Merge pull request #18 from mVenetos97/mrsimulator_max

Post Simulation signal processing

.flake8

@@ -1,7 +1,9 @@
 [flake8]
-ignore = E402 C901 E501 E265
+ignore = E402
 exclude = .eggs, *.egg,build, src/mrsimulator/__init__.py
 filename = *.pyx, *py
 max-line-length = 88
-max-complexity = 10
+max-complexity = 12
 select = C,E,F,W,N8
+count = True
+statistics = True

conftest.py

@@ -3,6 +3,8 @@
 
 import matplotlib
 import matplotlib.pyplot as plt
+import mrsimulator.signal_processing as sp
+import mrsimulator.signal_processing.apodization as apo
 import numpy as np
 import pytest
 from mrsimulator import Simulator
@@ -28,6 +30,8 @@ def add_site(doctest_namespace):
     doctest_namespace["st"] = SymmetricTensor
     doctest_namespace["pprint"] = pprint
     doctest_namespace["Isotope"] = Isotope
+    doctest_namespace["sp"] = sp
+    doctest_namespace["apo"] = apo
 
     site1 = Site(
         isotope="13C",

docs/api_py/fitting.rst

@@ -5,5 +5,5 @@ Fitting Utility Functions
 
 .. currentmodule:: mrsimulator.spectral_fitting
 
-.. autofunction:: make_fitting_parameters
-.. autofunction:: min_function
+.. autofunction:: make_LMFIT_parameters
+.. autofunction:: LMFIT_min_function

docs/api_py/operations/operation_documentation.rst

@@ -0,0 +1,15 @@
+
+
+Documentation
+-------------
+
+.. currentmodule:: mrsimulator.signal_processing
+
+.. autoclass:: Scale
+.. autoclass:: IFFT
+.. autoclass:: FFT
+
+.. currentmodule:: mrsimulator.signal_processing.apodization
+
+.. autoclass:: Gaussian
+.. autoclass:: Exponential

docs/api_py/operations/operations_summary.rst

@@ -0,0 +1,49 @@
+.. _operations_api:
+
+Operations
+==========
+
+Generic operations
+------------------
+
+.. currentmodule:: mrsimulator.signal_processing
+
+Import the module as
+
+.. doctest::
+
+    >>> import mrsimulator.signal_processing as sp
+
+.. rubric:: Operation Summary
+
+The following list of operations apply to **all dependent variables** within the
+simulation data object.
+
+.. autosummary::
+    :nosignatures:
+
+      ~Scale
+      ~IFFT
+      ~FFT
+
+Apodization
+-----------
+
+.. currentmodule:: mrsimulator.signal_processing.apodization
+
+Import the module as
+
+.. doctest::
+
+    >>> import mrsimulator.signal_processing.apodization as apo
+
+.. rubric:: Operation Summary
+
+The following list of operations apply to **selected dependent variables** within
+the simulation data object.
+
+.. autosummary::
+    :nosignatures:
+
+      ~Gaussian
+      ~Exponential

docs/api_py/py_api.rst

@@ -15,6 +15,8 @@ Python-API References
    method
    methods
    fitting
+   signal_processing
+   operations/operations_summary
 
 ..    parameterized_tensor
 ..    interaction

docs/api_py/signal_processing.rst

@@ -0,0 +1,15 @@
+.. _signal_processing_api:
+
+Signal Processing
+=================
+
+.. currentmodule:: mrsimulator.signal_processing
+
+.. autoclass:: SignalProcessor
+    :show-inheritance:
+
+    .. rubric:: Method Documentation
+
+    .. automethod:: parse_dict_with_units
+    .. automethod:: to_dict_with_units
+    .. automethod:: apply_operations

docs/api_py/simulator.rst

@@ -20,4 +20,3 @@ Simulator
     .. automethod:: run
     .. automethod:: save
     .. automethod:: load
-    .. automethod:: apodize

docs/index.rst

@@ -152,6 +152,7 @@ Our current objectives for the future are the following
     getting_started
     using_mrsimulator_objects
     configuring_simulator
+    signal_processing
     mrsim_IO
     benchmark
     auto_examples/index

docs/requirements.rst

@@ -15,7 +15,7 @@ Package dependencies
 - `requests>=2.22 <https://pypi.org/project/requests/>`_
 - cython>=0.29.14
 - `matplotlib>=3.1 <https://matplotlib.org>`_ for figures and visualization,
-- `csdmpy>=0.3 <https://csdmpy.readthedocs.io/en/latest/>`_
+- `csdmpy>=0.3.1 <https://csdmpy.readthedocs.io/en/latest/>`_
 - `pydantic>=1.0 <https://pydantic-docs.helpmanual.io>`_
 - monty>=2.0.4