PK ! &, dlc_gui/__init__.pyimport sys
if hasattr(sys, "_called_from_test"):
print("In pytest, skipping __init__.py")
else:
from .gui import show # pragma: no cover
__all__ = ["show"] # pragma: no cover
PK ! IZ dlc_gui/__main__.pyimport argparse
import dlc_gui
parser = argparse.ArgumentParser()
parser.add_argument("config", help="Abs path to config.yaml", nargs="?")
args = parser.parse_args()
config = args.config
dlc_gui.show(config)
PK ! 4Kq q dlc_gui/data.py"""
This module handles the data creation and handling of dlc_gui.
It creates the main pandas DataFrame, color palette, and `frames_dict`.
`frames_dict` is a dictionary of frame_name (str): frame_path (path object) pairs.
"""
# TODO make sure each exception encloses paths with quotes
from pathlib import Path
from typing import List, Tuple, Union
import numpy as np
import pandas as pd
import dlc_gui.util
class DataModel:
"""
Create useful data structures such as the main pandas DataFrame used by DeepLabCut,
the frames_dict which keeps allows translation between abs and rel paths,
and the color palette.
"""
def __init__(self, config_path):
# Initialize without a given directory of frames or a h5 file
# Define attributes as empty or None, because the rest of the code
# expects their existence
self.config_path = config_path
self.config_dict = dlc_gui.util.read_config_file(self.config_path)
self.scorer = self.config_dict["scorer"]
self.bodyparts = self.config_dict["bodyparts"]
# Make sure the project path is valid and exists
try:
self.project_path = Path(self.config_dict["project_path"]).resolve()
if not self.project_path.is_dir():
raise FileNotFoundError(
"'project_path' ({0}) in config.yaml does not exist.".format(
self.config_dict["project_path"]
)
)
except TypeError as e:
raise TypeError(
"'project_path' in config.yaml has an invalid type of {0}".format(
type(self.config_dict["project_path"])
)
) from e
self.colors, self.colors_opposite, self.colors_opaque = self.color_palette(
len(self.bodyparts)
)
# Define variables to be used in gui.py for QFileDialog default dirs
self.labeled_data_path = self.project_path / "labeled-data"
self.save_path_hdf = self.labeled_data_path / "CollectedData_{}.h5".format(
self.scorer
)
self.save_path_pkl = self.labeled_data_path / "CollectedData_{}.pkl".format(
self.scorer
)
# TODO find replacement for pd.concat to avoid defining as None
self.data_frame = None
self.frames_dict = {}
def init_from_dir(self, dir: Union[str, Path]) -> None:
# Defines self.frames_dict and self.data_frame based on a dir
dir = Path(dir)
if self.project_path not in dir.parents:
raise ValueError(
"'{0}' is not within the project path ('{1}').".format(
dir, self.project_path
)
)
try:
self.frames_paths = sorted(Path(dir).glob("*.png"))
# The commented out code causes an error with pytables.
# It is currently unknown why.
# init_nan = np.empty((len(self.images_paths), 2)).fill(np.nan)
init_nan = np.empty((len(self.frames_paths), 2))
init_nan[:] = np.nan
self.frames_names = [
str(Path(frame_path).relative_to(self.project_path))
for frame_path in self.frames_paths
]
self.frames_dict = dict(zip(self.frames_names, self.frames_paths))
for bodypart in self.bodyparts:
index = pd.MultiIndex.from_product(
[[self.scorer], [bodypart], ["x", "y"]],
names=["scorer", "bodyparts", "coords"],
)
frame = pd.DataFrame(init_nan, columns=index, index=self.frames_names)
self.data_frame = pd.concat([self.data_frame, frame], axis=1)
except (TypeError, ValueError):
pass
def init_from_file(self, file: Union[str, Path]) -> None:
# Defines self.frames_dict and self.data_frame based on a h5 file
# Due to the inconsistencies between ``to_csv``, ``from_csv``,
# ``read_csv``, etc., ONLY '.h5' files will be accepted.
# https://github.com/pandas-dev/pandas/issues/13262
# TODO Proper extension checking
file = Path(file)
if file.is_file():
if file.suffix in (".hdf", ".h5"):
try:
self.data_frame = pd.read_hdf(file, "df_with_missing")
except KeyError as e:
raise KeyError(
"The group 'df_with_missing' was not found in the .h5 file."
) from e
elif file.suffix in (".pkl", ".pickle"):
self.data_frame = pd.read_pickle(file)
try:
self.frames_names = sorted(self.data_frame.index.tolist())
except AttributeError as e:
raise AttributeError(
"Could not find the DataFrame index from the file ('{0}').".format(
file
)
) from e
self.frames_paths = [Path(self.project_path, _) for _ in self.frames_names]
# TODO avoid copy pasted code
self.frames_dict = dict(zip(self.frames_names, self.frames_paths))
def color_palette(self, number: int) -> Tuple[List, List, List]:
# Create a list of QColors and their opposites equal in length to the
# number of bodyparts
# TODO set alpha from config
hues = np.linspace(0, 1, number, endpoint=False)
colors = [(h, 1, 1, 0.5) for h in hues]
colors_opposite = [(abs(0.5 - h), 1, 1, 0.5) for h in hues]
colors_opaque = [(h, 1, 1, 1) for h in hues]
return colors, colors_opposite, colors_opaque
def add_coords_to_dataframe(self, frame, bodypart, coords):
if all(coord is None for coord in coords):
coords = (np.nan, np.nan)
try:
self.data_frame.loc[frame, self.scorer][bodypart, "x"] = coords[0]
self.data_frame.loc[frame, self.scorer][bodypart, "y"] = coords[1]
except KeyError as e:
raise KeyError(
"The scorer of the config.yaml does not match this .h5 file."
) from e
def get_coords_from_dataframe(self, frame, bodypart):
x = self.data_frame.loc[frame, self.scorer][bodypart, "x"]
y = self.data_frame.loc[frame, self.scorer][bodypart, "y"]
if np.isnan(x):
x = None
if np.isnan(y):
y = None
return (x, y)
def save_as_pkl(self, path):
if path:
pd.to_pickle(self.data_frame, path)
def save_as_hdf(self, path):
if path:
self.data_frame.to_hdf(path, "df_with_missing", format="table", mode="w")
PK ! 1xuH H dlc_gui/gui.py"""
This module handles all the GUI aspects of dlc_gui.
This module creates a main window containing the main widget containing subset widgets.
"""
# TODO add feature to specify project_path
import sys
from typing import Union
import webbrowser
from PySide2.QtCore import QEvent, QRectF, Qt
from PySide2.QtGui import QBrush, QColor, QKeySequence, QPen, QPixmap
from PySide2.QtWidgets import (
QAction,
QApplication,
QDesktopWidget,
QFileDialog,
QGraphicsEllipseItem,
QGraphicsScene,
QGraphicsView,
QGridLayout,
QLabel,
QListWidget,
QMainWindow,
QShortcut,
QSlider,
QSplitter,
QVBoxLayout,
QWidget,
)
import dlc_gui.data
import dlc_gui.util
class GraphicsScene(QGraphicsScene):
def __init__(self, parent):
super(GraphicsScene, self).__init__(parent)
def load_image(self, image: str) -> None:
# Load frame png into scene
self.frame_image = QPixmap()
self.frame_image.load(image)
self.addPixmap(self.frame_image)
class GraphicsView(QGraphicsView):
def __init__(self, parent):
super(GraphicsView, self).__init__(parent)
self.scene = GraphicsScene(self)
self.setScene(self.scene)
self.fitInView(self.scene.sceneRect(), aspectRadioMode=Qt.KeepAspectRatio)
self.viewport().setCursor(Qt.CrossCursor)
# keep track of the current scale value to prevent zooming too far out
self.current_scale = 1.0
def zoom(self, pos: tuple, scale: float, anchor: str = "NoAnchor") -> None:
if anchor == "NoAnchor":
self.setTransformationAnchor(QGraphicsView.NoAnchor)
self.setResizeAnchor(QGraphicsView.NoAnchor)
old_pos = self.mapToScene(*pos)
# Prevent zooming out beyond 0.3 or in beyond 3.33
if (self.current_scale > 0.3 or scale > 1) and (
self.current_scale < 3.33 or scale < 1
):
self.scale(scale, scale)
self.current_scale *= scale
new_pos = self.mapToScene(*pos)
translate_delta = (new_pos - old_pos).toTuple()
self.translate(*translate_delta)
# Scroll wheel to zoom in and out
def wheelEvent(self, event):
scale_factor = 1.25
if event.delta() > 0:
self.zoom(event.pos().toTuple(), scale_factor)
else:
self.zoom(event.pos().toTuple(), 1 / scale_factor)
# Toggle on dragging when middle mouse is pressed
def mousePressEvent(self, event):
if event.button() == Qt.MiddleButton:
self.__og_pos = event.pos()
self.viewport().setCursor(Qt.ClosedHandCursor)
else:
return super(GraphicsView, self).mousePressEvent(event)
# TODO find a legit way to engage the ScrollHandDrag mode
# rather than simply using it to change the cursor look
# Translate scene using scrollbars while middle button is held
def mouseMoveEvent(self, event):
if event.buttons() == Qt.MiddleButton:
offset = self.__og_pos - event.pos()
self.__og_pos = event.pos()
self.verticalScrollBar().setValue(
self.verticalScrollBar().value() + offset.y()
)
self.horizontalScrollBar().setValue(
self.horizontalScrollBar().value() + offset.x()
)
else:
super(GraphicsView, self).mouseMoveEvent(event)
# Toggle off dragging when middle mouse is pressed
def mouseReleaseEvent(self, event):
if event.button() == Qt.MiddleButton:
self.viewport().setCursor(Qt.CrossCursor)
else:
return super(GraphicsView, self).mouseReleaseEvent(event)
class MainWidget(QWidget):
"""
Create the main user interface and controls, connected to DataModel
"""
def __init__(self, parent, config_path):
super(MainWidget, self).__init__(parent)
# Create the main widgets
self.graphics_view = GraphicsView(self)
self.bodyparts_view = QListWidget()
self.dot_size_slider = QSlider(Qt.Horizontal)
self.dot_size_label = QLabel(parent=self.dot_size_slider)
self.frames_view = QListWidget()
# Setup the data_model, get config values, and setup widgets based on data_model
self.config_path = config_path
data_model = dlc_gui.data.DataModel(self.config_path)
self.init_from_data_model(data_model)
# Set up the dot_size_slider
dot_size_from_config = self.data_model.config_dict["dotsize"]
self.dot_size_slider.setMinimum(1)
self.dot_size_slider.setMaximum(100)
self.dot_size_slider.setValue(dot_size_from_config)
self.dot_size_slider.setTickPosition(QSlider.TicksBothSides)
self.dot_size_slider.setTickInterval(10)
self.dot_size_label.setText(
"Label dot size: {} (from config.yaml)".format(dot_size_from_config)
)
self.dot_size_slider.sliderReleased.connect(
lambda: self.dot_size_label.setText(
"Label dot size: {}".format(self.dot_size_slider.value())
)
)
self.dot_size_slider.sliderReleased.connect(lambda: self.update_scene())
# Add a widget to add a layout containing the bodyparts and the slider
labeling_widget = QWidget()
labeling_layout = QVBoxLayout()
labeling_layout.addWidget(self.bodyparts_view)
labeling_layout.addWidget(self.dot_size_label)
labeling_layout.addWidget(self.dot_size_slider)
labeling_widget.setLayout(labeling_layout)
# Set the main layout of Widget
main_layout = QGridLayout()
splitter = QSplitter()
splitter.addWidget(self.frames_view)
splitter.addWidget(self.graphics_view)
splitter.addWidget(labeling_widget)
splitter.setStretchFactor(1, 1)
main_layout.addWidget(splitter)
self.setLayout(main_layout)
# Set up events
self.frames_view.currentItemChanged.connect(lambda x: self.update_scene())
self.graphics_view.scene.installEventFilter(self)
shortcut_next_bodypart = QShortcut(QKeySequence("d"), self)
shortcut_prev_bodypart = QShortcut(QKeySequence("a"), self)
shortcut_next_frame = QShortcut(QKeySequence("s"), self)
shortcut_prev_frame = QShortcut(QKeySequence("w"), self)
# setattr is used as an assignment function, because lambdas cannot assign
# prior to python 3.8
shortcut_next_bodypart.activated.connect(
lambda: setattr(self, "current_bodypart_row", self.current_bodypart_row + 1)
)
shortcut_prev_bodypart.activated.connect(
lambda: setattr(self, "current_bodypart_row", self.current_bodypart_row - 1)
)
shortcut_next_frame.activated.connect(
lambda: setattr(self, "current_frame_row", self.current_frame_row + 1)
)
shortcut_prev_frame.activated.connect(
lambda: setattr(self, "current_frame_row", self.current_frame_row - 1)
)
self.save_file_dialog = QFileDialog()
self.save_file_dialog.setFileMode(QFileDialog.AnyFile)
self.save_file_dialog.setAcceptMode(QFileDialog.AcceptSave)
def init_from_data_model_from_file(self, dataframe_file) -> None:
data_model = dlc_gui.data.DataModel(self.config_path)
try:
data_model.init_from_file(dataframe_file)
except (KeyError, AttributeError) as e:
self.send_status(
"Error: {} is not structured correctly.".format(dataframe_file), 5
)
raise e
except Exception:
pass
self.init_from_data_model(data_model)
def init_from_data_model_from_dir(self, dir: str) -> None:
data_model = dlc_gui.data.DataModel(self.config_path)
try:
data_model.init_from_dir(dir)
except Exception:
pass
if not data_model.frames_dict and dir is not None:
self.send_status("Error: No frames (*.png) found in {}".format(dir), 5)
else:
self.init_from_data_model(data_model)
def init_from_data_model(self, data_model) -> None:
self.data_model = data_model
self.bodyparts = self.data_model.bodyparts
self.project_path = self.data_model.project_path
# Populate the frames and bodyparts lists
if self.data_model.frames_dict:
self.frames_dict = self.data_model.frames_dict
self.frames_view.clear()
for frame in self.frames_dict.keys():
self.frames_view.addItem(frame)
self.bodyparts_view.clear()
for bodypart in self.bodyparts:
self.bodyparts_view.addItem(bodypart)
# Convert tuples to QColors
self.data_model.colors = [
QColor.fromHsvF(*color) for color in self.data_model.colors
]
self.data_model.colors_opposite = [
QColor.fromHsvF(*color) for color in self.data_model.colors_opposite
]
self.data_model.colors_opaque = [
QColor.fromHsvF(*color) for color in self.data_model.colors_opaque
]
# Set initial selections for both listwidgets, load the first frame,
# and add color icons
frames_view_items = self.frames_view.findItems("*", Qt.MatchWildcard)
if frames_view_items:
self.frames_view.setCurrentItem(frames_view_items[0])
self.graphics_view.scene.load_image(str(list(self.frames_dict.values())[0]))
self.bodyparts_view_items = self.bodyparts_view.findItems("*", Qt.MatchWildcard)
if self.bodyparts_view_items:
self.bodyparts_view.setCurrentItem(self.bodyparts_view_items[0])
for item, color in zip(
self.bodyparts_view_items, self.data_model.colors_opaque
):
pixmap = QPixmap(100, 100)
pixmap.fill(color)
item.setIcon(pixmap)
self.update_scene()
def eventFilter(self, obj, event):
"""
Implement left and right mouse clicking functionalities
"""
# Check if the click is within the QGraphicsView
if (
obj is self.graphics_view.scene
and event.type() == QEvent.Type.GraphicsSceneMousePress
):
scene_pos = event.scenePos()
coords = (scene_pos.x(), scene_pos.y())
frame = self.current_frame_text
bodypart = self.current_bodypart_text
if frame and bodypart:
if event.buttons() == Qt.LeftButton:
self.data_model.add_coords_to_dataframe(frame, bodypart, coords)
elif event.buttons() == Qt.RightButton:
self.data_model.add_coords_to_dataframe(
frame, bodypart, (None, None)
)
self.update_scene()
return super(MainWidget, self).eventFilter(obj, event)
@property
def current_bodypart_row(self) -> int:
return self.bodyparts_view.currentRow()
@current_bodypart_row.setter
def current_bodypart_row(self, row) -> None:
self.bodyparts_view.setCurrentRow(row)
@property
def current_frame_row(self) -> int:
return self.frames_view.currentRow()
@current_frame_row.setter
def current_frame_row(self, row) -> None:
self.frames_view.setCurrentRow(row)
@property
def current_bodypart_text(self) -> Union[str, None]:
try:
return self.bodyparts_view.currentItem().text()
except AttributeError:
return None
@property
def current_frame_text(self) -> Union[str, None]:
try:
return self.frames_view.currentItem().text()
except AttributeError:
return None
def send_status(self, msg, timeout) -> None:
self.parent().status_bar.showMessage(msg, timeout * 1000)
def save_as_pkl(self) -> None:
self.save_file_dialog.selectFile(str(self.data_model.save_path_pkl))
self.save_file_dialog.setNameFilter("(*.pkl *.pickle)")
self.save_file_dialog.setDefaultSuffix(".pkl")
if self.save_file_dialog.exec():
save_path = self.save_file_dialog.selectedFiles()[0]
self.data_model.save_as_pkl(save_path)
def save_as_hdf(self) -> None:
self.save_file_dialog.selectFile(str(self.data_model.save_path_hdf))
self.save_file_dialog.setNameFilter("(*.h5 *.hdf)")
self.save_file_dialog.setDefaultSuffix(".h5")
if self.save_file_dialog.exec():
save_path = self.save_file_dialog.selectedFiles()[0]
self.data_model.save_as_hdf(save_path)
# Updating scene is in MainWidget and not GraphicsScene because it needs to know
# current frame and current bodypart, both properties of MainWidget
def update_scene(self) -> None:
def add_dots_to_scene(
coords: tuple,
size: float,
brush_color: QColor,
pen_color: QColor,
tooltip: str,
):
# Adds dots to the scene
x, y = coords
dot_rect = QRectF(x - size / 2, y - size / 2, size, size)
dot_brush = QBrush(Qt.SolidPattern)
dot_brush.setColor(brush_color)
dot_pen = QPen(dot_brush, size / 40)
dot_pen.setColor(pen_color)
dot_ellipse = QGraphicsEllipseItem(dot_rect)
dot_ellipse.setPen(dot_pen)
dot_ellipse.setBrush(dot_brush)
dot_ellipse.setToolTip(tooltip)
self.graphics_view.scene.addItem(dot_ellipse)
self.graphics_view.scene.clear()
frame = self.current_frame_text
if frame:
self.graphics_view.scene.load_image(str(self.frames_dict[frame]))
dot_size = self.dot_size_slider.value()
if self.data_model.data_frame is not None:
for bodypart, brush_color, pen_color in zip(
self.bodyparts,
self.data_model.colors,
self.data_model.colors_opposite,
):
coords = self.data_model.get_coords_from_dataframe(frame, bodypart)
if all(coord is not None for coord in coords):
add_dots_to_scene(
coords, dot_size, brush_color, pen_color, bodypart
)
class MainWindow(QMainWindow):
"""
Define the main window and its menubar and statusbar
"""
def __init__(self, config=None, relative_size=0.8):
super(MainWindow, self).__init__()
self.setWindowTitle("DeepLabCut Labeling GUI")
# Statusbar
# must be defined before children for children to access it
self.status_bar = self.statusBar()
self.open_file_dialog = QFileDialog()
if config is None:
config = self.open_file("(*.yml *.yaml)", "config.yaml")
if config == "" or config is None:
print("No config.yaml file provided, exiting...")
sys.exit()
self.main_widget = MainWidget(self, config)
self.open_file_dialog.setDirectory(
str(self.main_widget.data_model.labeled_data_path)
)
# Menubar
self.open_frames_dir = QAction("Open directory of frames", self)
self.open_frames_dir.setShortcut(QKeySequence("Ctrl+O"))
self.open_frames_dir.triggered.connect(
lambda x: self.main_widget.init_from_data_model_from_dir(self.open_dir())
)
self.open_dataframe_file = QAction("Open *.h5 or *.pkl file", self)
self.open_dataframe_file.setShortcut(QKeySequence("Ctrl+F"))
self.open_dataframe_file.triggered.connect(
lambda x: self.main_widget.init_from_data_model_from_file(
self.open_file(
"(*.h5 *.hdf *.pkl *.pickle)",
str(self.main_widget.data_model.save_path_hdf),
)
)
)
save_as_hdf = QAction("Save as .h5", self)
save_as_hdf.setShortcut(QKeySequence("Ctrl+S"))
save_as_hdf.triggered.connect(lambda x: self.main_widget.save_as_hdf())
save_as_pkl = QAction("Save as .pkl", self)
save_as_pkl.triggered.connect(lambda x: self.main_widget.save_as_pkl())
help_url = "https://dlc-gui.readthedocs.io/en/latest/README.html#using-the-gui"
open_help = QAction("Help", self)
open_help.setShortcut(QKeySequence("Ctrl+H"))
open_help.triggered.connect(lambda x: webbrowser.open(help_url))
self.menu_bar = self.menuBar()
self.file_menu = self.menu_bar.addMenu("File")
self.file_menu.addAction(self.open_frames_dir)
self.file_menu.addAction(self.open_dataframe_file)
self.file_menu.addAction(save_as_hdf)
self.file_menu.addAction(save_as_pkl)
self.help_menu = self.menu_bar.addMenu("Help")
self.help_menu.addAction(open_help)
# Window dimensions
self.resize(QDesktopWidget().availableGeometry(self).size() * relative_size)
self.setCentralWidget(self.main_widget)
#
## TODO fix bug of open_file_dialog object remembering
## selectedFiles and starting directory
#
def open_file(self, name_filter: str, select_file: str = None) -> Union[str, None]:
if select_file is not None:
self.open_file_dialog.selectFile(select_file)
self.open_file_dialog.setFileMode(QFileDialog.ExistingFile)
self.open_file_dialog.setNameFilter(name_filter)
if self.open_file_dialog.exec():
file = self.open_file_dialog.selectedFiles()[0]
return file
return None
def open_dir(self) -> Union[str, None]:
self.open_file_dialog.setFileMode(QFileDialog.Directory)
if self.open_file_dialog.exec():
dir = self.open_file_dialog.selectedFiles()[0]
return dir
return None
def show(config: Union[None, str] = None, relative_size: float = 0.8) -> None:
"""
Show the GUI.
Parameters
----------
config : str or None, optional (default None)
The config.yaml file to use.
May be None to use the GUI to pick the config.yaml file.
relative_size : float, optional (default 0.8)
What portion of the display to set the main window's size to.
"""
app = QApplication(sys.argv)
window = MainWindow(config, relative_size)
window.show()
sys.exit(app.exec_())
PK ! 䍇 dlc_gui/util.py# TODO use modern API
import ruamel.yaml
def read_config_file(config_path):
"""
Read a config.yaml file and return as a dictionary.
"""
with open(config_path, "r") as f:
config_dict = ruamel.yaml.load(f.read(), Loader=ruamel.yaml.Loader)
return config_dict
def write_config_file(write_path, config_dict):
"""
Write yaml dictionary to `write_path`.
"""
with open(write_path, "w") as f:
f.write(ruamel.yaml.dump(config_dict, default_flow_style=False))
PK ! p dlc_gui-0.3.1.dist-info/LICENSE GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
0. Additional Definitions.
As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.
"The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.
An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.
A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".
The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
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The "Corresponding Application Code" for a Combined Work means the
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