teng_ml/data_preprocess.py

@@ -1,14 +1,10 @@
 import pandas as pd
 import numpy as np
 import scipy.signal as signal
-import matplotlib as mpl
-mpl.use("TkAgg")  # fixes focus issues for me
 import matplotlib.pyplot as plt
 from time import sleep
 from random import choice as r_choice
 from sys import exit
-import os
-import re
 
 
 if __name__ == "__main__":
@@ -22,107 +18,36 @@ if __name__ == "__main__":
 
 from .util.transform import Normalize
 from .util.data_loader import get_datafiles
-from .util.file_io import get_next_digits
 
 file = "/home/matth/Uni/TENG/teng_2/data/2023-06-28_foam_black_1_188mm_06V001.csv"
 
-
 class InteractiveDataSelector:
-    re_file = r'\d{4}-\d{2}-\d{2}_([a-zA-Z0-9_]+)_([a-zA-Z0-9]+)_(\d+(?:\.\d+)?mm)_(\d+V)(\d+)\.csv'
-    re_index_group_nr = 5  # group number of the index part of the filename
     """
-    Go through all .csv files in a directory, split the data and exclude sections with the mouse, then write the sections as single files into a new directory
+    Helper class for "iterating" through selected peaks.
     """
-    def __init__(self, in_dir, out_dir, keep_index=True, split_at_exclude=True):
+    def __init__(self, out_name, out_dir, fig, ax):
-        """
-        @param keep_index:
-            If True: append the split number as triple digits to the existing filename (file001.csv -> file001001.csv, file001002.csv ...)
-            Else: remove the indices from the filename before adding the split number (file001.csv -> file001.csv, file002.csv ...)
-        @param split_at_exclude:
-            If True: When excluding an area, split the data before and after the excluded zone
-            Else: remove the excluded zone and join the previous and later part
-        """
-        if os.path.isdir(out_dir):
-            if os.listdir(out_dir):
-                raise ValueError(f"'out_dir' = '{out_dir}' is not empty")
-        else:
-            os.makedirs(out_dir)
         self._out_dir = out_dir
+        self._out_name = out_name
+        self._fig = fig
+        self._ax = ax
 
-        self._in_dir = in_dir
-        self._in_files = os.listdir(in_dir)
-        self._in_files.sort()
-        for i in reversed(range(len(self._in_files))):
-            if not re.fullmatch(InteractiveDataSelector.re_file, self._in_files[i]):
-                print(f"Dropping non-matching file '{self._in_files[i]}'")
-                self._in_files.pop(i)
-        if not self._in_files:
-            raise ValueError(f"No matching files in 'in_dir' = '{in_dir}'")
-
-        self._history: list[tuple[str, list]] = []   # (in_file, [out_files...])
-
-        self._keep_index = keep_index
-        self.split_at_exclude = split_at_exclude
-
-        plt.ion()
-        self._fig, self._ax = plt.subplots()
-
-        mpl.rcParams['keymap.save'].remove('s')  # s is used for split
-        mpl.rcParams['keymap.quit'].remove('q')
         self._fig.canvas.mpl_connect("button_press_event", lambda ev: self._fig_on_button_press(ev))
         self._fig.canvas.mpl_connect("key_press_event", lambda ev: self._fig_on_key_press(ev))
 
-    def run(self):
-        self._next_file()
-        while plt.fignum_exists(self._fig.number):
-            plt.pause(0.01)
-
-    def _set_titles(self):
-        help_str = "[(e)xclude, (s)plit, (w)rite+next, (U)ndo last file, (Q)uit]"
-        self._fig.suptitle(f"{help_str}\nuse left click to select, right click to undo\ncurret mode: {self._mode}")
-
-    def _undo_file(self):
-        if len(self._history) == 0:
-            print("Nothing to undo")
-            return
-        # delete written files
-        for outfile in self._history[-1][1]:
-            print(f"Deleting '{outfile}'")
-            os.remove(outfile)
-        self._in_files.insert(0, self._history[-1][0])
-        self._history.pop()
-        self._next_file()
-
-    def _next_file(self):
-        # runtime stuff
-        if len(self._in_files) == 0:
-            raise IndexError("No more files to process")
-        self._current_file = self._in_files.pop(0)
-        self._current_dataframe = pd.read_csv(os.path.join(self._in_dir, self._current_file))
-        self._current_array = self._current_dataframe.to_numpy()
-        self._current_array = np.loadtxt(os.path.join(self._in_dir, self._current_file), skiprows=1, delimiter=",")
-
-
-        # plot stuff
         self._splits_lines = None  # vlines
         self._excludes_lines = None
         self._excludes_areas = [] # list of areas
-        self._fig.clear()
-        self._ax = self._fig.subplots()
-        self._ax.plot(self._current_array[:,0], self._current_array[:,2])
-        self._ax.set_xlabel(self._current_file)
 
         self._splits: list[int] = []
         self._excludes: list[int] = []
-        self._mode = "exclude" # split or exclude
+        self._mode = None  # split or exclude
-        self._set_titles()
+        self._set_mode("split")
+
+    def run(self):
+        while plt.fignum_exists(self._fig.number):
+            plt.pause(0.01)
 
     def _fig_on_button_press(self, event):
-        """
-        left click: set split / exclude section (depends on mode)
-        right click: undo last action of selected mode
-        """
-        if event.xdata is None: return
         if event.xdata in self._excludes or event.xdata in self._splits: return
         if event.button == 1:  # left click, add position
             if self._mode == "split":
@@ -139,33 +64,22 @@ class InteractiveDataSelector:
         self._update_lines()
 
     def _fig_on_key_press(self, event):
-        """
+        if event.key == 'S':
-        s: set split mode
+            self._set_mode("split")
-        e: set exclude mode
-        w: write and got to next file
-        Q: quit all
-        """
-        if event.key == 's':
-            self._mode = "split"
         elif event.key == 'e':
-            self._mode = "exclude"
+            self._set_mode("exclude")
-        elif event.key == 'w':
-            self._save_as_new_files()
-            try:
-                self._next_file()
-            except IndexError:
-                print(f"All files processed.")
-                exit(0)
-        elif event.key == 'U':
-            self._undo_file()
-        elif event.key == 'Q':
-            print(f"Quitting before all files have been processed!")
-            exit(1)
-        self._set_titles()
 
+    def _set_mode(self, mode):
+        help_str = "[(e)xclude - (S)plit]"
+        if mode == "split":
+            self._mode = "split"
+            fig.suptitle(f"-> split mode {help_str}")
+        else:
+            self._mode = "exclude"
+            fig.suptitle(f"-> exclude mode {help_str}")
 
     def _update_lines(self):
-        # print(self._splits, self._excludes)
+        print(self._splits, self._excludes)
         ymin, ymax = self._ax.get_ylim()
 
         if self._splits_lines is not None: self._splits_lines.remove()
@@ -186,78 +100,28 @@ class InteractiveDataSelector:
         self._ax.set_ylim(ymin, ymax)  # reset, since margins are added to lines
         self._fig.canvas.draw()
 
-    def _get_next_filename(self):
-        if self._keep_index:
-            # 5th group is index
-            match = re.fullmatch(InteractiveDataSelector.re_file, self._current_file)
-            assert(type(match) is not None)
-            basename = self._current_file[:match.start(InteractiveDataSelector.re_index_group_nr)]
-        else:
-            basename = self._current_file[:-4]  # extension
-        index = get_next_digits(basename, self._out_dir, digits=3)
-        return f"{basename}{index}.csv"
-
     def _save_as_new_files(self):
-        # convert timestamps to their closest index
-        excludes_idx = [np.abs(self._current_array[:,0] - t).argmin() for t in self._excludes]
-        splits_idx = [np.abs(self._current_array[:,0] - t).argmin() for t in self._splits]
-        if self.split_at_exclude:
-            # split before the start of the exclucded range
-            splits_idx += [ excludes_idx[i]-1 for i in range(0, len(excludes_idx), 2) ]
-            # split after the end of the exclucded range
-            splits_idx += [ excludes_idx[i]+1 for i in range(1, len(excludes_idx), 2) ]
-        splits_idx = list(set(splits_idx))  # remove duplicates
-        splits_idx.sort()
 
-        df = self._current_dataframe.copy()
 
-        # 1) remove excluded parts
-        for i in range(1, len(excludes_idx), 2):
-            df = df.drop(index=range(excludes_idx[i-1], excludes_idx[i]+1))
-
-        # 2) splits
-        new_frames = []
-        start_i = df.index[0]
-        for i in range(0, len(splits_idx)):
-            end_i = splits_idx[i]
-            # print(start_i, end_i)
-            # check if valid start and end index
-            if start_i in df.index and end_i in df.index:
-                new_frames.append(df.loc[start_i:end_i])
-            start_i = end_i + 1
-        # append rest
-        if start_i in df.index:
-            new_frames.append(df.loc[start_i:])
-
-        # 3) remove empty
-        for i in reversed(range(len(new_frames))):
-            if len(new_frames[i]) == 0:
-                new_frames.pop(i)
-
-        self._history.append((self._current_file, []))
-        for frame in new_frames:
-            filename = self._get_next_filename()
-            pathname = os.path.join(self._out_dir, filename)
-            # until now, frame is a copy of a slice
-            frame = frame.copy()
-            # transform timestamps so that first value is 0
-            t_column_name = frame.columns[0]
-            frame[t_column_name] -= frame.iloc[0][t_column_name]
-            frame.to_csv(pathname, index=False)
-            self._history[-1][1].append(pathname)
-            print(f"Saved range of length {len(frame.index):04} to {pathname}")
 
 
 if __name__ == "__main__":
-    import argparse
+    """
-    parser = argparse.ArgumentParser("data_preprocess")
+    Peak identification:
-    parser.add_argument("in_dir")
+    plot, let user choose first, second, last and lowest peak for identification
-    parser.add_argument("out_dir")
+    """
-    parser.add_argument("-i", "--keep_index", action="store_true")
+    df = pd.read_csv(file)
-    parser.add_argument("-e", "--split_at_exclude", action="store_true")
+    a = df.to_numpy()
-    ns = parser.parse_args()
 
-    selector = InteractiveDataSelector(ns.in_dir, ns.out_dir, keep_index=ns.keep_index, split_at_exclude=ns.split_at_exclude)
+    # a2 = interpolate_to_linear_time()
+    # print(a2)
+    # exit()
+
+    vdata = Normalize(0, 1)(a[:,2])
+    plt.ion()
+    fig, ax = plt.subplots()
+    ax.plot(vdata)
+    ax.grid(True)
+    selector = InteractiveDataSelector("bla", "test", fig, ax)
     selector.run()
-    exit(2)  # selector should exit in _fig_on_key_press
 

teng_ml/tracker/epoch_tracker.py

@@ -1,6 +1,5 @@
 from ..util.data_loader import LabelConverter
 import matplotlib.pyplot as plt
-import matplotlib.colors as colors
 import time
 import torch
 import numpy as np
@@ -142,7 +141,8 @@ class EpochTracker:
         label_names = self.labels.get_labels()
 
         fig, ax = plt.subplots(layout="tight")
-        im = ax.imshow(normalized_predictions, cmap='Blues')  # cmap='BuPu', , norm=colors.PowerNorm(1./2.)
+
+        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)