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PierreGtch committed Feb 1, 2024
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},
"outputs": [],
"source": [
"# Authors: Igor Carrara <[email protected]>\n# Bruno Aristimunha <[email protected]>\n#\n# License: BSD (3-clause)\n\nimport matplotlib.pyplot as plt\nimport mne\nimport seaborn as sns\nimport torch\nfrom braindecode import EEGClassifier\nfrom braindecode.models import EEGNetv4\nfrom sklearn.pipeline import Pipeline\nfrom skorch.callbacks import EarlyStopping, EpochScoring\nfrom skorch.dataset import ValidSplit\n\nfrom moabb.datasets import BNCI2014_001\nfrom moabb.evaluations import CrossSessionEvaluation\nfrom moabb.paradigms import MotorImagery\nfrom moabb.pipelines.utils_pytorch import BraindecodeDatasetLoader, InputShapeSetterEEG\nfrom moabb.utils import setup_seed\n\n\nmne.set_log_level(False)\n\n# Print Information PyTorch\nprint(f\"Torch Version: {torch.__version__}\")\n\n# Set up GPU if it is there\ncuda = torch.cuda.is_available()\ndevice = \"cuda\" if cuda else \"cpu\"\nprint(\"GPU is\", \"AVAILABLE\" if cuda else \"NOT AVAILABLE\")"
"# Authors: Igor Carrara <[email protected]>\n# Bruno Aristimunha <[email protected]>\n#\n# License: BSD (3-clause)\n\nimport matplotlib.pyplot as plt\nimport mne\nimport seaborn as sns\nimport torch\nfrom braindecode import EEGClassifier\nfrom braindecode.models import EEGNetv4\nfrom sklearn.pipeline import make_pipeline\nfrom skorch.callbacks import EarlyStopping, EpochScoring\nfrom skorch.dataset import ValidSplit\n\nfrom moabb.datasets import BNCI2014_001\nfrom moabb.evaluations import CrossSessionEvaluation\nfrom moabb.paradigms import MotorImagery\nfrom moabb.utils import setup_seed\n\n\nmne.set_log_level(False)\n\n# Print Information PyTorch\nprint(f\"Torch Version: {torch.__version__}\")\n\n# Set up GPU if it is there\ncuda = torch.cuda.is_available()\ndevice = \"cuda\" if cuda else \"cpu\"\nprint(\"GPU is\", \"AVAILABLE\" if cuda else \"NOT AVAILABLE\")"
]
},
{
Expand All @@ -44,7 +44,7 @@
},
"outputs": [],
"source": [
"# Set random seed to be able to reproduce results\nseed = 42\nsetup_seed(seed)\n\n# Ensure that all operations are deterministic on GPU (if used) for reproducibility\ntorch.backends.cudnn.deterministic = True\ntorch.backends.cudnn.benchmark = False\n\n# Hyperparameter\nLEARNING_RATE = 0.0625 * 0.01 # parameter taken from Braindecode\nWEIGHT_DECAY = 0 # parameter taken from Braindecode\nBATCH_SIZE = 64 # parameter taken from BrainDecode\nEPOCH = 10\nPATIENCE = 3\nfmin = 4\nfmax = 100\ntmin = 0\ntmax = None\n\n# Load the dataset\ndataset = BNCI2014_001()\nevents = [\"right_hand\", \"left_hand\"]\nparadigm = MotorImagery(\n events=events, n_classes=len(events), fmin=fmin, fmax=fmax, tmin=tmin, tmax=tmax\n)\nsubjects = [1]\nX, _, _ = paradigm.get_data(dataset=dataset, subjects=subjects)\n# Define Transformer of Dataset compatible with Brain Decode\ncreate_dataset = BraindecodeDatasetLoader()"
"# Set random seed to be able to reproduce results\nseed = 42\nsetup_seed(seed)\n\n# Ensure that all operations are deterministic on GPU (if used) for reproducibility\ntorch.backends.cudnn.deterministic = True\ntorch.backends.cudnn.benchmark = False\n\n# Hyperparameter\nLEARNING_RATE = 0.0625 * 0.01 # parameter taken from Braindecode\nWEIGHT_DECAY = 0 # parameter taken from Braindecode\nBATCH_SIZE = 64 # parameter taken from BrainDecode\nEPOCH = 10\nPATIENCE = 3\nfmin = 4\nfmax = 100\ntmin = 0\ntmax = None\n\n# Load the dataset\ndataset = BNCI2014_001()\nevents = [\"right_hand\", \"left_hand\"]\nparadigm = MotorImagery(\n events=events, n_classes=len(events), fmin=fmin, fmax=fmax, tmin=tmin, tmax=tmax\n)\nsubjects = [1]\nX, _, _ = paradigm.get_data(dataset=dataset, subjects=subjects)"
]
},
{
Expand All @@ -62,7 +62,7 @@
},
"outputs": [],
"source": [
"model = EEGNetv4(in_chans=1, n_classes=1, input_window_samples=100)\n\n# Send model to GPU\nif cuda:\n model.cuda()\n\n# Define a Skorch classifier\nclf = EEGClassifier(\n module=model,\n criterion=torch.nn.CrossEntropyLoss,\n optimizer=torch.optim.Adam,\n optimizer__lr=LEARNING_RATE,\n batch_size=BATCH_SIZE,\n max_epochs=EPOCH,\n train_split=ValidSplit(0.2, random_state=seed),\n device=device,\n callbacks=[\n EarlyStopping(monitor=\"valid_loss\", patience=PATIENCE),\n EpochScoring(\n scoring=\"accuracy\", on_train=True, name=\"train_acc\", lower_is_better=False\n ),\n EpochScoring(\n scoring=\"accuracy\", on_train=False, name=\"valid_acc\", lower_is_better=False\n ),\n InputShapeSetterEEG(\n params_list=[\"in_chans\", \"input_window_samples\", \"n_classes\"],\n ),\n ],\n verbose=1, # Not printing the results for each epoch\n)\n\n# Create the pipelines\npipes = {}\npipes[\"EEGNetV4\"] = Pipeline([(\"Braindecode_dataset\", create_dataset), (\"Net\", clf)])"
"# Define a Skorch classifier\nclf = EEGClassifier(\n module=EEGNetv4,\n optimizer=torch.optim.Adam,\n optimizer__lr=LEARNING_RATE,\n batch_size=BATCH_SIZE,\n max_epochs=EPOCH,\n train_split=ValidSplit(0.2, random_state=seed),\n device=device,\n callbacks=[\n EarlyStopping(monitor=\"valid_loss\", patience=PATIENCE),\n EpochScoring(\n scoring=\"accuracy\", on_train=True, name=\"train_acc\", lower_is_better=False\n ),\n EpochScoring(\n scoring=\"accuracy\", on_train=False, name=\"valid_acc\", lower_is_better=False\n ),\n ],\n verbose=1, # Not printing the results for each epoch\n)\n\n# Create the pipelines\npipes = {}\npipes[\"EEGNetV4\"] = make_pipeline(clf)"
]
},
{
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},
"outputs": [],
"source": [
"# Authors: Igor Carrara <[email protected]>\n#\n# License: BSD (3-clause)\n\nfrom pickle import load\n\nimport keras\nimport torch\nfrom braindecode import EEGClassifier\nfrom braindecode.models import EEGInception\nfrom scikeras.wrappers import KerasClassifier\nfrom sklearn.pipeline import Pipeline\nfrom skorch.callbacks import EarlyStopping, EpochScoring\nfrom skorch.dataset import ValidSplit\n\nfrom moabb import set_log_level\nfrom moabb.pipelines.features import StandardScaler_Epoch\nfrom moabb.pipelines.utils_pytorch import BraindecodeDatasetLoader, InputShapeSetterEEG\nfrom moabb.utils import setup_seed\n\n\nset_log_level(\"info\")"
"# Authors: Igor Carrara <[email protected]>\n#\n# License: BSD (3-clause)\n\nfrom pickle import load\n\nimport keras\nimport torch\nfrom braindecode import EEGClassifier\nfrom braindecode.models import EEGInception\nfrom scikeras.wrappers import KerasClassifier\nfrom sklearn.pipeline import Pipeline, make_pipeline\nfrom skorch.callbacks import EarlyStopping, EpochScoring\nfrom skorch.dataset import ValidSplit\n\nfrom moabb import set_log_level\nfrom moabb.pipelines.features import StandardScaler_Epoch\nfrom moabb.utils import setup_seed\n\n\nset_log_level(\"info\")"
]
},
{
Expand Down Expand Up @@ -98,7 +98,7 @@
},
"outputs": [],
"source": [
"# Set EEG Inception model\nmodel = EEGInception(in_channels=22, n_classes=2)\n\n# Hyperparameter\nLEARNING_RATE = 0.0001\nWEIGHT_DECAY = 0\nBATCH_SIZE = 64\nSEED = 42\nVERBOSE = 1\nEPOCH = 2\nPATIENCE = 3\n\n# Define a Skorch classifier\nclf = EEGClassifier(\n module=model,\n criterion=torch.nn.CrossEntropyLoss,\n optimizer=torch.optim.Adam,\n optimizer__lr=LEARNING_RATE,\n batch_size=BATCH_SIZE,\n max_epochs=EPOCH,\n train_split=ValidSplit(0.2, random_state=SEED),\n callbacks=[\n EarlyStopping(monitor=\"valid_loss\", patience=PATIENCE),\n EpochScoring(\n scoring=\"accuracy\", on_train=True, name=\"train_acc\", lower_is_better=False\n ),\n EpochScoring(\n scoring=\"accuracy\", on_train=False, name=\"valid_acc\", lower_is_better=False\n ),\n InputShapeSetterEEG(\n params_list=[\"in_channels\", \"input_window_samples\", \"n_classes\"],\n ),\n ],\n verbose=VERBOSE, # Not printing the results for each epoch\n)\n\nclf.initialize()\n\nf_params = \"./results/Models_CrossSession/BNCI2014-001/1/braindecode_EEGInception/EEGInception_fitted_best_model.pkl\"\nf_optimizer = \"./results/Models_CrossSession/BNCI2014-001/1/braindecode_EEGInception/EEGInception_fitted_best_optim.pkl\"\nf_history = \"./results/Models_CrossSession/BNCI2014-001/1/braindecode_EEGInception/EEGInception_fitted_best_history.json\"\n\nclf.load_params(f_params=f_params, f_optimizer=f_optimizer, f_history=f_history)\n\n# Create the dataset\ncreate_dataset = BraindecodeDatasetLoader(drop_last_window=False)\n\n# Create the pipelines\npipes_pytorch = Pipeline([(\"Braindecode_dataset\", create_dataset), (\"EEGInception\", clf)])"
"# Hyperparameter\nLEARNING_RATE = 0.0001\nWEIGHT_DECAY = 0\nBATCH_SIZE = 64\nSEED = 42\nVERBOSE = 1\nEPOCH = 2\nPATIENCE = 3\n\n# Define a Skorch classifier\nclf = EEGClassifier(\n module=EEGInception,\n optimizer=torch.optim.Adam,\n optimizer__lr=LEARNING_RATE,\n batch_size=BATCH_SIZE,\n max_epochs=EPOCH,\n train_split=ValidSplit(0.2, random_state=SEED),\n callbacks=[\n EarlyStopping(monitor=\"valid_loss\", patience=PATIENCE),\n EpochScoring(\n scoring=\"accuracy\", on_train=True, name=\"train_acc\", lower_is_better=False\n ),\n EpochScoring(\n scoring=\"accuracy\", on_train=False, name=\"valid_acc\", lower_is_better=False\n ),\n ],\n verbose=VERBOSE, # Not printing the results for each epoch\n)\n\nclf.initialize()\n\nf_params = \"./results/Models_CrossSession/BNCI2014-001/1/braindecode_EEGInception/EEGInception_fitted_best_model.pkl\"\nf_optimizer = \"./results/Models_CrossSession/BNCI2014-001/1/braindecode_EEGInception/EEGInception_fitted_best_optim.pkl\"\nf_history = \"./results/Models_CrossSession/BNCI2014-001/1/braindecode_EEGInception/EEGInception_fitted_best_history.json\"\n\nclf.load_params(f_params=f_params, f_optimizer=f_optimizer, f_history=f_history)\n\n# Create the pipelines\npipes_pytorch = make_pipeline(clf)"
]
}
],
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17 changes: 3 additions & 14 deletions docs/_downloads/8fed52c2a57f02454c33ebb464a390de/load_model.py
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Expand Up @@ -16,13 +16,12 @@
from braindecode import EEGClassifier
from braindecode.models import EEGInception
from scikeras.wrappers import KerasClassifier
from sklearn.pipeline import Pipeline
from sklearn.pipeline import Pipeline, make_pipeline
from skorch.callbacks import EarlyStopping, EpochScoring
from skorch.dataset import ValidSplit

from moabb import set_log_level
from moabb.pipelines.features import StandardScaler_Epoch
from moabb.pipelines.utils_pytorch import BraindecodeDatasetLoader, InputShapeSetterEEG
from moabb.utils import setup_seed


Expand Down Expand Up @@ -70,9 +69,6 @@
###############################################################################
# Loading the PyTorch model

# Set EEG Inception model
model = EEGInception(in_channels=22, n_classes=2)

# Hyperparameter
LEARNING_RATE = 0.0001
WEIGHT_DECAY = 0
Expand All @@ -84,8 +80,7 @@

# Define a Skorch classifier
clf = EEGClassifier(
module=model,
criterion=torch.nn.CrossEntropyLoss,
module=EEGInception,
optimizer=torch.optim.Adam,
optimizer__lr=LEARNING_RATE,
batch_size=BATCH_SIZE,
Expand All @@ -99,9 +94,6 @@
EpochScoring(
scoring="accuracy", on_train=False, name="valid_acc", lower_is_better=False
),
InputShapeSetterEEG(
params_list=["in_channels", "input_window_samples", "n_classes"],
),
],
verbose=VERBOSE, # Not printing the results for each epoch
)
Expand All @@ -114,8 +106,5 @@

clf.load_params(f_params=f_params, f_optimizer=f_optimizer, f_history=f_history)

# Create the dataset
create_dataset = BraindecodeDatasetLoader(drop_last_window=False)

# Create the pipelines
pipes_pytorch = Pipeline([("Braindecode_dataset", create_dataset), ("EEGInception", clf)])
pipes_pytorch = make_pipeline(clf)
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Expand Up @@ -16,14 +16,13 @@
import torch
from braindecode import EEGClassifier
from braindecode.models import EEGNetv4
from sklearn.pipeline import Pipeline
from sklearn.pipeline import make_pipeline
from skorch.callbacks import EarlyStopping, EpochScoring
from skorch.dataset import ValidSplit

from moabb.datasets import BNCI2014_001
from moabb.evaluations import CrossSessionEvaluation
from moabb.paradigms import MotorImagery
from moabb.pipelines.utils_pytorch import BraindecodeDatasetLoader, InputShapeSetterEEG
from moabb.utils import setup_seed


Expand Down Expand Up @@ -81,8 +80,6 @@
)
subjects = [1]
X, _, _ = paradigm.get_data(dataset=dataset, subjects=subjects)
# Define Transformer of Dataset compatible with Brain Decode
create_dataset = BraindecodeDatasetLoader()

##############################################################################
# Create Pipelines
Expand All @@ -94,16 +91,9 @@
# callbacks InputShapeSetterEEG, where we have to specify the correct name of the parameter.
# Here, we will use the EEGNet v4 model [1]_ .

model = EEGNetv4(in_chans=1, n_classes=1, input_window_samples=100)

# Send model to GPU
if cuda:
model.cuda()

# Define a Skorch classifier
clf = EEGClassifier(
module=model,
criterion=torch.nn.CrossEntropyLoss,
module=EEGNetv4,
optimizer=torch.optim.Adam,
optimizer__lr=LEARNING_RATE,
batch_size=BATCH_SIZE,
Expand All @@ -118,16 +108,13 @@
EpochScoring(
scoring="accuracy", on_train=False, name="valid_acc", lower_is_better=False
),
InputShapeSetterEEG(
params_list=["in_chans", "input_window_samples", "n_classes"],
),
],
verbose=1, # Not printing the results for each epoch
)

# Create the pipelines
pipes = {}
pipes["EEGNetV4"] = Pipeline([("Braindecode_dataset", create_dataset), ("Net", clf)])
pipes["EEGNetV4"] = make_pipeline(clf)

##############################################################################
# Evaluation
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Expand Up @@ -781,7 +781,7 @@ <h2>Evaluation<a class="headerlink" href="#evaluation" title="Permalink to this
&#39;right_hand&#39;: 12&gt;
warn(f&quot;warnEpochs {epochs}&quot;)

BNCI2014-001-CrossSession: 50%|##### | 1/2 [00:05&lt;00:05, 5.58s/it]/home/runner/work/moabb/moabb/moabb/datasets/preprocessing.py:273: UserWarning: warnEpochs &lt;Epochs | 24 events (all good), 2 – 6 s, baseline off, ~4.1 MB, data loaded,
BNCI2014-001-CrossSession: 50%|##### | 1/2 [00:05&lt;00:05, 5.56s/it]/home/runner/work/moabb/moabb/moabb/datasets/preprocessing.py:273: UserWarning: warnEpochs &lt;Epochs | 24 events (all good), 2 – 6 s, baseline off, ~4.1 MB, data loaded,
&#39;left_hand&#39;: 12
&#39;right_hand&#39;: 12&gt;
warn(f&quot;warnEpochs {epochs}&quot;)
Expand Down Expand Up @@ -878,8 +878,8 @@ <h2>Evaluation<a class="headerlink" href="#evaluation" title="Permalink to this
&#39;right_hand&#39;: 12&gt;
warn(f&quot;warnEpochs {epochs}&quot;)

BNCI2014-001-CrossSession: 100%|##########| 2/2 [00:10&lt;00:00, 5.39s/it]
BNCI2014-001-CrossSession: 100%|##########| 2/2 [00:10&lt;00:00, 5.42s/it]
BNCI2014-001-CrossSession: 100%|##########| 2/2 [00:11&lt;00:00, 5.51s/it]
BNCI2014-001-CrossSession: 100%|##########| 2/2 [00:11&lt;00:00, 5.52s/it]
</pre></div>
</div>
<p>After processing the two, we simply concatenate the results.</p>
Expand Down Expand Up @@ -924,7 +924,7 @@ <h2>Plot Results<a class="headerlink" href="#plot-results" title="Permalink to t
<a href="https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.show.html#matplotlib.pyplot.show" title="matplotlib.pyplot.show" class="sphx-glr-backref-module-matplotlib-pyplot sphx-glr-backref-type-py-function"><span class="n">plt</span><span class="o">.</span><span class="n">show</span></a><span class="p">()</span>
</pre></div>
</div>
<img src="../../_images/sphx_glr_plot_filterbank_csp_vs_csp_001.png" srcset="../../_images/sphx_glr_plot_filterbank_csp_vs_csp_001.png" alt="plot filterbank csp vs csp" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> ( 0 minutes 13.040 seconds)</p>
<img src="../../_images/sphx_glr_plot_filterbank_csp_vs_csp_001.png" srcset="../../_images/sphx_glr_plot_filterbank_csp_vs_csp_001.png" alt="plot filterbank csp vs csp" class = "sphx-glr-single-img"/><p class="sphx-glr-timing"><strong>Total running time of the script:</strong> ( 0 minutes 13.249 seconds)</p>
<p><strong>Estimated memory usage:</strong> 282 MB</p>
<div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-advanced-examples-plot-filterbank-csp-vs-csp-py">
<div class="sphx-glr-download sphx-glr-download-python docutils container">
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Original file line number Diff line number Diff line change
Expand Up @@ -762,8 +762,8 @@ <h2>Running the Evaluation<a class="headerlink" href="#running-the-evaluation" t
&#39;left_hand&#39;: 12&gt;
warn(f&quot;warnEpochs {epochs}&quot;)

BNCI2014-001-WithinSession: 100%|##########| 1/1 [00:10&lt;00:00, 10.78s/it]
BNCI2014-001-WithinSession: 100%|##########| 1/1 [00:10&lt;00:00, 10.78s/it]
BNCI2014-001-WithinSession: 100%|##########| 1/1 [00:10&lt;00:00, 10.41s/it]
BNCI2014-001-WithinSession: 100%|##########| 1/1 [00:10&lt;00:00, 10.41s/it]
</pre></div>
</div>
</section>
Expand Down Expand Up @@ -837,8 +837,8 @@ <h2>Load Best Model Parameter<a class="headerlink" href="#load-best-model-parame
Best Parameter l1_ratio Session_T VanillaEN: 0.75
</pre></div>
</div>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> ( 0 minutes 13.269 seconds)</p>
<p><strong>Estimated memory usage:</strong> 181 MB</p>
<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> ( 0 minutes 12.873 seconds)</p>
<p><strong>Estimated memory usage:</strong> 143 MB</p>
<div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-advanced-examples-plot-grid-search-withinsession-py">
<div class="sphx-glr-download sphx-glr-download-python docutils container">
<p><a class="reference download internal" download="" href="../../_downloads/b298e4b36adf2bb5cb6f65682eec852f/plot_grid_search_withinsession.py"><code class="xref download docutils literal notranslate"><span class="pre">Download</span> <span class="pre">Python</span> <span class="pre">source</span> <span class="pre">code:</span> <span class="pre">plot_grid_search_withinsession.py</span></code></a></p>
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