py-neuromodulation 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

py_neuromodulation/utils/types.py

@@ -0,0 +1,251 @@
+from os import PathLike
+from math import isnan
+from typing import Any, Literal, Protocol, TYPE_CHECKING, runtime_checkable
+from pydantic import ConfigDict, Field, model_validator, BaseModel
+from pydantic_core import ValidationError, InitErrorDetails
+from pprint import pformat
+from collections.abc import Sequence
+
+if TYPE_CHECKING:
+    import numpy as np
+    from py_neuromodulation import NMSettings
+
+###################################
+########## TYPE ALIASES  ##########
+###################################
+
+_PathLike = str | PathLike
+
+FeatureName = Literal[
+    "raw_hjorth",
+    "return_raw",
+    "bandpass_filter",
+    "stft",
+    "fft",
+    "welch",
+    "sharpwave_analysis",
+    "fooof",
+    "nolds",
+    "coherence",
+    "bursts",
+    "linelength",
+    "mne_connectivity",
+    "bispectrum",
+]
+
+PreprocessorName = Literal[
+    "preprocessing_filter",
+    "notch_filter",
+    "raw_resampling",
+    "re_referencing",
+    "raw_normalization",
+]
+
+NormMethod = Literal[
+    "mean",
+    "median",
+    "zscore",
+    "zscore-median",
+    "quantile",
+    "power",
+    "robust",
+    "minmax",
+]
+
+###################################
+######## PROTOCOL CLASSES  ########
+###################################
+
+
+@runtime_checkable
+class NMFeature(Protocol):
+    def __init__(
+        self, settings: "NMSettings", ch_names: Sequence[str], sfreq: int | float
+    ) -> None: ...
+
+    def calc_feature(self, data: "np.ndarray") -> dict:
+        """
+        Feature calculation method. Each method needs to loop through all channels
+
+        Parameters
+        ----------
+        data : 'np.ndarray'
+            (channels, time)
+
+        Returns
+        -------
+        dict
+        """
+        ...
+
+
+class NMPreprocessor(Protocol):
+    def __init__(self, sfreq: float, settings: "NMSettings") -> None: ...
+
+    def process(self, data: "np.ndarray") -> "np.ndarray": ...
+
+
+###################################
+######## PYDANTIC CLASSES  ########
+###################################
+
+
+class NMBaseModel(BaseModel):
+    model_config = ConfigDict(validate_assignment=False, extra="allow")
+
+    def __init__(self, *args, **kwargs) -> None:
+        if kwargs:
+            super().__init__(**kwargs)
+        else:
+            field_names = list(self.model_fields.keys())
+            kwargs = {}
+            for i in range(len(args)):
+                kwargs[field_names[i]] = args[i]
+            super().__init__(**kwargs)
+
+    def __str__(self):
+        return pformat(self.model_dump())
+
+    def __repr__(self):
+        return pformat(self.model_dump())
+
+    def validate(self) -> Any:  # type: ignore
+        return self.model_validate(self.model_dump())
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def __setitem__(self, key, value) -> None:
+        setattr(self, key, value)
+
+
+class FrequencyRange(NMBaseModel):
+    frequency_low_hz: float = Field(gt=0)
+    frequency_high_hz: float = Field(gt=0)
+
+    def __init__(self, *args, **kwargs) -> None:
+        super().__init__(*args, **kwargs)
+
+    def __getitem__(self, item: int):
+        match item:
+            case 0:
+                return self.frequency_low_hz
+            case 1:
+                return self.frequency_high_hz
+            case _:
+                raise IndexError(f"Index {item} out of range")
+
+    def as_tuple(self) -> tuple[float, float]:
+        return (self.frequency_low_hz, self.frequency_high_hz)
+
+    def __iter__(self):  # type: ignore
+        return iter(self.as_tuple())
+
+    @model_validator(mode="after")
+    def validate_range(self):
+        if not (isnan(self.frequency_high_hz) or isnan(self.frequency_low_hz)):
+            assert (
+                self.frequency_high_hz > self.frequency_low_hz
+            ), "Frequency high must be greater than frequency low"
+        return self
+
+    @classmethod
+    def create_from(cls, input) -> "FrequencyRange":
+        match input:
+            case FrequencyRange():
+                return input
+            case dict() if "frequency_low_hz" in input and "frequency_high_hz" in input:
+                return FrequencyRange(
+                    input["frequency_low_hz"], input["frequency_high_hz"]
+                )
+            case Sequence() if len(input) == 2:
+                return FrequencyRange(input[0], input[1])
+            case _:
+                raise ValueError("Invalid input for FrequencyRange creation.")
+
+    @model_validator(mode="before")
+    @classmethod
+    def check_input(cls, input):
+        match input:
+            case dict() if "frequency_low_hz" in input and "frequency_high_hz" in input:
+                return input
+            case Sequence() if len(input) == 2:
+                return {"frequency_low_hz": input[0], "frequency_high_hz": input[1]}
+            case _:
+                raise ValueError(
+                    "Value for FrequencyRange must be a dictionary, "
+                    "or a sequence of 2 numeric values, "
+                    f"but got {input} instead."
+                )
+
+
+class BoolSelector(NMBaseModel):
+    def get_enabled(self):
+        return [
+            f
+            for f in self.model_fields.keys()
+            if (isinstance(self[f], bool) and self[f])
+        ]
+
+    def enable_all(self):
+        for f in self.model_fields.keys():
+            if isinstance(self[f], bool):
+                self[f] = True
+
+    def disable_all(self):
+        for f in self.model_fields.keys():
+            if isinstance(self[f], bool):
+                self[f] = False
+
+    def __iter__(self):  # type: ignore
+        return iter(self.model_dump().keys())
+
+    @classmethod
+    def list_all(cls):
+        return list(cls.model_fields.keys())
+
+    @classmethod
+    def print_all(cls):
+        for f in cls.list_all():
+            print(f)
+
+    @classmethod
+    def get_fields(cls):
+        return cls.model_fields
+
+
+def create_validation_error(
+    error_message: str,
+    loc: list[str | int] = None,
+    title: str = "Validation Error",
+    input_type: Literal["python", "json"] = "python",
+    hide_input: bool = False,
+) -> ValidationError:
+    """
+    Factory function to create a Pydantic v2 ValidationError instance from a single error message.
+
+    Args:
+    error_message (str): The error message for the ValidationError.
+    loc (List[str | int], optional): The location of the error. Defaults to None.
+    title (str, optional): The title of the error. Defaults to "Validation Error".
+    input_type (Literal["python", "json"], optional): Whether the error is for a Python object or JSON. Defaults to "python".
+    hide_input (bool, optional): Whether to hide the input value in the error message. Defaults to False.
+
+    Returns:
+    ValidationError: A Pydantic ValidationError instance.
+    """
+    if loc is None:
+        loc = []
+
+    line_errors = [
+        InitErrorDetails(
+            type="value_error", loc=tuple(loc), input=None, ctx={"error": error_message}
+        )
+    ]
+
+    return ValidationError.from_exception_data(
+        title=title,
+        line_errors=line_errors,
+        input_type=input_type,
+        hide_input=hide_input,
+    )

{py_neuromodulation-0.0.4.dist-info → py_neuromodulation-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.4
+Version: 0.0.6
 Summary: Real-time analysis of intracranial neurophysiology recordings.
 Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
 Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
@@ -33,40 +33,48 @@ Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
-Requires-Dist: black>=24.2.0
-Requires-Dist: filterpy>=1.4.5
+Requires-Python: >=3.11
 Requires-Dist: fooof
-Requires-Dist: hatch>=1.9.4
-Requires-Dist: imbalanced-learn
-Requires-Dist: ipython
 Requires-Dist: joblib>=1.3.2
-Requires-Dist: matplotlib>=3.3.4
+Requires-Dist: matplotlib>=3.9.0
 Requires-Dist: mne
 Requires-Dist: mne-bids>=0.8
 Requires-Dist: mne-connectivity
+Requires-Dist: mne-lsl>=1.2.0
 Requires-Dist: mrmr-selection
 Requires-Dist: nolds
-Requires-Dist: notebook
 Requires-Dist: numpy>=1.21.2
-Requires-Dist: pandas>=1.2.2
-Requires-Dist: pip
+Requires-Dist: pandas>=2.0.0
 Requires-Dist: pyarrow>=14.0.2
-Requires-Dist: pybids
-Requires-Dist: pybispectra>=1.0.0
-Requires-Dist: pynput
+Requires-Dist: pybispectra>=1.2.0
+Requires-Dist: pydantic>=2.7.3
 Requires-Dist: pyparrm
-Requires-Dist: pytest>=8.0.2
-Requires-Dist: scikit-image
+Requires-Dist: pyqt5
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: scikit-optimize
 Requires-Dist: scipy>=1.7.1
 Requires-Dist: seaborn>=0.11
-Requires-Dist: wget
 Provides-Extra: dev
-Requires-Dist: black; extra == 'dev'
-Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: notebook; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest-sugar; extra == 'dev'
+Requires-Dist: pytest>=8.0.2; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: notebook; extra == 'docs'
+Requires-Dist: numpydoc; extra == 'docs'
+Requires-Dist: pydata-sphinx-theme; extra == 'docs'
+Requires-Dist: pytest-cov; extra == 'docs'
+Requires-Dist: pytest-sugar; extra == 'docs'
+Requires-Dist: pytest>=8.0.2; extra == 'docs'
+Requires-Dist: recommonmark; extra == 'docs'
+Requires-Dist: ruff; extra == 'docs'
+Requires-Dist: sphinx; extra == 'docs'
+Requires-Dist: sphinx-gallery; extra == 'docs'
+Requires-Dist: sphinx-togglebutton; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: pytest-xdist; extra == 'test'
+Requires-Dist: pytest>=8.0.2; extra == 'test'
 Description-Content-Type: text/x-rst
 
 py_neuromodulation
@@ -111,23 +119,10 @@ py_neuromodulation requires at least python 3.10. For installation you can use p
 
     pip install py-neuromodulation
 
-
-We recommend however installing the package using `rye <https://rye-up.com/guide/installation/>`_:
-
-.. code-block::
-
-    git clone https://github.com/neuromodulation/py_neuromodulation.git
-    rye pin 3.11
-    rye sync
-
-And then activating the virtual environment e.g. in Windows using:
+Alternatively you can also install the package in a conda environment:
 
 .. code-block::
 
-    .\.venv\Scripts\activate
-
-Alternatively you can also install the package in a conda environment:
-
     conda create -n pynm-test python=3.11
     conda activate pynm-test
 

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@@ -0,0 +1,89 @@
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+py_neuromodulation/processing/resample.py,sha256=YwgGq900kGHhg1avmn-ju9M0mx9FvXQ06qj5-Ztv9Qk,1230
+py_neuromodulation/stream/__init__.py,sha256=R4Fm4ApFdnbG9x13fQm1uhslVf3P0mdtnexzDohEWF0,124
+py_neuromodulation/stream/data_processor.py,sha256=lODMA3DFxBfJPm4AeMLG6-e71pxj_6_EqevMrQmUSYY,11107
+py_neuromodulation/stream/generator.py,sha256=UKLuM8gz2YLBuVQnQNkkOOKhwsyW27ZgvRJ_5BK7Glo,1588
+py_neuromodulation/stream/mnelsl_player.py,sha256=e8l5ufEeCBljjl-oogi43TOmP7s_xQeVdpCREvtfWvk,2992
+py_neuromodulation/stream/mnelsl_stream.py,sha256=hsqkgo0mEzvP40M3vps4Ma7BX6R3wXx07TQpPSjnmUw,4603
+py_neuromodulation/stream/settings.py,sha256=19tRmjHDkkmgzdocBIa9tb-LyMPFlcoopuU7zsvrWZQ,10072
+py_neuromodulation/stream/stream.py,sha256=cstSVfmfJwReocAI88Pf-4VKMY0Qv53eJ1JyZMFe5zI,15599
+py_neuromodulation/utils/__init__.py,sha256=Ok3STMpsflCTclJC9C1iQgdT-3HNGMM7U45w5Oespr4,46
+py_neuromodulation/utils/channels.py,sha256=Y8hrJxEY_2MJEBlicRkJk04XsBUXEZ2NYYb1toEaDek,10632
+py_neuromodulation/utils/database.py,sha256=VEFsmbYDQWwaoZKmJCG8oyWoDTbfSiT_p0n7da9_Pn4,4755
+py_neuromodulation/utils/io.py,sha256=-qAwtFSsumfzY6dkYSKGySE8_RH1c2M1NDxC_ZQrUVM,10387
+py_neuromodulation/utils/keyboard.py,sha256=swoxYhf4Q3pj50EKALUFt6hREfXnoXq2Z2q01IahPe8,1505
+py_neuromodulation/utils/logging.py,sha256=eIBFBRaAMb3KJnoxNFiCkMrTGzWwgfeDs8m5iq6FxN8,2178
+py_neuromodulation/utils/types.py,sha256=QVq3wAgMcw5zKPa_Kj2QQ2Gt2CYavO_PAka3RAZdfwo,7310
+py_neuromodulation-0.0.6.dist-info/METADATA,sha256=UcYGczR0VlQ_98AKZe6J-x8Ml-wiie9d7Th7paCeziY,7216
+py_neuromodulation-0.0.6.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+py_neuromodulation-0.0.6.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
+py_neuromodulation-0.0.6.dist-info/RECORD,,

{py_neuromodulation-0.0.4.dist-info → py_neuromodulation-0.0.6.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.24.1
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

{py_neuromodulation-0.0.4.dist-info → py_neuromodulation-0.0.6.dist-info}/licenses/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.