.gitignore

@@ -1,2 +1 @@
 *__pycache__*
-.old

readme.md

@@ -1,13 +1,2 @@
 # Machine Learning stuff for TENG project
-(Bi)LSTM for name classification.  
-More information on the project are [on my website](https://quintern.xyz/en/teng.html).
-
-## Model training
-Adjust the parameters in `main.py` and run it.  
-All models and the settings they were trained with are automatically serialized with pickle and stored in a subfolder
-of the `<model_dir>` that was set in `main.py`.
-
-
-## Model evaluation
-Run `find_best_model.py <model_dir>` with the `<model_dir>` specified in `main.py` during training.
 

teng-ml/find_best_model.py

@@ -1,316 +0,0 @@
-from os import path, listdir
-
-import matplotlib.pyplot as plt
-import numpy as np
-from sys import exit, argv
-
-if __name__ == "__main__":
-    if __package__ is None:
-        # make relative imports work as described here: https://peps.python.org/pep-0366/#proposed-change
-        __package__ = "teng-ml"
-        import sys
-        from os import path
-        filepath = path.realpath(path.abspath(__file__))
-        sys.path.insert(0, path.dirname(path.dirname(filepath)))
-
-from .tracker.epoch_tracker import EpochTracker
-from .util.settings import MLSettings
-from .util import model_io as mio
-from .util.string import cleanup_str, fill_and_center
-
-
-cache = {}
-
-#
-# TOOLS
-#
-def get_model_dirs(models_dir):
-    """
-    return all model_dirs, relative to models_dir
-    """
-    if "model_dirs" in cache: return cache["model_dirs"].copy()
-    paths = listdir(models_dir)
-    model_dirs = []
-    for p in paths:
-        if not path.isdir(f"{models_dir}/{p}"): continue
-        if not path.isfile(f"{models_dir}/{p}/settings.pkl"): continue
-        if not path.isfile(f"{models_dir}/{p}/tracker_training.pkl"): continue
-        if not path.isfile(f"{models_dir}/{p}/tracker_validation.pkl"): continue
-        if not path.isfile(f"{models_dir}/{p}/model.pkl"): continue
-        model_dirs.append(f"{models_dir}/{p}")
-    cache["model_dirs"] = model_dirs.copy()
-    return model_dirs
-
-
-def resave_images_svg(model_dirs):
-    """
-    open all trackers and save all plots as svg
-    """
-    for model_dir in model_dirs:
-        val_tracker: EpochTracker = mio.load_tracker_validation(model_dir)
-        fig, _ = val_tracker.plot_predictions("Validation: Predictions", model_dir=model_dir, name="img_validation_predictions")
-        train_tracker: EpochTracker = mio.load_tracker_training(model_dir)
-        fig, _ = train_tracker.plot_predictions("Training: Predictions", model_dir=model_dir, name="img_training_predictions")
-        fig, _ = train_tracker.plot_training(model_dir=model_dir)
-        plt.close('all')
-
-
-
-#
-# MODEL RANKING
-#
-def get_model_info_md(model_dir):
-    st: MLSettings = mio.load_settings(model_dir)
-    validation_tracker = mio.load_tracker_validation(model_dir)
-    training_tracker = mio.load_tracker_training(model_dir)
-
-    s = f"""Model {model_dir[model_dir.rfind('/')+1:]}
-Model parameters:
-- num_features      = {st.num_features}
-- num_layers        = {st.num_layers}
-- hidden_size       = {st.hidden_size}
-- bidirectional     = {st.bidirectional}
-Training data:
-- transforms        = {st.transforms}
-- splitter          = {st.splitter}
-- labels            = {st.labels}
-Training info:
-- optimizer         = {cleanup_str(st.optimizer)}
-- scheduler         = {cleanup_str(st.scheduler)}
-- loss_func         = {st.loss_func}
-- num_epochs        = {st.num_epochs}
-- batch_size        = {st.batch_size}
-- n_predictions     = {np.sum(training_tracker.get_count_per_label())}
-- final accuracy    = {training_tracker.accuracies[-1]}
-- highest accuracy  = {np.max(training_tracker.accuracies)}
-Validation info:
-- n_predictions     = {np.sum(validation_tracker.get_count_per_label())}
-- accuracy          = {validation_tracker.accuracies[-1]}
-"""
-    return s
-
-
-def write_model_info(model_dir, model_info=None):
-    if model_info is None: model_info = get_model_info_md(model_dir)
-    with open(f"{model_dir}/model_info.md", "w") as file:
-        file.write(model_info)
-
-
-def get_model_ranking(model_dirs):
-    if "model_ranking" in cache: return cache["model_ranking"].copy()
-    model_ranking = []  # model, (model_dir | validation accuracy)
-    for model_dir in model_dirs:
-        model_ranking.append((model_dir, mio.load_tracker_validation(model_dir).accuracies[-1]))
-    model_ranking.sort(key=lambda t: t[1])   # sort accuracy
-    model_ranking.reverse()  # best to worst
-    cache["model_ranking"] = model_ranking.copy()
-    return model_ranking
-
-def get_model_ranking_md(model_dirs):
-    model_ranking = get_model_ranking(model_dirs)
-    ranking_md = ""
-    for i in range(len(model_ranking)):
-        model_dir = model_ranking[i][0]
-        model_name = model_dir[model_dir.rfind("/")+1:]
-        ranking_md += f"{i+1:3}. Model=`{model_name}`, Validation accuaracy={round(model_ranking[i][1], 2):.2f}%\n"
-    return ranking_md
-
-#
-# SETTINGS RANKING
-#
-def get_settings_ranking(model_dirs, use_ranking_instead_of_accuracy=False):
-    """
-    load the settings for each model and score them based on the performance of the model
-    This only works when all settings were the same number of times
-    (Example: 2 batch sizes x and y have to both to be used z times for the ranking to make sense)
-    """
-    if "settings_ranking" in cache: return cache["settings_ranking"].copy()
-    settings_ranking = {}  # parameter name: param_value: score
-
-    model_ranking = get_model_ranking(model_dirs)
-    model_ranking.reverse()  # worst to best
-    def score_ranking_based(i, param_name, param_value):
-        """
-        score settings depending on the ranking of the model
-        eg: best of 32 models has batch_size 10 -> batch_size 10 gets 32 points
-        """
-        param_value = cleanup_str(param_value)
-        if not param_name in settings_ranking.keys():
-            settings_ranking[param_name] = {}
-        if not param_value in settings_ranking[param_name].keys():
-            settings_ranking[param_name][param_value] = 0
-        settings_ranking[param_name][param_value] += i      # i+1 is reverse place in the ranking, worst model is at i=0
-
-    def score_accuracy_based(i, param_name, param_value):
-        """
-        score settings depending on the accuracy of the model
-        eg: models has batch_size 10 and accuracy 63% -> batch_size 10 gets 63 points
-        """
-        param_value = cleanup_str(param_value)
-        if not param_name in settings_ranking.keys():
-            settings_ranking[param_name] = {}
-        if not param_value in settings_ranking[param_name].keys():
-            settings_ranking[param_name][param_value] = 0
-        settings_ranking[param_name][param_value] += int(model_ranking[i][1])  # accuracy
-
-    if use_ranking_instead_of_accuracy:
-        score = lambda i, name, val : score_ranking_based(i, name, val)
-    else:
-        score = lambda i, name, val : score_accuracy_based(i, name, val)
-    for i in range(len(model_ranking)):
-        st = mio.load_settings(model_ranking[i][0])
-        score(i, "num_features", st.num_features)
-        score(i, "num_layers", st.num_layers)
-        score(i, "hidden_size", st.hidden_size)
-        score(i, "num_epochs", st.num_epochs)
-        score(i, "bidirectional", st.bidirectional)
-        score(i, "optimizer", st.optimizer)
-        score(i, "scheduler", st.scheduler)
-        score(i, "loss_func", st.loss_func)
-        score(i, "transforms", st.transforms)
-        score(i, "splitter", st.splitter)
-        score(i, "batch_size", st.batch_size)
-    # remove parameters with only one value
-    settings_ranking = { k: v for k, v in settings_ranking.items() if len(v) > 1 }
-    cache["settings_ranking"] = settings_ranking.copy()
-    return settings_ranking
-
-def get_settings_ranking_md(model_dirs):
-    """
-    turn the scores dict from rank_settings into a markdown string
-    """
-    settings_ranking = get_settings_ranking(model_dirs)
-    s = ""
-    for param_name, d in settings_ranking.items():
-        s += f"- {param_name}:\n"
-        sorted_scores = sorted(d.items(), key=lambda x: x[1], reverse=True)
-        for i in range(len(sorted_scores)):
-            param_value, score = sorted_scores[i]
-            s += f"\t{i+1}. `{param_value}` ({score} points)\n"
-    return s
-
-
-
-
-def interactive_model_inspector(models_dir: str):
-    model_dirs = get_model_dirs(models_dir)
-    model_dirs.sort()
-    model_names = [ mdir[mdir.rfind('/')+1:] for mdir in model_dirs ]
-
-    def print_options():
-        s = fill_and_center("Interactive Model Inspector") + "\n"
-        for i in range(len(model_names)):
-            s += f"{i+1:02}: {model_names[i]}\n"
-        s += """    ---
-x:  print model info for x. listed model (1-based)
-x.: print model info for x. ranked model (1-based)
-w:  write last model info
-wa: write info for all listed models
-q:  quit
-*:  name of model or path to model directory. If not found, reprint list."""
-        print(s)
-    last_model_info = None
-    last_model_dir = None
-
-    def print_model_info(model_dir):
-        last_model_dir = model_dir
-        last_model_info = get_model_info_md(last_model_dir)
-        print(last_model_info)
-    print_options()
-    loop = True
-    try:
-        while loop:
-            answer = input("> ")
-            if len(answer) == 0: continue
-            try:  # if x -> take x. from listed models
-                i = int(answer)
-                if 0 < i and i <= len(model_dirs):
-
-                    print_model_info(model_dirs[i-1])
-                    continue
-            except ValueError: pass
-            if answer.endswith('.'):  # if x. -> take x. from model ranking
-                try:
-                    i = int(answer[:-1])
-                    if 0 < i and i <= len(model_dirs):
-                        model_ranking = get_model_ranking(model_dirs)
-                        print_model_info(model_ranking[i-1][0])
-                        continue
-                except ValueError: pass
-
-            elif answer == "w":
-                if last_model_info is None:
-                    print("Print a model info first.")
-                    continue
-                write_model_info(last_model_dir, last_model_info)
-            elif answer == "wa":
-                for model_dir in model_dirs:
-                    write_model_info(model_dir)
-            elif answer == "q":
-                loop = False
-                continue
-            else:
-                if path.isdir(answer):  # if model dir
-                    print_model_info(answer)
-                elif path.isdir(f"{models_dir}/{answer}"):  # if model name
-                    print_model_info(f"{models_dir}/{answer}")
-                else:
-                    print(f"'{answer}' is not a model name in {models_dir} or path to a model directory.")
-                    print_options()
-    except KeyboardInterrupt:  # if <C-C>
-        pass
-    except EOFError:  # if <C-D>
-        exit(0)
-    return True
-
-
-
-if __name__ == "__main__":
-    if len(argv) != 2:
-        print(f"Exactly one argument (models directory) is required, but got {len(argv)-1}.")
-        exit(1)
-
-    # models_dir = "/home/matth/Uni/TENG/models_phase_2"  # where to save models, settings and results
-    models_dir = path.abspath(path.expanduser(argv[1]))
-
-    model_dirs = get_model_dirs(models_dir)
-
-    def save_model_ranking():
-        model_ranking = get_model_ranking_md(model_dirs)
-        with open(f"{models_dir}/ranking_models.md", "w") as file:
-            file.write(model_ranking)
-
-    def save_settings_ranking():
-        scores = get_settings_ranking(model_dirs)
-        with open(f"{models_dir}/ranking_settings.md", "w") as file:
-            file.write(get_settings_ranking_md(scores))
-
-
-    # if the functions return True, the options are printed again
-    options = {
-        '1':    ("Print model ranking", lambda: print(get_model_ranking_md(model_dirs))),
-        '2':    ("Save model ranking", save_model_ranking),
-        '3':    ("Print settings ranking", lambda: print(get_settings_ranking_md(model_dirs))),
-        '4':    ("Save settings ranking", save_settings_ranking),
-        '5':    ("Interactive model inspector", lambda: interactive_model_inspector(models_dir)),
-        '6':    ("Resave all images", lambda: resave_images_svg(model_dirs)),
-        'q':    ("quit", exit)
-    }
-
-    def print_options():
-        print(fill_and_center("Model Evaluator"))
-        for op, (name, _) in options.items():
-            print(f"{op:4}: {name}")
-    print(f"Using models directory '{models_dir}', which contains {len(model_dirs)} models")
-    print_options()
-    try:
-        while True:
-            answer = input("> ")
-            if answer in options.keys():
-                reprint = options[answer][1]()
-                if reprint == True: print_options()
-            else:
-                print(f"Invalid option: '{answer}'")
-                print_options()
-    except KeyboardInterrupt: pass
-    except EOFError: pass

teng-ml/main.py

@@ -7,22 +7,20 @@ if __name__ == "__main__":
         filepath = path.realpath(path.abspath(__file__))
         sys.path.insert(0, path.dirname(path.dirname(filepath)))
 
-from sys import exit
 import matplotlib.pyplot as plt
 import pandas as pd
 import torch
 import torch.nn as nn
+import torch.nn.utils.rnn as rnn_utils
 from torch.utils.data import DataLoader
-import itertools
+import json
 import time
-from os import makedirs, path
+import pickle
 
 from .util.transform import ConstantInterval, Normalize
 from .util.data_loader import load_datasets, LabelConverter
-from .util.split import DataSplitter
+from .util.epoch_tracker import EpochTracker
 from .util.settings import MLSettings
-from .rnn.rnn import RNN
-from .rnn.training import train_validate_save, select_device
 
 def test_interpol():
     file = "/home/matth/data/2023-04-27_glass_8.2V_179mm000.csv"
@@ -37,92 +35,187 @@ def test_interpol():
     ax1.plot(interp_array[:,0], interp_array[:,1], color="r", label="Interpolated")
     ax1.scatter(array[:,0], array[:,2], color="g", label="Original")
     ax1.legend()
-    # plt.show()
-
+    plt.show()
 
 if __name__ == "__main__":
+    device = (
+        "cuda"
+        if torch.cuda.is_available()
+        else "mps"
+        if torch.backends.mps.is_available()
+        else "cpu"
+    )
+
+
     labels = LabelConverter(["foam", "glass", "kapton", "foil", "cloth", "rigid_foam"])
-    models_dir = "/home/matth/Uni/TENG/models"  # where to save models, settings and results
-    if not path.isdir(models_dir):
-        makedirs(models_dir)
-    data_dir = "/home/matth/Uni/TENG/data"
-
-
-    # Test with
-    num_layers = [ 3 ]
-    hidden_size = [ 8 ]
-    bidirectional = [ True ]
     t_const_int = ConstantInterval(0.01)
     t_norm = Normalize(0, 1)
-    transforms = [[ t_const_int ]] #, [ t_const_int, t_norm ]]
-    batch_sizes = [ 64 ]  # , 16]
-    splitters = [ DataSplitter(100) ]
-    num_epochs = [ 80 ]
+    transforms = [ t_const_int, t_norm ]
+    st = MLSettings(num_features=1,
+                    num_layers=1,
+                    hidden_size=1,
+                    bidirectional=True,
+                    transforms=transforms,
+                    num_epochs=40,
+                    batch_size=3,
+                    labels=labels,
+                )
 
-     # num_layers=1,
-     # hidden_size=1,
-     # bidirectional=True,
-     # optimizer=None,
-     # scheduler=None,
-     # loss_func=None,
-     # transforms=[],
-     # splitter=None,
-     # num_epochs=10,
-     # batch_size=5,
-    args = [num_layers, hidden_size, bidirectional, [None], [None], [None], transforms, splitters, num_epochs, batch_sizes]
+    print(f"Using device: {device}")
 
-    # create settings for every possible combination
-    settings = [
-        MLSettings(1, *params, labels) for params in itertools.product(*args)
-    ]
 
-    loss_func = nn.CrossEntropyLoss()
-    optimizers = [
-        lambda model: torch.optim.Adam(model.parameters(), lr=0.03),
-        # lambda model: torch.optim.Adam(model.parameters(), lr=0.25),
-        # lambda model: torch.optim.Adam(model.parameters(), lr=0.50),
-    ]
-    schedulers = [
-        lambda optimizer, st: torch.optim.lr_scheduler.ExponentialLR(optimizer, gamma=0.9),
-        lambda optimizer, st: torch.optim.lr_scheduler.StepLR(optimizer, step_size=st.num_epochs // 10, gamma=0.40, verbose=False),
-        # lambda optimizer, st: torch.optim.lr_scheduler.StepLR(optimizer, step_size=st.num_epochs // 10, gamma=0.75, verbose=False),
-    ]
+    train_set, test_set = load_datasets("/home/matth/Uni/TENG/data", labels, voltage=8.2, transforms=st.transforms, train_to_test_ratio=0.7, random_state=42)
 
-    n_total = len(settings) * len(optimizers) * len(schedulers)
-    print(f"Testing {n_total} possible configurations")
-    # scheduler2 = 
-    def create_model(st, optimizer_f, scheduler_f):
-        model=RNN(input_size=st.num_features, hidden_size=st.hidden_size, num_layers=st.num_layers, num_classes=len(labels), bidirectional=st.bidirectional)
-        optimizer = optimizer_f(model)
-        scheduler = scheduler_f(optimizer, st)
-        return model, optimizer, scheduler
+    # train_loader = iter(DataLoader(train_set))
+    # test_loader = iter(DataLoader(test_set))
+    train_loader = DataLoader(train_set, batch_size=st.batch_size, shuffle=True)
+    test_loader = DataLoader(test_set, batch_size=st.batch_size, shuffle=True)
 
-    t_begin = time.time()
-    n = 1
-    for o in range(len(optimizers)):
-        for s in range(len(schedulers)):
-            for i in range(len(settings)):
-                st = settings[i]
-                # print(st.get_name())
-                train_set, test_set = load_datasets(data_dir, labels, voltage=8.2, transforms=st.transforms, split_function=st.splitter, train_to_test_ratio=0.7, random_state=42, num_workers=4)
+    class RNN(nn.Module):
+        def __init__(self, input_size, hidden_size, num_layers, num_classes, bidirectional):
+            super(RNN, self).__init__()
+            self.num_layers = num_layers
+            self.hidden_size = hidden_size
+            self.is_bidirectional = bidirectional
+            self.lstm = nn.LSTM(input_size, hidden_size, num_layers, batch_first=True, bidirectional=bidirectional)
+            # x = (batch_size, sequence, feature)
 
-                generator = torch.manual_seed(42)
-                # train_loader = iter(DataLoader(train_set))
-                # test_loader = iter(DataLoader(test_set))
-                train_loader = DataLoader(train_set, batch_size=st.batch_size, shuffle=True, generator=generator)
-                test_loader = DataLoader(test_set, batch_size=st.batch_size, shuffle=True, generator=generator)
-                print(f"Testing {n}/{n_total}: (o={o}, s={s}, i={i})")
-                model, optimizer, scheduler = create_model(st, optimizers[o], schedulers[s])
-                device = select_device(force_device="cpu")
-                try:
-                    train_validate_save(model, optimizer, scheduler, loss_func, train_loader, test_loader, st, models_dir, print_interval=4)
-                except KeyboardInterrupt:
-                    if input("Cancelled current training. Quit? (q/*): ") == "q":
-                        t_end = time.time()
-                        print(f"Testing took {t_end - t_begin:.2f}s = {(t_end-t_begin)/60:.1f}m")
-                        exit()
-                n += 1
+            if bidirectional == True:
+              self.fc = nn.Linear(hidden_size * 2, num_classes)
+            else:
+              self.fc = nn.Linear(hidden_size, num_classes)
 
+            self.softmax = nn.Softmax(dim=1)
+
+        def forward(self, x):
+            # x: batches, length, features
+            # print(f"forward pass")
+            D = 2 if self.is_bidirectional == True else 1
+
+            # print(f"x({x.shape})=...")
+            batch_size = x.shape[0]
+            # print(f"batch_size={batch_size}")
+
+            h0 = torch.zeros(D * self.num_layers, batch_size, self.hidden_size).to(device)
+            # print(f"h1({h0.shape})=...")
+            c0 = torch.zeros(D * self.num_layers, batch_size, self.hidden_size).to(device)
+            x.to(device)
+            _, (h_n, _) = self.lstm(x, (h0, c0))
+            # print(f"h_n({h_n.shape})=...")
+            final_state  = h_n.view(self.num_layers, D, batch_size, self.hidden_size)[-1]     # num_layers, num_directions, batch, hidden_size
+            # print(f"final_state({final_state.shape})=...")
+
+            if D == 1:
+                X = final_state.squeeze()  # TODO what if batch_size == 1
+            elif D == 2:
+              h_1, h_2 = final_state[0], final_state[1]  # forward & backward pass
+              #X = h_1 + h_2                        # Add both states
+              X = torch.cat((h_1, h_2), 1)          # Concatenate both states, X-size: (Batch, hidden_size * 2）
+            else:
+                raise ValueError("D must be 1 or 2")
+            # print(f"X({X.shape})={X}")
+            output = self.fc(X) # fully-connected layer
+            # print(f"out({output.shape})={output}")
+            output = self.softmax(output)
+            # print(f"out({output.shape})={output}")
+            return output
+
+    model=RNN(input_size=st.num_features, hidden_size=st.hidden_size, num_layers=st.num_layers, num_classes=len(labels), bidirectional=st.bidirectional).to(device)
+    loss_func = torch.nn.CrossEntropyLoss()
+    optimizer = torch.optim.Adam(model.parameters(), lr=0.02)
+    scheduler = torch.optim.lr_scheduler.ExponentialLR(optimizer, gamma=0.95)
+
+    print(f"model:", model)
+    print(f"loss_func={loss_func}")
+    print(f"optimizer={optimizer}")
+    print(f"scheduler={scheduler}")
+
+
+
+    epoch_tracker = EpochTracker(labels)
+
+    print(f"train_loader")
+    for i, (data, y) in enumerate(train_loader):
+        print(y)
+        print(f"{i:3} - {torch.argmax(y, dim=1, keepdim=False)}")
+
+
+# training 
+    epoch_tracker.train_begin()
+    for ep in range(st.num_epochs):
+        for i, (data, y) in enumerate(train_loader):
+            # print(data, y)
+            # data = batch, seq, features
+            # print(f"data({data.shape})={data}")
+            x = data[:,:,[2]].float()   # select voltage data
+            # print(f"x({x.shape}, {x.dtype})=...")
+            # print(f"y({y.shape}, {y.dtype})=...")
+            # length = torch.tensor([x.shape[1] for _ in range(x.shape[0])], dtype=torch.int64)
+            # print(f"length({length.shape})={length}")
+            # batch_size = x.shape[0]
+            # print(f"batch_size={batch_size}")
+            # v = x.view(batch_size, -1, feature_count)
+            # data = rnn_utils.pack_padded_sequence(v.type(torch.FloatTensor), length, batch_first=True).to(device)[0]
+            # print(f"data({data.shape})={data}")
+            # print(data.batch_sizes[0])
+            # print(data)
+            out = model(x)
+            # print(f"out({out.shape}={out})")
+            loss = loss_func(out, y)
+            # print(loss)
+
+            optimizer.zero_grad()   # clear gradients for next train
+            loss.backward()         # backpropagation, compute gradients
+            optimizer.step()        # apply gradients
+
+            # predicted = torch.max(torch.nn.functional.softmax(out), 1)[1]
+            predicted = torch.argmax(out, dim=1, keepdim=False)  # -> [ label_indices ]
+            correct = torch.argmax(y, dim=1, keepdim=False)  # -> [ label_indices ]
+            # print(f"predicted={predicted}, correct={correct}")
+            # train_total += y.size(0)
+            # train_correct += (predicted == correct).sum().item()
+            epoch_tracker.train(correct, predicted)
+        epoch_tracker.next_epoch(loss)
+        print(epoch_tracker.get_last_epoch_summary_str())
+        scheduler.step()
     t_end = time.time()
-    print(f"Testing took {t_end - t_begin:.2f}s = {(t_end-t_begin)/60:.1f}m")
+
+    with torch.no_grad():
+        for i, (data, y) in enumerate(test_loader):
+            # print(ep, "Test")
+            x = data[:,:,[2]].float()
+            out = model(x)
+            loss = loss_func(out, y)
+
+            predicted = torch.argmax(out, dim=1, keepdim=False)  # -> [ label_indices ]
+            correct = torch.argmax(y, dim=1, keepdim=False)  # -> [ label_indices ]
+            # print(f"predicted={predicted}, correct={correct}")
+            # val_total += y.size(0)
+            # val_correct += (predicted == correct).sum().item()
+
+            epoch_tracker.test(correct, predicted)
+
+        # print(f"train_total={train_total}, val_total={val_total}")
+        # if train_total == 0: train_total = -1
+        # if val_total == 0: val_total = -1
+
+        # print(f"epoch={ep+1:3}: Testing accuracy={100 * val_correct / val_total:.2f}")
+    # print(f"End result: Training accuracy={100 * train_correct / train_total:.2f}%, Testing accuracy={100 * val_correct / val_total:.2f}, training took {t_end - t_begin:.2f} seconds")
+
+    epoch_tracker.get_test_statistics()
+    # epoch_tracker.()
+
+    # print(epoch_tracker.get_training_summary_str())
+    print(epoch_tracker.get_training_count_per_label())
+
+    model_name = st.get_name()
+    # save the settings, results and model
+    with open(model_name + "_settings.pkl", "wb") as file:
+        pickle.dump(st, file)
+
+    with open(model_name + "_results.pkl", "wb") as file:
+        pickle.dump(epoch_tracker, file)
+
+    with open(model_name + "_model.pkl", "wb") as file:
+        pickle.dump(model, file)
 

teng-ml/peaks.py

@@ -17,7 +17,6 @@ if __name__ == "__main__":
         sys.path.insert(0, path.dirname(path.dirname(filepath)))
 
 from .util.transform import Normalize
-from .util.data_loader import get_datafiles
 
 file = "/home/matth/data/2023-04-25_kapton_8.2V_179mm002.csv"
 

teng-ml/rnn.py

@@ -0,0 +1,39 @@
+import torch
+import torch.nn as nn
+
+# BiLSTM Model
+
+class RNN(nn.Module):
+  def __init__(self, input_size, hidden_size, num_layers, num_classes, if_bidirectional):
+    super(RNN, self).__init__()
+    self.num_layers = num_layers
+    self.hidden_size = hidden_size
+    self.if_bidirectional = if_bidirectional
+    self.lstm = nn.LSTM(input_size, hidden_size, num_layers, batch_first=True, bidirectional=if_bidirectional)
+
+    if if_bidirectional == True:
+      self.fc = nn.Linear(hidden_size * 2, num_classes)
+    else:
+      self.fc = nn.Linear(hidden_size, num_classes)
+
+
+  def forward(self, x):
+    D = 2 if self.if_bidirectional == True else 1
+    Batch = x.batch_sizes[0]
+
+    h0 = torch.zeros(D * self.num_layers, Batch, self.hidden_size).to(device)
+    c0 = torch.zeros(D * self.num_layers, Batch, self.hidden_size).to(device)
+    x.to(device)
+    _, (h_n, _) = self.lstm(x, (h0, c0))
+    final_state  = h_n.view(self.num_layers, D, Batch, self.hidden_size)[-1]     # num_layers, num_directions, batch, hidden_size
+
+    if D == 1:
+      X = final_state.squeeze()
+    elif D == 2:
+      h_1, h_2 = final_state[0], final_state[1]  # forward & backward pass
+      # X = h_1 + h_2                # Add both states
+      X = torch.cat((h_1, h_2), 1)         # Concatenate both states, X-size: (Batch, hidden_size * 2）
+
+    output = self.fc(X) # fully-connected layer
+
+    return output

teng-ml/rnn/rnn.py

@@ -1,80 +0,0 @@
-import torch
-import torch.nn as nn
-
-class RNN(nn.Module):
-    """
-    (Bi)LSTM for name classification
-    """
-    def __init__(self, input_size, hidden_size, num_layers, num_classes, bidirectional):
-        super(RNN, self).__init__()
-        self.num_layers = num_layers
-        self.hidden_size = hidden_size
-        self.is_bidirectional = bidirectional
-        self.lstm = nn.LSTM(input_size=input_size, hidden_size=hidden_size, num_layers=num_layers, batch_first=True, bidirectional=bidirectional)
-        # x = (batch_size, sequence, feature)
-
-        if bidirectional == True:
-          self.fc = nn.Linear(hidden_size * 2, num_classes)
-        else:
-          self.fc = nn.Linear(hidden_size, num_classes)
-
-        self.softmax = nn.Softmax(dim=1)
-
-    def forward(self, x):
-        # x: batches, length, features
-        # print(f"forward pass")
-        D = 2 if self.is_bidirectional == True else 1
-        # print(f"x({x.shape})=...")
-        batch_size = x.shape[0]
-
-        device = x.device
-
-        h0 = torch.zeros(D * self.num_layers, batch_size, self.hidden_size).to(device)
-        # print(f"h1({h0.shape})=...")
-        c0 = torch.zeros(D * self.num_layers, batch_size, self.hidden_size).to(device)
-
-        out, (h_n, c_n) = self.lstm(x, (h0, c0))
-        # out: (N, L, D * hidden_size)
-        # h_n: (D * num_layers, hidden_size)
-        # c_n: (D * num_layers, hidden_size)
-        # print(f"out({out.shape})={out}")
-        # print(f"h_n({h_n.shape})={h_n}")
-        # print(f"c_n({c_n.shape})={c_n}")
-        # print(f"out({out.shape})=...")
-        # print(f"h_n({h_n.shape})=...")
-        # print(f"c_n({c_n.shape})=...")
-
-        """
-        # select only last layer [-1] -> last layer,
-        last_layer_state  = h_n.view(self.num_layers, D, batch_size, self.hidden_size)[-1]
-        if D == 1:
-            # [1, batch_size, hidden_size] -> [batch_size, hidden_size]
-            X = last_layer_state.squeeze()           # TODO what if batch_size == 1
-        elif D == 2:
-            h_1, h_2 = last_layer_state[0], last_layer_state[1]   # states of both directions
-            # concatenate both states, X-size: (Batch, hidden_size * 2）
-            X = torch.cat((h_1, h_2), dim=1)
-        else:
-            raise ValueError("D must be 1 or 2")
-        """  # all this is quivalent to line below
-        out = out[:,-1,:]  # select last time step
-
-        # fc: (*, hidden_size) -> (*, num_classes)
-        # print(f"X({X.shape})={X}")
-        # print(f"X({X.shape})=...")
-        out = self.fc(out) # fully-connected layer
-        # print(f"out({output.shape})={output}")
-        # print(f"output({output.shape})=...")
-        # softmax: (*) -> (*)
-        # out = self.softmax(out)
-        # print(f"output({output.shape})=...")
-        # print(f"output({output.shape})={output}")
-
-        """
-        out(torch.Size([15, 200, 10]))=...
-        h_n(torch.Size([3, 15, 10]))=...
-        c_n(torch.Size([3, 15, 10]))=...
-        X(torch.Size([3, 1, 15, 10]))=...
-        output(torch.Size([3, 1, 15, 6]))=...
-        output(torch.Size([3, 1, 15, 6]))=..."""
-        return out

teng-ml/rnn/training.py

@@ -1,150 +0,0 @@
-from os import makedirs, path
-import torch
-import pickle
-import matplotlib.pyplot as plt
-from torch.utils.data import DataLoader
-
-from ..util.settings import MLSettings
-from ..tracker.epoch_tracker import EpochTracker
-from ..util.file_io import get_next_digits
-from ..util.string import class_str
-
-from ..util import model_io as mio
-
-
-def select_device(force_device=None):
-    """
-    Select best device and move model
-    """
-    if force_device is not None:
-        device = force_device
-    else:
-        device = torch.device(
-            "cuda"
-            if torch.cuda.is_available()
-            # else "mps"
-            # if torch.backends.mps.is_available()
-            else "cpu"
-        )
-    # print(device, torch.cuda.get_device_name(device), torch.cuda.get_device_properties(device))
-    return device
-
-
-def train(model, optimizer, scheduler, loss_func, train_loader: DataLoader, st: MLSettings, print_interval=1) -> EpochTracker:
-    epoch_tracker = EpochTracker(st.labels)
-    epoch_tracker.begin()
-    for ep in range(st.num_epochs):
-        loss = -1
-        for i, (data, y) in enumerate(train_loader):
-            # print(data, y)
-            # data = batch, seq, features
-            # print(f"data({data.shape})={data}")
-            x = data[:,:,[2]].float()   # select voltage data
-            # print(f"x({x.shape}, {x.dtype})=...")
-            # print(f"y({y.shape}, {y.dtype})=...")
-            # length = torch.tensor([x.shape[1] for _ in range(x.shape[0])], dtype=torch.int64)
-            # print(f"length({length.shape})={length}")
-            # batch_size = x.shape[0]
-            # print(f"batch_size={batch_size}")
-            # v = x.view(batch_size, -1, feature_count)
-            # data = rnn_utils.pack_padded_sequence(v.type(torch.FloatTensor), length, batch_first=True).to(device)[0]
-            # print(f"data({data.shape})={data}")
-            out = model(x)
-
-            # print(f"out({out.shape}={out})")
-            # print(f"  y({y.shape}={y})")
-            with torch.no_grad():
-                predicted = torch.argmax(out, dim=1, keepdim=False)  # -> [ label_indices ]
-                correct = torch.argmax(y, dim=1, keepdim=False)  # -> [ label_indices ]
-                # print(f"predicted={predicted}, correct={correct}")
-                # train_total += y.size(0)
-                # train_correct += (predicted == correct).sum().item()
-                epoch_tracker.add_prediction(correct, predicted)
-                # predicted2 = torch.argmax(out, dim=1, keepdim=True)  # -> [ label_indices ]
-                # print(f"correct={correct}, y={y}")
-            loss = loss_func(out, correct)
-            # loss = loss_func(out, y)
-
-
-            optimizer.zero_grad()   # clear gradients for next train
-            loss.backward()         # backpropagation, compute gradients
-            optimizer.step()        # apply gradients
-
-            # predicted = torch.max(torch.nn.functional.softmax(out), 1)[1]
-        epoch_tracker.end_epoch(loss, optimizer.param_groups[0]["lr"])
-        if ep+1 % print_interval == 0:
-            print(f"Training:", epoch_tracker.get_epoch_summary_str())
-        scheduler.step()
-    print("Training:", epoch_tracker.end())
-    return epoch_tracker
-
-
-def validate(model, test_loader: DataLoader, st: MLSettings) -> EpochTracker:
-    epoch_tracker = EpochTracker(st.labels)
-    epoch_tracker.begin()
-    with torch.no_grad():
-        for i, (data, y) in enumerate(test_loader):
-            # print(ep, "Test")
-            x = data[:,:,[2]].float()
-            out = model(x)
-
-            predicted = torch.argmax(out, dim=1, keepdim=False)  # -> [ label_indices ]
-            correct = torch.argmax(y, dim=1, keepdim=False)  # -> [ label_indices ]
-
-            epoch_tracker.add_prediction(correct, predicted)
-    print("Validation:", epoch_tracker.end())
-    return epoch_tracker
-
-
-def train_validate_save(model, optimizer, scheduler, loss_func, train_loader: DataLoader, test_loader: DataLoader, st: MLSettings, models_dir, print_interval=1, show_plots=False):
-    # assumes model and data is already on correct device
-    # train_loader.to(device)
-    # test_loader.to(device)
-
-    # store optimizer, scheduler and loss_func in settings
-    st.optimizer = class_str(optimizer)
-    st.scheduler = class_str(scheduler)
-    st.loss_func = class_str(loss_func)
-
-    model_name = st.get_name()
-
-    def add_tab(s):
-        return "\t" + str(s).replace("\n", "\n\t")
-    print(100 * '=')
-    print("Model Name:", model_name)
-    print(f"model:\n", add_tab(model))
-    # print(f"loss_func:\n", add_tab(class_str(loss_func)))
-    # print(f"optimizer:\n", add_tab(class_str(optimizer)))
-    # print(f"scheduler:\n", add_tab(class_str(scheduler)))
-
-
-    print(100 * '-')
-    training_tracker = train(model, optimizer, scheduler, loss_func, train_loader, st, print_interval=print_interval)
-    # print("Training: Count per label:", training_tracker.get_count_per_label())
-    # print("Training: Predictions per label:", training_tracker.get_predictions_per_label())
-
-    print(100 * '-')
-    validation_tracker = validate(model, test_loader, st)
-    # print("Validation: Count per label:", validation_tracker.get_count_per_label())
-    # print("Validation: Predictions per label:", validation_tracker.get_predictions_per_label())
-
-
-    digits = get_next_digits(f"{model_name}_", models_dir)
-    model_dir = f"{models_dir}/{model_name}_{digits}"
-    # do not put earlier, since the dir should not be created if training is interrupted
-    if not path.isdir(model_dir):  # should always run, if not the digits function did not work
-        makedirs(model_dir)
-
-    fig, _ = validation_tracker.plot_predictions("Validation: Predictions", model_dir=model_dir, name="img_validation_predictions")
-    fig, _ = training_tracker.plot_predictions("Training: Predictions", model_dir=model_dir, name="img_training_predictions")
-    fig, _ = training_tracker.plot_training(model_dir=model_dir)
-
-    if show_plots:
-        plt.show()
-    plt.close('all')
-
-    # save the settings, results and model
-    mio.save_settings(model_dir, st)
-    mio.save_tracker_validation(model_dir, validation_tracker)
-    mio.save_tracker_training(model_dir, training_tracker)
-    mio.save_model(model_dir, model)

teng-ml/tracker/epoch_tracker.py

@@ -1,187 +0,0 @@
-from ..util.data_loader import LabelConverter
-import matplotlib.pyplot as plt
-import time
-import torch
-import numpy as np
-
-class EpochTracker:
-    """
-    Track accuracy, loss, learning_rate etc. during model training
-    Can also be used for validation (which will probably be only one epoch)
-    """
-    def __init__(self, labels: LabelConverter):
-        self.labels = labels
-
-        self.times: list[float] = []            # (epoch)
-        self.predictions = [[]]  # (epoch, batch_nr, (correct_indices | predicted_indices), ind:ex_nr)
-        self.loss: list[float] = []             # (epoch)
-        self.learning_rate: list[float] = []    # (epoch)
-        self.epochs: list[int] = []             # 1 based for FINISHED epochs
-        self._current_epoch = 0    # 0 based
-
-        # after training
-        self.accuracies: list[float] = []       # (epoch)
-
-    def begin(self):
-        self.times.append(time.time())
-
-    def end(self):
-        self.times.append(time.time())
-        # if end_epoch was called before end:
-        if len(self.predictions[-1]) == 0:
-            self.predictions.pop()
-            self._current_epoch -= 1
-        else:  # if end_epoch was not called
-            self.epochs.append(len(self.epochs) + 1)
-            self._calculate_accuracies(self._current_epoch)
-
-
-        s = f"Summary: After {self.epochs[-1]} epochs: "
-        s += f"Accuracy={self.accuracies[-1]:.2f}%"
-        s += f", Total time={self.get_total_time():.2f}s"
-        return s
-
-
-
-    def get_total_time(self):
-        if len(self.times) > 1: return self.times[-1] - self.times[0]
-        else: return -1
-
-    #
-    # EPOCH
-    #
-    def end_epoch(self, loss, learning_rate):
-        """
-        loss and learning_rate of last epoch
-        call before scheduler.step()
-        """
-        self.times.append(time.time())
-        self.epochs.append(len(self.epochs) + 1)
-        if type(loss) == torch.Tensor: self.loss.append(loss.item())
-        else: self.loss.append(loss)
-        self.learning_rate.append(learning_rate)
-        self._calculate_accuracies(self._current_epoch)
-
-        self._current_epoch += 1
-        self.predictions.append([])
-
-    def get_epoch_summary_str(self, ep=-1):
-        """call after next_epoch()"""
-        m = max(ep, 0)  # if ep == -1, check if len is > 0
-        assert(len(self.epochs) > m)
-        s = f"Epoch {self.epochs[ep]:3}"
-        if len(self.accuracies) > m:s += f", Accuracy={self.accuracies[ep]:.2f}%"
-        if len(self.loss) > m:      s += f", Loss={self.loss[ep]:.3f}"
-        if len(self.loss) > m:      s += f", lr={self.learning_rate[ep]:.4f}"
-        if len(self.times) > m+1:   s += f", dt={self.times[ep] - self.times[ep-1]:.2f}s"
-        return s
-
-    def add_prediction(self, correct_indices: torch.Tensor, predicted_indices: torch.Tensor):
-        """for accuracy calculation"""
-        self.predictions[self._current_epoch].append((correct_indices.detach().numpy(), predicted_indices.detach().numpy()))
-
-    #
-    # STATISTICS
-    #
-    def get_count_per_label(self, epoch=-1):
-        """
-        the number of times where <label> was the correct label, per label
-        @returns shape: (label)
-        """
-        count_per_label = [ 0 for _ in range(len(self.labels)) ]
-        for corr, _ in self.predictions[epoch]:
-            for batch in range(len(corr)):
-                count_per_label[corr[batch]] += 1
-        return count_per_label
-
-    def get_predictions_per_label(self, epoch=-1):
-        """
-        How often label_i was predicted, when label_j was the correct label
-        @returns shape: (label_j, label_i)
-        """
-        statistics = [ [ 0 for _ in range(len(self.labels)) ] for _ in range(len(self.labels)) ]
-        for corr, pred in self.predictions[epoch]:
-            for batch in range(len(corr)):
-                statistics[corr[batch]][pred[batch]] += 1
-        return statistics
-
-    def plot_training(self, title="Training Summary", model_dir=None, name="img_training"):
-        """
-        @param model_dir: Optional. If given, save to model_dir as svg
-        """
-        fig, ax = plt.subplots(nrows=3, ncols=1, sharex=True, layout="tight")
-
-        ax[0].plot(self.epochs, self.accuracies, color="red")
-        ax[0].set_ylabel("Accuracy")
-
-        ax[1].plot(self.epochs, self.learning_rate, color="green")
-        ax[1].set_ylabel("Learning Rate")
-
-        ax[2].plot(self.epochs, self.loss, color="blue")
-        ax[2].set_ylabel("Loss")
-
-        fig.suptitle(title)
-        ax[2].set_xlabel("Epoch")
-        plt.tight_layout()
-        if model_dir is not None:
-            fig.savefig(f"{model_dir}/{name}.svg")
-
-        return fig, ax
-
-    def plot_predictions(self, title="Predictions per Label", ep=-1, model_dir=None, name="img_training_predictions"):
-        """
-        @param model_dir: Optional. If given, save to model_dir as svg
-        @param ep: Epoch, defaults to last
-        """
-        # Normalize the data
-        predictions_per_label = self.get_predictions_per_label(ep)
-        normalized_predictions = predictions_per_label / np.sum(predictions_per_label, axis=1, keepdims=True)
-
-        N = len(self.labels)
-        label_names = self.labels.get_labels()
-
-        fig, ax = plt.subplots(layout="tight")
-
-        im = ax.imshow(normalized_predictions, cmap='Blues')  # cmap='BuPu'
-        ax.set_xticks(np.arange(N))
-        ax.set_yticks(np.arange(N))
-        ax.set_xticklabels(label_names)
-        ax.set_yticklabels(label_names)
-        ax.set_xlabel('Predicted Label')
-        ax.set_ylabel('Correct Label')
-
-        # horizontal lines between labels to better show that the sum of a row is 1
-        for i in range(1, N):
-            ax.axhline(i-0.5, color='black', linewidth=1)
-
-        # rotate the x-axis labels for better readability
-        plt.setp(ax.get_xticklabels(), rotation=45, ha="right", rotation_mode="anchor")
-
-        # create annotations
-        for i in range(N):
-            for j in range(N):
-                text = ax.text(j, i, round(normalized_predictions[i, j], 2),
-                               ha="center", va="center", color="black")
-
-        # add colorbar
-        cbar = ax.figure.colorbar(im, ax=ax)
-
-        ax.set_title(title)
-        plt.tight_layout()
-        if model_dir is not None:
-            fig.savefig(f"{model_dir}/{name}.svg")
-        return fig, ax
-
-    #
-    # CALCULATION
-    #
-    def _calculate_accuracies(self, ep):
-        correct_predictions = 0
-        total_predictions = 0
-        for correct_indices, predicted_indices in self.predictions[ep]:
-            correct_predictions += (predicted_indices == correct_indices).sum().item()
-            total_predictions += len(predicted_indices)
-        accuracy = correct_predictions / total_predictions * 100
-        while len(self.accuracies) <= ep:
-            self.accuracies.append(-1)
-        self.accuracies[ep] = accuracy

teng-ml/util/data_loader.py

@@ -3,9 +3,6 @@ from os import path, listdir
 import re
 import numpy as np
 import pandas as pd
-from scipy.sparse import data
-
-import threading
 
 from sklearn.model_selection import train_test_split
 
@@ -13,7 +10,7 @@ from sklearn.model_selection import train_test_split
 re_filename = r"(\d{4}-\d{2}-\d{2})_([a-zA-Z_]+)_(\d{1,2}(?:\.\d*)?)V_(\d+(?:\.\d*)?)mm(\d+).csv"
 
 class LabelConverter:
-    def __init__(self, class_labels: list[str]):
+    def __init__(self, class_labels):
         self.class_labels = class_labels.copy()
         self.class_labels.sort()
 
@@ -35,12 +32,10 @@ class LabelConverter:
     def get_labels(self):
         return self.class_labels.copy()
 
-    def __repr__(self):
-        return str(self.class_labels)
 
 
 class Datasample:
-    def __init__(self, date: str, label: str, voltage: str, distance: str, index: str, label_vec, datapath: str, init_data=False):
+    def __init__(self, date: str, label: str, voltage: str, distance: str, index: str, label_vec, datapath: str):
         self.date = date
         self.label = label
         self.voltage = float(voltage)
@@ -49,62 +44,50 @@ class Datasample:
         self.label_vec = label_vec
         self.datapath = datapath
         self.data = None
-        if init_data: self._load_data()
 
     def __repr__(self):
         size = self.data.size if self.data is not None else "Unknown"
         return f"{self.label}-{self.index}: dimension={size}, recorded at {self.date} with U={self.voltage}V, d={self.distance}mm"
 
     def _load_data(self):
-        # df = pd.read_csv(self.datapath)
-        self.data = np.loadtxt(self.datapath, skiprows=1, dtype=np.float32, delimiter=",")
+        df = pd.read_csv(self.datapath)
+        self.data = df.to_numpy(dtype=np.float32)
 
     def get_data(self):
-        """[[timestamp, idata, vdata]]"""
+        """[[timestamps, idata, vdata]]"""
         if self.data is None:
             self._load_data()
         return self.data
 
-
 class Dataset:
     """
     Store the whole dataset, compatible with torch.data.Dataloader
     """
-    def __init__(self, datasamples, transforms=[], split_function=None):
-        """
-        @param transforms: single callable or list of callables that are applied to the data (before eventual split)
-        @param split_function: (data) -> [data0, data1...] callable that splits the data
-        """
+    def __init__(self, datasamples, transforms=None):
+        self.datasamples = datasamples
         self.transforms = transforms
-        self.data = []  # (data, label)
-        for sample in datasamples:
-            data = self.apply_transforms(sample.get_data())
-            if split_function is None:
-                self.data.append((data, sample.label_vec))
-            else:
-                for data_split in split_function(data):
-                    self.data.append((data_split, sample.label_vec))
+        # self.labels = [ d.label_vec for d in datasamples ]
+        # self.data = [ d.get_data() for d in datasamples ]
 
-    def apply_transforms(self, data):
+    def __getitem__(self, index):
+        data, label = self.datasamples[index].get_data(), self.datasamples[index].label_vec
+        # print(f"loading dataset {self.datasamples[index]}")
         if type(self.transforms) == list:
             for t in self.transforms:
                 data = t(data)
-        elif self.transforms is not None:
+        elif self.transforms:
             data = self.transforms(data)
-        return data
-
-    def __getitem__(self, index):
-        return self.data[index]
+        # TODO
+        return data[:2000], label
 
     def __len__(self):
-        return len(self.data)
+        return len(self.datasamples)
 
-
-def get_datafiles(datadir, labels: LabelConverter, voltage=None):
+def load_datasets(datadir, labels: LabelConverter, transforms=None, voltage=None, train_to_test_ratio=0.7, random_state=None):
     """
-    get a list of all matching datafiles from datadir that are in the format: yyyy-mm-dd_label_x.xV_xxxmm.csv
+    load all data from datadir that are in the format: yyyy-mm-dd_label_x.xV_xxxmm.csv
     """
-    datafiles = []
+    datasamples = []
     files = listdir(datadir)
     files.sort()
     for file in files:
@@ -116,38 +99,9 @@ def get_datafiles(datadir, labels: LabelConverter, voltage=None):
 
         sample_voltage = float(match.groups()[2])
         if voltage and voltage != sample_voltage: continue
-        datafiles.append((datadir + "/" + file, match, label))
-    return datafiles
 
-
-def load_datasets(datadir, labels: LabelConverter, transforms=None, split_function=None, voltage=None, train_to_test_ratio=0.7, random_state=None, num_workers=None):
-    """
-    load all data from datadir that are in the format: yyyy-mm-dd_label_x.xV_xxxmm.csv
-    """
-    datasamples = []
-    if num_workers == None:
-        for file, match, label in get_datafiles(datadir, labels, voltage):
-            datasamples.append(Datasample(*match.groups(), labels.get_one_hot(label), file))
-    else:
-        files = get_datafiles(datadir, labels, voltage)
-        def worker():
-            while True:
-                try:
-                    file, match, label = files.pop()
-                except IndexError:
-                    # No more files to process
-                    return
-                datasamples.append(Datasample(*match.groups(), labels.get_one_hot(label), file, init_data=True))
-        threads = [threading.Thread(target=worker) for _ in range(num_workers)]
-        for t in threads:
-            t.start()
-        for t in threads:
-            t.join()
-
-
-    # TODO do the train_test_split after the Dataset split
-    # problem: needs to be after transforms
+        datasamples.append(Datasample(*match.groups(), labels.get_one_hot(label), datadir + "/" + file))
     train_samples, test_samples = train_test_split(datasamples, train_size=train_to_test_ratio, shuffle=True, random_state=random_state)
-    train_dataset = Dataset(train_samples, transforms=transforms, split_function=split_function)
-    test_dataset = Dataset(test_samples, transforms=transforms, split_function=split_function)
+    train_dataset = Dataset(train_samples, transforms=transforms)
+    test_dataset = Dataset(test_samples, transforms=transforms)
     return train_dataset, test_dataset

teng-ml/util/epoch_tracker.py

@@ -0,0 +1,83 @@
+from ..util.data_loader import LabelConverter
+import time
+import torch
+
+class EpochTracker:
+    """
+    Track progress through epochs and generate statistics
+    """
+    def __init__(self, labels: LabelConverter):
+        # Training
+        self.accuracy = []
+        self.loss = []
+        self.times = []  # timestamps for each epoch end
+        self.trainings = []
+        self.training_indices = [[]]  # epoch, batch_nr, (correct_indices, predicted_indices), ind:ex_nr
+        self._current_epoch = 0
+
+        self.labels = labels
+
+        # Testing
+        self.tests = []  # (correct_indices, predicted_indices)
+
+    def train_begin(self):
+        """for time tracking"""
+        self.times.append(time.time())
+
+    # TRAINING
+    def train(self, correct_indices: torch.Tensor, predicted_indices: torch.Tensor):
+        self.training_indices[self._current_epoch].append((correct_indices, predicted_indices))
+
+    def next_epoch(self, loss):
+        self.times.append(time.time())
+        self.loss.append(loss)
+        correct_predictions = 0
+        total_predictions = 0
+        for predicted_indices, correct_indices in self.training_indices[self._current_epoch]:
+            correct_predictions += (predicted_indices == correct_indices).sum().item()
+            total_predictions += predicted_indices.size(0)
+        accuracy = 100 * correct_predictions / total_predictions
+        self.accuracy.append(accuracy)
+        self._current_epoch += 1
+        self.training_indices.append([])
+
+    def get_last_epoch_summary_str(self):
+        """call after next_epoch()"""
+        return f"Epoch {self._current_epoch:3}: Accuracy={self.accuracy[-1]:.2f}, Loss={self.loss[-1]:.3f}, Training duration={self.times[-1] - self.times[0]:.2f}s"
+    def get_last_epoch_summary(self):
+        """
+        @returns accuracy, loss, training time
+        """
+        return self.accuracy[-1], self.loss[-1], self.times[-1] - self.times[0]
+
+    def get_training_count_per_label(self):
+        count_per_label = [ 0 for _ in range(len(self.labels)) ]
+        for i in range(len(self.training_indices)):
+            for j in range(len(self.training_indices[i])):
+                for k in range(self.training_indices[i][j][0].size(0)):
+                    # epoch, batch_nr, 0 = correct_indices, correct_index_nr
+                    count_per_label[self.training_indices[i][j][0][k]] += 1
+        return count_per_label
+
+    def __len__(self):
+        return len(self.accuracy)
+
+    def __getitem__(self, idx):
+        return (self.accuracy[idx], self.loss[idx])
+
+    # TESTING
+    def test(self, correct_indices: torch.Tensor, predicted_indices: torch.Tensor):
+        """
+        @param correct_indices and predicted_indices: 1 dim Tensor
+        """
+        for i in range(correct_indices.size(0)):
+            self.tests.append((correct_indices[i], predicted_indices[i]))
+
+
+    def get_test_statistics(self):
+        # label i, label_j was predicted when label_i was correct 
+        statistics = [ [ 0 for _ in range(len(self.labels))] for _ in range(len(self.labels)) ]
+        for corr, pred in self.tests:
+            statistics[corr][pred] += 1
+        print(statistics)
+        return statistics

teng-ml/util/file_io.py

@@ -1,34 +0,0 @@
-from os import listdir, path
-
-def add_zeros(v: int, digits=3):
-    """
-    return v as string, add leading zeros if len(str(v)) < digits
-    """
-    s = str(v)
-    return '0' * (max(digits - len(s), 0)) + s
-
-
-def get_next_digits(basename, directory=".", digits=3):
-    """
-    get the next filename digits
-    example:
-        basename = file
-        directory has file001.csv, file002.pkl, file004.csv
-        -> return 005
-    """
-    files = listdir(directory)
-    files.sort()
-    files.reverse()
-    lowest_number = -1
-    for file in files:
-        if not file.startswith(basename): continue
-        try:
-            dot = file.rfind('.')
-            if dot > 0: file = file[:dot]
-            number = int(file.replace(basename, ""))
-            if number < lowest_number: continue
-            lowest_number = number
-        except ValueError:
-            continue
-
-    return add_zeros(lowest_number+1)

teng-ml/util/model_io.py

@@ -1,45 +0,0 @@
-from ..tracker.epoch_tracker import EpochTracker
-from ..util.settings import MLSettings
-import pickle
-
-
-"""
-Load and save model, settings and EpochTrackers from/on disk
-"""
-
-def load_tracker_validation(model_dir):
-    with open(f"{model_dir}/tracker_validation.pkl", "rb") as file:
-        validation_tracker: EpochTracker = pickle.load(file)
-    return validation_tracker
-
-def load_tracker_training(model_dir):
-    with open(f"{model_dir}/tracker_training.pkl", "rb") as file:
-        training_tracker: EpochTracker = pickle.load(file)
-    return training_tracker
-
-def load_settings(model_dir):
-    with open(f"{model_dir}/settings.pkl", "rb") as file:
-        st: MLSettings = pickle.load(file)
-    return st
-
-def load_model(model_dir):
-    with open(f"{model_dir}/model.pkl", "rb") as file:
-        model = pickle.load(file)
-    return model
-
-
-def save_tracker_validation(model_dir, validation_tracker: EpochTracker):
-    with open(f"{model_dir}/tracker_validation.pkl", "wb") as file:
-        pickle.dump(validation_tracker, file)
-
-def save_tracker_training(model_dir, training_tracker: EpochTracker):
-    with open(f"{model_dir}/tracker_training.pkl", "wb") as file:
-        pickle.dump(training_tracker, file)
-
-def save_settings(model_dir, st):
-    with open(f"{model_dir}/settings.pkl", "wb") as file:
-        pickle.dump(st, file)
-
-def save_model(model_dir, model):
-    with open(f"{model_dir}/model.pkl", "wb") as file:
-        pickle.dump(model, file)

teng-ml/util/settings.py

@@ -1,5 +1,4 @@
 from ..util.data_loader import LabelConverter
-from ..util.split import DataSplitter
 
 class MLSettings:
     """
@@ -10,11 +9,7 @@ class MLSettings:
                  num_layers=1,
                  hidden_size=1,
                  bidirectional=True,
-                 optimizer=None,
-                 scheduler=None,
-                 loss_func=None,
                  transforms=[],
-                 splitter=None,
                  num_epochs=10,
                  batch_size=5,
                  labels=LabelConverter([]),
@@ -24,11 +19,7 @@ class MLSettings:
         self.hidden_size = hidden_size
         self.num_epochs = num_epochs
         self.bidirectional = bidirectional
-        self.optimizer = optimizer
-        self.scheduler = scheduler
-        self.loss_func = loss_func
         self.transforms = transforms
-        self.splitter = splitter
         self.batch_size = batch_size
         self.labels = labels
 
@@ -39,7 +30,6 @@ class MLSettings:
         H = hidden_size
         B = bidirectional
         T = #transforms
-        S = splitter
         E = #epochs
         """
-        return f"F{self.num_features}L{self.num_layers}H{self.hidden_size:02}B{'1' if self.bidirectional else '0'}T{len(self.transforms)}S{self.splitter.split_size if type(self.splitter) == DataSplitter is not None else 0:03}E{self.num_epochs:03}"
+        return f"F{self.num_features}L{self.num_layers}H{self.hidden_size}B{'1' if self.bidirectional else '0'}T{len(self.transforms)}"

teng-ml/util/split.py

@@ -1,23 +0,0 @@
-import numpy as np
-
-class DataSplitter:
-    r"""
-    Split a numpy array into smaller arrays of size datapoints_per_split
-    If data.shape(0) % datapoints_per_split != 0, the remaining datapoints are dropped
-    """
-    def __init__(self, datapoints_per_split):
-        self.split_size = datapoints_per_split
-
-    def __call__(self, data: np.ndarray):
-        """
-        data: [[t, i, v]]
-        """
-        ret_data = []
-        for i in range(self.split_size, data.shape[0], self.split_size):
-            ret_data.append(data[i-self.split_size:i, :])
-        if len(ret_data) == 0:
-            raise ValueError(f"data has only {data.shape[0]}, but datapoints_per_split is set to {self.split_size}")
-        return ret_data
-
-    def __repr__(self):
-        return f"DataSplitter({self.split_size})"

teng-ml/util/string.py

@@ -1,51 +0,0 @@
-import inspect
-import torch.optim.lr_scheduler as sd
-import re
-
-def fill_and_center(s: str, fill_char="=", length=100):
-    rs = fill_char * length
-    margin = (length - len(s)) // 2
-    if margin > 1:
-        rs = f"{fill_char*(margin-1)} {s} {fill_char*(margin-1)}"
-        if len(rs) == 99: rs = rs + "="
-        assert(len(rs) == 100)
-        return rs
-    else:
-        return s
-
-def class_str(x):
-    """
-    Return the constructor of the class of x with arguemnts
-    """
-    name = type(x).__name__
-    signature = inspect.signature(type(x))
-    params = []
-    for param_name, param_value in x.__dict__.items():
-        if param_name not in signature.parameters:
-            continue
-        default_value = signature.parameters[param_name].default
-        if param_value != default_value:
-            params.append(f"{param_name}={param_value!r}")
-    if params:
-        return f"{name}({', '.join(params)})"
-    else:
-        return name
-
-
-def cleanup_str(s):
-    """
-    convert to string if necessary and
-    if scheduler string:
-        remove unnecessary parameters
-    """
-    if not type(s) == str:
-        s = str(s)
-    # check if scheduler string
-    re_scheduler = r"(\w+)\((.*)(optimizer=[A-Za-z]+) \(.*(initial_lr: [\d.]+).*?\)(.*)\)"
-    # groups: (sched_name, sched_params1, optimizer=Name, initial_lr: digits, sched_params2)
-    match = re.fullmatch(re_scheduler, s.replace("\n", " "))
-    if match:
-        g = match.groups()
-        s = f"{g[0]}({g[1]}{g[2]}({g[3]}, ...){g[4]})"
-        return s
-    return s

teng-ml/util/transform.py

@@ -54,3 +54,4 @@ class ConstantInterval:
 
     def __repr__(self):
         return f"ConstantInterval(interval={self.interval})"
+