def __init__(self, parent):
"""Constructor"""
wx.Panel.__init__(self, parent=parent)
# load parameters to set dimension of frames and graphs
configs = ConfigFunctions.load_config('./config.yaml')
self.window_width = configs['window_width']
self.window_height = configs['window_height']
self.dirname = os.getcwd()
self.folder1 = ''
self.folder2 = ''
self.sizer = wx.GridBagSizer(0, 0)
self.header = wx.StaticText(self, -1, "Random Forest Classification", size=(500, 100))
font = wx.Font(20, wx.MODERN, wx.NORMAL, wx.NORMAL)
self.header.SetFont(font)
self.sizer.Add(self.header, pos=(0, 0), span=(2, 5), flag=wx.LEFT | wx.TOP, border=25)
instructions = "Classify animals using extracted gait kinematic parameters and identify important parameters."
self.instructions = wx.StaticText(self, -1, instructions, size=(self.window_width,50))
font = wx.Font(15, wx.MODERN, wx.NORMAL, wx.NORMAL)
self.instructions.SetFont(font)
self.sizer.Add(self.instructions, pos=(2, 0), span=(1, 6), flag=wx.LEFT, border=25)
self.data_widgets = []
#################################
self.select_group1_button = wx.Button(self, id=wx.ID_ANY, label="Group 1")
self.sizer.Add(self.select_group1_button, pos=(3, 0), flag=wx.LEFT | wx.TOP, border=25)
self.data_widgets.append(self.select_group1_button)
self.Bind(wx.EVT_BUTTON, lambda event, group_no = 0 : self.SelectGroupFolder(event, group_no), self.select_group1_button)
self.select_group1_text = wx.StaticText(self, label="\nPlease select kinematic data folder of the first group.")
self.sizer.Add(self.select_group1_text, pos=(3, 1), flag=wx.LEFT | wx.TOP, border=25)
self.data_widgets.append(self.select_group1_text)
#################################
self.select_group2_button = wx.Button(self, id=wx.ID_ANY, label="Group 2")
self.sizer.Add(self.select_group2_button, pos=(4, 0), flag=wx.LEFT | wx.TOP, border=25)
self.data_widgets.append(self.select_group2_button)
self.Bind(wx.EVT_BUTTON, lambda event, group_no = 1 : self.SelectGroupFolder(event, group_no), self.select_group2_button)
self.select_group2_text = wx.StaticText(self, label="\nPlease select kinematic data folder of the second group.")
self.sizer.Add(self.select_group2_text, pos=(4, 1), flag=wx.LEFT | wx.TOP, border=25)
self.data_widgets.append(self.select_group2_text)
#################################
self.select_output_folder_button = wx.Button(
self, id=wx.ID_ANY, label='Select output path')
self.sizer.Add(self.select_output_folder_button, pos=(
7, 1), flag=wx.TOP | wx.LEFT | wx.BOTTOM, border=25)
self.data_widgets.append(self.select_output_folder_button)
self.select_output_folder_button.Bind(wx.EVT_BUTTON, self.SelectOutputFolder)
self.select_output_folder_button.Show()
self.SetSizer(self.sizer)
self.GetParent().Layout()
def ImportKinematicsCSV(self, e):
import_dialog = wx.FileDialog(
self, 'Choose a file', self.dirname, '', 'CSV files (*.csv)|*.csv|All files(*.*)|*.*', wx.FD_OPEN)
if import_dialog.ShowModal() == wx.ID_OK:
self.csv_dirname = import_dialog.GetDirectory()
self.filename = os.path.join(
self.csv_dirname, import_dialog.GetFilename())
self.df, self.filename = KinematicsFunctions.read_file(
self.filename)
self.df, self.bodyparts = KinematicsFunctions.fix_column_names(
self.df)
try:
if self.df is not None:
self.has_imported_file = True
self.has_input_path = False
self.import_csv_text.SetLabel(
f"File imported! \n\n{self.filename}\n")
self.GetParent().Layout()
configs = ConfigFunctions.load_config('./config.yaml')
self.cutoff_f = configs['lowpass_filter_cutoff']
if self.analysis_type == 'Treadmill':
self.px_to_cm_speed_ratio = configs['px_to_cm_speed_ratio']
if configs['cm_speed'] == '':
self.cm_speed = 1
else:
self.cm_speed = configs['cm_speed']
elif self.analysis_type == 'Spontaneous walking':
self.pixels_per_cm = configs['pixels_per_cm']
self.method_label.Show()
self.method_choices.Show()
self.method_note_text.Show()
try:
self.select_output_folder_button.Hide()
self.select_output_folder_button.Destroy()
self.bulk_extract_parameters_button.Hide()
self.bulk_extract_parameters_button.Destroy()
self.extract_parameters_text.Hide()
self.extract_parameters_text.Destroy()
except:
pass
self.GetParent().Layout()
except AttributeError:
# user cancelled file import in pop up
self.GetParent().Layout()
pass
def __init__(self, parent):
"""Constructor"""
wx.Panel.__init__(self, parent=parent)
configs = ConfigFunctions.load_config('./config.yaml')
self.window_width = configs['window_width']
self.window_height = configs['window_height']
self.frame_rate = configs['frame_rate']
self.cutoff_f = configs['lowpass_filter_cutoff']
self.px_to_cm_speed_ratio = configs['px_to_cm_speed_ratio']
self.analysis_type = "Treadmill"
self.pixels_per_cm = configs['pixels_per_cm']
if configs['cm_speed'] == '':
self.cm_speed = None
else:
self.cm_speed = configs['cm_speed']
self.dragging_filter = bool(configs['dragging_filter'])
self.no_outlier_filter = bool(configs['no_outlier_filter'])
self.stride_widgets = []
self.has_input_path = False
self.has_imported_file = False
self.dirname = os.getcwd()
self.sizer = wx.GridBagSizer(0, 0)
self.header = wx.StaticText(
self, -1, "Kinematic Analysis", size=(500, 100))
font = wx.Font(20, wx.MODERN, wx.NORMAL, wx.NORMAL)
self.header.SetFont(font)
self.sizer.Add(self.header, pos=(0, 0), span=(
2, 4), flag=wx.LEFT | wx.TOP, border=25)
self.instructions = wx.StaticText(
self, -1, "Load the csv file of bodypart coordinates and extract kinematic parameters.", size=(self.window_width,50))
font = wx.Font(15,wx.MODERN,wx.NORMAL,wx.NORMAL)
self.instructions.SetFont(font)
self.sizer.Add(self.instructions, pos=(
2, 0), span=(1, 4), flag=wx.LEFT, border=25)
self.Stride_UI()
def BulkImportKinematicsCSV(self, e):
import_dialog = wx.DirDialog(
self, 'Choose a folder', self.dirname, style=wx.DD_DEFAULT_STYLE)
# Show the dialog and retrieve the user response.
if import_dialog.ShowModal() == wx.ID_OK:
self.input_path = import_dialog.GetPath()
self.files = []
for file in os.listdir(self.input_path):
if file.endswith('.csv'):
self.files.append(file)
try:
if len(self.files) > 0:
self.df = None
self.has_input_path = True
self.has_imported_file = False
self.import_csv_text.SetLabel(
f"Loaded {len(self.files)} csv files found in {self.input_path}.\n")
self.GetParent().Layout()
configs = ConfigFunctions.load_config('./config.yaml')
self.cutoff_f = configs['lowpass_filter_cutoff']
if self.analysis_type == 'Treadmill':
self.px_to_cm_speed_ratio = configs['px_to_cm_speed_ratio']
if configs['cm_speed'] == '':
self.cm_speed = None
else:
self.cm_speed = configs['cm_speed']
elif self.analysis_type == 'Spontaneous walking':
self.pixels_per_cm = configs['pixels_per_cm']
self.method_label.Show()
self.method_choices.Show()
self.method_note_text.Show()
self.GetParent().Layout()
try:
self.select_output_path_button.Hide()
self.select_output_path_button.Destroy()
self.extract_parameters_text.Hide()
self.extract_parameters_text.Destroy()
self.extract_parameters_button.Hide()
self.extract_parameters_button.Destroy()
except:
pass
self.GetParent().Layout()
return self.input_path, self.files, len(self.files)
else:
self.has_input_path = False
except AttributeError:
# user cancelled file import in pop up
self.GetParent().Layout()
pass
else:
self.input_path = ''
import_dialog.Destroy()
def __init__(self, parent):
"""Constructor"""
wx.Panel.__init__(self, parent=parent)
self.sizer = wx.GridBagSizer(0, 0)
#################################
configs = ConfigFunctions.load_config('./config.yaml')
self.window_width = configs['window_width']
self.window_height = configs['window_height']
self.header = wx.StaticText(self,
-1,
"Automated Limb Motion Analysis (ALMA)",
size=(self.window_width, 60))
font = wx.Font(30, wx.MODERN, wx.NORMAL, wx.NORMAL)
self.header.SetFont(font)
self.sizer.Add(self.header,
pos=(1, 0),
span=(1, 2),
flag=wx.ALL,
border=25)
self.intro_text = wx.StaticText(
self, label="Select behavioral test to analyze:\n")
font = wx.Font(15, wx.MODERN, wx.NORMAL, wx.NORMAL)
self.intro_text.SetFont(font)
ladder_rung_img = wx.Bitmap('./Resources/image_ladder_rung.png')
w, h = ladder_rung_img.GetWidth(), ladder_rung_img.GetHeight()
ladder_rung_img = wx.Bitmap.ConvertToImage(ladder_rung_img)
ladder_rung_img.Rescale(w // (3000 // self.window_width),
h // (3000 // self.window_width))
ladder_rung_img = wx.Bitmap(ladder_rung_img)
self.ladder_rung_button = wx.BitmapButton(self,
id=wx.ID_ANY,
bitmap=ladder_rung_img)
kinematics_img = wx.Bitmap('./Resources/image_kinematics.png')
kinematics_img = wx.Bitmap.ConvertToImage(kinematics_img)
kinematics_img.Rescale(w // (3000 // self.window_width),
h // (3000 // self.window_width))
kinematics_img = wx.Bitmap(kinematics_img)
self.kinematics_button = wx.BitmapButton(self,
id=wx.ID_ANY,
bitmap=kinematics_img)
self.sizer.Add(self.intro_text, pos=(2, 0), flag=wx.ALL, border=25)
self.sizer.Add(self.ladder_rung_button,
pos=(3, 0),
flag=wx.ALL,
border=25)
self.sizer.Add(self.kinematics_button,
pos=(3, 1),
flag=wx.ALL,
border=25)
# self.sizer.Add(control)
self.ladder_rung_button.Bind(wx.EVT_BUTTON, parent.on_analyze_footfall)
self.kinematics_button.Bind(wx.EVT_BUTTON, parent.on_analyze_stride)
self.SetSizer(self.sizer)
self.GetParent().Layout()
self.SetStatusText('Run PCA on extracted gait kinematic parameters')
self.Layout()
self.Refresh() # refresh to show slider in right proportion
def on_about(self, e):
wx.MessageBox( "This is a toolbox for fully automated (rodent) "\
"limb motion analysis with markerless bodypart tracking data. "\
"Compatible with csv output from DeepLabCut.",
"About ALMA",
wx.OK|wx.ICON_INFORMATION)
def on_help(self, event):
wx.MessageBox("Please go to our GitHub Wiki for help or email us :)",
"Support",
wx.OK|wx.ICON_INFORMATION)
if __name__ == '__main__':
from Functions import ConfigFunctions
configs = ConfigFunctions.load_config('./config.yaml')
window_width, window_height = configs['window_width'], configs['window_height']
app = wx.App(redirect = True)
home_frame = HomeFrame(None, title='ALMA - Automated Limb Motion Analysis', size=(window_width, window_height))
home_frame.Show()
app.MainLoop()