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Commit eafb2dcb authored by Ines Filipa Fernandes Ramos's avatar Ines Filipa Fernandes Ramos
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notebook example_plot(ax, fontsize=24)

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example_notebook_RGC_sim.ipynb
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......@@ -63,7 +63,6 @@
{
"cell_type": "code",
"execution_count": 34,
f38591a3e541db669b81e10e304f4f091346ce53
"metadata": {},
"outputs": [],
"source": [
......@@ -77,11 +76,12 @@ f38591a3e541db669b81e10e304f4f091346ce53
" 'batch_size': 64, \n",
" 'seed': 1, \n",
" 'cuda': True,\n",
" 'normalize': False, \n",
" 'normalize': True, \n",
" 'exclude': \"images\"}\n",
"\n",
"dataloaders_RGCs = static_loaders(**dataset_config)\n",
"dat = FileTreeDataset('D://inception_loop/RGC_sim_data/data/static15032021_oval_RF', \"images\", \"responses\")" ]
"dat = FileTreeDataset('D://inception_loop/RGC_sim_data/data/static15032021_oval_RF', \"images\", \"responses\")"
]
},
{
"cell_type": "code",
......@@ -3176,7 +3176,7 @@ f38591a3e541db669b81e10e304f4f091346ce53
},
{
"cell_type": "code",
"execution_count": 172,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
......@@ -3187,9 +3187,9 @@ f38591a3e541db669b81e10e304f4f091346ce53
"from bayes_opt.logger import JSONLogger\n",
"from bayes_opt.event import Events\n",
"\n",
"neurons = [556,771]\n",
"neurons = [0,10]\n",
"\n",
"responses_training_set = responses[:,neurons]\n",
"responses_training_set = responses\n",
"images_training_set = images\n",
"\n",
"tier = 'validation'\n",
......@@ -3200,11 +3200,11 @@ f38591a3e541db669b81e10e304f4f091346ce53
" responses_validation_set.append(y.squeeze().cpu().data.numpy())\n",
" \n",
"images_validation_set = np.vstack(images_validation_set)\n",
"responses_validation_set = np.vstack(responses_validation_set)[:,neurons]\n",
"responses_validation_set = np.vstack(responses_validation_set)\n",
"\n",
"#Estimation of rcond\n",
"\n",
"def STA_estim(responses_training_set, images_training_set, rcond):\n",
"def STA_estim(neurons, responses_training_set, images_training_set, rcond):\n",
" \n",
" S = []\n",
" for i in range(len(images_training_set)):\n",
......@@ -3216,7 +3216,7 @@ f38591a3e541db669b81e10e304f4f091346ce53
" \n",
" sta_neurons = []\n",
" sta_neurons_decorr = []\n",
" for neuron in range(responses_training_set.shape[1]):\n",
" for neuron in neurons:\n",
" pseudo_inv = linalg.pinv2(S, rcond)\n",
" sta = np.dot(pseudo_inv, responses_training_set[:,neuron])\n",
" sta_neurons_decorr.append((sta/sum(responses_training_set[:,neuron])).reshape(images_training_set.shape[1],images_training_set.shape[2]))\n",
......@@ -3236,17 +3236,19 @@ f38591a3e541db669b81e10e304f4f091346ce53
"def pred_RGC_response(rfs, images):\n",
" spikes = []\n",
" for image in images:\n",
" Img_barHat = image * rfs\n",
" Img_barHat = image * rf\n",
" g = ELU(np.sum(np.sum(Img_barHat,axis=1), axis=1))\n",
" spikes.append(np.random.poisson(lam=g, size=None))\n",
" \n",
" return np.array(spikes)\n",
" return spikes\n",
"\n",
"def grid_response_prediction(rcond):\n",
" y_true = responses_validation_set\n",
" rfs, rfs_decorr = STA_estim(responses_training_set, images_training_set, rcond)\n",
" y_true = responses_validation_set[:,neurons]\n",
" rfs, rfs_decorr = STA_estim(neurons, responses_training_set, images_training_set, rcond)\n",
" y_pred = pred_RGC_response(rfs_decorr, images_validation_set)\n",
" mse = mean_squared_error(y_true, y_pred)\n",
" \n",
" return corr"
" return 1/mse"
]
},
{
......@@ -3290,7 +3292,44 @@ f38591a3e541db669b81e10e304f4f091346ce53
},
{
"cell_type": "code",
"execution_count": 171,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"fig, ax = plt.subplots(1, figsize=(7,7))\n",
"plt.imshow(sta_neurons[20:56,20:84])\n",
"plt.title('STA of target unit '+str(neuron)+' with natural stimuli')\n",
"plt.savefig(\"D://inception_loop/RGC_sim_data/results/STA_natur_target_unit_\"+str(neuron)+\".png\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%time \n",
"%%memit\n",
"#Bounded region of parameter space\n",
"pbounds={'rcond' : (1, 100)}\n",
"\n",
"optimizer_rcond_ = BayesianOptimization(\n",
" f=grid_response_prediction,\n",
" pbounds=pbounds,\n",
" random_state=1,\n",
" verbose = 1,\n",
")\n",
"\n",
"#Run optimization to maximize the target \n",
"#init_points: number of random exploration points\n",
"#n_iter: number of exploitation points\n",
"\n",
"optimizer_rcond_.maximize(init_points=5, n_iter=5)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
......@@ -3312,13 +3351,20 @@ f38591a3e541db669b81e10e304f4f091346ce53
"metadata": {},
"outputs": [],
"source": [
"TargetUnit = 556\n",
"TargetUnit = 570\n",
"#rf = np.load('D://inception_loop/RGC_sim/data/static27012021/RFs/'+str(TargetUnit)+'.npy')\n",
"rf =np.load('C://Users/Asus/Desktop/Intership EMBL/Python docs/Inception_loop/RGC_sim_data/data/static27012021/RFs/'+str(TargetUnit)+'.npy')\n",
"rf =np.load('C://Users/Asus/Desktop/Intership EMBL/Python docs/Inception_loop/Lurz_2020_code/notebooks/data/RGC_sim/static27012021/RFs/'+str(TargetUnit)+'.npy')\n",
"fig, axs = plt.subplots(figsize=(20,4))\n",
"axs.imshow(rf, vmin=-1, vmax=1, cmap=\"gray\")\n",
"axs.set_title(\"RGC RF\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"-----------------------------"
]
}
],
"metadata": {
......@@ -3337,7 +3383,7 @@ f38591a3e541db669b81e10e304f4f091346ce53
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.9"
"version": "3.8.5"
}
},
"nbformat": 4,
......
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