From c9c0915779134adff6704adc65187f8d8d061860 Mon Sep 17 00:00:00 2001
From: Schneider Leo <leo.schneider@etu.ec-lyon.fr>
Date: Tue, 30 Jan 2024 13:32:00 +0100
Subject: [PATCH] add test
---
.gitignore | 2 -
test.py | 132 +++++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 132 insertions(+), 2 deletions(-)
create mode 100644 test.py
diff --git a/.gitignore b/.gitignore
index 1f8b308..749ec53 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,7 +2,5 @@
/fig/
/venv/
/dataset/
-/test.py
/database/
-
/wandb_run/
diff --git a/test.py b/test.py
new file mode 100644
index 0000000..59f1279
--- /dev/null
+++ b/test.py
@@ -0,0 +1,132 @@
+import os
+import wandb as wdb
+import torch.nn as nn
+import torch.optim as optim
+import torch
+from dataloader import load_data, load_split_intensity, Intentsity_Dataset, load_intensity_from_files
+from model import RT_pred_model, Intensity_pred_model_multi_head, RT_pred_model_self_attention
+from config import load_args
+
+
+def train(model, data_train, epoch, optimizer, criterion, cuda=False):
+ losses = 0.
+ distance = 0.
+ for data1, data2, data3, target in data_train:
+ if torch.cuda.is_available():
+ data1, data2, data3, target = data1.cuda(), data2.cuda(), data3.cuda(), target.cuda()
+ pred_rt = model.forward(data1, data2, data3)
+ target.float()
+ loss = criterion(pred_rt, target)
+ dist = torch.mean(torch.abs(pred_rt - target))
+ distance += dist.item()
+ optimizer.zero_grad()
+ loss.backward()
+ optimizer.step()
+ losses += loss.item()
+
+ # wdb.log({"train loss": losses / len(data_train), "train mean distance": distance / len(data_train)})
+
+ print('epoch : ', epoch, ',train losses : ', losses / len(data_train), " ,mean distance : ",
+ distance / len(data_train))
+
+
+def eval(model, data_test, epoch, criterion=nn.MSELoss(reduction='mean'), cuda=False):
+ losses = 0.
+ distance = 0.
+ for data, target in data_test:
+ if torch.cuda.is_available():
+ data, target = data.cuda(), target.cuda()
+ pred_rt = model(data)
+ loss = criterion(pred_rt, target)
+ losses += loss.item()
+ dist = torch.mean(torch.abs(pred_rt - target))
+ distance += dist.item()
+ # wdb.log({"eval loss": losses / len(data_test), "eval mean distance": distance / len(data_test)})
+ print('epoch : ', epoch, ',eval losses : ', losses / len(data_test), " ,eval mean distance: :",
+ distance / len(data_test))
+
+
+def save(model, optimizer, epoch, checkpoint_name):
+ print('\nModel Saving...')
+ model_state_dict = model.state_dict()
+ os.makedirs('checkpoints', exist_ok=True)
+ torch.save({
+ 'model_state_dict': model_state_dict,
+ 'global_epoch': epoch,
+ 'optimizer_state_dict': optimizer.state_dict(),
+ }, os.path.join('checkpoints', checkpoint_name))
+
+
+def run(epochs, eval_inter, save_inter, model, data_train, data_test, optimizer, criterion=nn.MSELoss(reduction='mean'),
+ cuda=False):
+ for e in range(1, epochs + 1):
+ train(model, data_train, e, optimizer, criterion, cuda=cuda)
+ if e % eval_inter == 0:
+ eval(model, data_test, e, cuda=cuda)
+ if e % save_inter == 0:
+ save(model, optimizer, epochs, 'model_self_attention_' + str(e) + '.pt')
+
+
+def main(args):
+ os.environ["WANDB_API_KEY"] = 'b4a27ac6b6145e1a5d0ee7f9e2e8c20bd101dccd'
+ os.environ["WANDB_MODE"] = "offline"
+
+ config = {
+ "model": "RT prediction GRU/selfAtt+ GRU",
+ "learning_rate": args.lr,
+ "batch_size": args.batch_size,
+ }
+
+ # wdb.init(project="RT prediction", dir='wandb_run')
+
+ print('Cuda : ', torch.cuda.is_available())
+ data_train, data_test = load_data(args.batch_size, args.n_train, args.n_test, data_source='database/data.csv')
+ print('\nData loaded')
+ model = RT_pred_model_self_attention()
+ if torch.cuda.is_available():
+ model = model.cuda()
+ optimizer = optim.Adam(model.parameters(), lr=args.lr)
+ print('\nModel initialised')
+ run(args.epochs, args.eval_inter, args.save_inter, model, data_train, data_test, optimizer=optimizer, cuda=True)
+ # wdb.finish()
+
+
+def main2(args):
+ print(torch.cuda.is_available())
+ # sources_train = ('data/intensity/sequence_train.npy',
+ # 'data/intensity/intensity_train.npy',
+ # 'data/intensity/collision_energy_train.npy',
+ # 'data/intensity/precursor_charge_train.npy')
+ #
+ # sources_test = ('data/intensity/sequence_test.npy',
+ # 'data/intensity/intensity_test.npy',
+ # 'data/intensity/collision_energy_test.npy',
+ # 'data/intensity/precursor_charge_test.npy')
+ #
+ # data_train = load_intensity_from_files(sources_train[0], sources_train[1], sources_train[2], sources_train[3])
+ # data_test = load_intensity_from_files(sources_test[0], sources_test[1], sources_test[2], sources_test[3])
+
+ sources = ('data/intensity/sequence_header.npy',
+ 'data/intensity/intensity_header.npy',
+ 'data/intensity/collision_energy_header.npy',
+ 'data/intensity/precursor_charge_header.npy')
+
+ data_train, data_test, data_validation = load_split_intensity(sources, (0.5, 0.25, 0.25))
+ train = Intentsity_Dataset(data_train)
+ test = Intentsity_Dataset(data_test)
+
+
+
+ print('\nData loaded')
+ model = Intensity_pred_model_multi_head()
+ if torch.cuda.is_available():
+ model = model.cuda()
+ optimizer = optim.Adam(model.parameters(), lr=0.001)
+ print('\nModel initialised')
+ run(args.epochs, args.eval_inter, args.save_inter, model, train, test, optimizer=optimizer, cuda=True)
+
+
+if __name__ == "__main__":
+ args = load_args()
+ print(args)
+ main2(args)
--
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