pytour 3.0.0__tar.gz

pytour-3.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2018 Jin Dou
+
+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.

pytour-3.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pytour
+Version: 3.0.0
+Home-page: https://github.com/powerfulbean/pytour
+Author: Powerfulbean
+Author-email: powerfulbean@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mne
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: h5py
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+
+# tour | 托
+A framework for boosting the implementation of stimulus-response research code in the field of cognitive science and neuroscience 

pytour-3.0.0/README.md

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+# tour | 托
+A framework for boosting the implementation of stimulus-response research code in the field of cognitive science and neuroscience 

pytour-3.0.0/pytour.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: pytour
+Version: 3.0.0
+Home-page: https://github.com/powerfulbean/pytour
+Author: Powerfulbean
+Author-email: powerfulbean@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mne
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: h5py
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+
+# tour | 托
+A framework for boosting the implementation of stimulus-response research code in the field of cognitive science and neuroscience 

pytour-3.0.0/pytour.egg-info/SOURCES.txt

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+LICENSE
+README.md
+setup.py
+pytour.egg-info/PKG-INFO
+pytour.egg-info/SOURCES.txt
+pytour.egg-info/dependency_links.txt
+pytour.egg-info/requires.txt
+pytour.egg-info/top_level.txt
+tests/test_dataset.py
+tour/__init__.py
+tour/artifacts_removal.py
+tour/backend.py
+tour/package_manage.py
+tour/torch_trainer.py
+tour/vis.py
+tour/dataclass/__init__.py
+tour/dataclass/dataset.py
+tour/dataclass/io.py
+tour/dataclass/stim.py

pytour-3.0.0/pytour.egg-info/dependency_links.txt

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+

pytour-3.0.0/pytour.egg-info/requires.txt

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+mne
+numpy
+scipy
+matplotlib
+h5py

pytour-3.0.0/pytour.egg-info/top_level.txt

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+tour

pytour-3.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

pytour-3.0.0/setup.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Sat Aug 31 00:52:16 2019
+
+@author: Jin Dou
+"""
+
+import setuptools
+import re
+
+with open("./README.md", "r", encoding='UTF-8') as fh:
+  long_description = fh.read()
+
+with open("tour/__init__.py") as file:
+    for line in file.readlines():
+        m = re.match("__version__ *= *['\"](.*)['\"]", line)
+        if m:
+            version = m.group(1)
+
+setuptools.setup(
+  name="pytour",
+  version=version,
+  author="Powerfulbean",
+  author_email="powerfulbean@gmail.com",
+  long_description=long_description,
+  long_description_content_type="text/markdown",
+  url="https://github.com/powerfulbean/pytour",
+  packages=setuptools.find_packages(),
+  classifiers=[
+      "Programming Language :: Python :: 3",
+      "License :: OSI Approved :: MIT License",
+      "Operating System :: OS Independent",
+  ],
+  install_requires=[
+      "mne",
+      "numpy",
+      "scipy",
+      "matplotlib",
+      "h5py"
+  ],
+)

pytour-3.0.0/tests/test_dataset.py

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+import os
+import mne
+import h5py
+import json
+import numpy as np
+from collections import OrderedDict
+from StellarInfra import siIO
+from tour.dataclass.io import (
+    mne_montage_to_h5py_group,
+    mne_montage_from_h5py_group,
+    data_record_from_h5py_group,
+    data_record_to_h5py_group,
+    stim_dict_to_hdf5,
+    stim_dict_from_hdf5
+)
+from tour.dataclass.dataset import Dataset, DataRecord
+from StimRespFlow.DataStruct.DataSet import CDataSet, CDataRecord
+
+
+current_folder = os.path.dirname(os.path.abspath(__file__))
+
+def to_impulses(vectors, timestamps, f:float,padding_s = 0):
+    '''
+    # align the vectors into impulses with specific sampling rate 
+    '''
+    startTimes = timestamps[0]
+    endTimes = timestamps[1]
+    secLen = endTimes[-1] + padding_s
+    nLen = np.ceil( secLen * f).astype(int)
+    nDim = vectors.shape[0]
+    out = np.zeros((nDim,nLen))
+    
+    timeIndices = np.round(startTimes * f).astype(int)
+    out[:,timeIndices] = vectors
+    return out
+
+def test_save_mne_montage():
+    output_fd = os.environ['box_root']
+    montage = mne.channels.make_standard_montage('biosemi128')
+    fig = montage.plot(show = False)
+    fig.savefig(f"{current_folder}/target_montage.png")
+    # pos_dict = montage.get_positions()
+    with h5py.File(f"{output_fd}/Collab-Project/CompiledDataset/biosemi128_montage.h5", "w") as f:
+        mne_montage_to_h5py_group(montage, f)
+    
+def test_load_montage_in_mne():
+    output_fd = os.environ['box_root']
+    with h5py.File(f"{output_fd}/Collab-Project/CompiledDataset/biosemi128_montage.h5", "r") as f:
+        montage = mne_montage_from_h5py_group(f)
+    fig = montage.plot(show = False)
+    fig.savefig(f"{current_folder}/loaded_montage.png")
+
+
+data_path = f"{os.environ['box_root']}/Collab-Project/CompiledDataset/ns.pkl"
+dataset:CDataSet = CDataSet.load(siIO.loadObject(data_path))
+# print(dataset.records[0])
+
+
+dataset_name = 'lalorlab_oldman'
+dataset_new = Dataset(
+    name = dataset_name,
+    srate = dataset.srate
+)
+
+stim_dict = dataset.stimuliDict
+old_stim_ids = list(stim_dict.keys())
+for old_stim_id in old_stim_ids:
+    values = stim_dict[old_stim_id]
+    # print(old_stim_id, values.keys())
+    new_stim_id = old_stim_id.replace('phonemes','oldman')
+    words = values['words']
+    timeinfo = values['lex_sur']['timeinfo']
+    x = values['lex_sur']['x']
+    uniqueness_point = values['uni_pnt']['x']
+    values['lexical_surprisal'] = {
+        'tag': words,
+        'timeinfo': timeinfo,
+        'x': x
+    }
+    values['uniqueness_point'] = {
+        'tag': words,
+        'timeinfo': timeinfo,
+        'x': uniqueness_point
+    }
+    values['lexical_surprisal_fs64'] = to_impulses(
+        x,
+        timeinfo,
+        dataset.srate
+    )
+    ones = np.ones(x.shape)
+    # print(x.shape, timeinfo.shape)
+    values['word_onset_fs64'] = to_impulses(
+        ones,
+        timeinfo,
+        dataset.srate
+    )
+    values['envelope_fs64'] = values['env']
+    del values['lex_sur']
+    del values['onset']
+    del values['words']
+    del values['env']
+    del values['uni_pnt']
+    stim_dict[new_stim_id] = stim_dict[old_stim_id]
+    del stim_dict[old_stim_id]
+
+# print(stim_dict)
+for record in dataset.records:
+    record:CDataRecord
+    data = record.data
+    old_info = record.descInfo
+    stim_id = 'oldman' + str(old_info['stim'])
+    trial_id = old_info['stim']
+    subj_id = old_info['subj']
+    meta_info = dict(
+        subj_id = subj_id,
+        trial_id = trial_id,
+        dataset_name = dataset_name
+    )
+    record_new = DataRecord(
+        data,
+        stim_id,
+        meta_info,
+        srate = dataset.srate
+    )
+    dataset_new.append(record_new)
+
+
+stim_dict_to_hdf5(
+    f"{os.environ['box_root']}/Collab-Project/CompiledDataset/ns_unipnt_lexsur_env_onset.h5",
+    stim_dict
+)
+
+stim_dict_new = stim_dict_from_hdf5(
+    f"{os.environ['box_root']}/Collab-Project/CompiledDataset/ns_unipnt_lexsur_env_onset.h5",
+)
+
+# test_save_mne_montage()
+# test_load_montage_in_mne()
+    
+dataset_new.dump(f"{os.environ['box_root']}/Collab-Project/CompiledDataset/ns.h5")
+new_dataset_new = Dataset.load(f"{os.environ['box_root']}/Collab-Project/CompiledDataset/ns.h5")

pytour-3.0.0/tour/__init__.py

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+__version__ = "3.0.0"

pytour-3.0.0/tour/artifacts_removal.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jul  8 14:41:55 2021
+
+@author: Jin Dou
+"""
+import mne
+import numpy as np
+from scipy.stats import zscore
+
+def mneWrap_lalorlab_detect_EEG_badChannels(mneraw:mne.io.RawArray, montage = None, nNearest = 10):
+    oRaw = mneraw.copy()
+    data = oRaw.get_data()
+    if montage is None:
+        badChansIdx = lalorlab_detect_EEG_badChannels(data,False)
+    else:
+        badChansIdx = lalorlab_detect_EEG_badChannels_covVarNear(data,montage, nNearest = nNearest)
+    oRaw.info['bads'] = [oRaw.info['ch_names'][i] for i in badChansIdx]
+    print(f'bad channels: {",".join(oRaw.info["bads"])}')
+    return oRaw
+
+
+def lalorlab_detect_EEG_badChannels(eegarray,verbose = True):
+    '''
+    we assume the first dimension is channel dimension
+
+    Parameters
+    ----------
+    eegarray : TYPE
+        DESCRIPTION.
+
+    Returns
+    -------
+    None.
+
+    '''
+    eegarray = np.array(eegarray)
+    assert len(eegarray.shape) == 2 
+    stdChans = list()
+    badChansIdx = list()
+    for chan in eegarray:
+        stdChans.append(np.std(chan))
+    
+    for idx,chan in enumerate(eegarray):
+        if np.std(chan) > 2.5 * np.mean(stdChans):
+            badChansIdx.append(idx)
+        
+    stdChans.clear()
+    
+    for idx,chan in enumerate(eegarray):
+        if idx not in badChansIdx:
+            stdChans.append(np.std(chan))
+    
+    for idx,chan in enumerate(eegarray):
+        if np.std(chan) < np.mean(stdChans) / 2.5:
+            badChansIdx.append(idx)
+        
+    if verbose:
+        print(badChansIdx)
+    
+    return badChansIdx
+
+def lalorlab_detect_EEG_badChannels_covVarNear(data, montage, th1 = 2, th2 = 2, nNearest = 6):
+    # data: (nChan, nSamples)
+    data = np.array(data)
+    assert data.ndim == 2
+    
+    ### prepare the nearest channels
+    if nNearest > 0:
+        chanloc = montage.get_positions()['ch_pos']
+        chnames = []
+        poses = []
+        for n,pos in chanloc.items():
+            chnames.append(n)
+            poses.append(pos)
+            
+        assert data.shape[0] == len(chnames)
+        chanDistMat = np.zeros((len(chanloc), len(chanloc)))
+        
+        fDist = lambda pos1,pos2: np.sqrt(np.sum((pos1 - pos2)**2))
+        
+        for i in range(len(chnames)):
+            for j in range(len(chnames)):
+                chanDistMat[i,j] = fDist(poses[i], poses[j])
+        
+        nearChanIdx = []
+        for i in range(len(chnames)):
+            nearChanIdx.append(np.argsort(chanDistMat[i])[1:nNearest+1])
+    else:
+        nearChanIdx = [None] * data.shape[1]
+    ### find the bad channels
+    dataz = zscore(data, axis = 1)
+    XTX = np.matmul(dataz ,dataz.T)
+    stdXTX = np.std(XTX, axis = 1)
+    stdEEG = np.std(data, axis = 1)
+    
+    badChans = []
+    if nNearest <=0 :
+        badChans.append(np.where(stdXTX < np.mean(stdXTX) / th1))
+        badChans.append(np.where(stdEEG > np.mean(stdEEG) * th2))
+    else:
+        for chanIdx in range(data.shape[0]):
+            # print(stdXTX[chanIdx],
+            #       stdEEG[chanIdx],
+            #       np.mean(stdXTX[nearChanIdx[chanIdx]]) / th1,
+            #       np.mean(stdEEG[nearChanIdx[chanIdx]]) * th2)
+            if stdXTX[chanIdx] < np.mean(stdXTX[nearChanIdx[chanIdx]]) / th1:
+                badChans.append(chanIdx)
+            if stdEEG[chanIdx] > np.mean(stdEEG[nearChanIdx[chanIdx]]) * th2:
+                badChans.append(chanIdx)
+            
+    return list(set(badChans))
+    
+def plotChanWithNamesAtIdx(montage, idxs):
+    chnames = montage.ch_names
+    montage.plot(show_names = [chnames[idx] for idx in idxs])
+    
+            
+# def      
+        
+    
+        

pytour-3.0.0/tour/backend.py

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+import numbers
+from typing import TypeVar
+
+try:
+    import torch
+except:
+    torch = None
+
+try:
+    import numpy as np
+except:
+    np = None
+
+Array = TypeVar("Array")
+
+def get_numeric_backend(data: Array):
+    if isinstance(data, torch.Tensor):
+        return torch
+    elif isinstance(data, np.ndarray):
+        return np
+    elif isinstance(data, numbers.Number):
+        return np
+    else:
+        raise ValueError(f"input is not an numeric variable")
+
+def is_tensor(data: Array):
+    if isinstance(data, torch.Tensor):
+        return True
+    elif isinstance(data, np.ndarray):
+        return False
+    elif isinstance(data, numbers.Number):
+        return False
+    else:
+        raise ValueError(f"input is not an numeric variable")