sortion/TensorBird
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity

Add image dataset, batch convertion bash script,

Browse Source 
jupyter-notebook...
This commit is contained in:
Samuel Ortion 2021-03-06 18:27:41 +01:00
parent 504dd98b9d
commit cd8eca013e
9 changed files with 2760 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.gitignore vendored Normal file
View File

@ -0,0 +1,2 @@
.vscode/
tb-venv/

11
data/sp_names.csv Normal file
View File

@ -0,0 +1,11 @@
sp_code,sp_latin,sp_fr
cyacae,Cyanistes caeruleus,Mésange bleue
parmaj,Parus major,Mésange charbonnière
erirub,Erithacus rubecula,Rougegorge familier
prumod,Prunella modularis,Accenteur mouchet
pasdom,Passer domesticus,Moineau domestique
turmer,Turdus merula,Merle noir
felcat,Felix catus,Chat domestique
fricoe,Fringilla coelebs,Pinson des arbres
stedec,Streptopelia decaocto,Tourterelle turque
carcar,Carduelis carduelis,Chardonneret élégant
1 sp_code sp_latin sp_fr
2 cyacae Cyanistes caeruleus Mésange bleue
3 parmaj Parus major Mésange charbonnière
4 erirub Erithacus rubecula Rougegorge familier
5 prumod Prunella modularis Accenteur mouchet
6 pasdom Passer domesticus Moineau domestique
7 turmer Turdus merula Merle noir
8 felcat Felix catus Chat domestique
9 fricoe Fringilla coelebs Pinson des arbres
10 stedec Streptopelia decaocto Tourterelle turque
11 carcar Carduelis carduelis Chardonneret élégant

1
data/species_dataset Symbolic link
View File

@ -0,0 +1 @@
/home/ortion/Documents/PiCameraTrap/captures/species_dataset/

899
src/.ipynb_checkpoints/Bird_ID_404_species_CNN_TL_clean-checkpoint.ipynb Normal file
View File

@ -0,0 +1,899 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "z-7UORN7Ymoo"
},
"source": [
"Mount the drive to the instance."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "9X2hja-OpXM9"
},
"outputs": [],
"source": [
"from google.colab import drive\n",
"drive.mount('/content/gdrive')"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "fjU2n68zYxU3"
},
"source": [
"Import various modules.\n",
"\n",
"I used Tnesorflow and its Keras library as the backend. The Keras module is for preprocessing images. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "QIR81L-ArDn3"
},
"outputs": [],
"source": [
"!pip install -q tensorflow-gpu==2.0.0-alpha0\n",
"import cv2\n",
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt\n",
"import matplotlib.patches as patches\n",
"from __future__ import absolute_import, division, print_function\n",
"import os\n",
"import tensorflow as tf\n",
"from sklearn.model_selection import train_test_split\n",
"from keras.utils import to_categorical\n",
"from keras.callbacks import ModelCheckpoint, ReduceLROnPlateau, EarlyStopping\n",
"from keras.preprocessing import image\n",
"keras = tf.keras\n",
"datapath = '/content/gdrive/My Drive/Bird_ID_project/nabirds'"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "GVPN6iW0IvZ5"
},
"source": [
"Reading in the pandas dataframe. It actually doesn't provide much beside the unique species class names."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "K99e_KEnkN4p"
},
"outputs": [],
"source": [
"train_frame = pd.read_csv(datapath+'/train.csv')\n",
"val_frame = pd.read_csv(datapath+'/val.csv')\n",
"test_frame = pd.read_csv(datapath+'/test.csv')\n",
"# train_frame\n",
"Bird_list=train_frame.class_name_sp.unique()\n",
"Bird_id=train_frame.class_id_sp.unique()\n",
"# print(Bird_list, Bird_id)\n",
"Birds = dict(zip(Bird_id, Bird_list))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "R9pJGyS8b83K"
},
"source": [
"Unzip the tar.gz files **to the Google Colab instance**. This drastically increased the training speed."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "cYGuyyUINUQ3"
},
"outputs": [],
"source": [
"!tar -xzf \"gdrive/My Drive/Bird_ID_project/nabirds/data.tar.gz\"\n",
"!tar -xzf \"gdrive/My Drive/Bird_ID_project/nabirds/Darren_data.tar.gz\""
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "GWP0UQZdBDk1"
},
"outputs": [],
"source": [
"!mv /content/Darren_test/0289 /content/Darren_test/0867\n",
"!mv /content/Darren_test/0095 /content/Darren_test/0553\n",
"!rm -rf /content/Darren_test/NIL"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "0vRSm4DVI9Jd"
},
"source": [
"Using Keras image generator to reduce RAM footprint (instead of using a large numpy array)."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "BxCuJxxxl2ge"
},
"outputs": [],
"source": [
"train_datagen = image.ImageDataGenerator(\n",
" rescale=1./255,\n",
"# width_shift_range=0.1,\n",
"# height_shift_range=0.1,\n",
"# zoom_range=0.1,\n",
" fill_mode='constant',\n",
" horizontal_flip=True,\n",
" dtype=np.float32)\n",
"\n",
"val_datagen = image.ImageDataGenerator(\n",
" rescale=1./255, \n",
" dtype=np.float32)\n",
"\n",
"test_datagen = image.ImageDataGenerator(\n",
" rescale=1./255,\n",
" dtype=np.float32)\n",
"\n",
"train_generator = train_datagen.flow_from_directory(\n",
" directory='/content/data/train/',\n",
" #directory=datapath + '/data/train/',\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')\n",
"\n",
"validation_generator = val_datagen.flow_from_directory(\n",
" #directory=datapath + '/data/val/',\n",
" directory='/content/data/val/',\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')\n",
"\n",
"test_generator = test_datagen.flow_from_directory(\n",
" #directory=datapath + '/data/test/',\n",
" directory='/content/data/test/',\n",
" shuffle=False,\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "HlsRpRXDMicF"
},
"source": [
"Research has shown that starting from scratch will not work. So we use MobileNet V2 as our feature extractor. This is a relatively small network, which will help in the future when we want to run near real time inferences. We also add two layers: One global average and one prediction. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "ytj6wsAdM7Un"
},
"outputs": [],
"source": [
"IMG_SHAPE = (224,224,3)\n",
"base_model = tf.keras.applications.MobileNetV2(input_shape=IMG_SHAPE,\n",
" include_top=False, \n",
" weights='imagenet')\n",
"\n",
"base_model.trainable = False\n",
"\n",
"global_average_layer = tf.keras.layers.GlobalAveragePooling2D()\n",
"prediction_layer = keras.layers.Dense(404,activation='softmax')\n",
"base_learning_rate = 0.0001\n",
"model = tf.keras.Sequential([\n",
" base_model,\n",
" global_average_layer,\n",
" prediction_layer\n",
"])\n",
"model.compile(optimizer=tf.keras.optimizers.RMSprop(lr=base_learning_rate), \n",
" loss='categorical_crossentropy', \n",
" metrics=['accuracy'])\n",
"model.summary()"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "bGi69hxZRSvy"
},
"outputs": [],
"source": [
"def fit_model(model, batch_size=32, epochs=10): \n",
" history = model.fit_generator(\n",
" generator=train_generator,\n",
" steps_per_epoch=(len(train_frame) // batch_size),\n",
" epochs=epochs,\n",
" validation_data=validation_generator,\n",
" callbacks=None\n",
" )\n",
" score = model.evaluate_generator(train_generator, verbose=1)\n",
" probs = model.predict_generator(test_generator, verbose=1)\n",
" return model, score, probs, history\n"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "dt80nu7nQlzm"
},
"outputs": [],
"source": [
"fit_model, score, probs, history = fit_model(model, batch_size=32, epochs=10)"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "YdfI5Fzw6CRx"
},
"outputs": [],
"source": [
"def top3(probs, GT):\n",
" t3 = np.argsort(probs)[-3:]\n",
" #print(t3)\n",
" if GT in t3:\n",
" return 1\n",
" else:\n",
" return 0\n",
" \n",
"def top5(probs, GT):\n",
" t5 = np.argsort(probs)[-5:]\n",
" if GT in t5:\n",
" return 1\n",
" else:\n",
" return 0\n",
" \n",
"def top3_idx(probs):\n",
" return np.flip(np.argsort(probs)[-3:],0), np.flip(probs[np.argsort(probs)[-3:]],0)\n",
" #print(t3)\n",
"\n",
"def top5_idx(probs):\n",
" return np.flip(np.argsort(probs)[-5:])\n",
" #print(t3)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "-Kb1Q3eeP7DI"
},
"source": [
"After 10 epochs we achieve 44, 64, and 72 % top 1, 3, and 5 hit rate. Not bad! But it can be better. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "2iQYi1kdSLtF"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(probs)):\n",
" P_this = np.argmax(probs[ii])\n",
" GT_this = test_generator.labels[ii]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(probs[ii],GT_this)\n",
" correct_top5 += top5(probs[ii],GT_this)\n",
" if ii < 10:\n",
" print(\"Prediction: {} ({})\".format(P_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(P_this)])]))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
" print(\"Prediction: {} \".format(P_this))\n",
" print(\"Actual: {} \".format(GT_this))\n",
" #plt.figure()\n",
" #plt.imshow(X_test[ii,:,:,:])\n",
" #plt.show()\n",
"print(correct_prediction, correct_prediction/len(probs))\n",
"print(correct_top3, correct_top3/len(probs))\n",
"print(correct_top5, correct_top5/len(probs))\n",
"print(len(probs))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "2ou1-W3SQYOK"
},
"source": [
"We see overfitting after second epoch, which seems to be a common thing when training models for bird IDs. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "7tJdIW8F6mIv"
},
"outputs": [],
"source": [
"acc = history.history['accuracy']\n",
"val_acc = history.history['val_accuracy']\n",
"\n",
"loss = history.history['loss']\n",
"val_loss = history.history['val_loss']\n",
"\n",
"plt.figure(figsize=(8, 8))\n",
"plt.subplot(2, 1, 1)\n",
"plt.plot(acc, label='Training Accuracy')\n",
"plt.plot(val_acc, label='Validation Accuracy')\n",
"plt.legend(loc='lower right')\n",
"plt.ylabel('Accuracy')\n",
"plt.ylim([min(plt.ylim()),1])\n",
"plt.title('Training Accuracy')\n",
"\n",
"plt.subplot(2, 1, 2)\n",
"plt.plot(loss, label='Training Loss')\n",
"plt.plot(val_loss, label='Validation Loss')\n",
"plt.legend(loc='upper right')\n",
"plt.ylabel('Cross Entropy')\n",
"# plt.ylim([0,1.0])\n",
"plt.title('Training Loss')\n",
"plt.xlabel('epoch')\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "FK_OysQzQ4_S"
},
"source": [
"We start to fine tune the model by allowing the last 55 layers to be trained."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "BffxJucn6wlf"
},
"outputs": [],
"source": [
"base_model.trainable = True"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "WCA4VLaUYr7P"
},
"outputs": [],
"source": [
"# Let's take a look to see how many layers are in the base model\n",
"print(\"Number of layers in the base model: \", len(base_model.layers))\n",
"\n",
"# Fine tune from this layer onwards\n",
"fine_tune_at = 100\n",
"\n",
"# Freeze all the layers before the `fine_tune_at` layer\n",
"for layer in base_model.layers[:fine_tune_at]:\n",
" layer.trainable = False"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "fbNXMyuEZd2h"
},
"outputs": [],
"source": [
"model.compile(loss='categorical_crossentropy',\n",
" optimizer = tf.keras.optimizers.RMSprop(lr=base_learning_rate/10),\n",
" metrics=['accuracy'])"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "JmYtpM-GZit-"
},
"outputs": [],
"source": [
"initial_epochs = 10\n",
"fine_tune_epochs = 10\n",
"total_epochs = initial_epochs + fine_tune_epochs\n",
"\n",
"\n",
"def fit_model_FT(model, batch_size=32, epochs=10): \n",
" history = model.fit_generator(\n",
" generator=train_generator,\n",
" steps_per_epoch=(len(train_frame) // batch_size),\n",
" epochs=total_epochs,\n",
" initial_epoch=initial_epochs,\n",
" validation_data=validation_generator,\n",
" callbacks=None\n",
" )\n",
" score = model.evaluate_generator(train_generator, verbose=1)\n",
" probs = model.predict_generator(test_generator, verbose=1)\n",
" return model, score, probs, history"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "Ng5tOm_VZ2LZ"
},
"outputs": [],
"source": [
"fit_model, score, probs, history = fit_model_FT(model, batch_size=32, epochs=10)"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "ee6U1HZLWnK8"
},
"outputs": [],
"source": [
"acc = history.history['accuracy']\n",
"val_acc = history.history['val_accuracy']\n",
"\n",
"loss = history.history['loss']\n",
"val_loss = history.history['val_loss']\n",
"\n",
"plt.figure(figsize=(8, 8))\n",
"plt.subplot(2, 1, 1)\n",
"plt.plot(acc, label='Training Accuracy')\n",
"plt.plot(val_acc, label='Validation Accuracy')\n",
"plt.legend(loc='lower right')\n",
"plt.ylabel('Accuracy')\n",
"plt.ylim([min(plt.ylim()),1])\n",
"plt.title('Training Accuracy')\n",
"\n",
"plt.subplot(2, 1, 2)\n",
"plt.plot(loss, label='Training Loss')\n",
"plt.plot(val_loss, label='Validation Loss')\n",
"plt.legend(loc='upper right')\n",
"plt.ylabel('Cross Entropy')\n",
"# plt.ylim([0,1.0])\n",
"plt.title('Training Loss')\n",
"plt.xlabel('epoch')\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "bFU-cJgNRNr3"
},
"source": [
"After 10 fine tuning epochs the hit rates increased to 63 (top), 82 (top3), and 88 % (top5)."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "fJWas9HFIm8p"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(probs)):\n",
" P_this = np.argmax(probs[ii])\n",
" GT_this = test_generator.labels[ii]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(probs[ii],GT_this)\n",
" correct_top5 += top5(probs[ii],GT_this)\n",
" if ii % 100 == 20:\n",
" t3, p3 = top3_idx(probs[ii])\n",
" print(\"Prediction: {}, {}, or {} ({} ({:.1f} %), {} ({:.1f} %), or {} ({:.1f} %))\".format(t3[0], t3[1], t3[2] ,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[0])])], p3[0] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[1])])], p3[1] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[2])])], p3[2] * 100))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
"\n",
" \n",
" plt.figure()\n",
" image = plt.imread('data/test/'+test_generator.filenames[ii])\n",
" plt.imshow(image)\n",
" plt.show()\n",
"print(correct_prediction, correct_prediction/len(probs))\n",
"print(correct_top3, correct_top3/len(probs))\n",
"print(correct_top5, correct_top5/len(probs))\n",
"print(len(probs))"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "5BfjDfYfSaGs"
},
"outputs": [],
"source": [
"Prediction = []\n",
"Prediction3 = []\n",
"Correct_prediction3 = []\n",
"for ii in range(len(probs)):\n",
" Prediction.append(np.argmax(probs[ii]))\n",
" Prediction3.append(top3_idx(probs[ii])[0])\n",
" Correct_prediction3.append(np.asscalar(np.in1d(test_generator.labels[ii],Prediction3[ii])))\n",
"\n",
" \n",
"Correct_predicted = []\n",
"Correct_predicted3 = []\n",
"Species_length = []\n",
"for ii in range(len(np.unique(test_generator.labels))):\n",
" Species_length.append(sum((test_generator.labels == ii)))\n",
" Correct_predicted.append((sum((test_generator.labels == ii) & (Prediction == test_generator.labels)))/sum(test_generator.labels == ii))\n",
" Correct_predicted3.append(sum((test_generator.labels == ii) & (Correct_prediction3))/sum(test_generator.labels == ii))\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "y090L25JReE_"
},
"source": [
"For some species the model performed terribly. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "hYumabaNVOMA"
},
"outputs": [],
"source": [
"for ii in range(len(np.unique(test_generator.labels))):\n",
"# if sum((test_generator.labels == ii)) < 8:\n",
" if Correct_predicted3[ii] < 0.4:\n",
" print('{}: {:.2f}, {:.2f}, {}, {}'.format(ii, Correct_predicted[ii], Correct_predicted3[ii], sum((train_generator.labels == ii)), Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(ii)])]))"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "eWALVyB-PwNz"
},
"outputs": [],
"source": [
"initial_epochs = 20\n",
"fine_tune_epochs = 10\n",
"total_epochs = initial_epochs + fine_tune_epochs\n",
"\n",
"\n",
"def fit_model_FT2(model, batch_size=32, epochs=10): \n",
" history = model.fit_generator(\n",
" generator=train_generator,\n",
" steps_per_epoch=(len(train_frame) // batch_size),\n",
" epochs=total_epochs,\n",
" initial_epoch=initial_epochs,\n",
" validation_data=validation_generator,\n",
" callbacks=None\n",
" )\n",
" score = model.evaluate_generator(train_generator, verbose=1)\n",
" probs = model.predict_generator(test_generator, verbose=1)\n",
" return model, score, probs, history"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "sqEGCIJmP3aC"
},
"outputs": [],
"source": [
"#fit_model, score, probs, history = fit_model_FT(model, X_train, X_test, Y_train, Y_test, batch_size=32, epochs=15)\n",
"fit_model, score, probs, history = fit_model_FT2(model, batch_size=32, epochs=10)\n",
"model.save(datapath + '/model3_30.h5')\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "4DyFi0YJH5iv"
},
"outputs": [],
"source": [
"probs = model.predict_generator(test_generator, verbose=1)\n",
"np.savetxt(datapath + '/probs30.txt', probs)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "fB66sNewSaue"
},
"source": [
"After another 10 fine tuning epochs (total = 30 epochs) we have 66, 84, 89 % top 1, 3, 5 hit rate. At this point it may be more helpful to refine the probability based on the location and time of year that the picture is taken. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "bjudiCZmKEe3"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(probs)):\n",
" P_this = np.argmax(probs[ii])\n",
" GT_this = test_generator.labels[ii]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(probs[ii],GT_this)\n",
" correct_top5 += top5(probs[ii],GT_this)\n",
" if ii % 100 == 26:\n",
"# if test_generator.labels[ii] == 10: # Gadwall\n",
" #print(\"Prediction: {} ({})\".format(P_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(top3_idx(probs[ii]))])]))\n",
" t3, p3 = top3_idx(probs[ii])\n",
" print(\"Prediction: {}, {}, or {} ({} ({:.1f} %), {} ({:.1f} %), or {} ({:.1f} %))\".format(t3[0], t3[1], t3[2] ,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[0])])], p3[0] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[1])])], p3[1] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[2])])], p3[2] * 100))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
"# print(\"Prediction: {} \".format(P_this))\n",
"# print(\"Actual: {} \".format(GT_this))\n",
"# print('data/test/'+test_generator.filenames[ii])\n",
" \n",
" plt.figure()\n",
" image = plt.imread('data/test/'+test_generator.filenames[ii])\n",
" plt.imshow(image)\n",
" plt.show()\n",
"print(correct_prediction, correct_prediction/len(probs))\n",
"print(correct_top3, correct_top3/len(probs))\n",
"print(correct_top5, correct_top5/len(probs))\n",
"print(len(probs))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "RlxJGKb8TNYY"
},
"source": [
"Using my photos to test."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "TRgQdjw7APzO"
},
"outputs": [],
"source": [
"Darren_test_generator = test_datagen.flow_from_directory(\n",
" #directory=datapath + '/data/test/',\n",
" directory='/content/Darren_test/',\n",
" shuffle=False,\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "FbuTUb_6AaGy"
},
"outputs": [],
"source": [
"Darren_probs = model.predict_generator(Darren_test_generator, verbose=1)"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "bf_PABndAb7s"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(Darren_probs)):\n",
"# for ii in [0]:\n",
" P_this = np.argmax(Darren_probs[ii])\n",
" GT_this = test_generator.class_indices[list(Darren_test_generator.class_indices.keys())[Darren_test_generator.labels[ii]]]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(Darren_probs[ii],GT_this)\n",
" correct_top5 += top5(Darren_probs[ii],GT_this)\n",
"# if ii % 100 == 26:\n",
"# if test_generator.labels[ii] == 10: # Gadwall\n",
" #print(\"Prediction: {} ({})\".format(P_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(top3_idx(probs[ii]))])]))\n",
" t3, p3 = top3_idx(Darren_probs[ii])\n",
" print(\"Prediction: {}, {}, or {} ({} ({:.1f} %), {} ({:.1f} %), or {} ({:.1f} %))\".format(\n",
" t3[0], t3[1], t3[2] ,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[0])])], p3[0] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[1])])], p3[1] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[2])])], p3[2] * 100))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
"# print(\"Prediction: {} \".format(P_this))\n",
"# print(\"Actual: {} \".format(GT_this))\n",
"# print('data/test/'+test_generator.filenames[ii])\n",
" \n",
" plt.figure()\n",
" image = plt.imread('Darren_test/'+Darren_test_generator.filenames[ii])\n",
" plt.imshow(image)\n",
" plt.show()\n",
"print(correct_prediction, correct_prediction/len(Darren_probs))\n",
"print(correct_top3, correct_top3/len(Darren_probs))\n",
"print(correct_top5, correct_top5/len(Darren_probs))\n",
"print(len(Darren_probs))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "Yg-w5GA6TIZy"
},
"source": [
"Below are scratch codes."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "h_6UTR_-hBIs"
},
"outputs": [],
"source": [
"#Birds\n",
"class_indices_inv_map = {v: k for k, v in test_generator.class_indices.items()} \n",
"\n",
"import pickle\n",
"\n",
"# write python dict to a file\n",
"output = open(datapath+'/class_indices_inv_map.pkl', 'wb')\n",
"pickle.dump(class_indices_inv_map, output)\n",
"output.close()\n",
"output = open(datapath+'/Birds.pkl', 'wb')\n",
"pickle.dump(Birds, output)\n",
"output.close()"
]
}
],
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [],
"name": "Bird_ID_404_species_CNN_TL_clean.ipynb",
"provenance": [],
"version": "0.3.2"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
}
},
"nbformat": 4,
"nbformat_minor": 1
}

467
src/.ipynb_checkpoints/TensorBirdId-checkpoint.ipynb Normal file
View File

File diff suppressed because one or more lines are too long

899
src/Bird_ID_404_species_CNN_TL_clean.ipynb Normal file
View File

@ -0,0 +1,899 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "z-7UORN7Ymoo"
},
"source": [
"Mount the drive to the instance."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "9X2hja-OpXM9"
},
"outputs": [],
"source": [
"from google.colab import drive\n",
"drive.mount('/content/gdrive')"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "fjU2n68zYxU3"
},
"source": [
"Import various modules.\n",
"\n",
"I used Tnesorflow and its Keras library as the backend. The Keras module is for preprocessing images. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "QIR81L-ArDn3"
},
"outputs": [],
"source": [
"!pip install -q tensorflow-gpu==2.0.0-alpha0\n",
"import cv2\n",
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt\n",
"import matplotlib.patches as patches\n",
"from __future__ import absolute_import, division, print_function\n",
"import os\n",
"import tensorflow as tf\n",
"from sklearn.model_selection import train_test_split\n",
"from keras.utils import to_categorical\n",
"from keras.callbacks import ModelCheckpoint, ReduceLROnPlateau, EarlyStopping\n",
"from keras.preprocessing import image\n",
"keras = tf.keras\n",
"datapath = '/content/gdrive/My Drive/Bird_ID_project/nabirds'"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "GVPN6iW0IvZ5"
},
"source": [
"Reading in the pandas dataframe. It actually doesn't provide much beside the unique species class names."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "K99e_KEnkN4p"
},
"outputs": [],
"source": [
"train_frame = pd.read_csv(datapath+'/train.csv')\n",
"val_frame = pd.read_csv(datapath+'/val.csv')\n",
"test_frame = pd.read_csv(datapath+'/test.csv')\n",
"# train_frame\n",
"Bird_list=train_frame.class_name_sp.unique()\n",
"Bird_id=train_frame.class_id_sp.unique()\n",
"# print(Bird_list, Bird_id)\n",
"Birds = dict(zip(Bird_id, Bird_list))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "R9pJGyS8b83K"
},
"source": [
"Unzip the tar.gz files **to the Google Colab instance**. This drastically increased the training speed."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "cYGuyyUINUQ3"
},
"outputs": [],
"source": [
"!tar -xzf \"gdrive/My Drive/Bird_ID_project/nabirds/data.tar.gz\"\n",
"!tar -xzf \"gdrive/My Drive/Bird_ID_project/nabirds/Darren_data.tar.gz\""
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "GWP0UQZdBDk1"
},
"outputs": [],
"source": [
"!mv /content/Darren_test/0289 /content/Darren_test/0867\n",
"!mv /content/Darren_test/0095 /content/Darren_test/0553\n",
"!rm -rf /content/Darren_test/NIL"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "0vRSm4DVI9Jd"
},
"source": [
"Using Keras image generator to reduce RAM footprint (instead of using a large numpy array)."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "BxCuJxxxl2ge"
},
"outputs": [],
"source": [
"train_datagen = image.ImageDataGenerator(\n",
" rescale=1./255,\n",
"# width_shift_range=0.1,\n",
"# height_shift_range=0.1,\n",
"# zoom_range=0.1,\n",
" fill_mode='constant',\n",
" horizontal_flip=True,\n",
" dtype=np.float32)\n",
"\n",
"val_datagen = image.ImageDataGenerator(\n",
" rescale=1./255, \n",
" dtype=np.float32)\n",
"\n",
"test_datagen = image.ImageDataGenerator(\n",
" rescale=1./255,\n",
" dtype=np.float32)\n",
"\n",
"train_generator = train_datagen.flow_from_directory(\n",
" directory='/content/data/train/',\n",
" #directory=datapath + '/data/train/',\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')\n",
"\n",
"validation_generator = val_datagen.flow_from_directory(\n",
" #directory=datapath + '/data/val/',\n",
" directory='/content/data/val/',\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')\n",
"\n",
"test_generator = test_datagen.flow_from_directory(\n",
" #directory=datapath + '/data/test/',\n",
" directory='/content/data/test/',\n",
" shuffle=False,\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "HlsRpRXDMicF"
},
"source": [
"Research has shown that starting from scratch will not work. So we use MobileNet V2 as our feature extractor. This is a relatively small network, which will help in the future when we want to run near real time inferences. We also add two layers: One global average and one prediction. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "ytj6wsAdM7Un"
},
"outputs": [],
"source": [
"IMG_SHAPE = (224,224,3)\n",
"base_model = tf.keras.applications.MobileNetV2(input_shape=IMG_SHAPE,\n",
" include_top=False, \n",
" weights='imagenet')\n",
"\n",
"base_model.trainable = False\n",
"\n",
"global_average_layer = tf.keras.layers.GlobalAveragePooling2D()\n",
"prediction_layer = keras.layers.Dense(404,activation='softmax')\n",
"base_learning_rate = 0.0001\n",
"model = tf.keras.Sequential([\n",
" base_model,\n",
" global_average_layer,\n",
" prediction_layer\n",
"])\n",
"model.compile(optimizer=tf.keras.optimizers.RMSprop(lr=base_learning_rate), \n",
" loss='categorical_crossentropy', \n",
" metrics=['accuracy'])\n",
"model.summary()"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "bGi69hxZRSvy"
},
"outputs": [],
"source": [
"def fit_model(model, batch_size=32, epochs=10): \n",
" history = model.fit_generator(\n",
" generator=train_generator,\n",
" steps_per_epoch=(len(train_frame) // batch_size),\n",
" epochs=epochs,\n",
" validation_data=validation_generator,\n",
" callbacks=None\n",
" )\n",
" score = model.evaluate_generator(train_generator, verbose=1)\n",
" probs = model.predict_generator(test_generator, verbose=1)\n",
" return model, score, probs, history\n"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "dt80nu7nQlzm"
},
"outputs": [],
"source": [
"fit_model, score, probs, history = fit_model(model, batch_size=32, epochs=10)"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "YdfI5Fzw6CRx"
},
"outputs": [],
"source": [
"def top3(probs, GT):\n",
" t3 = np.argsort(probs)[-3:]\n",
" #print(t3)\n",
" if GT in t3:\n",
" return 1\n",
" else:\n",
" return 0\n",
" \n",
"def top5(probs, GT):\n",
" t5 = np.argsort(probs)[-5:]\n",
" if GT in t5:\n",
" return 1\n",
" else:\n",
" return 0\n",
" \n",
"def top3_idx(probs):\n",
" return np.flip(np.argsort(probs)[-3:],0), np.flip(probs[np.argsort(probs)[-3:]],0)\n",
" #print(t3)\n",
"\n",
"def top5_idx(probs):\n",
" return np.flip(np.argsort(probs)[-5:])\n",
" #print(t3)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "-Kb1Q3eeP7DI"
},
"source": [
"After 10 epochs we achieve 44, 64, and 72 % top 1, 3, and 5 hit rate. Not bad! But it can be better. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "2iQYi1kdSLtF"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(probs)):\n",
" P_this = np.argmax(probs[ii])\n",
" GT_this = test_generator.labels[ii]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(probs[ii],GT_this)\n",
" correct_top5 += top5(probs[ii],GT_this)\n",
" if ii < 10:\n",
" print(\"Prediction: {} ({})\".format(P_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(P_this)])]))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
" print(\"Prediction: {} \".format(P_this))\n",
" print(\"Actual: {} \".format(GT_this))\n",
" #plt.figure()\n",
" #plt.imshow(X_test[ii,:,:,:])\n",
" #plt.show()\n",
"print(correct_prediction, correct_prediction/len(probs))\n",
"print(correct_top3, correct_top3/len(probs))\n",
"print(correct_top5, correct_top5/len(probs))\n",
"print(len(probs))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "2ou1-W3SQYOK"
},
"source": [
"We see overfitting after second epoch, which seems to be a common thing when training models for bird IDs. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "7tJdIW8F6mIv"
},
"outputs": [],
"source": [
"acc = history.history['accuracy']\n",
"val_acc = history.history['val_accuracy']\n",
"\n",
"loss = history.history['loss']\n",
"val_loss = history.history['val_loss']\n",
"\n",
"plt.figure(figsize=(8, 8))\n",
"plt.subplot(2, 1, 1)\n",
"plt.plot(acc, label='Training Accuracy')\n",
"plt.plot(val_acc, label='Validation Accuracy')\n",
"plt.legend(loc='lower right')\n",
"plt.ylabel('Accuracy')\n",
"plt.ylim([min(plt.ylim()),1])\n",
"plt.title('Training Accuracy')\n",
"\n",
"plt.subplot(2, 1, 2)\n",
"plt.plot(loss, label='Training Loss')\n",
"plt.plot(val_loss, label='Validation Loss')\n",
"plt.legend(loc='upper right')\n",
"plt.ylabel('Cross Entropy')\n",
"# plt.ylim([0,1.0])\n",
"plt.title('Training Loss')\n",
"plt.xlabel('epoch')\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "FK_OysQzQ4_S"
},
"source": [
"We start to fine tune the model by allowing the last 55 layers to be trained."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "BffxJucn6wlf"
},
"outputs": [],
"source": [
"base_model.trainable = True"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "WCA4VLaUYr7P"
},
"outputs": [],
"source": [
"# Let's take a look to see how many layers are in the base model\n",
"print(\"Number of layers in the base model: \", len(base_model.layers))\n",
"\n",
"# Fine tune from this layer onwards\n",
"fine_tune_at = 100\n",
"\n",
"# Freeze all the layers before the `fine_tune_at` layer\n",
"for layer in base_model.layers[:fine_tune_at]:\n",
" layer.trainable = False"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "fbNXMyuEZd2h"
},
"outputs": [],
"source": [
"model.compile(loss='categorical_crossentropy',\n",
" optimizer = tf.keras.optimizers.RMSprop(lr=base_learning_rate/10),\n",
" metrics=['accuracy'])"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "JmYtpM-GZit-"
},
"outputs": [],
"source": [
"initial_epochs = 10\n",
"fine_tune_epochs = 10\n",
"total_epochs = initial_epochs + fine_tune_epochs\n",
"\n",
"\n",
"def fit_model_FT(model, batch_size=32, epochs=10): \n",
" history = model.fit_generator(\n",
" generator=train_generator,\n",
" steps_per_epoch=(len(train_frame) // batch_size),\n",
" epochs=total_epochs,\n",
" initial_epoch=initial_epochs,\n",
" validation_data=validation_generator,\n",
" callbacks=None\n",
" )\n",
" score = model.evaluate_generator(train_generator, verbose=1)\n",
" probs = model.predict_generator(test_generator, verbose=1)\n",
" return model, score, probs, history"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "Ng5tOm_VZ2LZ"
},
"outputs": [],
"source": [
"fit_model, score, probs, history = fit_model_FT(model, batch_size=32, epochs=10)"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "ee6U1HZLWnK8"
},
"outputs": [],
"source": [
"acc = history.history['accuracy']\n",
"val_acc = history.history['val_accuracy']\n",
"\n",
"loss = history.history['loss']\n",
"val_loss = history.history['val_loss']\n",
"\n",
"plt.figure(figsize=(8, 8))\n",
"plt.subplot(2, 1, 1)\n",
"plt.plot(acc, label='Training Accuracy')\n",
"plt.plot(val_acc, label='Validation Accuracy')\n",
"plt.legend(loc='lower right')\n",
"plt.ylabel('Accuracy')\n",
"plt.ylim([min(plt.ylim()),1])\n",
"plt.title('Training Accuracy')\n",
"\n",
"plt.subplot(2, 1, 2)\n",
"plt.plot(loss, label='Training Loss')\n",
"plt.plot(val_loss, label='Validation Loss')\n",
"plt.legend(loc='upper right')\n",
"plt.ylabel('Cross Entropy')\n",
"# plt.ylim([0,1.0])\n",
"plt.title('Training Loss')\n",
"plt.xlabel('epoch')\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "bFU-cJgNRNr3"
},
"source": [
"After 10 fine tuning epochs the hit rates increased to 63 (top), 82 (top3), and 88 % (top5)."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "fJWas9HFIm8p"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(probs)):\n",
" P_this = np.argmax(probs[ii])\n",
" GT_this = test_generator.labels[ii]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(probs[ii],GT_this)\n",
" correct_top5 += top5(probs[ii],GT_this)\n",
" if ii % 100 == 20:\n",
" t3, p3 = top3_idx(probs[ii])\n",
" print(\"Prediction: {}, {}, or {} ({} ({:.1f} %), {} ({:.1f} %), or {} ({:.1f} %))\".format(t3[0], t3[1], t3[2] ,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[0])])], p3[0] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[1])])], p3[1] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[2])])], p3[2] * 100))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
"\n",
" \n",
" plt.figure()\n",
" image = plt.imread('data/test/'+test_generator.filenames[ii])\n",
" plt.imshow(image)\n",
" plt.show()\n",
"print(correct_prediction, correct_prediction/len(probs))\n",
"print(correct_top3, correct_top3/len(probs))\n",
"print(correct_top5, correct_top5/len(probs))\n",
"print(len(probs))"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "5BfjDfYfSaGs"
},
"outputs": [],
"source": [
"Prediction = []\n",
"Prediction3 = []\n",
"Correct_prediction3 = []\n",
"for ii in range(len(probs)):\n",
" Prediction.append(np.argmax(probs[ii]))\n",
" Prediction3.append(top3_idx(probs[ii])[0])\n",
" Correct_prediction3.append(np.asscalar(np.in1d(test_generator.labels[ii],Prediction3[ii])))\n",
"\n",
" \n",
"Correct_predicted = []\n",
"Correct_predicted3 = []\n",
"Species_length = []\n",
"for ii in range(len(np.unique(test_generator.labels))):\n",
" Species_length.append(sum((test_generator.labels == ii)))\n",
" Correct_predicted.append((sum((test_generator.labels == ii) & (Prediction == test_generator.labels)))/sum(test_generator.labels == ii))\n",
" Correct_predicted3.append(sum((test_generator.labels == ii) & (Correct_prediction3))/sum(test_generator.labels == ii))\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "y090L25JReE_"
},
"source": [
"For some species the model performed terribly. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "hYumabaNVOMA"
},
"outputs": [],
"source": [
"for ii in range(len(np.unique(test_generator.labels))):\n",
"# if sum((test_generator.labels == ii)) < 8:\n",
" if Correct_predicted3[ii] < 0.4:\n",
" print('{}: {:.2f}, {:.2f}, {}, {}'.format(ii, Correct_predicted[ii], Correct_predicted3[ii], sum((train_generator.labels == ii)), Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(ii)])]))"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "eWALVyB-PwNz"
},
"outputs": [],
"source": [
"initial_epochs = 20\n",
"fine_tune_epochs = 10\n",
"total_epochs = initial_epochs + fine_tune_epochs\n",
"\n",
"\n",
"def fit_model_FT2(model, batch_size=32, epochs=10): \n",
" history = model.fit_generator(\n",
" generator=train_generator,\n",
" steps_per_epoch=(len(train_frame) // batch_size),\n",
" epochs=total_epochs,\n",
" initial_epoch=initial_epochs,\n",
" validation_data=validation_generator,\n",
" callbacks=None\n",
" )\n",
" score = model.evaluate_generator(train_generator, verbose=1)\n",
" probs = model.predict_generator(test_generator, verbose=1)\n",
" return model, score, probs, history"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "sqEGCIJmP3aC"
},
"outputs": [],
"source": [
"#fit_model, score, probs, history = fit_model_FT(model, X_train, X_test, Y_train, Y_test, batch_size=32, epochs=15)\n",
"fit_model, score, probs, history = fit_model_FT2(model, batch_size=32, epochs=10)\n",
"model.save(datapath + '/model3_30.h5')\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "4DyFi0YJH5iv"
},
"outputs": [],
"source": [
"probs = model.predict_generator(test_generator, verbose=1)\n",
"np.savetxt(datapath + '/probs30.txt', probs)"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "fB66sNewSaue"
},
"source": [
"After another 10 fine tuning epochs (total = 30 epochs) we have 66, 84, 89 % top 1, 3, 5 hit rate. At this point it may be more helpful to refine the probability based on the location and time of year that the picture is taken. "
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "bjudiCZmKEe3"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(probs)):\n",
" P_this = np.argmax(probs[ii])\n",
" GT_this = test_generator.labels[ii]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(probs[ii],GT_this)\n",
" correct_top5 += top5(probs[ii],GT_this)\n",
" if ii % 100 == 26:\n",
"# if test_generator.labels[ii] == 10: # Gadwall\n",
" #print(\"Prediction: {} ({})\".format(P_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(top3_idx(probs[ii]))])]))\n",
" t3, p3 = top3_idx(probs[ii])\n",
" print(\"Prediction: {}, {}, or {} ({} ({:.1f} %), {} ({:.1f} %), or {} ({:.1f} %))\".format(t3[0], t3[1], t3[2] ,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[0])])], p3[0] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[1])])], p3[1] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[2])])], p3[2] * 100))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
"# print(\"Prediction: {} \".format(P_this))\n",
"# print(\"Actual: {} \".format(GT_this))\n",
"# print('data/test/'+test_generator.filenames[ii])\n",
" \n",
" plt.figure()\n",
" image = plt.imread('data/test/'+test_generator.filenames[ii])\n",
" plt.imshow(image)\n",
" plt.show()\n",
"print(correct_prediction, correct_prediction/len(probs))\n",
"print(correct_top3, correct_top3/len(probs))\n",
"print(correct_top5, correct_top5/len(probs))\n",
"print(len(probs))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "RlxJGKb8TNYY"
},
"source": [
"Using my photos to test."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "TRgQdjw7APzO"
},
"outputs": [],
"source": [
"Darren_test_generator = test_datagen.flow_from_directory(\n",
" #directory=datapath + '/data/test/',\n",
" directory='/content/Darren_test/',\n",
" shuffle=False,\n",
" #classes=list(Bird_list),\n",
" target_size=(224, 224),\n",
" batch_size=32,\n",
" class_mode='categorical')"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "FbuTUb_6AaGy"
},
"outputs": [],
"source": [
"Darren_probs = model.predict_generator(Darren_test_generator, verbose=1)"
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "bf_PABndAb7s"
},
"outputs": [],
"source": [
"correct_prediction = 0\n",
"correct_top3 = 0\n",
"correct_top5 = 0\n",
"for ii in range(len(Darren_probs)):\n",
"# for ii in [0]:\n",
" P_this = np.argmax(Darren_probs[ii])\n",
" GT_this = test_generator.class_indices[list(Darren_test_generator.class_indices.keys())[Darren_test_generator.labels[ii]]]\n",
" if P_this == GT_this:\n",
" correct_prediction += 1\n",
" correct_top3 += top3(Darren_probs[ii],GT_this)\n",
" correct_top5 += top5(Darren_probs[ii],GT_this)\n",
"# if ii % 100 == 26:\n",
"# if test_generator.labels[ii] == 10: # Gadwall\n",
" #print(\"Prediction: {} ({})\".format(P_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(top3_idx(probs[ii]))])]))\n",
" t3, p3 = top3_idx(Darren_probs[ii])\n",
" print(\"Prediction: {}, {}, or {} ({} ({:.1f} %), {} ({:.1f} %), or {} ({:.1f} %))\".format(\n",
" t3[0], t3[1], t3[2] ,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[0])])], p3[0] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[1])])], p3[1] * 100,\n",
" Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(t3[2])])], p3[2] * 100))\n",
" print(\"Actual: {} ({})\".format(GT_this,Birds[int(list(test_generator.class_indices.keys())[list(test_generator.class_indices.values()).index(GT_this)])]))\n",
"# print(\"Prediction: {} \".format(P_this))\n",
"# print(\"Actual: {} \".format(GT_this))\n",
"# print('data/test/'+test_generator.filenames[ii])\n",
" \n",
" plt.figure()\n",
" image = plt.imread('Darren_test/'+Darren_test_generator.filenames[ii])\n",
" plt.imshow(image)\n",
" plt.show()\n",
"print(correct_prediction, correct_prediction/len(Darren_probs))\n",
"print(correct_top3, correct_top3/len(Darren_probs))\n",
"print(correct_top5, correct_top5/len(Darren_probs))\n",
"print(len(Darren_probs))"
]
},
{
"cell_type": "markdown",
"metadata": {
"colab_type": "text",
"id": "Yg-w5GA6TIZy"
},
"source": [
"Below are scratch codes."
]
},
{
"cell_type": "code",
"execution_count": 0,
"metadata": {
"colab": {},
"colab_type": "code",
"id": "h_6UTR_-hBIs"
},
"outputs": [],
"source": [
"#Birds\n",
"class_indices_inv_map = {v: k for k, v in test_generator.class_indices.items()} \n",
"\n",
"import pickle\n",
"\n",
"# write python dict to a file\n",
"output = open(datapath+'/class_indices_inv_map.pkl', 'wb')\n",
"pickle.dump(class_indices_inv_map, output)\n",
"output.close()\n",
"output = open(datapath+'/Birds.pkl', 'wb')\n",
"pickle.dump(Birds, output)\n",
"output.close()"
]
}
],
"metadata": {
"accelerator": "GPU",
"colab": {
"collapsed_sections": [],
"name": "Bird_ID_404_species_CNN_TL_clean.ipynb",
"provenance": [],
"version": "0.3.2"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
}
},
"nbformat": 4,
"nbformat_minor": 1
}

467
src/TensorBirdId.ipynb Normal file
View File

File diff suppressed because one or more lines are too long

14
src/resize_img.sh Executable file
View File

@ -0,0 +1,14 @@
# !/bin/bash
FOLDER="/home/ortion/Documents/projects/TensorBird/data/species_dataset/"
cd $FOLDER
N_FILES=`ls -ApR | grep -v /$ | wc -l`
i=0
for PHOTO in */*/*.jpg
do
i=$(($i+1))
BASE=`basename $PHOTO`
echo "convert $BASE $i/$N_FILES"
convert "$PHOTO" -resize 100x75 $PHOTO
done

0
src/run_tf_lite_classify_bird_pict.py Normal file
View File