pymodaq_data 0.0.1__tar.gz → 0.0.3__tar.gz

{pymodaq_data-0.0.1 → pymodaq_data-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pymodaq_data
-Version: 0.0.1
+Version: 0.0.3
 Summary: Modular Data Acquisition with Python
 Project-URL: Homepage, http://pymodaq.cnrs.fr
 Project-URL: Source, https://github.com/PyMoDAQ/PyMoDAQ
@@ -135,7 +135,6 @@ or calculated from theory:
 
 
 .. figure:: https://pymodaq.cnrs.fr/en/latest/_images/data.png
-   :alt: What is data?
 
    What is PyMoDAQ's data?.
 

{pymodaq_data-0.0.1 → pymodaq_data-0.0.3}/README.rst

@@ -78,7 +78,6 @@ or calculated from theory:
 
 
 .. figure:: https://pymodaq.cnrs.fr/en/latest/_images/data.png
-   :alt: What is data?
 
    What is PyMoDAQ's data?.
 

pymodaq_data-0.0.3/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.3'
+__version_tuple__ = version_tuple = (0, 0, 3)

{pymodaq_data-0.0.1 → pymodaq_data-0.0.3}/pyproject.toml

@@ -56,3 +56,6 @@ source = "vcs"
 include = [
     "/src",
 ]
+
+[tool.hatch.build.hooks.vcs]
+version-file = "_version.py"

{pymodaq_data-0.0.1 → pymodaq_data-0.0.3}/src/pymodaq_data/__init__.py

@@ -43,7 +43,7 @@ try:
     logger.info(f"Done")
     logger.info('************************')
 
-    from pymodaq_data.data import (DataRaw, DataFromPlugins, DataWithAxes, DataToExport, Axis,
+    from pymodaq_data.data import (DataRaw, DataWithAxes, DataToExport, Axis,
                                    DataCalculated, DataDim, DataDistribution, DataSource, DataBase)
 
 except Exception as e:

{pymodaq_data-0.0.1 → pymodaq_data-0.0.3}/src/pymodaq_data/data.py

@@ -9,6 +9,7 @@ from __future__ import annotations
 from abc import ABCMeta, abstractmethod, abstractproperty
 import numbers
 import numpy as np
+from numpy.lib.mixins import NDArrayOperatorsMixin
 from typing import List, Tuple, Union, Any, Callable
 from typing import Iterable as IterableType
 from collections.abc import Iterable
@@ -19,6 +20,7 @@ import warnings
 from time import time
 import copy
 import pint
+
 from multipledispatch import dispatch
 
 from pymodaq_utils.enums import BaseEnum, enum_checker
@@ -29,7 +31,7 @@ from pymodaq_data.slicing import SpecialSlicersData
 from pymodaq_utils import math_utils as mutils
 from pymodaq_utils.config import Config
 from pymodaq_data.plotting.plotter.plotter import PlotterFactory
-
+from pymodaq_data.numpy_func import HANDLED_FUNCTIONS, HANDLED_UFUNCS, process_arguments_for_ufuncs
 from pymodaq_data import Q_, ureg, Unit
 
 config = Config()
@@ -515,7 +517,7 @@ class DataLowLevel:
         self._timestamp = timestamp
 
 
-class DataBase(DataLowLevel):
+class DataBase(DataLowLevel, NDArrayOperatorsMixin):
     """Base object to store homogeneous data and metadata generated by pymodaq's objects.
 
     To be inherited for real data
@@ -672,6 +674,10 @@ class DataBase(DataLowLevel):
             new_data._units = units
             return new_data
 
+    def force_units(self, units: str):
+        """ Change immediately the units to whatever else. Use this with care!"""
+        self._units = units
+
     def as_dte(self, name: str = 'mydte') -> DataToExport:
         """Convenience method to wrap the DataWithAxes object into a DataToExport"""
         return DataToExport(name, data=[self])
@@ -726,70 +732,40 @@ class DataBase(DataLowLevel):
         else:
             raise IndexError(f'The index should be an positive integer lower than the data length')
 
-    def __add__(self, other: object):
-        if isinstance(other, DataBase) and len(other) == len(self):
-            new_data = copy.deepcopy(self)
-            for ind_array in range(len(new_data)):
-                if self[ind_array].shape != other[ind_array].shape:
-                    raise ValueError('The shapes of arrays stored into the data are not consistent')
-                try:
-                    new_data[ind_array] = (Q_(self[ind_array], self.units) +
-                                           Q_(other[ind_array], other.units)).m_as(self.units)
-                except pint.errors.DimensionalityError as e:
-                    raise DataUnitError(
-                        f'Cannot sum Data objects not having the same dimension: {e}')
-            return new_data
+    def __array_ufunc__(self, ufunc, method, *inputs, **kwargs):
+        ufunc_name = ufunc.__name__
+        if ufunc_name not in HANDLED_UFUNCS:
+            raise NotImplementedError
         else:
-            raise TypeError(f'Could not add a {other.__class__.__name__} or a {self.__class__.__name__} '
-                            f'of a different length')
-
-    def __sub__(self, other: object):
-        return self.__add__(other * -1)
-        #
-        # if isinstance(other, DataBase) and len(other) == len(self):
-        #     new_data = copy.deepcopy(self)
-        #     for ind_array in range(len(new_data)):
-        #         new_data[ind_array] = self[ind_array] - other[ind_array]
-        #     return new_data
-        # elif isinstance(other, numbers.Number) and self.length == 1 and self.size == 1:
-        #     new_data = copy.deepcopy(self)
-        #     new_data = new_data - DataActuator(data=other)
-        #     return new_data
-        # else:
-        #     raise TypeError(f'Could not substract a {other.__class__.__name__} or a {self.__class__.__name__} '
-        #                     f'of a different length')
-
-    def __mul__(self, other):
-        if (isinstance(other, numbers.Number) or
-                (isinstance(other, np.ndarray) and other.shape == self._shape)):
-            new_data = copy.deepcopy(self)
-            for ind_array in range(len(new_data)):
-                new_data[ind_array] = self[ind_array] * other
-            return new_data
-        elif isinstance(other, DataBase) and other.shape == self._shape:
-            new_data = copy.deepcopy(self)
-            new_unit = str((Q_(self[0], self.units) *
-                           Q_(other[0], other.units)).to_base_units().units)
-            for ind_array in range(len(new_data)):
-                new_data[ind_array] = \
-                    ((Q_(self[ind_array], self.units) * Q_(other[ind_array], other.units))
-                     .to_base_units()).magnitude
-            new_data._units = new_unit
-            return new_data
+            ufunc = HANDLED_UFUNCS[ufunc_name]
+        if method == '__call__':
+            elts = process_arguments_for_ufuncs(self, inputs)
+            dwa = self.deepcopy()
+            dwa.name = f'{self.name}_{ufunc_name}'
+            units = dwa.units
+            ufunc_results = [ufunc(*zipped, **kwargs) for zipped in list(zip(*elts))]
+            if isinstance(ufunc_results[0], Q_):
+                units = str(ufunc_results[0].units)
+                ufunc_results = [ufunc_result.magnitude for ufunc_result in ufunc_results]
+            dwa.data = ufunc_results
+            dwa.force_units(units)
+            return dwa
         else:
-            raise TypeError(f'Could not multiply a {other.__class__.__name__} and a {self.__class__.__name__} '
-                            f'of a different length')
+            return NotImplemented
 
-    def __truediv__(self, other):
-        if isinstance(other, numbers.Number):
-            return self * (1 / other)
+    def __array_function__(self, func, types, args, kwargs):
+        func_name = func.__name__
+        if func_name not in HANDLED_FUNCTIONS:
+            return NotImplemented
         else:
-            raise TypeError(f'Could not divide a {other.__class__.__name__} and a {self.__class__.__name__} '
-                            f'of a different length')
+            func = HANDLED_FUNCTIONS[func_name]
+        if not all(issubclass(t, self.__class__) for t in types):
+            return NotImplemented
+        return func(*args, **kwargs)
 
     def _comparison_common(self, other, operator='__eq__'):
         if isinstance(other, DataBase):
-            if not (self.name == other.name and
+            if not (#self.name == other.name and  # who cares if the name is not the same?
                     len(self) == len(other) and
                     Unit(self.units).is_compatible_with(other.units)):
                 return False
@@ -800,7 +776,10 @@ class DataBase(DataLowLevel):
                 if self[ind].shape != other[ind].shape:
                     eq = False
                     break
-                eq = eq and np.all(getattr(self.quantities[ind], operator)(other.quantities[ind]))
+                if operator == '__eq__':
+                    eq = eq and np.allclose(self.quantities[ind], other.quantities[ind])
+                else:
+                    eq = eq and np.all(getattr(self.quantities[ind], operator)(other.quantities[ind]))
             # extra attributes are not relevant as they may contain module specific data...
             # eq = eq and (self.extra_attributes == other.extra_attributes)
             # for attribute in self.extra_attributes:
@@ -811,9 +790,15 @@ class DataBase(DataLowLevel):
         else:
             raise TypeError()
 
+    def __bool__(self):
+        return all([np.all(array) for array in self])
+
     def __eq__(self, other):
         return self._comparison_common(other, '__eq__')
 
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
     def __le__(self, other):
         return self._comparison_common(other, '__le__')
 
@@ -849,27 +834,19 @@ class DataBase(DataLowLevel):
 
     def abs(self):
         """ Take the absolute value of itself"""
-        new_data = copy.copy(self)
-        new_data.data = [np.abs(dat) for dat in new_data]
-        return new_data
+        return np.abs(self)
 
     def angle(self):
         """ Take the phase value of itself"""
-        new_data = copy.copy(self)
-        new_data.data = [np.angle(dat) for dat in new_data]
-        return new_data
+        return np.angle(self)
 
     def real(self):
         """ Take the real part of itself"""
-        new_data = copy.copy(self)
-        new_data.data = [np.real(dat) for dat in new_data]
-        return new_data
+        return np.real(self)
 
     def imag(self):
         """ Take the imaginary part of itself"""
-        new_data = copy.copy(self)
-        new_data.data = [np.imag(dat) for dat in new_data]
-        return new_data
+        return np.imag(self)
 
     def flipud(self):
         """Reverse the order of elements along axis 0 (up/down)"""
@@ -1091,11 +1068,7 @@ class DataBase(DataLowLevel):
 
         new in 4.3.0
         """
-        new_data = copy.deepcopy(self)
-        for ind_array in range(len(new_data)):
-            new_data[ind_array] = 10 * np.log10(self[ind_array] / self[ind_array].max())
-        new_data._units = 'dB'
-        return new_data
+        return 10 * np.log10(self / np.max(self))
 
 
 class AxesManagerBase:
@@ -2274,14 +2247,14 @@ class DataWithAxes(DataBase):
 
         data = DataWithAxes(self.name, data=new_arrays_data, nav_indexes=tuple(nav_indexes),
                             axes=axes,
-                            source='calculated', origin=self.origin,
+                            source=DataSource.calculated, origin=self.origin,
                             labels=self.labels[:],
                             distribution=distribution)
         return data
 
     def deepcopy_with_new_data(self, data: List[np.ndarray] = None,
                                remove_axes_index: Union[int, List[int]] = None,
-                               source: DataSource = 'calculated',
+                               source: DataSource = DataSource.calculated,
                                keep_dim=False) -> DataWithAxes:
         """deepcopy without copying the initial data (saving memory)
 

{pymodaq_data-0.0.1 → pymodaq_data-0.0.3}/src/pymodaq_data/h5modules/data_saving.py

@@ -283,7 +283,7 @@ class DataSaverLoader(DataManagement):
 
         if isinstance(h5saver, Path) or isinstance(h5saver, str):
             h5saver_tmp = H5SaverLowLevel()
-            h5saver_tmp.init_file(addhoc_file_path=Path(h5saver))
+            h5saver_tmp.init_file(file_name=Path(h5saver))
             h5saver = h5saver_tmp
 
         self._h5saver = h5saver

pymodaq_data-0.0.3/src/pymodaq_data/numpy_func.py

@@ -0,0 +1,158 @@
+from typing import Union, List, TYPE_CHECKING, Iterable, Optional, Callable
+import numbers
+
+import numpy as np
+from pint.facets.numpy.numpy_func import HANDLED_UFUNCS  # imported by the data module
+from pymodaq_data import Q_
+from pymodaq_data import data as data_mod
+
+if TYPE_CHECKING:
+    from pymodaq_data.data import DataBase, DataWithAxes
+
+HANDLED_FUNCTIONS = {}
+
+
+def process_arguments_for_ufuncs(input: 'DataBase',
+                      inputs: List[Union[numbers.Number, Q_, np.ndarray, 'DataBase']]):
+    """
+
+    Parameters
+    ----------
+    input: 'DataBase'
+    inputs: list of elts in a numpy operation, could be numbers, quantities, ndarray, or 'DataBase'
+
+    Returns
+    -------
+    list of numbers, quantities or numpy arrays for applying to pint handled functions
+    """
+    elts = []
+    for elt in inputs:
+        if isinstance(elt, numbers.Number):
+            elts.append([elt for _ in range(input.length)])
+        elif isinstance(elt, Q_):  # take its magnitude
+            elts.append([elt for _ in range(input.length)])
+        elif isinstance(elt, np.ndarray):
+            if elt.size != input.size:
+                raise TypeError("inconsistent sizes")
+            elts.append([elt for _ in range(input.length)])
+        else:
+            try:
+                elts.append([Q_(array, elt.units) for array in elt.data])
+            except:
+                return NotImplementedError
+    return elts
+
+
+def implements(np_function):
+    """Register an __array_function__ implementation for DataWithAxes."""
+    def decorator(func):
+        HANDLED_FUNCTIONS[np_function] = func
+        return func
+    return decorator
+
+# ********* FUNCTIONS that reduce dimensions *****************
+
+def process_with_reduced_dimensions(func: Callable, dwa: 'DataWithAxes',
+                                    axis: Optional[Union[int, Iterable[int]]] = None,
+                                    *args, **kwargs):
+    all_axes = list(dwa.nav_indexes) + list(dwa.sig_indexes)
+    if axis is None:
+        remove_axis = all_axes
+    elif isinstance(axis, int):
+        remove_axis = all_axes[axis]
+    else:
+        remove_axis = [all_axes[axis_index] for axis_index in axis]
+    dwa_func = dwa.deepcopy_with_new_data(
+        data=[np.atleast_1d(func(dwa.data[ind], axis, *args, **kwargs)) for ind in range(len(dwa))],
+        remove_axes_index=remove_axis
+    )
+    dwa_func.name += f'_{func.__name__}'
+    return dwa_func
+
+
+@implements('max')
+def _max(dwa: 'DataWithAxes', *args, axis: Optional[Union[int, Iterable[int]]] = None, **kwargs):
+    return process_with_reduced_dimensions(np.max, dwa, *args, axis=axis, **kwargs)
+
+
+@implements('min')
+def _min(dwa: 'DataWithAxes', *args, axis: Optional[Union[int, Iterable[int]]] = None, **kwargs):
+    return process_with_reduced_dimensions(np.min, dwa, *args, axis=axis, **kwargs)
+
+
+@implements("std")
+def _std(dwa: 'DataWithAxes', *args, axis: Optional[Union[int, Iterable[int]]] = None, **kwargs):
+    return process_with_reduced_dimensions(np.std, dwa, *args, axis=axis, **kwargs)
+
+@implements("mean")
+def _mean(dwa: 'DataWithAxes', *args, axis: Optional[Union[int, Iterable[int]]] = None, **kwargs):
+    return process_with_reduced_dimensions(np.mean, dwa, *args, axis=axis, **kwargs)
+
+
+# ************* FUNCTIONS that apply with units ********
+
+@implements('angle')
+def _angle(dwa: 'DataWithAxes', *args, **kwargs):
+
+    dwa_func = dwa.deepcopy_with_new_data(
+        data=[np.angle(array, *args, **kwargs) for array in dwa.data])
+    dwa_func.name += f"_{'angle'}"
+    return dwa_func
+
+
+@implements('real')
+def _real(dwa: 'DataWithAxes', *args, **kwargs):
+
+    dwa_func = dwa.deepcopy_with_new_data(
+        data=[np.real(array, *args, **kwargs) for array in dwa.data])
+    dwa_func.name += f"_{'real'}"
+    return dwa_func
+
+
+@implements('imag')
+def _imag(dwa: 'DataWithAxes', *args, **kwargs):
+
+    dwa_func = dwa.deepcopy_with_new_data(
+        data=[np.imag(array, *args, **kwargs) for array in dwa.data])
+    dwa_func.name += f"_{'imag'}"
+    return dwa_func
+
+
+@implements('absolute')
+def _absolute(dwa: 'DataWithAxes', *args, **kwargs):
+
+    dwa_func = dwa.deepcopy_with_new_data(
+        data=[np.absolute(array, *args, **kwargs) for array in dwa.data])
+    dwa_func.name += f"_{'absolute'}"
+    return dwa_func
+
+
+@implements('abs')
+def _abs(dwa: 'DataWithAxes', *args, **kwargs):
+    return np.absolute(dwa, *args, **kwargs)
+
+
+# ******** functions that return booleans ***********
+@implements('all')
+def _all(dwa: 'DataWithAxes', *args, axis: Optional[Union[int, Iterable[int]]] = None, **kwargs):
+    return process_with_reduced_dimensions(np.all, dwa, *args, axis=axis, **kwargs)
+
+
+@implements('any')
+def _any(dwa: 'DataWithAxes', *args, axis: Optional[Union[int, Iterable[int]]] = None, **kwargs):
+    return process_with_reduced_dimensions(np.any, dwa, *args, axis=axis, **kwargs)
+
+
+@implements('allclose')
+def _allclose(dwa_a: 'DataWithAxes', dwa_b: 'DataWithAxes', *args,
+              **kwargs):
+    if dwa_a.size != dwa_b.size or dwa_a.length != dwa_b.length or dwa_a.shape != dwa_b.shape:
+        raise ValueError("The two DataWithAxes objects doesn't have arrays of same shape, "
+                         "size or length")
+    dwa = data_mod.DataCalculated(
+        f'allclose_{dwa_a.name}_{dwa_b.name}',
+        data=[np.atleast_1d(np.allclose(Q_(dwa_a[ind], dwa_a.units),
+                                        Q_(dwa_b[ind], dwa_b.units),
+                                        *args, **kwargs)) for ind in range(len(dwa_a))])
+
+    return dwa