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PyEcog2 is a python software package aimed at exploring, visualizing and analyzing (video) EEG telemetry data

License: GNU General Public License v3.0

Python 3.71% Jupyter Notebook 96.29% Shell 0.01% Batchfile 0.01%

pyecog2's Introduction

Pyecog2

Under construction.

PyEcog2 is a python software package aimed at exploring, visualizing and analysing (video) EEG telemetry data

Installation instructions

For alpha testing:

clone the repository to your local machine
create a dedicated python 3.8 environment for pyecog2 (e.g. a conda environment)

conda create --name pyecog2 python=3.8

activate the environment with activate pyecog2 in Windows or source activate pyecog2 in MacOS/Linux
run pip install with the development option :

python -m pip install -e <repository directory>

To launch PyEcog you should now, from any directory, be able to call:

python -m pyecog2

Hopefully in the future:

pip install pyecog2

pyecog2's People

Contributors

Stargazers

Watchers

pyecog2's Issues

pyside updates prevent starting on Windows

New pyecog2 environment and setup.py run. Error on attempting to start:

(pyecog2) C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2>python main.py
Traceback (most recent call last):
  File "main.py", line 7, in <module>
    from PySide2 import QtCore, QtGui
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyside2-5.15.2-py3.8-win-amd64.egg\PySide2\__init__.py", line 107, in <module>
    _setupQtDirectories()
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyside2-5.15.2-py3.8-win-amd64.egg\PySide2\__init__.py", line 54, in _setupQtDirectories
    for dir in _additional_dll_directories(pyside_package_dir):
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyside2-5.15.2-py3.8-win-amd64.egg\PySide2\__init__.py", line 26, in _additional_dll_directories    raise ImportError(shiboken2 + ' does not exist')
ImportError: C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\shiboken2\libshiboken does not exist

Avoid Loading all data when computing scalles

Timeline minimum height

The timeline sometimes disapears when resizing the windows around. Fix this by setting a minimum height for the timeline.

First use of global classifier sometimes raises error and fails

Repeated tries seem to work. Double check classifier import and assimilation

Classifier not being trained when there are no labels

This might be a symptom of a greater issue with the training of the Gaussian Classifiers.
Double check events that cross file boundaries as well

unable to convert ndf files

line 198 in convert_ndf_folder_gui.py:

        for a in self.p.param.get:
            print('***\n Starting to convert', a['name'], a['value'],'\n***')
            tids = a['value']
            dh.convert_ndf_directory_to_h5(self.files2convert,tids=tids,save_dir=self.destination_folder)

self.p.param.get:

IndexError: tuple index out of range

feature extractor failing

OrderedDict([('window_length', 5.0), ('overlap', 0.5), ('window', 'rectangular'), ('feature_labels', ['min', 'max', 'mean', 'log std', 'kurtosis', 'skewness', 'log coastline (log sum of abs diff)', 'log power in band (1, 4) Hz', 'log power in band (4, 8) Hz', 'log power in band (8, 12) Hz', 'log power in band (12, 30) Hz', 'log power in band (30, 50) Hz', 'log power in band (50, 70) Hz', 'log power in band (70, 120) Hz', 'Spectrum entropy']), ('feature_time_functions', ['np.min', 'np.max', 'np.mean', 'lambda x:np.log(np.std(x))', 'stats.kurtosis', 'stats.skew', 'lambda d:np.log(np.mean(np.abs(np.diff(d,axis=0))))']), ('feature_freq_functions', ['fe.powerf(1, 4)', 'fe.powerf(4, 8)', 'fe.powerf(8, 12)', 'fe.powerf(12, 30)', 'fe.powerf(30, 50)', 'fe.powerf(50, 70)', 'fe.powerf(70, 120)', 'fe.reg_entropy']), ('function_module_dependencies', [('numpy', 'np'), ('pyecog2.feature_extractor', 'fe'), ('scipy.stats', 'stats')])])
OrderedDict([('window_length', 5.0), ('overlap', 0.5), ('window', 'rectangular'), ('feature_labels', ['min', 'max', 'mean', 'log std', 'kurtosis', 'skewness', 'log coastline (log sum of abs diff)', 'log power in band (1, 4) Hz', 'log power in band (4, 8) Hz', 'log power in band (8, 12) Hz', 'log power in band (12, 30) Hz', 'log power in band (30, 50) Hz', 'log power in band (50, 70) Hz', 'log power in band (70, 120) Hz', 'Spectrum entropy']), ('feature_time_functions', ['np.min', 'np.max', 'np.mean', 'lambda x:np.log(np.std(x))', 'stats.kurtosis', 'stats.skew', 'lambda d:np.log(np.mean(np.abs(np.diff(d,axis=0))))']), ('feature_freq_functions', ['fe.powerf(1, 4)', 'fe.powerf(4, 8)', 'fe.powerf(8, 12)', 'fe.powerf(12, 30)', 'fe.powerf(30, 50)', 'fe.powerf(50, 70)', 'fe.powerf(70, 120)', 'fe.reg_entropy']), ('function_module_dependencies', [('numpy', 'np'), ('pyecog2.feature_extractor', 'fe'), ('scipy.stats', 'stats')])])
Starting feature extraction...
Starting FE worker
 calling feature_extractor.extract_features_from_animal
Extracting features for animal 1163812_45_46
multiprocessing.pool.RemoteTraceback: : F:\NP_test\H5\1163812_45_46\M1615232310_2021-03-08-19-38-30_tids_[45, 46].metaa
"""
TypeError: only size-1 arrays can be converted to Python scalars

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyecog2-0.0.1rc0-py3.8.egg\pyecog2\feature_extractor.py", line 154, in extract_features_from_file
    self.extract_features_from_time_range(file_buffer, time_range, feature_fname, feature_metafname,animal_id)
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyecog2-0.0.1rc0-py3.8.egg\pyecog2\feature_extractor.py", line 177, in extract_features_from_time_range
    features[i,j] = func(data)
ValueError: setting an array element with a sequence.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyecog2-0.0.1rc0-py3.8.egg\pyecog2\coding_tests\WaveletWidget.py", line 147, in run
    result = self.fn(*self.args, **self.kwargs)
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyecog2-0.0.1rc0-py3.8.egg\pyecog2\coding_tests\FeatureExtractorGUI.py", line 241, in extractFeatures
    self.feature_extractor.extract_features_from_animal(animal, re_write = self.re_write.isChecked(), n_cores = -1,
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyecog2-0.0.1rc0-py3.8.egg\pyecog2\feature_extractor.py", line 134, in extract_features_from_animal
    for i, _ in enumerate(pool.imap(self.extract_features_from_file, tuples)):
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\pool.py", line 868, in next
    raise value
ValueError: setting an array element with a sequence.

MacOS Big Sur sollution

os.environ['QT_MAC_WANTS_LAYER'] = '1'

this will solve the issue that Qt fails to show windows on macos big sur +

Time stamp on seizure annotations

It would be very useful to have the date and time of day of each annotation when exporting the csv file. In the meantime, could you share the formula that allows to onvert the current time stamp into date and time please?

feature extractor crash

On commencing feature extraction:

Starting feature extraction... Traceback (most recent call last): File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\coding_tests\WaveletWidget.py", line 147, in run result = self.fn(*self.args, **self.kwargs) File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\coding_tests\FeatureExtractorGUI.py", line 230, in extractFeatures self.feature_extractor.extract_features_from_animal(animal, re_write = self.re_write.isChecked(), n_cores = -1, File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\feature_extractor.py", line 130, in extract_features_from_animal with multiprocessing.Pool(processes=n_cores,initializer=my_worker_flist_init, File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\context.py", line 119, in Pool return Pool(processes, initializer, initargs, maxtasksperchild, File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\pool.py", line 212, in __init__ self._repopulate_pool() File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\pool.py", line 303, in _repopulate_pool return self._repopulate_pool_static(self._ctx, self.Process, File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\pool.py", line 326, in _repopulate_pool_static w.start() File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\process.py", line 121, in start self._popen = self._Popen(self) File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\context.py", line 327, in _Popen return Popen(process_obj) File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\popen_spawn_win32.py", line 93, in __init__ reduction.dump(process_obj, to_child) File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\reduction.py", line 60, in dump ForkingPickler(file, protocol).dump(obj) _pickle.PicklingError: Can't pickle <function <lambda> at 0x0000020A21CB5AF0>: attribute lookup <lambda> on __main__ failed Traceback (most recent call last): File "<string>", line 1, in <module> File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\spawn.py", line 116, in spawn_main exitcode = _main(fd, parent_sentinel) File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\multiprocessing\spawn.py", line 126, in _main self = reduction.pickle.load(from_parent) EOFError: Ran out of input

Bug when trying to plot files with different number of channels from the previous file

reminder to solve this bug - hack solution: restart pyecog

shift select

using shift select for both start and end of selection leads to programme hanging:

shift-left click to select start of annotation

-> skip to another distant file

-> shift select to select start of new annotation (without ending first annotation selection)

programme then adds all files in between to buffer: this may be hundreds of files

Segmentation fault on closeevent

Need to close all widgets before closing main application either by setting up automatic close or explicitly on close event

Handle better moving files around

try to base the data files as relative paths and avoid global paths

NDF converter bug: unusable

On using NDF converter:

when you press the convert button, PyEcog main window opens n_core times and no conversion starts

Typo

Plot controls
High pass freuency

Traces not shown on animal change

When first changing animals with different acquisition dates, EEG traces are not shown. Maybe trying to show time interva that does not have data?

sample rate bug when creating new project file

On clicking update project file button:

Error message:

Looking for files: F:\20210301_IntraHippoKA_DREADD\Left_virus\H5\1193429 \ *.h5
===== 2021.05.30 00:05:10 =====
Traceback (most recent call last):
File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\coding_tests\ProjectGUI.py", line 209, in update_project_settings
self.project.add_animal(Animal(id=id,eeg_folder=eeg_dir,video_folder=video_dir))
File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ProjectClass.py", line 91, in init
self.update_eeg_folder(eeg_folder)
File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ProjectClass.py", line 129, in update_eeg_folder
create_metafile_from_h5(file,duration)
File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ProjectClass.py", line 27, in create_metafile_from_h5
assert fs == int(fs_dict[tid]) # Check all tids have the same sampling rate

three files emailed to you: one that works, it's meta file and ne that creating a metafile fails

NDF converter issues

When trying to convert NDF files to H5:

leaving fs at 'auto' does not work well with many bad messages or files with missing data:

Progress: |--------------------------------------------------| 0.0% CompleteERROR:root: >half messages detected as bad messages. Probably change fs from auto to the correct frequency

But manually setting fs in ndf_converter.py line 552 as follows:

class DataHandler:

    def convert_ndf_directory_to_h5(self, ndf_dir,
                                    tids='all',
                                    save_dir='same_level',
                                    n_cores=9,
                                    fs=1024,
                                    glitch_detection=True,
                                    high_pass_filter=False,
                                    gui_object=False):

results in this error:



Progress: |*-------------------------------------------------| 1.0% Complete
Something unexpected went wrong loading [97, 98] from F:/epilepsy files/Rat telemetry/Rig4/2021/ndf\M1611780237.ndf :
Traceback (most recent call last):
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ndf_converter.py", line 647, in convert_ndf
    ndf.load(tids,
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ndf_converter.py", line 469, in load
    self.correct_sampling_frequency()
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ndf_converter.py", line 320, in correct_sampling_frequency
    regularised_time = np.linspace(0, self.file_length, num= self.file_length * self.tid_to_fs_dict[tid])
  File "<__array_function__ internals>", line 5, in linspace
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\numpy-1.20.0rc1-py3.8-win-amd64.egg\numpy\core\function_base.py", line 120, in linspace
    num = operator.index(num)
TypeError: 'float' object cannot be interpreted as an integer
None

Creating a new project from H5 files, if no TID is not found (empty file):

Looking for files: F:\epilepsy files\Rat telemetry\Rig4\2021\H5_Py2\210.97_98 \ *.h5
Traceback (most recent call last):
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\coding_tests\ProjectGUI.py", line 208, in update_project_settings
    self.project.add_animal(Animal(id=id,eeg_folder=eeg_dir,video_folder=video_dir))
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ProjectClass.py", line 75, in __init__
    self.update_eeg_folder(eeg_folder)
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ProjectClass.py", line 113, in update_eeg_folder
    create_metafile_from_h5(file,duration)
  File "C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\ProjectClass.py", line 18, in create_metafile_from_h5
    fs = fs_dict[int(h5_file.attributes['t_ids'][0])]
IndexError: index 0 is out of bounds for axis 0 with size 0

Video naming convention is too restrictive

It would be important to have a way of changing the video naming convention to synch with EEG

Feature request

When converting NDF to H5: Ability to load a csv file with animal ID and channel IDs

I have 32 animals in 4 rigs and need to convert NDFs iteratively as they are required.
Each time I load the NDF converter I need to manually input animal ID, TIDs and date/time range.

either ability to save and load each conversion session to a csv file, or somehow save this information within the project file

Shift + scroll on x axis sends errors

Error when selecting the channel for an annotation

Actions leading to error with printed messages in console and traceback:

Add label

adding label Label 1 (242, 12, 12)
Label 1 (242, 12, 12) []
Annotations Table widget Set Data called. Annotations page length: 0 row count: 0
Annotations Table widget Set Data ran in 0.0015999000024748966 seconds
AnnotationParameterTree Re_init Called  Label 1
AnnotationParameterTree Re_init finished ( 0.6638855999917723 seconds )
add label

Renamed

autosave_save action triggered
warning - project file does not exist yet
Key press captured by Main 16777248
tree changes:
  parameter: Annotation Labels.bad_chan
  change:    name
  data:      bad_chan
  ----------
new labels: ['bad_chan']
Annotations Table widget Set Data called. Annotations page length: 0 row count: 0
Annotations Table widget Set Data ran in 0.001363400006084703 seconds
AnnotationParameterTree Re_init Called  bad_chan
AnnotationParameterTree Re_init finished ( 0.6440338999964297 seconds )
change label name

Add a number to channel range :

setting new channel range 191 for label bad_chan
Annotations Table widget Set Data called. Annotations page length: 0 row count: 0
Annotations Table widget Set Data ran in 0.0014507000014418736 seconds
AnnotationParameterTree Re_init Called  bad_chan
AnnotationParameterTree Re_init finished ( 0.6674226999894017 seconds )
change label range
===== 2021.07.19 15:07:24 =====
Key press captured by Main 16777221
Traceback (most recent call last):
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyqtgraph\parametertree\parameterTypes.py", line 177, in valueChanged
    self.widget.sigChanged.disconnect(self.widgetValueChanged)
RuntimeError: Internal C++ object (PySide2.QtWidgets.QLineEdit) already deleted.

Result is that number is Not changed in channel range

Trying to add number with square brackets [ ] is successful but there is still a PySide2 runtime error

autosave_save action triggered
warning - project file does not exist yet
autosave_save action triggered
warning - project file does not exist yet
tree changes:
  parameter: Annotation Labels.bad_chan.Channel range
  change:    value
  data:      [191]
  ----------
setting new channel range [191] for label bad_chan
Annotations Table widget Set Data called. Annotations page length: 0 row count: 0
Annotations Table widget Set Data ran in 0.0009036999981617555 seconds
AnnotationParameterTree Re_init Called  bad_chan
AnnotationParameterTree Re_init finished ( 0.6499142999964533 seconds )
change label range
===== 2021.07.19 15:07:20 =====
Key press captured by Main 16777220
Traceback (most recent call last):
  File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyqtgraph\parametertree\parameterTypes.py", line 177, in valueChanged
    self.widget.sigChanged.disconnect(self.widgetValueChanged)
RuntimeError: Internal C++ object (PySide2.QtWidgets.QLineEdit) already deleted.

project setting saver

1.unable to automatically update animals from folders if '.'s in folder path

double check for this issue everywhere else

unable to save project file (.pyecog)
saves without pyecog suffix
update filetree in GUI after changing anything in project settings

Project GUI not very responsive

ProjectGUI stalls while large projects are being created - this needs to be threaded and a progress bar should be included

video not found

video files listed in project file under animal ID, but when try to play in GUI, states no file found for time

When updating project annotations are deleted

NDF converter project file and folders

Ideally a project file should automatically be created and the animals with specified transmitters IDs should have folders automatically created for all their files. Otherwise all files with the same start times will be lumped into one folder and will need to be manually separated into folders + project file created manually

Scale bar misplaced when using filters in plot controls

that

Very slow loading neuropixel binary data

Error with concurrent plotting of data that overlaps in time

By default all NP data is acquired at the same time: multiple LF and AP files per folder, 1 each for each probe.

If there is more than one file in the folder PyEcog plots all data from the same folder concurrently even if only one file is selected in the file tree

300s to display 30s of 385 channel data from 4 files (2 x LF and 2 x AP)

Work around: put each file in a separate folder

Data loading still slow

LF data: 25s for 385 channels (sample rate ~2500 Hz)
AP data: 120s for 385 channels (sample rat ~30,000 Hz)

@mfpleite Would it be possible to plot down sampled array as a whole rather than each channel individually?

Deleting multiple annotations is very slow

I'll have to block the annotation table refresh when deleting multiple annotations in one go.

NP data timescale for overview

X axis is date and time of recording, not duration of current recording.

Bug allows x axis to extend beyond current recording. If you accidentally scroll past the start or end, it can be difficult to go back to start of file without closing it and reopening.

Classifier window not updating when project settings change

e.g. when deleting an animal, the animal doesn't disappear from the classifier window

NDF converter add animal list error

remove animal, then try to add it again when it already exists (eg Animal 5)

===== 2021.06.11 18:06:10 =====
Traceback (most recent call last):
  File "C:\Users\Synapse\.conda\envs\pyecog2\lib\site-packages\pyqtgraph-0.11.0-py3.8.egg\pyqtgraph\parametertree\parameterTypes.py", line 426, in addChanged
    self.param.addNew(typ)
  File "C:\Users\Synapse\.conda\envs\pyecog2\lib\site-packages\pyecog2-0.0.1b0-py3.8.egg\pyecog2\coding_tests\convert_ndf_folder_gui.py", line 50, in addNew
  File "C:\Users\Synapse\.conda\envs\pyecog2\lib\site-packages\pyqtgraph-0.11.0-py3.8.egg\pyqtgraph\parametertree\Parameter.py", line 519, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
  File "C:\Users\Synapse\.conda\envs\pyecog2\lib\site-packages\pyqtgraph-0.11.0-py3.8.egg\pyqtgraph\parametertree\Parameter.py", line 562, in insertChild
    raise Exception("Already have child named %s" % str(name))
Exception: Already have child named Animal 5

license error

Using latest version of Development_ML this error constantly pops up:

Invalid license_reg file signature:  C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\license\license_reg.txt

Feature extractor run time error

On extracting features, I occasionally get this error. I am not sure which files it is referring to :

Extracting features for animal 1238529_39_40 Building File Tree... Building File Tree... Building File Tree... Building File Tree... Building File Tree... Building File Tree... <string>:1: RuntimeWarning: divide by zero encountered in log C:\Users\mweston\Documents\GitHub\pyecog2\pyecog2\feature_extractor.py:16: RuntimeWarning: divide by zero encountered in log return np.log(np.mean(np.abs(fdata[int(len(fdata)*band[0]/fs):int(len(fdata)*band[1]/fs)]))) # todo consider making this with proper units

paired view scaling resets when file selected in file tree

auto-scaling re-applied when a file is selected from the file tree

erratic filter behaviour

high pass filter does not apply properly over 50Hz
filter bug.pptx

Remove annotation on right click menu not working

Units on plot controls

missing units on filter options

NDF converter should only launch one process when clicking Convert NDF multiple times

Plot controls GUI not correctly updated upon start-up

Plot controls like filtering options are correctly applied to paired graphics view, but not to the GUI of plot controls

unable to load NP data

when attempting to load a NP data file

===== 2021.10.31 13:10:23 =====
Traceback (most recent call last):
File "c:\users\mweston\documents\github\pyecog2\pyecog2\pyecog_plot_item.py", line 152, in itemChange
return super().itemChange(*args)
File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyqtgraph\graphicsItems\GraphicsObject.py", line 23, in itemChange
self.parentChanged()
File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyqtgraph\graphicsItems\GraphicsItem.py", line 458, in parentChanged
self._updateView()
File "C:\Users\mweston\Anaconda3\envs\pyecog2\lib\site-packages\pyqtgraph\graphicsItems\GraphicsItem.py", line 514, in _updateView
self.viewRangeChanged()
File "c:\users\mweston\documents\github\pyecog2\pyecog2\pyecog_plot_item.py", line 47, in viewRangeChanged
self.setData_with_envelope()
File "c:\users\mweston\documents\github\pyecog2\pyecog2\pyecog_plot_item.py", line 145, in setData_with_envelope
self.scale_Bar.update_from_curve_item()
File "c:\users\mweston\documents\github\pyecog2\pyecog2\pyecog_plot_item.py", line 213, in update_from_curve_item
data_range = int(data_range/(data_range10))*data_range10
ValueError: cannot convert float NaN to integer
Paired graphics view plot channels finnished in 11.130413599999997 seconds