diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..1b607862ab354a72e8a64f9306e954eb9d87d3fb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+
+audio_examples/SCW1807_20200713_064545.wav
diff --git a/PyAVA.py b/PyAVA.py
index b054f7b4445bbcda1c80dc337c5a2534ac4f48cf..98c0d3b2d98a74934804a948e46fb0df82f42121 100644
--- a/PyAVA.py
+++ b/PyAVA.py
@@ -1,20 +1,40 @@
##### IMPORTATIONS #####
+import os
+import json
from tkinter import *
-from classes import FileExplorer, App
+from interface import FileExplorer, App
from args import fetch_inputs
##### MAIN #####
if __name__ == '__main__':
# fetching inputs.
- dir_explore, max_traj, new_sr, output = fetch_inputs()
+ dir_explore, max_traj, new_sr, output, modify, initial_basename = fetch_inputs()
- # open explorer to select firt file
- groot = Tk()
- initial_file = FileExplorer(dir_explore).file
- groot.quit()
- groot.destroy()
+ if modify:
+ with open(os.path.join(output, modify), "r") as f:
+ coords_to_change = json.load(f)
- if len(initial_file) > 0:
- # launch UI
- MainWindow = App(dir_explore, max_traj, new_sr, output, initial_file)
\ No newline at end of file
+ MainWindow = App(
+ dir_explore,
+ max_traj,
+ new_sr,
+ output,
+ os.path.join(dir_explore, initial_basename),
+ coords_to_change)
+
+ else:
+ # open explorer to select firt file
+ groot = Tk()
+ initial_file = FileExplorer(dir_explore).file
+ groot.quit()
+ groot.destroy()
+
+ if len(initial_file) > 0:
+ # launch UI
+ MainWindow = App(
+ dir_explore,
+ max_traj,
+ new_sr,
+ output,
+ initial_file)
diff --git a/README.md b/README.md
index 24102004712bf6e2dccfbac9dfc59115fa9f4a12..9f1c8986c3564c4a84e671e05a5136993f4991b6 100644
--- a/README.md
+++ b/README.md
@@ -11,21 +11,17 @@
- [x] Spectrogram contour annotations.
- [x] Spectrogram automatically computed from waveform.
-- [x] Switch between custom spectrogram resolutions (fft, hop length, clipping dB value).
+- [x] Choose custom spectrogram resolutions (fft, hop length, clipping dB value and PCEN).
- [x] Select a new file directly from the interface.
- [x] Exportation of contours to local `.json`.
-
-
-## TODO
-
-- [ ] Switch between waveform and spectrogram views.
-- [ ] Bounding Box, time segments and pixel selection.
+- [x] Move points once they are placed (with mouse wheel).
+- [x] Modification of previous annotation. Save & return later!
## Requirements
-- Ubuntu / Windows / macOS (tested only on Ubuntu but it *should* work on all OS).
-- Python3
+- Ubuntu / Windows / macOS (tested only on Ubuntu but it *should* work on any OS).
+- Python 3.9.7
- Packages in `requirements.txt`
Install packages in your python environment with `$ pip install -r requirements.txt`.
@@ -34,55 +30,48 @@ Install packages in your python environment with `$ pip install -r requirements.
## Usage
### Execution
-For classic use, run `$python PyAVA.py -dir myWavefileFolder -out myOutputFolder` in terminal.
+For classic use, download PyAVA folder, then run `$python PyAVA.py -dir myWavefileFolder -out myOutputFolder` in terminal.
Run `$python PyAVA.py --help` for details.
The annotations are saved in [JSON](http://www.json.org/) files. Each file contains a dict of contours. For each contour there is a list of points, each point is defined by a list of two elements : [time (in sec), frequency (in kHz)].
### User interaction
- Use the toolbar to interact with the plot.
-- No toolbar item must be selected in order to annotate.
-- Left-click on a name in the legend to activate annotation with it.
+- User must not have any toolbar item selected in order to annotate the image.
+- Left-click on a name in the listbox to activate annotation with it.
- Left-click to place a point from the selected category.
- Right-click to remove the nearest point from the selected category.
- Click on `Open file explorer` Button to change Wavefile (will end annotation of the current file).
- Change resolution of the spectrogram with `FFT`, `Hop length` and `clipping fields`.
- Click on `Update display` button to validate inputs.
-- Add more contours by clicking on the `MORE CONTOURS` button.
### Re-use data
-Two functions are available to load and display the saved annotations : `load_contours_file` and `display_contours`.
+To load and display the saved annotations, use the "Results" object. It contains several infos: coordinates of the annotations, spectrogram, waveform and more.
-Run the following lines in a python terminal to see an exemple of use :
+Open a terminal window in PyAVA folder and run the following lines with Python to see an exemple of use:
```python
import os
import json
-from functions import load_contours_file, display_contours # load functions
-
-# load annotations
-contours = load_contours_file(
- os.path.join(
- ".",
- "outputs",
- "SCW6070_20220717_174215-contours.json")
- )
-print(json.dumps(contours, indent=4)) # show file content
+from post_annotation import Results # load functions
-# display annotations
-display_contours(
- os.path.join(
- ".",
+# load object with annotation data
+annot_data = Results(os.path.join(
+ ".",
"audio_examples",
- "SCW1807_20200713_064545.wav"),
+ "SCW1807_20200713_064554.wav"),
os.path.join(
- ".",
+ ".",
"outputs",
- "SCW1807_20200713_064545-contours.json"),
- cmap='jet'
- )
+ "SCW1807_20200713_064554-contours.json"))
+print(json.dumps(annot_data.coords, indent=4)) # show file content
+# display annotations
+annot_data.display_contours() # or annot_data.display_contours(img="pcen")
```
+To modify previous annotations, run the following line (using annotations on file SCW6070_20220717_174215.wav as an example):
+`$python PyAVA_V2.py --modify SCW6070_20220717_174215-contours.json SCW6070_20220717_174215.wav`
+
## Support
Please contact [me](mailto:loic.lehnhoff@gmail.com) for any question and/or idea.
diff --git a/args.py b/args.py
index efc65dc431ed032ad4ef6cf2bf92ccaa4e5040ce..7298bce485a494e520475261e105b741d87960d8 100644
--- a/args.py
+++ b/args.py
@@ -26,6 +26,10 @@ def fetch_inputs():
Resampling rate for audio data.
outputs : int
Path to folder that will contain outputs.
+ modify_file : str or False
+ Path to a json file containing annotations.
+ from_wav : str or False
+ Path to a wavefile.
"""
# setting up arg parser
@@ -39,8 +43,8 @@ def fetch_inputs():
parser.add_argument(
'-dir', '--directory',
type=str,
- default=".",
- nargs=1,
+ default="./audio_examples",
+ nargs='?',
required=False,
help=("Directory in which the file explorer will open."
"\nPick any .wav file to begin annotation. "
@@ -51,7 +55,7 @@ def fetch_inputs():
'-max', '--max_contours',
type=int,
default=15,
- nargs=1,
+ nargs='?',
required=False,
help=("Number of contours that can be annotated at the same time."
"\nDue to restrictions with the module used,"
@@ -63,7 +67,7 @@ def fetch_inputs():
'-new', '--resampling_rate',
type=int,
default=96_000,
- nargs=1,
+ nargs='?',
required=False,
help=("Resampling rate for the Wavefile. "
"\nCan be used to speed up spectrogram visualisation. "
@@ -73,7 +77,7 @@ def fetch_inputs():
parser.add_argument(
'-out', '--output',
type=str,
- nargs=1,
+ nargs='?',
default=os.path.join(".","outputs"),
required=False,
help=("Path where the contours will be saved."
@@ -81,28 +85,48 @@ def fetch_inputs():
"\nDefault value is './outputs'.\n\n")
)
+ parser.add_argument(
+ '-m', '--modify',
+ type=str,
+ nargs=2,
+ required=False,
+ help=("Name of a file generated by a previous annitation,"
+ "\nand name of the associated wavefile."
+ "\nThis will open the interface with the contours from this file"
+ "\nand enable modification of these contours."))
+
# fetching arguments
args = parser.parse_args()
outputs = args.output
explore = args.directory
contour = args.max_contours
resampl = args.resampling_rate
+ if args.modify == None:
+ modify_file, from_wav = False, False
+ else:
+ modify_file, from_wav = args.modify
+
# verifying arguments
try:
assert (os.path.exists(outputs)), (
- f"\nInputError: Could not find dir {outputs}."
+ f"\nInputError: Could not find dir '{outputs}'."
"\n\tCreate a folder that will contain outputs,"
" or type in an existing folder with `-out folder_name`.")
assert (os.path.exists(explore)), (
- f"\nInputError: Could not find dir {explore}.")
+ f"\nInputError: Could not find dir '{explore}'.")
+ if modify_file:
+ assert (os.path.exists(os.path.join(outputs, modify_file))), (
+ f"\nInputError: Could not find file '{modify_file}' in '{outputs}'.")
+ assert (os.path.exists(os.path.join(explore, from_wav))), (
+ f"\nInputError: Could not find file '{from_wav}' in '{explore}'.")
assert (contour <= 50), (
f"\nInputError: Max number of contours cannot exceed 50, got {contour}.")
except Exception as e:
print(e)
exit()
- return (explore, contour, resampl, outputs)
+ return (explore, contour, resampl, outputs, modify_file, from_wav)
# if running `$python ARGS.py -h` for help.
if __name__ == '__main__':
diff --git a/audio_examples/SCW1807_20200713_064545.wav b/audio_examples/SCW1807_20200713_064545.wav
deleted file mode 100644
index 05b0a36a62220beb1d02328ab3fcc3bc95111cb2..0000000000000000000000000000000000000000
Binary files a/audio_examples/SCW1807_20200713_064545.wav and /dev/null differ
diff --git a/audio_examples/SCW1807_20200713_064554.wav b/audio_examples/SCW1807_20200713_064554.wav
new file mode 100644
index 0000000000000000000000000000000000000000..9bb76a7725268b0417beeecc152657695a77165b
Binary files /dev/null and b/audio_examples/SCW1807_20200713_064554.wav differ
diff --git a/classes.py b/classes.py
deleted file mode 100644
index 121de7f8d64a3282fd1d0e57b159f217b3562c70..0000000000000000000000000000000000000000
--- a/classes.py
+++ /dev/null
@@ -1,427 +0,0 @@
-##### IMPORTATIONS #####
-import os
-import numpy as np
-from tkinter import *
-from tkinter import filedialog as fd
-from matplotlib.backends.backend_tkagg import (NavigationToolbar2Tk,
- FigureCanvasTkAgg)
-from matplotlib.figure import Figure
-from mpl_point_clicker import clicker
-
-# Import external functions
-from functions import (load_waveform, wave_to_spectrogram, get_contours,
- save_dict)
-
-
-##### CLASSES #####
-class FileExplorer(object):
- """
- A Class to open a file explorer when it is run in an active Tkinter loop.
-
- ...
-
- Attributes
- ----------
- path : str
- Path to a folder in which the file explorer will be opened.
- file : str
- Path to a file selected by the user in the file explorer window.
-
- Methods
- -------
- explorer_window():
- Calls the tkinter functions that opens a file explorer window.
-
- """
-
- def __init__(self, path):
- """
- Constructs all the necessary attributes for the FileExplorer object.
-
- Parameters
- ----------
- path : str
- Path to a folder in which the file explorer will be opened.
- file : str
- Path to a file selected by the user in the file explorer window.
- """
- self.path = path # folder to be opened
- self.file = "" # file to be returned
- self.explorer_window() # start function auto
-
- def explorer_window(self):
- """
- Calls the tkinter function that opens a file explorer window.
- Affect the select pass to 'file' attribute.
-
- ...
-
- Parameters
- ----------
- path : str
- Path to the directory in which the file explorer will be opened.
- """
- self.file = fd.askopenfilename(
- title='Open a file',
- initialdir=self.path,
- filetypes=(
- ('Audio Files', '*.wav'),
- ('All files', '*.*')
- ))
-
-class App(object):
- """
- A Class to construct an contours annotation tool for audio data.
-
- ...
-
- Attributes
- ----------
- WIDTH (init with DEFAULT_WIDTH) : int
- (Default) width of the window in which the app will run, in pixels.
- (Default value is loaded from 'PARAMETERS.py' file).
- HEIGHT (init with DEFAULT_HEIGHT) : int
- Default height of the window in which the app will run, in pixels.
- (Default value is loaded from 'PARAMETERS.py' file).
- LEFT_WIDTH (init with DEFAULT_LEFT_WIDTH) : int
- Default width for the left panel of the window of the app.
- (Default value is loaded from 'PARAMETERS.py' file).
- NFFT (init with DEFAULT_NFFT) : int
- Default fft size for spectrogram, in samples.
- (Default value is loaded from 'PARAMETERS.py' file).
- HOP_LENGTH (init with DEFAULT_HOP_LENGTH) : int
- Default hop length for spectrogram, in samples.
- (Default value is loaded from 'PARAMETERS.py' file).
- CLIPPING (init with DEFAULT_CLIPPING) : int
- Default clipping value for spectrogram, in dB.
- (Default value is loaded from 'PARAMETERS.py' file).
- CMAP (init with DEFAULT_CMAP) : str
- Name of a matplotlib.pyplot color map.
- (Default value is loaded from 'PARAMETERS.py' file).
- COORDS (init with DEFAULT_COORDS) : dict
- Empty dictionary.
- DIR : str
- Path to a folder in which the file explorer will be opened.
- MAX_C : int
- Maximum number of contours that can be drawn at once.
- NEW_SR : int
- Resampling rate of the audio recording.
- DIR_OUT : str
- Path to a folder where the contours will be saved.
- WAVEFILE : str
- Path to the audio recording to be opened. Should be a '.wav' file.
- NAME0 : int
- Number used to name the first contour available for annotation.
- NAME1 : int
- Number used to name the last contour available for annotation.
- root : tkinter Tk instance
- Initialises tkinter interpreter and creates root window.
- klicker : mpl_point_clicker instance
- Adds widgets to matplotlib plot that allows to draw contours.
- waveform : numpy array
- Waveform of the audio recording.
- spectrogram : numpy array
- Spectrogram of the waveform.
- audio_duration : int
- Duration of the audio recording in seconds.
- FFT_IN : int
- User input for fft.
- HOP_IN : int
- User input for hop length.
- CLIP_IN : float
- User input for clipping value.
- figure, axis, data_showed : matplotlib objects
- Objects used to show matplotlib.pyplot plot.
- canvas : matplotlib object
- Interface to include matplotlib plot in tkinter canvas.
- Other buttons and labels have self explenatory names.
-
- Methods
- -------
- load_audio():
- Loads audio data. Waveform and spectrogram.
- layout():
- Lays the main structure of the tkinter window.
- setup():
- Loads default variables to local variables.
- entry_setup():
- Creates variables that save inputs from the user in the entry fields.
- create_canvas():
- Creates matplotlib figure to be shown in tkinter canvas.
- reset_toolbar():
- Resets the toolbar associated to the matplotlib figure,
- this is to avoid overlapping when the canvas is updated.
- submit():
- Loads user inputs to local variables.
- select_file():
- Opens a file explorer window to select a new wavefile.
- Saves contours if a new file is selected.
- Updates the canvas to show the new spectrogram.
- add_contours():
- Saves current drawn contours, add new contours that can be drawn.
- Draws previous contours in a different color/style on the same image.
- Previous contours are no longer editable.
- _quit():
- Saves contours and closes the app.
- """
-
- from parameters import (width, height, left_panel_width, nfft, hop_length,
- clipping, cmap)
-
- DEFAULT_WIDTH = width
- DEFAULT_HEIGHT = height
- DEFAULT_LEFT_WIDTH = left_panel_width
- DEFAULT_NFFT = nfft
- DEFAULT_HOP_LENGTH = hop_length
- DEFAULT_CLIPPING = clipping
- DEFAULT_CMAP = cmap
- DEFAULT_COORDS = {}
-
- def __init__(self, DIR, MAX_C, NEW_SR, DIR_OUT, WAVEFILE):
- # init variables
- self.setup()
- self.DIR = DIR
- self.MAX_C = MAX_C
- self.NEW_SR = NEW_SR
- self.DIR_OUT = DIR_OUT
- self.WAVEFILE = WAVEFILE
- self.NAME0 = 0
- self.NAME1 = MAX_C
-
- # load audio data
- self.load_audio()
-
- # init interface
- self.root = Tk()
- self.entry_setup()
- self.create_canvas()
- self.layout()
-
- # addon
- self.klicker = clicker(
- ax=self.axis,
- classes=["Line" + str(i+1) for i in range(self.NAME0, self.NAME1)],
- **{"linestyle":"solid", "mfc":"white"})
-
- # main loop
- self.root.mainloop()
-
-
- def load_audio(self):
- self.waveform = load_waveform(self.WAVEFILE, self.NEW_SR)
- self.spectrogram, self.audio_duration = wave_to_spectrogram(
- self.waveform,
- self.NEW_SR,
- self.NFFT,
- self.HOP_LENGTH,
- self.CLIPPING)
-
-
- def layout(self):
- self.root.wm_title("Spectrogram annotator")
- self.root.geometry(f"{str(self.WIDTH)}x{str(self.HEIGHT)}")
- self.root.rowconfigure(1, weight=1)
- self.root.rowconfigure(10, weight=1)
-
-
- self.fft_label = Label(
- self.root,
- width=self.LEFT_WIDTH,
- text='FFT window size:',
- font=('calibre',10, 'bold'))
- self.fft_label.grid(row=2, column=0)
-
- self.fft_entry = Entry(
- self.root,
- width=self.LEFT_WIDTH,
- textvariable=self.FFT_IN,
- font=('calibre',10,'normal'))
- self.fft_entry.grid(row=3, column=0)
-
- self.win_label = Label(
- self.root,
- width=self.LEFT_WIDTH,
- text='Hop length:',
- font=('calibre',10,'bold'))
- self.win_label.grid(row=4, column=0)
-
- self.win_entry = Entry(
- self.root,
- width=self.LEFT_WIDTH,
- textvariable=self.HOP_IN,
- font=('calibre',10,'normal'))
- self.win_entry.grid(row=5, column=0)
-
- self.clip_label = Label(
- self.root,
- width=self.LEFT_WIDTH,
- text='Clipping (dB):',
- font=('calibre',10,'bold'))
- self.clip_label.grid(row=6, column=0)
-
- self.clip_entry = Entry(
- self.root,
- width=self.LEFT_WIDTH,
- textvariable=self.CLIP_IN,
- font=('calibre',10,'normal'))
- self.clip_entry.grid(row=7, column=0)
-
- self.submit_button = Button(
- self.root,
- text='Update display',
- width=self.LEFT_WIDTH,
- command=self.submit)
- self.submit_button.grid(row=8, column=0)
-
- self.more_button = Button(
- self.root,
- width=self.LEFT_WIDTH,
- fg="white", bg="tomato",
- activeforeground="white", activebackground="red",
- text = ('MORE CONTOURS\nWARNING: current contours'
- '\nwill no longer be editable.'),
- command=self.add_contours)
- self.more_button.grid(row=9, column=0)
-
- self.quit_button = Button(self.root, text="Save & Quit", command=self._quit)
- self.quit_button.grid(row=11, column=0)
-
- self.explore_button = Button(
- self.root,
- text="Open file explorer",
- command=self.select_file)
- self.explore_button.grid(row=11, column=1)
-
- self.toolbarFrame = Frame(self.root)
- self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbarFrame)
- self.toolbar.update()
- self.toolbarFrame.grid(row=0, column=1, sticky='W')
-
- self.canvas.get_tk_widget().grid(row=1, column=1, rowspan=10)
-
- self.loading_screen = Label(
- self.root,
- text="LOADING SPECTROGRAM... \nThis can take a few seconds.",
- font=("gothic", 30),
- justify=LEFT)
-
-
- def setup(self):
- self.WIDTH = self.DEFAULT_WIDTH
- self.HEIGHT = self.DEFAULT_HEIGHT
- self.LEFT_WIDTH = self.DEFAULT_LEFT_WIDTH
- self.NFFT = self.DEFAULT_NFFT
- self.HOP_LENGTH = self.DEFAULT_HOP_LENGTH
- self.CLIPPING = self.DEFAULT_CLIPPING
- self.CMAP = self.DEFAULT_CMAP
- self.COORDS = self.DEFAULT_COORDS.copy()
-
-
- def entry_setup(self):
- self.FFT_IN = IntVar(value=self.DEFAULT_NFFT)
- self.HOP_IN = IntVar(value=self.DEFAULT_HOP_LENGTH)
- self.CLIP_IN = DoubleVar(value=self.DEFAULT_CLIPPING)
-
-
- def create_canvas(self):
- self.figure = Figure(figsize=(16, 9))
- self.axis = self.figure.add_subplot()
- self.data_showed = self.axis.imshow(
- self.spectrogram[::-1],
- cmap=self.CMAP,
- interpolation='nearest', aspect='auto',
- extent=(0, self.audio_duration, 0, self.NEW_SR/2))
- self.axis.set_xlabel("Time (in sec)")
- self.axis.set_ylabel("Frequencies (in Hz)")
- self.axis.set_title(f"Spectrogram of {os.path.basename(self.WAVEFILE)}")
- self.canvas = FigureCanvasTkAgg(self.figure, master=self.root)
- self.canvas.draw()
-
-
- def reset_toolbar(self):
- self.toolbar.destroy()
- self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbarFrame)
- self.toolbar.update()
-
-
- def submit(self):
- if ((self.FFT_IN != self.NFFT) or
- (self.HOP_IN != self.HOP_LENGTH) or
- (self.CLIP_IN != self.CLIPPING)):
-
- self.NFFT = self.FFT_IN.get()
- self.HOP_LENGTH = self.HOP_IN.get()
- self.CLIPPING = self.CLIP_IN.get()
-
- self.spectrogram, self.audio_duration = wave_to_spectrogram(
- self.waveform,
- self.NEW_SR,
- self.NFFT,
- self.HOP_LENGTH,
- self.CLIPPING)
- self.data_showed.set_data(self.spectrogram[::-1])
- self.canvas.draw()
-
-
- def select_file(self):
- self.new_wavefile = FileExplorer(self.DIR).file
-
- if len(self.new_wavefile) > 0 :
- self.COORDS = get_contours(self.klicker, self.COORDS)
- save_dict(self.COORDS, self.DIR_OUT,
- os.path.basename(self.WAVEFILE)[:-4]+"-contours.json")
- self.COORDS = self.DEFAULT_COORDS.copy()
- self.WAVEFILE = self.new_wavefile
- del self.new_wavefile
-
- self.loading_screen.grid(row=1, column=1, rowspan=10)
- self.canvas.get_tk_widget().destroy()
-
- self.load_audio()
- self.create_canvas()
- self.NAME0 = 0
- self.NAME1 = self.MAX_C
- self.klicker = clicker(
- ax=self.axis,
- classes=["Line"+str(i+1) for i in range(self.NAME0,self.NAME1)],
- **{"linestyle":"solid", "mfc":"white"})
-
- self.canvas.get_tk_widget().grid(row=1, column=1, rowspan=10)
- self.loading_screen.grid_forget()
- self.reset_toolbar()
-
-
- def add_contours(self):
- self.loading_screen.grid(row=1, column=1, rowspan=10)
- self.canvas.get_tk_widget().destroy()
-
- self.COORDS = get_contours(self.klicker, self.COORDS)
-
- self.create_canvas()
- self.NAME0 = self.NAME0 + self.MAX_C
- self.NAME1 = self.NAME1 + self.MAX_C
- self.klicker = clicker(
- ax=self.axis,
- classes=["Line"+str(i+1) for i in range(self.NAME0,self.NAME1)],
- **{"linestyle":"solid", "mfc":"white"})
-
- for key in list(self.COORDS.keys()):
- self.axis.plot(
- np.array(self.COORDS[key])[:,0],
- np.array(self.COORDS[key])[:,1],
- "black", marker="s", mfc="white")
- self.canvas.draw()
-
- self.canvas.get_tk_widget().grid(row=1, column=1, rowspan=10)
- self.loading_screen.grid_forget()
- self.reset_toolbar()
-
-
- def _quit(self):
- save_dict(
- get_contours(self.klicker, self.COORDS),
- self.DIR_OUT,
- os.path.basename(self.WAVEFILE)[:-4]+"-contours.json")
-
- self.root.quit()
- self.root.destroy()
\ No newline at end of file
diff --git a/functions.py b/functions.py
index 50439e319f99ccd3b7dea583966c74c54d766229..ae8ceb51e73cd8da6f46fdbd5bf8f0db075b2f24 100644
--- a/functions.py
+++ b/functions.py
@@ -3,187 +3,112 @@ import os
import json
import numpy as np
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
-import matplotlib.pyplot as plt
-
-import tkinter as tk
-from tkinter import filedialog as fd
-
-from librosa import load, amplitude_to_db, stft
+from librosa import load, amplitude_to_db, stft, pcen
from scipy.signal import resample
+from line_clicker.line_clicker import to_curve
-##### FUNCTIONS ######
+
+##### FUNCTIONS #####
def save_dict(dictionary, folder, name):
- """
- A function that saves a dictionary to a given path.
-
- ...
-
- Parameters
- ----------
- dictionary : dict
- Any dictionary.
- folder : str
- Path to the folder where the dictionary will be saved.
- name : str
- Name of the file in which the dictionary will be saved.
- If there is an extension, should not be different than '.json' extension.
- """
- if len(dictionary) > 0:
- with open(os.path.join(folder, name), "w") as f:
- json.dump(dictionary, f, indent=4)
+ """
+ A function that saves a dictionary to a given path.
+
+ ...
+
+ Parameters
+ ----------
+ dictionary : dict
+ Any dictionary.
+ folder : str
+ Path to the folder where the dictionary will be saved.
+ name : str
+ Name of the file in which the dictionary will be saved.
+ If there is an extension, should not be different than .json extension.
+
+ Returns
+ -------
+ None : save dict to json file.
+ """
+ if len(dictionary) > 0:
+ with open(os.path.join(folder, name), "w") as f:
+ json.dump(dictionary, f, indent=4)
def load_waveform(wavefile_name, sr_resample):
- """
- A function that loads any given wavefile
- and it resamples it to a given sampling rate.
-
- ...
-
- Parameters
- ----------
- wavefile_name : str
- Path of the wavefile that will be loaded.
- sr_resample : int
- Resampling rate for the waveform.
-
- Returns
- -------
- wavefile_dec : numpy array
- Loaded and resampled waveform
- """
- wavefile, sr = load(wavefile_name, sr=None)
- wavefile_dec = resample(wavefile,
- int(((len(wavefile)/sr)*sr_resample)))
-
- return wavefile_dec
-
-def wave_to_spectrogram(waveform, SR, n_fft, w_size, clip):
- """
- A function that transforms any given waveform to a spectrogram.
-
- ...
-
- Parameters
- ----------
- waveform : numpy array
- Waveform of an audio recording. Shape should be (N, 1).
- SR : int
- Sampling rate of the waveform
- n_fft : int
- Desired size for fft window. Should be in [1, N-1].
- w_size : int
- Desired size for hop length between two fft. Should be in [1, N-1].
- clip : int
- Clipping value for dB. If pixel value < clip, pixel is turned into a NaN.
-
- Returns
- -------
- spectro : numpy array
- Spectrogram of the waveform using the provided parameters.
- audio_length : float
- Duration of the audio in seconds.
- """
- spectro = amplitude_to_db(np.abs(stft(waveform,
- n_fft=n_fft, hop_length=w_size)))
- spectro = spectro - (np.max(spectro))
- spectro[spectro < clip] = np.nan
-
- audio_length = len(waveform)/SR
-
- return spectro, audio_length
-
-def get_contours(clicker, coords):
- """
- A function to get the positions of the clicks
- contained in a mpl_point_clicker OBJECT
-
- ...
-
- Parameters
- ----------
- clicker : mpl_point_clicker object
- Object containing the positions of mouse-drawn points in a plt plot.
-
- Returns
- -------
- coords : dict
- Gives coordinates of contours in lists [[time (in sec), freq (in Hz)]].
- """
- temp_coords = clicker.get_positions()
- for key in list(temp_coords.keys()):
- if len(temp_coords[key])>0:
- coords[key] = temp_coords[key].tolist()
-
- return coords
-
-def load_contours_file(jsonfile):
- """
- A function to import the contours saved from the interface.
-
- ...
-
- Parameters
- ----------
- jsonfile : str
- Path to a json file.
-
- Returns
- -------
- contours : dict
- Data contained in json file.
- """
- with open(jsonfile, "r") as f:
- contours = json.load(f)
- return contours
-
-def display_contours(wavefile, jsonfile,
- SR=96_000, n_fft=4098, w_size=156, clip=-80, cmap="viridis"):
- """
- A function to show the results of annotations, after using the interface.
-
- ...
-
- Parameters
- ----------
- wavefile : str
- Path to a wavefile.
- jsonfile : str
- Path to a json file.
- SR : int
- Sampling rate of the waveform
- n_fft : int
- Desired size for fft window. Should be in [1, N-1].
- w_size : int
- Desired size for hop length between two fft. Should be in [1, N-1].
- clip : int
- Clipping value for dB. If pixel value < clip, pixel is turned into a NaN.
- cmap : str
- Color map for matplotlib.pyplot plot.
-
- Returns
- -------
- None. Plots the contours fetched from a jsonfile onto a specgram.
- """
- lines = load_contours_file(jsonfile)
-
- waveform = load_waveform(wavefile, SR)
- specgram, duration = wave_to_spectrogram(waveform, SR, n_fft, w_size, clip)
-
- fig, ax = plt.subplots(figsize=(16,9))
- ax.imshow(specgram[::-1], cmap=cmap, interpolation='nearest', aspect='auto',
- extent=(0, duration, 0, SR/2))
-
- ax.set_xlabel("Time (in sec)")
- ax.set_ylabel("Frequencies (in Hz)")
- ax.set_title(f"Spectrogram of {os.path.basename(wavefile)}")
-
- for key in list(lines.keys()):
- ax.plot(
- np.array(lines[key])[:,0],
- np.array(lines[key])[:,1],
- marker="s", mfc="white")
-
- plt.show()
\ No newline at end of file
+ """
+ A function that loads any given wavefile
+ and it resamples it to a given sampling rate.
+
+ ...
+
+ Parameters
+ ----------
+ wavefile_name : str
+ Path of the wavefile that will be loaded.
+ sr_resample : int
+ Resampling rate for the waveform.
+
+ Returns
+ -------
+ wavefile_dec : numpy array
+ Loaded and resampled waveform
+ """
+ wavefile, sr = load(wavefile_name, sr=None)
+ wavefile_dec = resample(wavefile,
+ int(((len(wavefile)/sr)*sr_resample)))
+
+ return wavefile_dec
+
+def wave_to_spectrogram(waveform, SR, n_fft, w_size, clip, as_pcen=False):
+ """
+ A function that transforms any given waveform to a spectrogram.
+
+ ...
+
+ Parameters
+ ----------
+ waveform : numpy array
+ Waveform of an audio recording. Shape should be (N, 1).
+ SR : int
+ Sampling rate of the waveform
+ n_fft : int
+ Desired size for fft window. Should be in [1, N-1].
+ w_size : int
+ Desired size for hop length between two fft. Should be in [1, N-1].
+ clip : int
+ Clipping value for dB. If pixel value < clip, pixel is turned into NaN.
+ If as_pcen is selected, clipping will be applied using the values of pixels
+ in the orgiginal spectrogram.
+ as_pcen : bool, optional.
+ Whether the returned image should be a PCEN or not.
+ Aka : spectrogram with enhanced contrast.
+ Default is False.
+
+ Returns
+ -------
+ spectro : numpy array
+ Spectrogram of the waveform using the provided parameters.
+ audio_length : float
+ Duration of the audio in seconds.
+ """
+ base = np.abs(stft(
+ waveform,
+ n_fft=n_fft,
+ hop_length=w_size))
+
+
+ spectro_pcen = pcen(base * (2**31), bias=10)
+ spectro_og = amplitude_to_db(base)
+ spectro_og = spectro_og - (np.max(spectro_og))
+ spectro_og[spectro_og < clip] = np.nan
+
+ if as_pcen:
+ spectro_pcen[np.isnan(spectro_og)] = np.nan
+ spectro = spectro_pcen
+ else:
+ spectro = spectro_og
+
+ audio_length = len(waveform)/SR
+
+ return spectro, audio_length
+
diff --git a/images/PyAVA_show.gif b/images/PyAVA_show.gif
index 8ba57d86bfe069b86537aea85226f3b78c3593aa..4b02cb6a8fa9cb43ac7bba8d169205e9f836216f 100644
Binary files a/images/PyAVA_show.gif and b/images/PyAVA_show.gif differ
diff --git a/interface.py b/interface.py
new file mode 100644
index 0000000000000000000000000000000000000000..0dc89000fd6baa4968b9702ac47622ab0323a329
--- /dev/null
+++ b/interface.py
@@ -0,0 +1,711 @@
+##### IMPORTATIONS #####
+import os
+import numpy as np
+from tkinter import *
+from tkinter import filedialog as fd
+from tkinter import ttk
+from matplotlib.backends.backend_tkagg import (NavigationToolbar2Tk,
+ FigureCanvasTkAgg)
+from matplotlib.figure import Figure
+import matplotlib.colors as mc
+from line_clicker.line_clicker import clicker
+
+# Import external functions
+from functions import load_waveform, wave_to_spectrogram, save_dict
+
+
+##### CLASSES #####
+class FileExplorer(object):
+ """
+ A Class that opens a file explorer when it runs in an active Tkinter loop.
+
+ ...
+
+ Parameters
+ ----------
+ path : str
+ Path to a folder in which the file explorer will be opened.
+
+ Attributes
+ ----------
+ file : str
+ Path to a file selected by the user in the file explorer window.
+
+ Methods
+ -------
+ explorer_window():
+ Calls the tkinter functions that opens a file explorer window.
+
+ """
+
+ def __init__(self, path):
+ """
+ Constructs all the necessary attributes for the FileExplorer object.
+
+ Parameters
+ ----------
+ path : str
+ Path to a folder in which the file explorer will be opened.
+ file : str
+ Path to a file selected by the user in the file explorer window.
+ """
+ self.path = path # folder to be opened
+ self.explorer_window() # start function auto
+
+ def explorer_window(self):
+ """
+ Calls the tkinter function that opens a file explorer window.
+ Affect the select pass to 'file' attribute.
+
+ ...
+
+ Parameters
+ ----------
+ path : str
+ Path to the directory in which the file explorer will be opened.
+ """
+ self.file = fd.askopenfilename(
+ title='Open a file',
+ initialdir=self.path,
+ filetypes=(
+ ('Audio Files', '*.wav'),
+ ('All files', '*.*')
+ ))
+
+class App(object):
+ """
+ A Class to construct an contours annotation tool for audio data.
+
+ ...
+
+ Parameters
+ ----------
+ DIR : str
+ Path to a folder in which the file explorer will be opened.
+ DIR_OUT : str
+ Path to a folder where the contours will be saved.
+ MAX_C : int
+ Maximum number of contours that can be drawn at once.
+ NEW_SR : int
+ Resampling rate of the audio recording.
+ WAVEFILE : str
+ Path to the audio recording to be opened. Should be a '.wav' file.
+ coords_to_modify : dict
+ Coordinates of points (from a previous annotation) that can be used
+ as input to add modifications.
+
+ Attributes
+ ----------
+ _default_bounds : list of float
+ Boundaries for the matplotlib canvas.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_clipping : int
+ Default clipping value for spectrogram, in dB.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_cmap : str
+ Name of a matplotlib.pyplot color map.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_height : int
+ Default height of the window in which the app will run, in pixels.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_hop_length : int
+ Default hop length for spectrogram, in samples.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_left_panel_width : int
+ Default width for the left panel of the window of the app.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_nfft : int
+ Default fft size for spectrogram, in samples.
+ (Default value is loaded from 'PARAMETERS.py' file).
+ _default_width: int
+ (Default) width of the window in which the app will run, in pixels.
+ (Default value is loaded from 'PARAMETERS.py' file).
+
+ canvas : matplotlib object
+ Interface to include matplotlib plot in tkinter canvas.
+ CHECK_bspline : tkinter int variable
+ User checkbox about plotting curves or not.
+ CLIP_IN : tkinter float variable (Double)
+ User input for clipping value.
+ FFT_IN : tkinter int variable
+ User input for fft.
+ figure, axis, data_showed : matplotlib objects
+ Objects used to show matplotlib.pyplot plot.
+ HOP_IN : tkinter int variable
+ User input for hop length.
+ klicker : mpl_point_clicker instance
+ Adds widgets to matplotlib plot that allows to draw contours.
+ NAME0 : int
+ Number used to name the first contour available for annotation.
+ NAME1 : int
+ Number used to name the last contour available for annotation.
+ OPTIONS : tkinter list variable
+ User listbox to select category item.
+ root : tkinter Tk instance
+ Initialises tkinter interpreter and creates root window.
+ spectrogram : numpy array
+ Spectrogram of the waveform.
+ waveform : numpy array
+ Waveform of the audio recording.
+
+ Other attributes, buttons and labels have self explenatory names.
+
+ Methods
+ -------
+ bspline_activation():
+ Activates/deactivates the visualisation of lines as curves.
+ create_canvas():
+ Creates matplotlib figure to show spectrogram in tkinter canvas.
+ entry_setup():
+ Creates variables that save inputs from the user in the entry fields.
+ get_key_pressed(event):
+ Updates plot and tkinter interface
+ when a key is pressed to add a new category.
+ layout():
+ Lays the main structure of the tkinter window.
+ link_select(event):
+ Changes the focus to be on a new category, corresponding to
+ the selected item in listbox widget.
+ load_audio():
+ Loads audio data. Waveform and spectrogram.
+ reset_toolbar():
+ Resets the toolbar associated to the matplotlib figure,
+ this is to avoid overlapping when the canvas is updated.
+ select_file():
+ Opens a file explorer window to select a new wavefile.
+ Saves contours if a new file is selected.
+ Updates the canvas to show the new spectrogram.
+ setup():
+ Loads default variables to local variables.
+ submit():
+ Loads user inputs to local variables.
+ switch(self)
+ Updates spectrogram displayed to PCEN (and conversely).
+ _frame_listbox_scroll():
+ Just a callable part of layout()
+ _quit():
+ Saves contours and closes the app.
+ """
+
+ from parameters import (_default_width, _default_height, _default_hop_length,
+ _default_nfft, _default_clipping, _default_cmap, _default_bounds,
+ _default_left_panel_width)
+
+ def __init__(
+ self,
+ DIR,
+ MAX_C,
+ NEW_SR,
+ DIR_OUT,
+ WAVEFILE,
+ coords_to_modify={}):
+
+ # init variables
+ self.DIR = DIR
+ self.MAX_C = MAX_C
+ self.NEW_SR = NEW_SR
+ self.DIR_OUT = DIR_OUT
+ self.WAVEFILE = WAVEFILE
+ self.NAME0 = 0
+ self.NAME1 = MAX_C
+ self.setup()
+
+ # load audio data
+ self.load_audio()
+
+ # init interface
+ self.root = Tk()
+ self.root.style = ttk.Style()
+ self.root.style.theme_use('clam')
+ self.create_canvas()
+
+ # addon
+ self.klicker = clicker(
+ axis=self.axis,
+ names=["Line" + str(i+1) for i in range(self.NAME0, self.NAME1)],
+ bspline='quadratic', maxlines=99, legend_bbox=(2,0.5),
+ coords=coords_to_modify)
+
+ # main loop
+ self.entry_setup()
+ self.layout()
+ self.axis.set_position(self._default_bounds)
+
+ # To avoid probles, disconnect matplotlib keypress
+ # and replace it with tkinter keypress.
+ self.figure.canvas.mpl_disconnect(self.klicker.key_press)
+ self.root.bind('<Key>', self.get_key_pressed)
+
+ self.root.mainloop()
+
+ def bspline_activation(self):
+ """
+ Activates/deactivates the visualisation of lines as curves.
+
+ ...
+
+ Returns
+ -------
+ None : Updates klicker.
+ (It uses the "wait" parameter to force straigth lines).
+ """
+ if self.CHECK_bspline.get():
+ self.klicker.wait = 2
+ else:
+ self.klicker.wait = np.inf
+ self.klicker.update_lines()
+ self.klicker.figure.canvas.draw()
+
+ def create_canvas(self):
+ """
+ Creates a figure based on imported spectrogram.
+
+ ...
+
+ Returns
+ -------
+ None : Creates figure, axis, data_showed and canvas variables.
+ """
+ self.figure = Figure(figsize=(16, 9))
+ self.axis = self.figure.add_subplot()
+ self.data_showed = self.axis.imshow(
+ self.spectrogram[::-1],
+ cmap=self._default_cmap,
+ interpolation='nearest', aspect='auto',
+ extent=(0, self.audio_duration, 0, self.NEW_SR/2))
+ self.data_showed.set_clim(
+ vmin=np.nanmin(self.spectrogram),
+ vmax=np.nanmax(self.spectrogram))
+ self.axis.set_xlabel("Time (in sec)")
+ self.axis.set_ylabel("Frequencies (in Hz)")
+ self.axis.set_title(f"Spectrogram of {os.path.basename(self.WAVEFILE)}")
+ self.axis.set_position(self._default_bounds)
+ self.figure.set_facecolor("gainsboro")
+ self.canvas = FigureCanvasTkAgg(self.figure, master=self.root)
+ self.canvas.draw()
+
+ def entry_setup(self):
+ """
+ Creates tkinter variables that will be used in entry fields.
+ (Objects that are specific to tkinter)
+
+ ...
+
+ Returns
+ -------
+ None : Creates FFT_IN, HOP_IN, CHECK_bspline, CLIP_IN and OPTIONS,
+ variables that are tkinter variables (3 integers, 1 float, 1 list).
+ """
+ self.FFT_IN = IntVar(value=self._default_nfft)
+ self.HOP_IN = IntVar(value=self._default_hop_length)
+ self.CHECK_bspline = IntVar(value=1)
+ self.CLIP_IN = DoubleVar(value=self._default_clipping)
+ self.OPTIONS = Variable(value=self.klicker.legend_labels)
+
+ def get_key_pressed(self, event):
+ """
+ Updates plot and tkinter interface
+ when a key is pressed to add a new category.
+
+ ...
+
+ Parameters
+ ----------
+ event : tkinter event
+ tkinter object containing the name of the key pressed.
+
+ Returns
+ -------
+ None : updates klicker, listbox, axis and figure.
+ """
+ class EmptyObject(object):
+ """
+ Empty class that is just a hacky of creating an object that
+ can be used in matplotlib.
+ """
+ pass
+
+ # create key attribute and use it
+ dummy_event = EmptyObject()
+ dummy_event.key = event.char
+ self.klicker.get_key_event(dummy_event, show=False)
+
+ # if a category is added. Update listbox and canvas.
+ if len(self.klicker.legend_labels) > self.listbox.size():
+ self.listbox.insert(
+ self.listbox.size(),
+ self.klicker.legend_labels[-1])
+ self.listbox.itemconfig(
+ self.listbox.size()-1,
+ {
+ 'bg': self.klicker.colors[
+ (self.listbox.size()-1)%len(self.klicker.colors)],
+ 'selectbackground': mc.to_hex(tuple([min(0.1+x,1)
+ for x in mc.to_rgb(
+ self.klicker.colors[
+ (self.listbox.size()-1)%len(self.klicker.colors)])])),
+ 'selectforeground': 'white'})
+ self.listbox.select_clear(0, END)
+ self.listbox.select_set(self.listbox.size()-1)
+ self.listbox.see(self.listbox.size()-1)
+ self.listbox.activate(self.listbox.size()-1)
+ self.listbox.selection_anchor(self.listbox.size()-1)
+ self.axis.set_position(self._default_bounds)
+ self.figure.canvas.draw()
+
+ def layout(self):
+ """
+ This *long* function lays the structure of the tkinter interface
+
+ ...
+
+ Returns
+ -------
+ None :
+ Updates root
+ Creates list_label, frame_list, listbox, scrollbar, empty_frame,
+ activate_bspline, fft_label, fft_entry,win_label, win_entry,
+ clip_label, clip_entry, submit_button, quit_button, explore_button
+ toolbarFrame, toolbar, loading_screen
+ """
+ # configure main window
+ self.root.wm_title("Spectrogram annotator")
+ self.root.geometry(
+ f"{str(self._default_width)}x{str(self._default_height)}")
+ self.root.rowconfigure(1, weight=1)
+ self.root.rowconfigure(14, weight=1)
+ self.root.configure(bg='gainsboro')
+
+ # Add Panel for line selection on Left side
+ self.list_label = Label(
+ self.root,
+ width=self._default_left_panel_width,
+ text='Pick a line to draw.\n(Shift+a adds a new line)',
+ font=('calibre',10,'bold'))
+ self.list_label.grid(row=2, column=0)
+
+ self._frame_listbox_scroll()
+
+ self.activate_bspline = Checkbutton(
+ self.root,
+ text='Activate interpolation',
+ variable=self.CHECK_bspline,
+ command=self.bspline_activation)
+ self.activate_bspline.grid(row=4, column=0)
+
+ # Add space between panels
+ self.empty_frame = Label(
+ self.root,
+ width=self._default_left_panel_width,
+ height=30)
+ self.empty_frame.grid(row=5, column=0)
+
+ # Add panel for spectrogram personalisation on Left side.
+ self.fft_label = Label(
+ self.root,
+ width=self._default_left_panel_width,
+ text='FFT window size:',
+ font=('calibre',10, 'bold'))
+ self.fft_label.grid(row=6, column=0)
+
+ self.fft_entry = Entry(
+ self.root,
+ width=self._default_left_panel_width,
+ textvariable=self.FFT_IN,
+ font=('calibre',10,'normal'))
+ self.fft_entry.grid(row=7, column=0)
+
+ self.win_label = Label(
+ self.root,
+ width=self._default_left_panel_width,
+ text='Hop length:',
+ font=('calibre',10,'bold'))
+ self.win_label.grid(row=8, column=0)
+
+ self.win_entry = Entry(
+ self.root,
+ width=self._default_left_panel_width,
+ textvariable=self.HOP_IN,
+ font=('calibre',10,'normal'))
+ self.win_entry.grid(row=9, column=0)
+
+ self.clip_label = Label(
+ self.root,
+ width=self._default_left_panel_width,
+ text='Clipping (dB):',
+ font=('calibre',10,'bold'))
+ self.clip_label.grid(row=10, column=0)
+
+ self.clip_entry = Entry(
+ self.root,
+ width=self._default_left_panel_width,
+ textvariable=self.CLIP_IN,
+ font=('calibre',10,'normal'))
+ self.clip_entry.grid(row=11, column=0)
+
+ self.submit_button = Button(
+ self.root,
+ text='Update display',
+ width=self._default_left_panel_width,
+ command=self.submit)
+ self.submit_button.grid(row=12, column=0)
+
+ self.switch_view_button = Button(
+ self.root,
+ text="Switch to PCEN",
+ width=self._default_left_panel_width,
+ command=self.switch)
+ self.switch_view_button.grid(row=13, column=0)
+
+ # Add buttons at the bottom of the interface
+ self.quit_button = Button(
+ self.root,
+ text="Save & Quit",
+ command=self._quit)
+ self.quit_button.grid(row=15, column=0)
+
+ self.explore_button = Button(
+ self.root,
+ text="Open file explorer",
+ command=self.select_file)
+ self.explore_button.grid(row=15, column=1)
+
+ # Add matplotlib tools at the top of the interface
+ self.toolbarFrame = Frame(self.root)
+ self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbarFrame)
+ self.toolbar.update()
+ self.toolbarFrame.grid(row=0, column=1, sticky='W')
+
+ # Add main panel : canvas.
+ self.canvas.get_tk_widget().grid(row=1, column=1, rowspan=14)
+ self.loading_screen = Label(
+ self.root,
+ text="LOADING SPECTROGRAM... \nThis can take a few seconds.",
+ font=("gothic", 30),
+ justify=LEFT)
+
+ def link_select(self, event):
+ """
+ Changes the focus to be on a new category, corresponding to
+ the selected item in listbox widget.
+
+ ...
+
+ Parameters
+ ----------
+ event : tkinter object
+ event containing the item clicked in listbox widget.
+
+ Returns
+ -------
+ None : Updates klicker.
+ """
+ if len(event.widget.curselection()):
+ self.klicker.current_line = event.widget.curselection()[0]
+
+ # Manually update display
+ for legend_line in self.klicker.legend.get_lines():
+ legend_line.set_alpha(0.2)
+ self.klicker.legend.get_lines()[self.klicker.current_line].set_alpha(1)
+ self.klicker.figure.canvas.draw()
+
+ def load_audio(self):
+ """
+ A class to load the waveform and spectrogram of a wavefile.
+
+ ...
+
+ Returns
+ -------
+ None : Creates waveform and spectrogram arrays.
+ """
+ self.waveform = load_waveform(self.WAVEFILE, self.NEW_SR)
+ self.spectrogram, self.audio_duration = wave_to_spectrogram(
+ self.waveform,
+ self.NEW_SR,
+ self.NFFT,
+ self.HOP_LENGTH,
+ self.CLIPPING)
+
+ def reset_toolbar(self):
+ """
+ A function to destroy and create a new toolbar
+ that interacts with matplotlib canvas.
+ """
+ self.toolbar.destroy()
+ self.toolbar = NavigationToolbar2Tk(self.canvas, self.toolbarFrame)
+ self.toolbar.update()
+
+ def select_file(self):
+ """
+ A function that calls a new window to select a wavefile.
+ Then replaces spectrogram in canvas using the newly selected file.
+
+ ...
+
+ Returns
+ -------
+ None : If a new file is selected, saves current coordinates to json file
+ and generate a new window for annotation.
+ """
+ new_wavefile = FileExplorer(self.DIR).file
+
+ if len(new_wavefile) > 0 :
+ # save current coords
+ save_dict(self.klicker.coords, self.DIR_OUT,
+ os.path.basename(self.WAVEFILE)[:-4]+"-contours.json")
+ self.WAVEFILE = new_wavefile
+
+ # display loading scree
+ self.loading_screen.grid(row=1, column=1, rowspan=13)
+ self.canvas.get_tk_widget().destroy()
+
+ # load new data
+ self.load_audio()
+ self.create_canvas()
+ self.NAME0 = 0
+ self.NAME1 = self.MAX_C
+
+ # display new data
+ self.klicker = clicker(
+ axis=self.axis,
+ names=["Line" + str(i+1) for i in range(self.NAME0, self.NAME1)],
+ bspline='quadratic', maxlines=99, legend_bbox=(2,0.5))
+ self.axis.set_position(self._default_bounds)
+ self.figure.canvas.mpl_disconnect(self.klicker.key_press)
+
+ # update interface
+ self.entry_setup()
+ self._frame_listbox_scroll()
+ self.canvas.get_tk_widget().grid(row=1, column=1, rowspan=13)
+ self.loading_screen.grid_forget()
+ self.reset_toolbar()
+
+ def setup(self):
+ """
+ A function to create variables based on default values
+ This is a security to avoid mixing default values with new values
+ during use... But it could be removed.
+ """
+ self.NFFT = self._default_nfft
+ self.HOP_LENGTH = self._default_hop_length
+ self.CLIPPING = self._default_clipping
+
+ def submit(self):
+ """
+ A function that fetches the new values in entry fields.
+ Updates spectrogram accordingly.
+
+ ---
+
+ Returns
+ -------
+ None : Updates spectrogram and data_showed
+ according to new fft, hop_length and clipping values.
+ """
+ if ((self.FFT_IN != self.NFFT) or
+ (self.HOP_IN != self.HOP_LENGTH) or
+ (self.CLIP_IN != self.CLIPPING)):
+
+ self.NFFT = self.FFT_IN.get()
+ self.HOP_LENGTH = self.HOP_IN.get()
+ self.CLIPPING = self.CLIP_IN.get()
+
+ self.spectrogram, self.audio_duration = wave_to_spectrogram(
+ self.waveform,
+ self.NEW_SR,
+ self.NFFT,
+ self.HOP_LENGTH,
+ self.CLIPPING)
+ self.data_showed.set_data(self.spectrogram[::-1])
+ self.data_showed.set_clim(
+ vmin=np.nanmin(self.spectrogram),
+ vmax=np.nanmax(self.spectrogram))
+ self.canvas.draw()
+
+ def switch(self):
+ """
+ Updates spectrogram displayed to PCEN (and conversely).
+
+ ---
+
+ Returns
+ -------
+ None : Updates switch_view_button, spectrogram and data_showed.
+ """
+ current_text = self.switch_view_button['text']
+
+ if current_text == "Switch to PCEN":
+ self.spectrogram, _ = wave_to_spectrogram(
+ self.waveform,
+ self.NEW_SR,
+ self.NFFT,
+ self.HOP_LENGTH,
+ self.CLIPPING,
+ as_pcen=True)
+ self.switch_view_button['text'] = "Switch to Spectrogram"
+ else:
+ self.spectrogram, _ = wave_to_spectrogram(
+ self.waveform,
+ self.NEW_SR,
+ self.NFFT,
+ self.HOP_LENGTH,
+ self.CLIPPING)
+ self.switch_view_button['text'] = "Switch to PCEN"
+
+ self.data_showed.set_data(self.spectrogram[::-1])
+ self.data_showed.set_clim(
+ vmin=np.nanmin(self.spectrogram),
+ vmax=np.nanmax(self.spectrogram))
+ self.canvas.draw()
+
+ def _frame_listbox_scroll(self):
+ """
+ Just a callable part of "layout"
+ """
+ self.frame_list = Frame(
+ self.root,
+ width=self._default_left_panel_width,
+ height=50)
+ self.frame_list.grid(row=3, column=0)
+
+ self.listbox = Listbox(
+ self.frame_list,
+ height=9,
+ width=self._default_left_panel_width,
+ selectmode=SINGLE,
+ listvariable=self.OPTIONS)
+ for idx in range(len(self.klicker.legend_labels)):
+ self.listbox.itemconfig(idx,
+ {
+ 'bg': self.klicker.colors[idx%len(self.klicker.colors)],
+ 'selectbackground': mc.to_hex(tuple([min(0.1+x,1)
+ for x in mc.to_rgb(
+ self.klicker.colors[idx%len(self.klicker.colors)])])),
+ 'selectforeground': 'white'})
+ self.listbox.pack(side="left", fill="y")
+ self.listbox.bind("<<ListboxSelect>>", self.link_select)
+ self.listbox.select_set(0)
+
+ self.scrollbar = Scrollbar(self.frame_list, orient="vertical")
+ self.scrollbar.config(command=self.listbox.yview)
+ self.scrollbar.pack(side="right", fill="y")
+ self.listbox.config(yscrollcommand=self.scrollbar.set)
+
+ def _quit(self):
+ """
+ A function that saves coordinates of lines before closing app.
+
+ ...
+
+ Returns
+ -------
+ None : Saves coords in a json file, quits and destroys root.
+ """
+ save_dict(
+ self.klicker.coords,
+ self.DIR_OUT,
+ os.path.basename(self.WAVEFILE)[:-4]+"-contours.json")
+
+ self.root.quit()
+ self.root.destroy()
\ No newline at end of file
diff --git a/line_clicker/__init__.py b/line_clicker/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/line_clicker/line_clicker.py b/line_clicker/line_clicker.py
new file mode 100644
index 0000000000000000000000000000000000000000..103db70fcf7d583c4ad81eba03345e937ccd02b0
--- /dev/null
+++ b/line_clicker/line_clicker.py
@@ -0,0 +1,735 @@
+"""
+Add default parameters for keys and mousebutton so it can be customized
+"""
+
+##### IMPORTATIONS ######
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.backend_bases import MouseButton
+import matplotlib.lines as mlines
+
+from scipy.interpolate import interp1d
+
+##### FUNCTIONS #####
+def to_curve(x, y, kind):
+ """
+ A function to compute a curvy line between two points.
+ It interpolates a line with 100 points.
+
+ ...
+
+ Parameters
+ ----------
+ x : list or numpy array
+ List of coordinates on x axis.
+ y : list or numpy array
+ List of coordinates on y axis.
+ kind : string
+ The interpolation method to use. Can be any method in : ‘linear’,
+ ‘nearest’, ‘nearest-up’, ‘zero’, ‘slinear’, ‘quadratic’, ‘cubic’,
+ ‘previous’, or ‘next’.
+
+ Returns
+ -------
+ xi : numpy array
+ List of the coordinates of the curve on x-axis.
+ yi : numpy array
+ List of the coordinates of the curve on y-axis.
+ """
+ i = np.arange(len(x))
+
+ interp_i = np.linspace(0, i.max(), 100 * i.max())
+
+ xi = interp1d(i, x, kind=kind)(interp_i)
+ yi = interp1d(i, y, kind=kind)(interp_i)
+
+ return xi, yi
+
+##### CLASSES #####
+class clicker(object):
+ """
+ A Class that is an "add-on" for an existing matplotlib figure axis.
+ Added to an axis, it allows to draw lines from mouse clicks.
+ Points can be removed using the right click.
+
+ Different categories can be selected using the generated legend :
+ by clicking on a line or by using up/down arrows.
+ It is also possible to add more categories using with 'ctrl+a' shortcut
+
+ ...
+
+ Params
+ ----------
+ axis : matplotlib object
+ Axis instance.
+ bspline : string or boolean, optional.
+ If False, app will plot points linked by lines.
+ If string, app will plot points linked by curve.
+ For curves, use 'cubic' or 'quadratic'
+ colors : list, optional.
+ List of color (hexadecimal) to cycle over when plotting lines.
+ Default is the default list of colors from matplotlib.
+ legend_bbox : tuple, optional.
+ The position of the legend (x-axis, y-axis) relative to the figure.
+ marker : dict, optional.
+ Additional parameters to change the look of the lines.
+ Default is None, lines will be solid with points as white dots.
+ maxlines : int, optional.
+ Maximum number of labels in legend.
+ Default is 30.
+ Default is False.
+ names : str or list, optional.
+ Names for legend labels.
+ If string, names will be name+{line number}
+ If list, when a category is added, it will have the name "DefaultNameX".
+ Default is "Line".
+ n_names : int, optional.
+ Number of categories at launch when name is a string.
+ Default is 10.
+ pick_dist : int, optional.
+ Distance to legend category for picking mouse.
+ Default is 10.
+ wraplines : int, optional.
+ Maximum number of labels in legend before creating a new column.
+ Default is 15.
+ Default is (1, 0.5)
+ coords : dict, optional.
+ Coordinates of each point for each category (line, key of the dict).
+ Coordinates are expressed in (time, frequency)
+ or (pixel, pixel) if no extent given.
+ Default is {}. If given, initates figure with annotations.
+
+
+ Attributes
+ ----------
+ current_line : int
+ Index of the ctegory (line) currently selected
+ figure : matplotlib object
+ Abbreviation for axis.figure.
+ figure_bsplines : list of matplotlib 2D lines
+ Secondary lines, in use if bspline mode is selected.
+ Draws curves instead of straight lines.
+ figure_lines : list of matplotlib 2D lines
+ Main lines, displayed on image as straight lines if bspline is False.
+ If bspline is true, linestyle is removed and they are displayed as dots.
+ key_press : matplotlib event
+ Information on the last key_press event.
+ legend : matplotlib object
+ legend of the plot
+ legend_labels : list of str
+ labels of the categories in legend.
+ linestyle : str
+ If bspline is True, saves linestyle.
+ mouse_press : matplotlib event
+ Information on the last mouse click in matplotlib canvas.
+ pick_press : matplotlib event
+ Information on the last mouse click event in matplotlib legend.
+ pressed : bool
+ Is used to check if a specific mouse button is pressed or not.
+
+ Other attributes have self explenatory names.
+
+ Methods
+ -------
+ add_category(show):
+ Adds a category to the list in legend.
+ add_point(x,y):
+ Adds a point to the category in focus at the given coordinates.
+ Focus is updated to be on this new category.
+ clear_category():
+ Clears all points from the category in focus.
+ double_lines():
+ Creates a copy of the current set of lines from figure_lines.
+ It is used to interpolate curves between figure_lines points.
+ distance_mouse(points, mouse_x, mouse_y):
+ Gets the distance bewteen a mouse position and the currently
+ selected category (points).
+ get_focus(event):
+ Puts focus on a category in legend. Allows the user to interact with it.
+ get_key_event(event):
+ Activates functions when specific keyboard keys are pressed.
+ get_mouse_press(event, show=True):
+ Activates functions when specific mouse buttons are pressed.
+ move_point(event):
+ Moves a selected point of the currently selected category to a new
+ position (event). Updates figure accordingly.
+ rm_point(x,y):
+ Removes a point from the category in focus at the given coordinates.
+ set_legend():
+ Adds legend to axis given.
+ switch_line(arrow):
+ Puts focus on previous/next category in legend based on arrow input.
+ update_lines():
+ Updates data in lines. Called when coords is changed.
+
+ References
+ ----------
+ Heavily inspired from mpl_point_clicker :
+ mpl-point-clicker.readthedocs.io/
+ """
+
+ DEFAULT_marker = { # Markerstyle for categories.
+ "marker":"o",
+ "mfc":"white",
+ "linestyle":"-",
+ }
+
+ DEFAULT_colors = [ # Colors for categories. Will cycle through them.
+ '#1f77b4', # List can be appened or reduced.
+ '#ff7f0e',
+ '#2ca02c',
+ '#d62728',
+ '#9467bd',
+ '#8c564b',
+ '#e377c2',
+ '#7f7f7f',
+ '#bcbd22',
+ '#17becf'
+ ]
+
+ DEFAULT_param = {
+ "add_point" : MouseButton.LEFT,
+ "rm_point" : MouseButton.RIGHT,
+ "move_point" : MouseButton.MIDDLE,
+ "add_category" : "A", # shift+a
+ "clear_category" : "R", # shift+r
+ "focus_up" : "up",
+ "focus_down" : "down",
+ }
+
+
+ def __init__(
+ self,
+ axis,
+ marker=None,
+ bspline=False,
+ colors=None,
+ names="Line",
+ maxlines=30,
+ wraplines=15,
+ legend_bbox=(1,0.5),
+ pick_dist=10,
+ n_names=10,
+ coords={}):
+
+ # Variable assignement
+ self.axis = axis
+ self.legend_bbox = legend_bbox
+ self.pick_dist = pick_dist
+ self.param = self.DEFAULT_param.copy()
+
+ if isinstance(marker, dict):
+ self.marker = marker
+ else:
+ self.marker = self.DEFAULT_marker.copy()
+ if bspline=="quadratic":
+ self.bspline = bspline
+ else:
+ self.bspline = False
+ self.wait = 2
+ if isinstance(colors, list):
+ self.colors = colors
+ else:
+ self.colors = self.DEFAULT_colors.copy()
+ if isinstance(names, str):
+ self.names = names
+ self.legend_labels = [self.names + str(i+1) for i in range(n_names)]
+ elif isinstance(names, list):
+ self.legend_labels = names.copy()
+ self.names = "DefaultName"
+ else:
+ self.names = self.DEFAULT_name
+ self.legend_labels = [self.names + str(i+1) for i in range(n_names)]
+ if isinstance(maxlines, int):
+ self.maxlines = maxlines
+ else:
+ self.maxlines = self.DEFAULT_maxlines
+ if isinstance(wraplines, int):
+ self.wraplines = wraplines
+ else:
+ self.wraplines = self.DEFAULT_wraplines
+
+ if self.bspline:
+ # replace linestyle
+ self.linestyle = self.marker['linestyle']
+ self.marker['linestyle'] = ""
+
+ if isinstance(coords, dict) and coords != {}:
+ self.coords = coords
+ self.legend_labels = list(self.coords.keys()).copy()
+ self.figure_lines = [mlines.Line2D(
+ np.array(self.coords[legend_label])[:,0],
+ np.array(self.coords[legend_label])[:,1],
+ label=legend_label,
+ color=self.colors[idx%len(self.colors)], **self.marker)
+ for idx, legend_label in enumerate(self.legend_labels)]
+ else:
+ self.coords = {}
+ self.figure_lines = [mlines.Line2D([], [], label=legend_label,
+ color=self.colors[idx%len(self.colors)], **self.marker)
+ for idx, legend_label in enumerate(self.legend_labels)]
+
+ # Creation of lines
+ if self.bspline:
+ self.double_lines()
+
+ # Creation of legend
+ self.figure = self.axis.figure
+ self.current_line = 0
+ self.set_legend()
+
+ # Linking actions in matplotlib canvas
+ self.mouse_press_event = self.figure.canvas.mpl_connect(
+ 'button_press_event',
+ self.get_mouse_press)
+ self.mouse_release_event = self.figure.canvas.mpl_connect(
+ 'button_release_event',
+ self.get_mouse_press)
+ self.motoin_event = self.figure.canvas.mpl_connect(
+ 'motion_notify_event',
+ self.move_point)
+ self.currently_pressed = False
+
+ self.pick_event = self.figure.canvas.mpl_connect(
+ 'pick_event',
+ self.get_focus)
+ self.key_press = self.figure.canvas.mpl_connect(
+ 'key_press_event',
+ self.get_key_event)
+
+
+
+ def add_category(self, show):
+ """
+ A method to add a line (therefore a new category) to the plot.
+ Also change current focus to be on the newly created category.
+
+ ...
+
+ Parameters
+ ----------
+ show : boolean
+ Shows change in legend.
+
+ Returns
+ -------
+ None : updates legend_labels, figure_lines, legend, figure
+ and current_line.
+ """
+ # make new name
+ self.legend_labels += [self.names + str(len(self.legend_labels)+1)]
+
+ # add to categories
+ self.figure_lines += [mlines.Line2D([], [],
+ label=self.legend_labels[len(self.legend_labels)-1],
+ color=self.colors[(len(self.legend_labels)-1)%len(self.colors)],
+ **self.marker)]
+
+ if self.bspline:
+ self.figure_bsplines += [mlines.Line2D([], [],
+ label=self.legend_labels[len(self.legend_labels)-1],
+ color=self.colors[(len(self.legend_labels)-1)%len(self.colors)],
+ **{'linestyle':self.linestyle})]
+
+ self.set_legend()
+
+ # focus auto on new category
+ self.current_line = len(self.legend_labels)-1
+
+ for legend_line in self.legend.get_lines():
+ legend_line.set_alpha(0.2)
+ self.legend.get_lines()[self.current_line].set_alpha(1)
+ if show:
+ self.figure.canvas.draw()
+
+ def add_point(self, x, y):
+ """
+ A method to add a point on plot at given coordinates.
+
+ ...
+
+ Parameters
+ ----------
+ x : float
+ x-axis coordinate.
+ y : float
+ y-axis coordinate.
+
+ Returns
+ -------
+ None : updates coords, figure_lines, figure.
+ """
+ if self.legend_labels[self.current_line] in list(self.coords.keys()):
+ self.coords[self.legend_labels[self.current_line]] += [[x, y]]
+ else:
+ self.coords[self.legend_labels[self.current_line]] = [[x, y]]
+
+ self.update_lines()
+ self.figure.canvas.draw()
+
+ def double_lines(self):
+ """
+ Creates an other set of lines, additionnally to figure_lines.
+ It is necessary to display curves instead of straight lines.
+
+ ...
+
+ Returns
+ -------
+ None : Updates linestyle and marker. Creates figure_bsplines.
+ """
+ # create new lines
+ if self.coords == {}:
+ self.figure_bsplines = [mlines.Line2D([], [],
+ label=legend_label,
+ color=self.colors[idx%len(self.colors)],
+ **{'linestyle':self.linestyle})
+ for idx, legend_label in enumerate(self.legend_labels)]
+
+ else:
+ self.figure_bsplines = []
+ for idx, legend_label in enumerate(self.legend_labels):
+ curves = to_curve(
+ np.array(self.coords[legend_label])[:,0],
+ np.array(self.coords[legend_label])[:,1],
+ kind="quadratic")
+ self.figure_bsplines += [mlines.Line2D(curves[0], curves[1],
+ label=legend_label,
+ color=self.colors[idx%len(self.colors)],
+ **{'linestyle':self.linestyle})]
+
+ def clear_category(self):
+ """
+ A method to remove a line (therefore a whole category) from the plot.
+ Removes the category that is in focus.
+
+ ...
+
+ Returns
+ -------
+ None : updates legend_labels, figure_lines, legend, figure.
+ """
+
+ # we only need to remove data from coords
+ if self.legend_labels[self.current_line] in list(self.coords.keys()):
+ del self.coords[self.legend_labels[self.current_line]]
+ # set data to have no point in memory
+ self.figure_lines[self.current_line].set_data([], [])
+ if self.bspline:
+ self.figure_bsplines[self.current_line].set_data([], [])
+ # update plot
+ self.figure.canvas.draw()
+
+ def distance_mouse(self, points, mouse_x, mouse_y):
+ """
+ Gets the distance bewteen a mouse position
+ and the currently selected category (points).
+
+ ...
+ Parameters
+ ----------
+ points : numpy array
+ A list of coordinates with shape (2,n).
+ mouse_x : int or float
+ Coordinate of the mouse on x-axis.
+ mouse_y : int or float
+ Coordinate of the mouse on y-axis.
+ Returns
+ -------
+ distances : numpy array
+ Distances of each point to mous coordinates.
+ """
+ size_x, size_y = self.figure.get_size_inches()
+ max_x, max_y=self.axis.get_xbound()[1],self.axis.get_ybound()[1]
+
+ # look for closest coordinates of the category currently selected.
+ distances = [np.linalg.norm([(point[0]/max_x)*size_x,
+ (point[1]/max_y)*size_y] - np.array([(mouse_x/max_x)*size_x,
+ (mouse_y/max_y)*size_y]))
+ for point in points]
+
+ return distances
+
+ def get_focus(self, event):
+ """
+ A method to highlight a given marker in legend.
+ Points can be added/removed only to the category in focus.
+
+ ...
+
+ Parameters
+ ----------
+ event : matplotlib object
+ Is used to acces event.artist attribute.
+
+ Returns
+ -------
+ None : updates figure, current_line and legend attributes.
+ """
+ # set all legend lines to alpha = 0.2
+ for legend_line in self.legend.get_lines():
+ legend_line.set_alpha(0.2)
+ # set legend line in focus to alpha = 1
+ selected_legend = event.artist
+ current_alpha = selected_legend._alpha
+ selected_legend.set_alpha(1.0 if (current_alpha==0.2) else 0.2)
+ self.figure.canvas.draw()
+
+ # new focus
+ self.current_line = int(np.where(
+ np.array(self.legend.get_lines()) == event.artist)[0])
+
+ def get_mouse_press(self, event):
+ """
+ A Method that retrieves mouse interactions with matplotlib plot.
+
+ ...
+
+ Parameters
+ ----------
+ event : matplotlib object
+ Contains 3 attributes : button pressed, x and y at that time.
+
+ Returns
+ -------
+ None : is used to trigger methods add_points and rm_points().
+ """
+ if self.figure.canvas.widgetlock.available(self):
+ pressed, x, y = event.button, event.xdata, event.ydata
+ if ((pressed is self.param["add_point"]) and
+ (isinstance(x, float)) and
+ (isinstance(y, float)) and
+ event.name == 'button_press_event'):
+ self.add_point(x, y)
+
+ elif ((pressed is self.param["rm_point"]) and
+ (isinstance(x, float)) and
+ (isinstance(y, float)) and
+ event.name == 'button_press_event'):
+ self.rm_point(x, y)
+
+ elif ((pressed is self.param["move_point"]) and
+ (isinstance(x, float)) and
+ (isinstance(y, float)) and
+ event.name == 'button_press_event'):
+ distances = self.distance_mouse(
+ np.array(self.coords[self.legend_labels[self.current_line]]),
+ event.xdata, event.ydata)
+ self.index, dist = np.argmin(distances), np.min(distances)
+ if dist < 0.1:
+ self.currently_pressed = True
+
+ elif ((pressed is self.param["move_point"]) and
+ (isinstance(x, float)) and
+ (isinstance(y, float)) and
+ event.name == 'button_release_event'):
+ self.currently_pressed = False
+ self.index = False
+
+ def get_key_event(self, event, show=True):
+ """
+ A method that retrieve key interactions with matplotlib plot.
+
+ ...
+
+ Parameters
+ ----------
+ event : matplotlib object
+ Contains 3 attributes : button pressed, x and y at that time.
+ show : boolean
+ Parameter passed to add_category()
+
+ Returns
+ -------
+ None : is used to trigger other functions.
+ """
+ key = event.key
+ if ((key == self.param["add_category"]) and
+ (len(self.legend_labels) < self.maxlines)):
+ self.add_category(show)
+
+ elif ((key == self.param["clear_category"]) and
+ (len(self.legend_labels) > 1)):
+ self.clear_category()
+
+ elif ((key == self.param["focus_up"]) and
+ (self.current_line != 0)):
+ self.switch_line(-1)
+
+ elif ((key == self.param["focus_down"]) and
+ (self.current_line != len(self.legend_labels)-1)):
+ self.switch_line(1)
+
+ def move_point(self, event):
+ """
+ Moves a selected point of the currently selected category to a new
+ position (event). Updates figure accordingly.
+
+ ...
+
+ Parameters
+ ----------
+ event : matplotlib object
+ Matplotlib event containig information on positions.
+
+ Returns
+ -------
+ None : it updates the coordinates of a point in a category
+ and re-draws the figure.
+ """
+ if (self.currently_pressed and
+ event.xdata != None and
+ event.ydata != None):
+ # update coords
+ current_lines = self.figure_lines[self.current_line].get_data()
+ current_lines[0][self.index] = event.xdata
+ current_lines[1][self.index] = event.ydata
+ self.coords[self.legend_labels[self.current_line]][self.index] = [event.xdata, event.ydata]
+
+ # update plot
+ self.update_lines()
+ self.figure.canvas.draw()
+
+ def set_legend(self):
+ """
+ A method to create matplotlib.pyplot legend.
+ Legend contains empty lines and can be clicked.
+
+ ...
+
+ Returns
+ -------
+ None : updates axis, creates legend.
+ """
+ # Make some space to include legend
+ scale = (19-((len(self.legend_labels)//self.wraplines)+1))/19
+ self.axis.set_position([0, 0, scale, 1])
+
+ # Add legend to plot
+ self.legend = self.axis.legend(
+ loc="center left",
+ bbox_to_anchor=self.legend_bbox,
+ ncol=(len(self.legend_labels)//self.wraplines)+1,
+ title="Selection of lines",
+ handles=self.figure_bsplines if self.bspline else self.figure_lines)
+
+ # Add lines to plot
+ if self.bspline:
+ for bspline in self.figure_bsplines:
+ self.axis.add_line(bspline)
+
+ for legend_l, line in zip(self.legend.get_lines(), self.figure_lines):
+ legend_l.set_picker(True)
+ legend_l.set_pickradius(self.pick_dist)
+ legend_l.set_alpha(0.2)
+ self.axis.add_line(line)
+
+ # Focus on selected line
+ self.legend.get_lines()[self.current_line].set_alpha(1)
+
+ def switch_line(self, arrow):
+ """
+ Puts focus on previous/next category in legend based on arrow input.
+
+ ...
+
+ Parameters
+ ----------
+ arrow : int
+ Can be 1 or -1. Change the index of the current category in focus.
+
+ Returns
+ -------
+ None : updates currentline, legend and figures attributes.
+ """
+ # new focus
+ self.current_line += arrow
+
+ # adapt alpha
+ for legend_line in self.legend.get_lines():
+ legend_line.set_alpha(0.2)
+ self.legend.get_lines()[self.current_line].set_alpha(1)
+ self.figure.canvas.draw()
+
+ def rm_point(self, x, y):
+ """
+ A method to remove closest point in plot to given coordinates.
+
+ ...
+
+ Parameters
+ ----------
+ x : float
+ x-axis coordinate.
+ y : float
+ y-axis coordinate.
+
+ Returns
+ -------
+ None : updates coords, figure_lines, figure.
+ """
+ if self.legend_labels[self.current_line] in list(self.coords.keys()):
+ list_coords = np.array(
+ self.coords[self.legend_labels[self.current_line]])
+
+ if len(list_coords) > 1:
+ # figure is distorted on screen
+ # we want to look for coordinated based on what the user sees
+ # not the actual coordinates of the pixels in the image.
+ distances = self.distance_mouse(list_coords, x, y)
+
+ # remove it
+ list_coords = np.delete(list_coords, np.argmin(distances),
+ axis=0)
+ self.coords[self.legend_labels[self.current_line]] = list_coords.tolist()
+
+ self.update_lines()
+
+ else:
+ del self.coords[self.legend_labels[self.current_line]]
+ self.figure_lines[self.current_line].set_data([], [])
+ if self.bspline:
+ self.figure_bsplines[self.current_line].set_data([],[])
+
+ self.figure.canvas.draw()
+
+ def update_lines(self):
+ """
+ Updates data in lines. Called when coords is changed.
+
+ ...
+
+ Returns
+ -------
+ None : Updates figure_lines and figure_bsplines (if bspline is True).
+ """
+ if self.bspline:
+ if len(self.coords[self.legend_labels[self.current_line]]) > self.wait:
+ curvex, curvey = to_curve(
+ np.array(self.coords[
+ self.legend_labels[self.current_line]])[:,0],
+ np.array(self.coords[
+ self.legend_labels[self.current_line]])[:,1],
+ kind=self.bspline)
+ self.figure_bsplines[self.current_line].set_data(curvex, curvey)
+ else:
+ self.figure_bsplines[self.current_line].set_data(
+ np.array(self.coords[
+ self.legend_labels[self.current_line]])[:,0],
+ np.array(self.coords[
+ self.legend_labels[self.current_line]])[:,1])
+
+ self.figure_lines[self.current_line].set_data(
+ np.array(self.coords[self.legend_labels[self.current_line]])[:,0],
+ np.array(self.coords[self.legend_labels[self.current_line]])[:,1])
+
+
+##### MAIN #####
+if __name__ == '__main__':
+ # dummy example
+ img = np.array([[0,1,0],[1,0,1],[0,1,0]])
+
+ fig, ax = plt.subplots(figsize=(16, 9))
+ ax.imshow(img, cmap="viridis")
+ base = clicker(axis=ax, bspline="quadratic")
+ plt.show(block=True)
\ No newline at end of file
diff --git a/outputs/SCW1807_20200713_064545-contours.json b/outputs/SCW1807_20200713_064545-contours.json
deleted file mode 100644
index 966d1d53f1a3ecf0ffc5131647d6cc173db70a65..0000000000000000000000000000000000000000
--- a/outputs/SCW1807_20200713_064545-contours.json
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new file mode 100644
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diff --git a/outputs/SCW6070_20220717_174215-contours.json b/outputs/SCW6070_20220717_174215-contours.json
index 66bfb03d3ecd6f6a6301c45033af58566087d251..6306a0489c0024b03c20456d5e52ce4bd68fc650 100644
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diff --git a/parameters.py b/parameters.py
index 2d35979ee6e7962a07c06cc50d0b91b9c6803aa4..e259304d3c559c5352014fb6c6a810caa0ab2670 100644
--- a/parameters.py
+++ b/parameters.py
@@ -3,10 +3,11 @@ from screeninfo import get_monitors
##### FIXED PARAMETERS ######
-width = get_monitors()[0].width # width of tk window
-height = get_monitors()[0].height # height of tk window
-left_panel_width = 26 # Size of window's left panel
-nfft = 2048 # default fft value (can be changed by user)
-hop_length = 512 # default hop_length value (can be changed by user)
-clipping = -80 # default clipping value in dB (can be changed by user)
-cmap = "viridis" # default cmap for spectrogram visualisation
+_default_width = get_monitors()[0].width # width of tk window
+_default_height = get_monitors()[0].height # height of tk window
+_default_left_panel_width = 26 # Size of window's left panel
+_default_nfft = 2048 # default fft value (can be changed by user)
+_default_hop_length = 512 # default hop_length value (can be changed by user)
+_default_clipping = -80 # default clipping value in dB (can be changed by user)
+_default_cmap = "viridis" # default cmap for spectrogram visualisation
+_default_bounds = [0.05, 0.05, 0.94, 0.9] # default boundaries for canvas in tkinter
\ No newline at end of file
diff --git a/post_annotation.py b/post_annotation.py
new file mode 100644
index 0000000000000000000000000000000000000000..e0dc1305a7dfe2c74b1725225071d4fd4f582426
--- /dev/null
+++ b/post_annotation.py
@@ -0,0 +1,190 @@
+##### IMPORTATIONS #####
+import os
+import json
+import numpy as np
+
+from matplotlib.patches import Rectangle
+import matplotlib.pyplot as plt
+
+from line_clicker.line_clicker import to_curve
+
+# Import external functions
+from functions import load_waveform, wave_to_spectrogram, save_dict
+
+##### CLASS ######
+class Results(object):
+ """
+ SR : int, optional.
+ Sampling rate of the waveform.
+ Default is 96 kHz.
+ n_fft : int, optional.
+ Desired size for fft window. Should be in [1, N-1].
+ Default is 4098.
+ w_size : int, optional.
+ Desired size for hop length between two fft. Should be in [1, N-1].
+ Default is 156.
+ clip : int, optional.
+ Clipping value for dB. If pixel value < clip, pixel is turned into NaN.
+ Default is -80.
+ cmap : str, optional.
+ Color map for matplotlib.pyplot plot.
+ Default is viridis.
+ """
+
+ colors = [ # Colors for categories. Will cycle through them.
+ '#1f77b4', # List can be appened or reduced.
+ '#ff7f0e',
+ '#2ca02c',
+ '#d62728',
+ '#9467bd',
+ '#8c564b',
+ '#e377c2',
+ '#7f7f7f',
+ '#bcbd22',
+ '#17becf'
+ ]
+
+ def __init__(
+ self,
+ wavefile_name,
+ jsonfile_name,
+ SR = 96_000,
+ NFFT = 4098,
+ HOP_LENGTH = 156,
+ CLIPPING = -80,
+ cmap = 'viridis'):
+
+ self.wavefile_name = wavefile_name
+ self.jsonfile_name = jsonfile_name
+ self.SR = SR
+ self.NFFT = NFFT
+ self.HOP_LENGTH = HOP_LENGTH
+ self.CLIPPING = CLIPPING
+ self.cmap = cmap
+
+ self.coords = self.load_contours_file()
+ self.waveform = load_waveform(self.wavefile_name, self.SR)
+ self.spectrogram, self.duration = wave_to_spectrogram(
+ self.waveform,
+ self.SR,
+ self.NFFT,
+ self.HOP_LENGTH,
+ self.CLIPPING)
+ self.pcen, _ = wave_to_spectrogram(
+ self.waveform,
+ self.SR,
+ self.NFFT,
+ self.HOP_LENGTH,
+ self.CLIPPING,
+ as_pcen=True)
+
+ def load_contours_file(self):
+ """
+ A function to import the contours saved from the interface.
+
+ ...
+
+ Returns
+ -------
+ contours : dict
+ Data contained in json file.
+ """
+ with open(self.jsonfile_name, "r") as f:
+ contours = json.load(f)
+ return contours
+
+ def display_image(self, img="spec"):
+ fig, ax = plt.subplots(figsize=(16,9))
+ ax.imshow(
+ self.pcen[::-1] if img=="pcen" else self.spectrogram[::-1],
+ cmap=self.cmap,
+ interpolation='nearest', aspect='auto',
+ extent=(0, self.duration, 0, self.SR/2))
+
+ ax.set_xlabel("Time (in sec)")
+ ax.set_ylabel("Frequencies (in Hz)")
+ ax.set_title(f"Spectrogram of {os.path.basename(self.wavefile_name)}")
+ return fig, ax
+
+ def display_contours(self, mode="curves", img="spec"):
+ """
+ A function to show the results of annotations, after using the interface.
+
+ ...
+
+ Parameters
+ ----------
+ mode : str
+ Wether to plot curves or straight lines between each point.
+ "curves" or any other string for straight lines. Default is "curves".
+
+ Returns
+ -------
+ None. Plots the contours fetched from a jsonfile onto a specgram.
+ """
+ fig, ax = self.display_image(img)
+
+ for idx, key in enumerate(list(self.coords.keys())):
+ if mode=="curves":
+ cx, cy = to_curve(
+ np.array(self.coords[key])[:,0],
+ np.array(self.coords[key])[:,1],
+ kind="quadratic")
+ ax.plot(cx, cy, color=self.colors[idx%len(self.colors)])
+
+ else:
+ ax.plot(
+ np.array(self.coords[key])[:,0],
+ np.array(self.coords[key])[:,1],
+ linestyle="-", color=self.colors[idx%len(self.colors)])
+
+ ax.plot(
+ np.array(self.coords[key])[:,0],
+ np.array(self.coords[key])[:,1],
+ marker="s", mfc="white", linestyle="",
+ color=self.colors[idx%len(self.colors)])
+
+ plt.show()
+
+ def display_as_BB(self, img="spec", tol=1/100):
+ fig, ax = self.display_image(img)
+
+ for idx, key in enumerate(list(self.coords.keys())):
+ min_min = (min(np.array(annot_data.coords[key])[:,0]),
+ min(np.array(annot_data.coords[key])[:,1]))
+ max_max = (max(np.array(annot_data.coords[key])[:,0]),
+ max(np.array(annot_data.coords[key])[:,1]))
+
+ min_min = (min_min[0]-tol*min_min[0], min_min[1]-tol*min_min[1])
+ max_max = (max_max[0]+tol*max_max[0], max_max[1]+tol*max_max[1])
+
+ ax.add_patch(Rectangle(
+ min_min,
+ max_max[0]-min_min[0],
+ max_max[1]-min_min[1],
+ facecolor='none',
+ edgecolor=self.colors[idx%len(self.colors)],
+ lw=1))
+
+ ax.text(min_min[0], max_max[1], key,
+ color="white",
+ bbox=dict(
+ boxstyle='square, pad=0',
+ fc=self.colors[idx%len(self.colors)],
+ ec='none'))
+
+ plt.show()
+
+##### EXAMPLE #####
+if __name__ == '__main__':
+
+ annot_data = Results(os.path.join(
+ ".",
+ "audio_examples",
+ "SCW1807_20200713_064554.wav"),
+ os.path.join(
+ ".",
+ "outputs",
+ "SCW1807_20200713_064554-contours.json"))
+
+ annot_data.display_contours() # or annot_data.display_contours(img="pcen")
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index dbccbca594fea5908dbc0ceb42e87b6cb6cf0af1..a0c2d324fd6db14ae7e41b45893d41d895f7f870 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,9 +1,9 @@
appdirs==1.4.4
audioread==3.0.0
-certifi @ file:///croot/certifi_1665076670883/work/certifi
+certifi @ file:///croot/certifi_1671487769961/work/certifi
cffi==1.15.1
-charset-normalizer==2.1.1
-contourpy==1.0.6
+charset-normalizer==3.0.1
+contourpy==1.0.7
cycler==0.11.0
decorator==5.1.1
fonttools==4.38.0
@@ -12,21 +12,22 @@ joblib==1.2.0
kiwisolver==1.4.4
librosa==0.9.2
llvmlite==0.39.1
-matplotlib==3.6.2
-mpl-point-clicker==0.3.1
+matplotlib==3.6.3
numba==0.56.4
numpy==1.23.5
-packaging==22.0
-Pillow==9.3.0
+packaging==23.0
+Pillow==9.4.0
pooch==1.6.0
pycparser==2.21
pyparsing==3.0.9
python-dateutil==2.8.2
-requests==2.28.1
+requests==2.28.2
resampy==0.4.2
scikit-learn==1.2.0
-scipy==1.9.3
+scipy==1.10.0
+screeninfo==0.8.1
six==1.16.0
soundfile==0.11.0
threadpoolctl==3.1.0
-urllib3==1.26.13
+tk==0.1.0
+urllib3==1.26.14