py-neuromodulation 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

py_neuromodulation/{nm_IO.py → utils/io.py}

@@ -3,34 +3,32 @@ from pathlib import PurePath, Path
 from typing import TYPE_CHECKING
 
 import numpy as np
-import pandas as pd
 
-from py_neuromodulation.nm_types import _PathLike
+from py_neuromodulation.utils.types import _PathLike
 from py_neuromodulation import logger, PYNM_DIR
 
 if TYPE_CHECKING:
     from mne_bids import BIDSPath
     from mne import io as mne_io
+    import pandas as pd
 
 
-def load_nm_channels(
-    nm_channels: pd.DataFrame | _PathLike,
+def load_channels(
+    channels: "pd.DataFrame | _PathLike",
 ) -> "pd.DataFrame":
-    """Read nm_channels from path or specify via BIDS arguments.
+    """Read channels from path or specify via BIDS arguments.
     Necessary parameters are then ch_names (list), ch_types (list), bads (list), used_types (list),
     target_keywords (list) and reference Union[list, str].
     """
+    import pandas as pd
 
-    if isinstance(nm_channels, pd.DataFrame):
-        nm_ch_return = nm_channels
-    elif nm_channels:
-        if not Path(nm_channels).is_file():
-            raise ValueError(
-                "PATH_NM_CHANNELS is not a valid file. Got: " f"{nm_channels}"
-            )
-        nm_ch_return = pd.read_csv(nm_channels)
+    if isinstance(channels, pd.DataFrame):
+        return channels
 
-    return nm_ch_return
+    if not Path(channels).is_file():
+        raise ValueError("PATH_CHANNELS is not a valid file. Got: " f"{channels}")
+
+    return pd.read_csv(channels)
 
 
 def read_BIDS_data(
@@ -150,7 +148,7 @@ def get_coord_list(
     return coord_list, coord_names
 
 
-def read_grid(PATH_GRIDS: _PathLike | None, grid_str: str) -> pd.DataFrame:
+def read_grid(PATH_GRIDS: _PathLike | None, grid_str: str) -> "pd.DataFrame":
     """Read grid file from path or PYNM_DIR
 
     Parameters
@@ -165,6 +163,8 @@ def read_grid(PATH_GRIDS: _PathLike | None, grid_str: str) -> pd.DataFrame:
     pd.DataFrame
         pd.DataFrame including mni x,y,z coordinates for each grid point
     """
+    import pandas as pd
+
     if PATH_GRIDS is None:
         grid = pd.read_csv(PYNM_DIR / ("grid_" + grid_str.lower() + ".tsv"), sep="\t")
     else:
@@ -190,46 +190,6 @@ def get_annotations(PATH_ANNOTATIONS: str, PATH_RUN: str, raw_arr: "mne_io.RawAr
     return annot, annot_data, raw_arr
 
 
-def read_plot_modules(
-    PATH_PLOT: _PathLike = PYNM_DIR / "plots",
-):
-    """Read required .mat files for plotting
-
-    Parameters
-    ----------
-    PATH_PLOT : regexp, optional
-        path to plotting files, by default
-    """
-
-    faces = loadmat(PurePath(PATH_PLOT, "faces.mat"))
-    vertices = loadmat(PurePath(PATH_PLOT, "Vertices.mat"))
-    grid = loadmat(PurePath(PATH_PLOT, "grid.mat"))["grid"]
-    stn_surf = loadmat(PurePath(PATH_PLOT, "STN_surf.mat"))
-    x_ver = stn_surf["vertices"][::2, 0]
-    y_ver = stn_surf["vertices"][::2, 1]
-    x_ecog = vertices["Vertices"][::1, 0]
-    y_ecog = vertices["Vertices"][::1, 1]
-    z_ecog = vertices["Vertices"][::1, 2]
-    x_stn = stn_surf["vertices"][::1, 0]
-    y_stn = stn_surf["vertices"][::1, 1]
-    z_stn = stn_surf["vertices"][::1, 2]
-
-    return (
-        faces,
-        vertices,
-        grid,
-        stn_surf,
-        x_ver,
-        y_ver,
-        x_ecog,
-        y_ecog,
-        z_ecog,
-        x_stn,
-        y_stn,
-        z_stn,
-    )
-
-
 def write_csv(df, path_out):
     """
     Function to save Pandas dataframes to disk as CSV using
@@ -242,31 +202,31 @@ def write_csv(df, path_out):
     csv.write_csv(Table.from_pandas(df), path_out)
 
 
-def save_nm_channels(
-    nmchannels: pd.DataFrame,
-    out_dir: _PathLike,
+def save_channels(
+    nmchannels: "pd.DataFrame",
+    out_dir: _PathLike = "",
     prefix: str = "",
 ) -> None:
-    filename = f"{prefix}_nm_channels.csv" if prefix else "nm_channels.csv"
-    path_out = PurePath(out_dir, filename)
-    write_csv(nmchannels, path_out)
-    logger.info(f"nm_channels.csv saved to {path_out}")
+    out_dir = Path.cwd() if not out_dir else Path(out_dir)
+    filename = "channels.csv" if not prefix else prefix + "_channels.csv"
+    write_csv(nmchannels, out_dir / filename)
+    logger.info(f"{filename} saved to {out_dir}")
 
 
 def save_features(
-    df_features: pd.DataFrame,
-    out_dir: _PathLike,
+    df_features: "pd.DataFrame",
+    out_dir: _PathLike = "",
     prefix: str = "",
 ) -> None:
+    out_dir = Path.cwd() if not out_dir else Path(out_dir)
     filename = f"{prefix}_FEATURES.csv" if prefix else "_FEATURES.csv"
-    out_dir = PurePath(out_dir, filename)
-    write_csv(df_features, out_dir)
-    logger.info(f"FEATURES.csv saved to {str(out_dir)}")
+    write_csv(df_features, out_dir / filename)
+    logger.info(f"{filename} saved to {str(out_dir)}")
 
 
 def save_sidecar(
     sidecar: dict,
-    out_dir: _PathLike,
+    out_dir: _PathLike = "",
     prefix: str = "",
 ) -> None:
     save_general_dict(sidecar, out_dir, prefix, "_SIDECAR.json")
@@ -274,15 +234,14 @@ def save_sidecar(
 
 def save_general_dict(
     dict_: dict,
-    out_dir: _PathLike,
+    out_dir: _PathLike = "",
     prefix: str = "",
     str_add: str = "",
 ) -> None:
-    # We should change this to a proper experiment name
+    out_dir = Path.cwd() if not out_dir else Path(out_dir)
+    filename = f"{prefix}{str_add}"
 
-    path_out = PurePath(out_dir, f"{prefix}{str_add}")
-
-    with open(path_out, "w") as f:
+    with open(out_dir / filename, "w") as f:
         json.dump(
             dict_,
             f,
@@ -290,10 +249,12 @@ def save_general_dict(
             indent=4,
             separators=(",", ": "),
         )
-    logger.info(f"{str_add} saved to {path_out}")
+    logger.info(f"{filename} saved to {out_dir}")
 
 
 def default_json_convert(obj) -> list | float:
+    import pandas as pd
+
     if isinstance(obj, np.ndarray):
         return obj.tolist()
     if isinstance(obj, pd.DataFrame):
@@ -310,12 +271,16 @@ def read_sidecar(PATH: _PathLike) -> dict:
         return json.load(f)
 
 
-def read_features(PATH: _PathLike) -> pd.DataFrame:
+def read_features(PATH: _PathLike) -> "pd.DataFrame":
+    import pandas as pd
+
     return pd.read_csv(str(PATH) + "_FEATURES.csv", engine="pyarrow")
 
 
-def read_nm_channels(PATH: _PathLike) -> pd.DataFrame:
-    return pd.read_csv(str(PATH) + "_nm_channels.csv")
+def read_channels(PATH: _PathLike) -> "pd.DataFrame":
+    import pandas as pd
+
+    return pd.read_csv(str(PATH) + "_channels.csv")
 
 
 def get_run_list_indir(PATH: _PathLike) -> list:

py_neuromodulation/utils/keyboard.py

@@ -0,0 +1,52 @@
+import asyncio
+import sys
+from typing import Callable
+
+if sys.platform.startswith("win"):
+    import msvcrt
+else:
+    import termios
+    import tty
+
+
+class KeyboardListener:
+    def __init__(self, event_callback: tuple[str, Callable] | None = None):
+        self.callbacks = {}
+        self.running = False
+
+        if event_callback is not None:
+            self.on_press(*event_callback)
+
+    def on_press(self, key, callback):
+        self.callbacks[key] = callback
+
+    async def _windows_listener(self):
+        while self.running:
+            if msvcrt.kbhit():
+                key = msvcrt.getch().decode("utf-8").lower()
+                if key in self.callbacks:
+                    await self.callbacks[key]()
+            await asyncio.sleep(0.01)
+
+    async def _unix_listener(self):
+        fd = sys.stdin.fileno()
+        old_settings = termios.tcgetattr(fd)
+        try:
+            tty.setraw(fd)
+            while self.running:
+                key = sys.stdin.read(1).lower()
+                if key in self.callbacks:
+                    await self.callbacks[key]()
+                await asyncio.sleep(0.01)
+        finally:
+            termios.tcsetattr(fd, termios.TCSADRAIN, old_settings)
+
+    async def start(self):
+        self.running = True
+        if sys.platform.startswith("win"):
+            await self._windows_listener()
+        else:
+            await self._unix_listener()
+
+    def stop(self):
+        self.running = False

py_neuromodulation/{nm_logger.py → utils/logging.py}

@@ -1,5 +1,5 @@
 from pathlib import Path
-from py_neuromodulation.nm_types import _PathLike
+from py_neuromodulation.utils.types import _PathLike
 import logging
 
 INFOFORMAT = "%(name)s:\t%(message)s"
@@ -52,12 +52,12 @@ class NMLogger(logging.Logger):
         path = Path(path)
         path.mkdir(parents=True, exist_ok=True)
 
-        self.debug_file_handler = logging.FileHandler(path / "logfile_pynm_debug.log")
+        self.debug_file_handler = logging.FileHandler(path / "logfile_pydebug.log")
         self.debug_file_handler.setLevel(logging.DEBUG)
         self.debug_file_handler.setFormatter(logging.Formatter(DEBUGFORMAT))
 
         self.info_file_handler = logging.FileHandler(
-            path / "logfile_pynm_info.log", mode=mode
+            path / "logfile_pyinfo.log", mode=mode
         )
         self.info_file_handler.setLevel(logging.INFO)
         self.info_file_handler.setFormatter(logging.Formatter(INFOFORMAT))

py_neuromodulation/{nm_types.py → utils/types.py}

@@ -1,11 +1,15 @@
 from os import PathLike
 from math import isnan
-from typing import NamedTuple, Type, Any, Literal
-from importlib import import_module
+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  ##########
 ###################################
@@ -48,20 +52,37 @@ NormMethod = Literal[
     "minmax",
 ]
 
-
 ###################################
-###### LAZY MODULE IMPORTS  #######
+######## PROTOCOL CLASSES  ########
 ###################################
-class ImportDetails(NamedTuple):
-    module_name: str
-    class_name: str
 
 
-def get_class(module_details: ImportDetails) -> Type[Any]:
-    return getattr(
-        import_module("py_neuromodulation." + module_details.module_name),
-        module_details.class_name,
-    )
+@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": ...
 
 
 ###################################
@@ -99,8 +120,8 @@ class NMBaseModel(BaseModel):
 
 
 class FrequencyRange(NMBaseModel):
-    frequency_low_hz: float = Field(default=0, gt=0)
-    frequency_high_hz: float = Field(default=0, gt=0)
+    frequency_low_hz: float = Field(gt=0)
+    frequency_high_hz: float = Field(gt=0)
 
     def __init__(self, *args, **kwargs) -> None:
         super().__init__(*args, **kwargs)
@@ -191,3 +212,40 @@ class BoolSelector(NMBaseModel):
     @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-0.0.5.dist-info → py_neuromodulation-0.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.5
+Version: 0.0.7
 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
@@ -33,35 +33,28 @@ 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: filterpy>=1.4.5
+Requires-Python: >=3.11
 Requires-Dist: fooof
-Requires-Dist: hatch>=1.9.4
-Requires-Dist: imbalanced-learn
 Requires-Dist: joblib>=1.3.2
+Requires-Dist: llvmlite>=0.43.0
 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: nibabel>=5.2.1
-Requires-Dist: nolds
+Requires-Dist: nolds>=0.6.1
+Requires-Dist: numba>=0.60.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pandas>=2.0.0
-Requires-Dist: pip>=24.2
 Requires-Dist: pyarrow>=14.0.2
-Requires-Dist: pybispectra>=1.0.0
+Requires-Dist: pybispectra>=1.2.0
 Requires-Dist: pydantic>=2.7.3
-Requires-Dist: pynput
 Requires-Dist: pyparrm
-Requires-Dist: pyqt5
-Requires-Dist: scikit-image
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: scikit-optimize
 Requires-Dist: scipy>=1.7.1
 Requires-Dist: seaborn>=0.11
-Requires-Dist: statsmodels
 Provides-Extra: dev
 Requires-Dist: notebook; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
@@ -116,7 +109,7 @@ The original intention for writing this toolbox was movement decoding from invas
 The application however could be any neural decoding problem.
 *py_neuromodulation* offers wrappers around common practice machine learning methods for efficient analysis.
 
-Find the documentation here http://py-neuromodulation.readthedocs.io for example usage and parametrization.
+Find the documentation here neuromodulation.github.io/py_neuromodulation/ for example usage and parametrization.
 
 Installation
 ============
@@ -127,25 +120,15 @@ py_neuromodulation requires at least python 3.10. For installation you can use p
 
     pip install py-neuromodulation
 
-Alternatively you can also install the package in a conda environment:
+Alternatively you can also clone the pacakge and install it using `uv <https://docs.astral.sh/uv/>`_:
 
 .. code-block::
 
-    conda create -n pynm-test python=3.11
-    conda activate pynm-test
+    uv python install 3.10
+    uv venv
+    . .venv/bin/activate
+    uv sync
 
-Then install the packages listed in the `pyproject.toml`:
-
-.. code-block::
-
-    pip install .
-
-
-Optionally the ipython kernel can be specified for the installed pynm-test conda environment:
-
-.. code-block::
-
-    ipython kernel install --user --name=pynm-test
 
 Then *py_neuromodulation* can be imported via:
 

py_neuromodulation-0.0.7.dist-info/RECORD

@@ -0,0 +1,89 @@
+py_neuromodulation/__init__.py,sha256=MaOF7mCNRjR9MgcCnk9b7dYJICVJthiWlZVf365lXOo,2831
+py_neuromodulation/default_settings.yaml,sha256=06KzRz8eLAa5--gmrYsr_bn9UOzSMIpuktrPKNaSc4A,5568
+py_neuromodulation/grid_cortex.tsv,sha256=k2QOkHY1ej3lJ33LD6DOPVlTynzB3s4BYaoQaoUCyYc,643
+py_neuromodulation/grid_subcortex.tsv,sha256=oCQDYLDdYSa1DAI9ybwECfuzWulFzXqKHyf7oZ1oDBM,25842
+py_neuromodulation/ConnectivityDecoding/Automated Anatomical Labeling 3 (Rolls 2020).nii,sha256=Sp-cjF_AuT0Tlilb5s8lB14hVgkXJiR2uKMS9nOQOeg,902981
+py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m,sha256=2RPDGotbLsCzDJLFB2JXatJtfOMno9UUBCBnsOuse8A,714
+py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py,sha256=VsInAIADIf9d3unxUSN0B50aU472IQocGZ-kyG8A7Fc,3066
+py_neuromodulation/ConnectivityDecoding/_helper_write_connectome.py,sha256=1DNrccrJqrH5PIW2yp24xbyqRrsRz98Gof5aPQZUUUE,3423
+py_neuromodulation/ConnectivityDecoding/mni_coords_cortical_surface.mat,sha256=AZc0mgiAiqXVAxAnfxwICeh-dQX62RfTeRN_knS-i60,11622
+py_neuromodulation/ConnectivityDecoding/mni_coords_whole_brain.mat,sha256=YxT9nrXZ2IECheEhN1SgSsqNyihHUTLuZQ7o5yP4Q-c,29864
+py_neuromodulation/ConnectivityDecoding/rmap_func_all.nii,sha256=WjVA02B2cGNi670_45fdNssspf8GKbkKgRStZ2d4_FU,7221384
+py_neuromodulation/ConnectivityDecoding/rmap_struc.nii,sha256=XsEMjsCxjAsMFvw1_jpQ-wIU2BUuZ_lISPwMa7zDmDk,7221384
+py_neuromodulation/analysis/RMAP.py,sha256=e5qTZ680NkLZbI0cpVpsIqDy7OEhsoabedv5pVq6bG0,15001
+py_neuromodulation/analysis/__init__.py,sha256=x9lKfCnOaawYdil39CWszpDNNtXFckF__RxbE0HnwKA,116
+py_neuromodulation/analysis/decode.py,sha256=eK-jfrHmfthVQbpYCM8E2DbYOUD-AyLSSumXrrXt67E,33167
+py_neuromodulation/analysis/feature_reader.py,sha256=Nyb2OLLX-jCVrFy_CI0FWzd7mCeqUG-MdHT4gj3bR3Y,35596
+py_neuromodulation/analysis/plots.py,sha256=B625WZaLOm4Z6oQ5nrqnM77WaU9C1Ezn8UGggHAfIF8,17728
+py_neuromodulation/analysis/stats.py,sha256=ZZIXTGh6r9gfiJV1RwZpLzDgqyia9mIDt8yNEN8cSw8,15094
+py_neuromodulation/data/README,sha256=8PhEkUm8F2NgL7A5co1CgfumAMB14v5XPIbk54SvtAE,708
+py_neuromodulation/data/dataset_description.json,sha256=HMHtmF0bbw9XO79GAyRt8urpEyxRJ5A1REcYos8D2s0,122
+py_neuromodulation/data/participants.json,sha256=S4rrcSAmLcL_jLk9IY_cwJBipl8OwwCvouZ7tsgdldw,756
+py_neuromodulation/data/participants.tsv,sha256=-dg_i5N4I-Cp1l21433z1lDjXUmcuTn8S3UqkxPvgdI,77
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/sub-testsub_ses-EphysMedOff_scans.tsv,sha256=iz6Nvf_E5jChjacmO_eAxX7Y8rR8v03-gGdUeBlyDVY,89
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_coordsystem.json,sha256=dq0Vc2fIR-YvbCEqBb7lq3P_YkOOzkKe1Hh-a1gd46E,118
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_electrodes.tsv,sha256=Kr9vKh1qnnwFQE0Cet7PkeVuuGx1u-CT_xXs4qucezg,722
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_channels.tsv,sha256=ZSixrfpSlNEfmv0diaJ96usFPwPtO_dA6CCDYDp85KY,779
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg,sha256=NnQeMDrKpeK3lctIZ5Bzh85UMTs5OCUCaivn_NU5rc4,760040
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.json,sha256=nRPEWAa0isyDKbeW1IPhL9ECWkzqfQw1sKwJkZU3vbk,474
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr,sha256=-QEHwQjJb9Hp9yudEawqhQl8vrD8bYqiuvlF4cyPNg0,988
+py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk,sha256=BD-VmcKe7dR0vGzzkv4c09QnSwc3zYeAWDGJIzWEOI0,540
+py_neuromodulation/features/__init__.py,sha256=zpulQ3IaKh6yNSnCBIRa5IC3SZ7FlKNQxHLF50yTdQU,1567
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