format version for this file. if new: if params['PYTABLES_SYS_ATTRS']: root._v_attrs._g__setattr( 'PYTABLES_FORMAT_VERSION', format_version) # If the file is old, and not opened in "read-only" mode, # check if it has a transaction log if not new and self.mode != "r" and _trans_group_path in self: # It does. Enable the undo. self.enable_undo() # Set the maximum number of threads for Numexpr ne.set_vml_num_threads(params['MAX_NUMEXPR_THREADS'])
(self, filename, mode='r', title='', root_uep='/', filters=None, **kwargs)
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728,402
tables.file
__iter__
Recursively iterate over the nodes in the tree. This is equivalent to calling :meth:`File.walk_nodes` with no arguments. Examples -------- :: # Recursively list all the nodes in the object tree. h5file = tables.open_file('vlarray1.h5') print("All nodes in the object tree:") for node in h5file: print(node)
def __iter__(self): """Recursively iterate over the nodes in the tree. This is equivalent to calling :meth:`File.walk_nodes` with no arguments. Examples -------- :: # Recursively list all the nodes in the object tree. h5file = tables.open_file('vlarray1.h5') print("All nodes in the object tree:") for node in h5file: print(node) """ return self.walk_nodes('/')
(self)
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728,403
tables.file
__repr__
Return a detailed string representation of the object tree.
def __repr__(self): """Return a detailed string representation of the object tree.""" if not self.isopen: return "<closed File>" # Print all the nodes (Group and Leaf objects) on object tree lines = [ f'File(filename={self.filename!s}, title={self.title!r}, ' f'mode={self.mode!r}, root_uep={self.root_uep!r}, ' f'filters={self.filters!r})'] for group in self.walk_groups("/"): lines.append(f'{group}') for kind in self._node_kinds[1:]: for node in self.list_nodes(group, kind): lines.append(f'{node!r}') return '\n'.join(lines) + '\n'
(self)
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728,404
tables.file
__str__
Return a short string representation of the object tree. Examples -------- :: >>> import tables >>> f = tables.open_file('tables/tests/Tables_lzo2.h5') >>> print(f) tables/tests/Tables_lzo2.h5 (File) 'Table Benchmark' Last modif.: '...' Object Tree: / (RootGroup) 'Table Benchmark' /tuple0 (Table(100,)lzo(1)) 'This is the table title' /group0 (Group) '' /group0/tuple1 (Table(100,)lzo(1)) 'This is the table title' /group0/group1 (Group) '' /group0/group1/tuple2 (Table(100,)lzo(1)) 'This is the table title' /group0/group1/group2 (Group) '' >>> f.close()
def __str__(self): """Return a short string representation of the object tree. Examples -------- :: >>> import tables >>> f = tables.open_file('tables/tests/Tables_lzo2.h5') >>> print(f) tables/tests/Tables_lzo2.h5 (File) 'Table Benchmark' Last modif.: '...' Object Tree: / (RootGroup) 'Table Benchmark' /tuple0 (Table(100,)lzo(1)) 'This is the table title' /group0 (Group) '' /group0/tuple1 (Table(100,)lzo(1)) 'This is the table title' /group0/group1 (Group) '' /group0/group1/tuple2 (Table(100,)lzo(1)) 'This is the table title' /group0/group1/group2 (Group) '' >>> f.close() """ if not self.isopen: return "<closed File>" # Print all the nodes (Group and Leaf objects) on object tree try: date = datetime.datetime.fromtimestamp( Path(self.filename).stat().st_mtime, datetime.timezone.utc ).isoformat(timespec='seconds') except OSError: # in-memory file date = "<in-memory file>" lines = [f'{self.filename} (File) {self.title!r}', f'Last modif.: {date!r}', 'Object Tree: '] for group in self.walk_groups("/"): lines.append(f'{group}') for kind in self._node_kinds[1:]: for node in self.list_nodes(group, kind): lines.append(f'{node}') return '\n'.join(lines) + '\n'
(self)
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728,405
tables.file
_check_group
null
def _check_group(self, node): # `node` must already be a node. if not isinstance(node, Group): raise TypeError(f"node ``{node._v_pathname}`` is not a group")
(self, node)
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728,406
tables.file
_check_open
Check the state of the file. If the file is closed, a `ClosedFileError` is raised.
def _check_open(self): """Check the state of the file. If the file is closed, a `ClosedFileError` is raised. """ if not self.isopen: raise ClosedFileError("the file object is closed")
(self)
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728,407
tables.file
_check_undo_enabled
null
def _check_undo_enabled(self): if not self._undoEnabled: raise UndoRedoError("Undo/Redo feature is currently disabled!")
(self)
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728,408
tables.file
_check_writable
Check whether the file is writable. If the file is not writable, a `FileModeError` is raised.
def _check_writable(self): """Check whether the file is writable. If the file is not writable, a `FileModeError` is raised. """ if not self._iswritable(): raise FileModeError("the file is not writable")
(self)
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728,409
tables.file
_create_mark
null
def _create_mark(self, trans, mid): return MarkG( trans, _markName % mid, "Mark number %d" % mid, new=True)
(self, trans, mid)
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728,410
tables.file
_create_path
Create the groups needed for the `path` to exist. The group associated with the given `path` is returned.
def _create_path(self, path): """Create the groups needed for the `path` to exist. The group associated with the given `path` is returned. """ if not hasattr(path, 'split'): raise TypeError("when creating parents, parent must be a path") if path == '/': return self.root parent, create_group = self.root, self.create_group for pcomp in path.split('/')[1:]: try: child = parent._f_get_child(pcomp) except NoSuchNodeError: child = create_group(parent, pcomp) parent = child return parent
(self, path)
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728,411
tables.file
_create_transaction
null
def _create_transaction(self, troot, tid): return TransactionG( troot, _trans_name % tid, "Transaction number %d" % tid, new=True)
(self, troot, tid)
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728,412
tables.file
_create_transaction_group
null
def _create_transaction_group(self): tgroup = TransactionGroupG( self.root, _trans_group_name, "Transaction information container", new=True) # The format of the transaction container. tgroup._v_attrs._g__setattr('FORMATVERSION', _trans_version) return tgroup
(self)
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728,413
tables.file
_doundo
Undo/Redo actions up to final action in the specificed direction.
def _doundo(self, finalaction, direction): """Undo/Redo actions up to final action in the specificed direction.""" if direction < 0: actionlog = \ self._actionlog[finalaction + 1:self._curaction + 1][::-1] else: actionlog = self._actionlog[self._curaction:finalaction] # Uncomment this for debugging # print("curaction, finalaction, direction", \ # self._curaction, finalaction, direction) for i in range(len(actionlog)): if actionlog['opcode'][i] != _op_to_code["MARK"]: # undo/redo the action if direction > 0: # Uncomment this for debugging # print("redo-->", \ # _code_to_op[actionlog['opcode'][i]],\ # actionlog['arg1'][i],\ # actionlog['arg2'][i]) undoredo.redo(self, # _code_to_op[actionlog['opcode'][i]], # The next is a workaround for python < 2.5 _code_to_op[int(actionlog['opcode'][i])], actionlog['arg1'][i].decode('utf8'), actionlog['arg2'][i].decode('utf8')) else: # Uncomment this for debugging # print("undo-->", \ # _code_to_op[actionlog['opcode'][i]],\ # actionlog['arg1'][i].decode('utf8'),\ # actionlog['arg2'][i].decode('utf8')) undoredo.undo(self, # _code_to_op[actionlog['opcode'][i]], # The next is a workaround for python < 2.5 _code_to_op[int(actionlog['opcode'][i])], actionlog['arg1'][i].decode('utf8'), actionlog['arg2'][i].decode('utf8')) else: if direction > 0: self._curmark = int(actionlog['arg1'][i]) else: self._curmark = int(actionlog['arg1'][i]) - 1 # Protection against negative marks if self._curmark < 0: self._curmark = 0 self._curaction += direction
(self, finalaction, direction)
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728,414
tables.file
_get_final_action
Get the action to go. It does not touch the self private attributes
def _get_final_action(self, markid): """Get the action to go. It does not touch the self private attributes """ if markid > self._nmarks - 1: # The required mark is beyond the end of the action log # The final action is the last row return self._actionlog.nrows elif markid <= 0: # The required mark is the first one # return the first row return 0 return self._seqmarkers[markid]
(self, markid)
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728,415
tables.file
_get_mark_id
Get an integer markid from a mark sequence number or name.
def _get_mark_id(self, mark): """Get an integer markid from a mark sequence number or name.""" if isinstance(mark, int): markid = mark elif isinstance(mark, str): if mark not in self._markers: lmarkers = sorted(self._markers) raise UndoRedoError("The mark that you have specified has not " "been found in the internal marker list: " "%r" % lmarkers) markid = self._markers[mark] else: raise TypeError("Parameter mark can only be an integer or a " "string, and you passed a type <%s>" % type(mark)) # print("markid, self._nmarks:", markid, self._nmarks) return markid
(self, mark)
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728,416
tables.file
_get_node
null
def _get_node(self, nodepath): # The root node is always at hand. if nodepath == '/': return self.root node = self._node_manager.get_node(nodepath) assert node is not None, "unable to instantiate node ``%s``" % nodepath return node
(self, nodepath)
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728,417
tables.file
_get_or_create_path
Get the given `path` or create it if `create` is true. If `create` is true, `path` *must* be a string path and not a node, otherwise a `TypeError`will be raised.
def _get_or_create_path(self, path, create): """Get the given `path` or create it if `create` is true. If `create` is true, `path` *must* be a string path and not a node, otherwise a `TypeError`will be raised. """ if create: return self._create_path(path) else: return self.get_node(path)
(self, path, create)
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