py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

docs/source/_build/html/_downloads/3b4900a2b2818ff30362215b76f7d5eb/plot_1_example_BIDS.py

@@ -1,240 +0,0 @@
-"""
-ECoG Movement decoding example 
-==============================
-
-"""
-
-# %%
-# This example notebook read openly accessible data from the publication
-# *Electrocorticography is superior to subthalamic local field potentials
-# for movement decoding in Parkinson’s disease*
-# (`Merk et al. 2022 <https://elifesciences.org/articles/75126>_`).
-# The dataset is available `here <https://doi.org/10.7910/DVN/IO2FLM>`_.
-#
-# For simplicity one example subject is automatically shipped within
-# this repo at the *py_neuromodulation/data* folder, stored in
-# `iEEG BIDS <https://www.nature.com/articles/s41597-019-0105-7>`_ format.
-
-# %%
-from sklearn import metrics, model_selection, linear_model
-import matplotlib.pyplot as plt
-
-import py_neuromodulation as nm
-from py_neuromodulation import (
-    nm_analysis,
-    nm_decode,
-    nm_define_nmchannels,
-    nm_IO,
-    nm_plots,
-    nm_settings,
-)
-
-# %%
-# Let's read the example using `mne_bids <https://mne.tools/mne-bids/stable/index.html>`_.
-# The resulting raw object is of type `mne.RawArray <https://mne.tools/stable/generated/mne.io.RawArray.html>`_.
-# We can use the properties such as sampling frequency, channel names, channel types all from the mne array and create the *nm_channels* DataFrame:
-
-(
-    RUN_NAME,
-    PATH_RUN,
-    PATH_BIDS,
-    PATH_OUT,
-    datatype,
-) = nm_IO.get_paths_example_data()
-
-(
-    raw,
-    data,
-    sfreq,
-    line_noise,
-    coord_list,
-    coord_names,
-) = nm_IO.read_BIDS_data(
-    PATH_RUN=PATH_RUN, BIDS_PATH=PATH_BIDS, datatype=datatype
-)
-
-nm_channels = nm_define_nmchannels.set_channels(
-    ch_names=raw.ch_names,
-    ch_types=raw.get_channel_types(),
-    reference="default",
-    bads=raw.info["bads"],
-    new_names="default",
-    used_types=("ecog", "dbs", "seeg"),
-    target_keywords=["MOV_RIGHT"],
-)
-
-nm_channels
-
-# %%
-# This example contains the grip force movement traces, we'll use the *MOV_RIGHT* channel as a decoding target channel.
-# Let's check some of the raw feature and time series traces:
-
-plt.figure(figsize=(12, 4), dpi=300)
-plt.subplot(121)
-plt.plot(raw.times, data[-1, :])
-plt.xlabel("Time [s]")
-plt.ylabel("a.u.")
-plt.title("Movement label")
-plt.xlim(0, 20)
-
-plt.subplot(122)
-for idx, ch_name in enumerate(nm_channels.query("used == 1").name):
-    plt.plot(raw.times, data[idx, :] + idx * 300, label=ch_name)
-plt.legend(bbox_to_anchor=(1, 0.5), loc="center left")
-plt.title("ECoG + STN-LFP time series")
-plt.xlabel("Time [s]")
-plt.ylabel("Voltage a.u.")
-plt.xlim(0, 20)
-
-# %%
-settings = nm_settings.get_default_settings()
-settings = nm_settings.set_settings_fast_compute(settings)
-
-settings["features"]["welch"] = True
-settings["features"]["fft"] = True
-settings["features"]["bursts"] = True
-settings["features"]["sharpwave_analysis"] = True
-settings["features"]["coherence"] = True
-settings["coherence"]["channels"] = [["LFP_RIGHT_0", "ECOG_RIGHT_0"]]
-settings["coherence"]["frequency_bands"] = ["high beta", "low gamma"]
-settings["sharpwave_analysis_settings"]["estimator"]["mean"] = []
-for sw_feature in list(
-    settings["sharpwave_analysis_settings"]["sharpwave_features"].keys()
-):
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        sw_feature
-    ] = True
-    settings["sharpwave_analysis_settings"]["estimator"]["mean"].append(
-        sw_feature
-    )
-
-# %%
-stream = nm.Stream(
-    sfreq=sfreq,
-    nm_channels=nm_channels,
-    settings=settings,
-    line_noise=line_noise,
-    coord_list=coord_list,
-    coord_names=coord_names,
-    verbose=True,
-)
-
-# %%
-features = stream.run(
-    data=data,
-    out_path_root=PATH_OUT,
-    folder_name=RUN_NAME,
-)
-
-# %%
-# Feature Analysis Movement
-# -------------------------
-# The obtained performances can now be read and visualized using the :class:`nm_analysis.Feature_Reader`.
-
-# initialize analyzer
-feature_reader = nm_analysis.Feature_Reader(
-    feature_dir=PATH_OUT,
-    feature_file=RUN_NAME,
-)
-feature_reader.label_name = "MOV_RIGHT"
-feature_reader.label = feature_reader.feature_arr["MOV_RIGHT"]
-
-# %%
-feature_reader.feature_arr.iloc[100:108, -6:]
-
-# %%
-print(feature_reader.feature_arr.shape)
-
-# %%
-feature_reader._get_target_ch()
-
-# %%
-feature_reader.plot_target_averaged_channel(
-    ch="ECOG_RIGHT_0",
-    list_feature_keywords=None,
-    epoch_len=4,
-    threshold=0.5,
-    ytick_labelsize=7,
-    figsize_x=12,
-    figsize_y=12,
-)
-
-# %%
-feature_reader.plot_all_features(
-    ytick_labelsize=6,
-    clim_low=-2,
-    clim_high=2,
-    ch_used="ECOG_RIGHT_0",
-    time_limit_low_s=0,
-    time_limit_high_s=20,
-    normalize=True,
-    save=True,
-)
-
-# %%
-nm_plots.plot_corr_matrix(
-    feature=feature_reader.feature_arr.filter(regex="ECOG_RIGHT_0"),
-    ch_name="ECOG_RIGHT_0-avgref",
-    feature_names=feature_reader.feature_arr.filter(
-        regex="ECOG_RIGHT_0-avgref"
-    ).columns,
-    feature_file=feature_reader.feature_file,
-    show_plot=True,
-    figsize=(15, 15),
-)
-
-# %%
-# Decoding
-# --------
-#
-# The main focus of the *py_neuromodulation* pipeline is feature estimation.
-# Nevertheless, the user can also use the pipeline for machine learning decoding.
-# It can be used for regression and classification problems and also dimensionality reduction such as PCA and CCA.
-#
-# Here, we show an example using the XGBOOST classifier. The used labels came from a continuous grip force movement target, named "MOV_RIGHT".
-#
-# First we initialize the :class:`~nm_decode.Decoder` class, which the specified *validation method*, here being a simple 3-fold cross validation,
-# the evaluation metric, used machine learning model, and the channels we want to evaluate performances for.
-#
-# There are many more implemented methods, but we will here limit it to the ones presented.
-
-model = linear_model.LinearRegression()
-
-feature_reader.decoder = nm_decode.Decoder(
-    features=feature_reader.feature_arr,
-    label=feature_reader.label,
-    label_name=feature_reader.label_name,
-    used_chs=feature_reader.used_chs,
-    model=model,
-    eval_method=metrics.r2_score,
-    cv_method=model_selection.KFold(n_splits=3, shuffle=True),
-)
-
-# %%
-performances = feature_reader.run_ML_model(
-    estimate_channels=True,
-    estimate_gridpoints=False,
-    estimate_all_channels_combined=True,
-    save_results=True,
-)
-
-# %%
-# The performances are a dictionary that can be transformed into a DataFrame:
-
-df_per = feature_reader.get_dataframe_performances(performances)
-
-df_per
-
-# %%
-ax = nm_plots.plot_df_subjects(
-    df_per,
-    x_col="sub",
-    y_col="performance_test",
-    hue="ch_type",
-    PATH_SAVE=PATH_OUT / RUN_NAME / (RUN_NAME + "_decoding_performance.png"),
-    figsize_tuple=(8, 5),
-)
-ax.set_ylabel(r"$R^2$ Correlation")
-ax.set_xlabel("Subject 000")
-ax.set_title("Performance comparison Movement decoding")
-plt.tight_layout()

docs/source/_build/html/_downloads/5d73cadc59a8805c47e3b84063afc157/plot_example_BIDS.py

@@ -1,233 +0,0 @@
-"""
-ECoG Movement decoding example 
-==============================
-
-"""
-
-# %%
-# This example notebook read openly accessible data from the publication
-# *Electrocorticography is superior to subthalamic local field potentials
-# for movement decoding in Parkinson’s disease*
-# (`Merk et al. 2022 <https://elifesciences.org/articles/75126>_`).
-# The dataset is available `here <https://doi.org/10.7910/DVN/IO2FLM>`_.
-#
-# For simplicity one example subject is automatically shipped within
-# this repo at the *py_neuromodulation/data* folder, stored in
-# `iEEG BIDS <https://www.nature.com/articles/s41597-019-0105-7>`_ format.
-
-# %%
-from sklearn import metrics, model_selection, linear_model
-import matplotlib.pyplot as plt
-
-import py_neuromodulation as nm
-from py_neuromodulation import (
-    nm_analysis,
-    nm_decode,
-    nm_define_nmchannels,
-    nm_IO,
-    nm_plots,
-    nm_settings,
-)
-
-# %%
-# Let's read the example using `mne_bids <https://mne.tools/mne-bids/stable/index.html>`_.
-# The resulting raw object is of type `mne.RawArray <https://mne.tools/stable/generated/mne.io.RawArray.html>`_.
-# We can use the properties such as sampling frequency, channel names, channel types all from the mne array and create the *nm_channels* DataFrame:
-
-RUN_NAME, PATH_RUN, PATH_BIDS, PATH_OUT, datatype = nm_IO.get_paths_example_data()
-
-(
-    raw,
-    data,
-    sfreq,
-    line_noise,
-    coord_list,
-    coord_names,
-) = nm_IO.read_BIDS_data(
-    PATH_RUN=PATH_RUN, BIDS_PATH=PATH_BIDS, datatype=datatype
-)
-
-nm_channels = nm_define_nmchannels.set_channels(
-    ch_names=raw.ch_names,
-    ch_types=raw.get_channel_types(),
-    reference="default",
-    bads=raw.info["bads"],
-    new_names="default",
-    used_types=("ecog", "dbs", "seeg"),
-    target_keywords=["MOV_RIGHT"],
-)
-
-nm_channels
-
-# %%
-# This example contains the grip force movement traces, we'll use the *MOV_RIGHT_CLEAN* channel as a decoding target channel.
-# Let's check some of the raw feature and time series traces:
-
-plt.figure(figsize=(12, 4), dpi=300)
-plt.subplot(121)
-plt.plot(raw.times, data[-1, :])
-plt.xlabel("Time [s]")
-plt.ylabel("a.u.")
-plt.title("Movement label")
-plt.xlim(0, 20)
-
-plt.subplot(122)
-for idx, ch_name in enumerate(nm_channels.query("used == 1").name):
-    plt.plot(raw.times, data[idx, :] + idx * 300, label=ch_name)
-plt.legend(bbox_to_anchor=(1, 0.5), loc="center left")
-plt.title("ECoG + STN-LFP time series")
-plt.xlabel("Time [s]")
-plt.ylabel("Voltage a.u.")
-plt.xlim(0, 20)
-
-# %%
-settings = nm_settings.get_default_settings()
-settings = nm_settings.set_settings_fast_compute(settings)
-
-settings["features"]["fft"] = True
-settings["features"]["bursts"] = False
-settings["features"]["sharpwave_analysis"] = False
-settings["features"]["coherence"] = False # True
-settings["coherence"]["channels"] = [["LFP_RIGHT_0", "ECOG_RIGHT_0"]]
-settings["coherence"]["frequency_bands"] = ["high beta", "low gamma"]
-settings["sharpwave_analysis_settings"]["estimator"]["mean"] = []
-for sw_feature in list(
-    settings["sharpwave_analysis_settings"]["sharpwave_features"].keys()
-):
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        sw_feature
-    ] = True
-    settings["sharpwave_analysis_settings"]["estimator"]["mean"].append(
-        sw_feature
-    )
-
-# %%
-stream = nm.Stream(
-    sfreq=sfreq,
-    nm_channels=nm_channels,
-    settings=settings,
-    line_noise=line_noise,
-    coord_list=coord_list,
-    coord_names=coord_names,
-    verbose=True,
-)
-
-# %%
-features = stream.run(
-    data=data,
-    out_path_root=PATH_OUT,
-    folder_name=RUN_NAME,
-)
-
-# %%
-# Feature Analysis
-# ----------------
-# The obtained performances can now be read and visualized using the :class:`nm_analysis.Feature_Reader`.
-
-# initialize analyzer
-feature_reader = nm_analysis.Feature_Reader(
-    feature_dir=PATH_OUT,
-    feature_file=RUN_NAME,
-)
-feature_reader.label_name = "MOV_RIGHT"
-feature_reader.label = feature_reader.feature_arr["MOV_RIGHT"]
-
-# %%
-feature_reader.feature_arr.iloc[100:108, -6:]
-
-# %%
-print(feature_reader.feature_arr.shape)
-
-# %%
-feature_reader._get_target_ch()
-
-# %%
-feature_reader.plot_target_averaged_channel(
-    ch="ECOG_RIGHT_0",
-    list_feature_keywords=None,
-    epoch_len=4,
-    threshold=0.5,
-    ytick_labelsize=7,
-    figsize_x=12,
-    figsize_y=12,
-)
-
-# %%
-feature_reader.plot_all_features(
-    ytick_labelsize=3,
-    clim_low=-2,
-    clim_high=2,
-    ch_used="ECOG_RIGHT_0",
-    time_limit_low_s=0,
-    time_limit_high_s=20,
-    normalize=True,
-    save=True,
-)
-
-# %%
-nm_plots.plot_corr_matrix(
-    feature=feature_reader.feature_arr.filter(regex="ECOG_RIGHT_0"),
-    ch_name="ECOG_RIGHT_0-avgref",
-    feature_names=feature_reader.feature_arr.filter(
-        regex="ECOG_RIGHT_0-avgref"
-    ).columns,
-    feature_file=feature_reader.feature_file,
-    show_plot=True,
-    figsize=(15, 15),
-)
-
-# %%
-# Decoding
-# --------
-#
-# The main focus of the *py_neuromodulation* pipeline is feature estimation.
-# Nevertheless, the user can also use the pipeline for machine learning decoding.
-# It can be used for regression and classification problems and also dimensionality reduction such as PCA and CCA.
-#
-# Here, we show an example using the XGBOOST classifier. The used labels came from a continuous grip force movement target, named "MOV_LEFT_CLEAN".
-#
-# First we initialize the :class:`~nm_decode.Decoder` class, which the specified *validation method*, here being a simple 3-fold cross validation, 
-# the evaluation metric, used machine learning model, and the channels we want to evaluate performances for.
-#
-# There are many more implemented methods, but we will here limit it to the ones presented.
-
-model = linear_model.LinearRegression()
-
-feature_reader.decoder = nm_decode.Decoder(
-    features=feature_reader.feature_arr,
-    label=feature_reader.label,
-    label_name=feature_reader.label_name,
-    used_chs=feature_reader.used_chs,
-    model=model,
-    eval_method=metrics.r2_score,
-    cv_method=model_selection.KFold(n_splits=3, shuffle=True),
-)
-
-# %%
-performances = feature_reader.run_ML_model(
-    estimate_channels=True,
-    estimate_gridpoints=False,
-    estimate_all_channels_combined=True,
-    save_results=True,
-)
-
-# %%
-# The performances are a dictionary that can be transformed into a DataFrame:
-
-df_per = feature_reader.get_dataframe_performances(performances)
-
-df_per
-
-# %%
-ax = nm_plots.plot_df_subjects(
-    df_per,
-    x_col="sub",
-    y_col="performance_test",
-    hue="ch_type",
-    PATH_SAVE=PATH_OUT / RUN_NAME / (RUN_NAME + "_decoding_performance.png"),
-    figsize_tuple=(8, 5)
-)
-ax.set_ylabel(r"$R^2$ Correlation")
-ax.set_xlabel("Subject 000")
-ax.set_title("Performance comparison Movement decoding")
-plt.tight_layout()

docs/source/_build/html/_downloads/7660317fa5a6bfbd12fcca9961457fc4/plot_example_rmap_computing.py

@@ -1,63 +0,0 @@
-"""
-R-Map computation
-=================
-
-"""
-# %%
-# sphinx_gallery_thumbnail_path = '_static/RMAP_figure.png'
-
-# %%
-# Across patient decoding using R-Map optimal connectivity
-# --------------------------------------------------------
-# 
-# ECoG electrode placement is commonly very heterogeneous across patients and cohorts. 
-# To still facilitate approaches that are able to perform decoding applications without patient individual training, 
-# two across-patient decoding approaches were previously investigated for movement decoding:
-# 
-# 
-# * grid-point decoding
-# * optimal connectivity channel decoding
-# 
-# First, the grid-point decoding approach relies on definition of a cortical or subcortical grid. 
-# Data from individual grid points is then interpolated onto those common grid points. 
-# The approach was also explained in the :ref:`/auto_examples/plot_example_gridPointProjection.rst` notebook.
-# 
-# .. image:: ../_static/RMAP_figure.png
-#     :alt: R-Map and grid point approach for decoding without patient-individual training 
-# 
-# The R-Map decoding approach relies on the other hand on computation of whole brain connectivity. The electrode MNI space locations need to be known,
-# then the following steps can be performed for decoding without patient individual training:
-# 
-# #. Using the `wjn_toolbox <https://github.com/neuromodulation/wjn_toolbox>`_ *wjn_specrical_roi* function, the MNI coordinates can be transformed into NIFTI (.nii) files,
-# containing the electrode contact region of interest (ROI):
-# 
-#    .. code-block:: python
-# 
-#      wjn_spherical_roi(roiname, mni, 4)
-# 
-# #. For the given *ROI.nii* files, the LeadDBS `LeadMapper <https://netstim.gitbook.io/leaddbs/connectomics/lead-mapper>`_ tool can be used for functional or structural connectivity estimation. 
-# #. The py_neuromodulation :class:`~nm_RMAP.py` module can then compute the R-Map given the contact-individual connectivity fingerprints:
-# 
-#    .. code-block:: python
-# 
-#        nm_RMAP.calculate_RMap_numba(fingerprints, performances)
-# 
-# #. The fingerprints from test-set patients can then be correlated with the calculated R-Map:
-# 
-#    .. code-block:: python
-# 
-#       nm_RMAP.get_corr_numba(fp, fp_test)
-# 
-# #. The channel with highest correlation can then be selected for decoding without individual training. :class:`~nm_RMAP.py` contain already leave one channel
-#  and leave one patient out cross validation functions:
-# 
-#    .. code-block:: python
-# 
-#       nm_RMAP.leave_one_sub_out_cv(l_fps_names, l_fps_dat, l_per, sub_list)
-# 
-# #. The obtained R-Map correlations can then be estimated statistically and plotted against true correlates:
-# 
-#    .. code-block:: python
-# 
-#       nm_RMAP.plot_performance_prediction_correlation(per_left_out, per_predict, out_path_save)
-#