https://github.com/scw97/PiezoPaperExpressoCode
Tip revision: bd8a58fa0e4f796e2ed0b72fe807862305b84b6b authored by scw97 on 05 February 2021, 20:18:22 UTC
changed to exact version used in paper
changed to exact version used in paper
Tip revision: bd8a58f
expresso_gui_rough_mk2.py
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 09 17:11:07 2016
@author: Fruit Flies
"""
import matplotlib
matplotlib.use('TkAgg')
import os
import sys
if sys.version_info[0] < 3:
from Tkinter import *
import tkFileDialog
from ttk import *
import tkMessageBox
else:
from tkinter import *
from tkinter.ttk import *
from tkinter import filedialog as tkFileDialog
from tkinter import messagebox as tkMessageBox
import h5py
import numpy as np
from scipy import interpolate
#from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider
#from matplotlib.figure import Figure
from load_hdf5_data import load_hdf5
from bout_analysis_func import bout_analysis
from batch_bout_analysis_func import batch_bout_analysis, save_batch_xlsx
#from PIL import ImageTk, Image
import csv
#------------------------------------------------------------------------------
class DirectoryFrame(Frame):
""" Top UI frame containing the list of directories to be scanned. """
def __init__(self, parent, col=0, row=0, filedir=None):
Frame.__init__(self, parent)
self.lib_label = Label(parent, text='Directory list:')
#foreground=guiParams['textcolor'],
#background=guiParams['bgcolor'])
self.lib_label.grid(column=col, row=row, padx=10, pady=2, sticky=NW)
# listbox containing all selected additional directories to scan
self.dirlist = Listbox(parent, width=64, height=8,
selectmode=EXTENDED, exportselection=False)
#foreground=guiParams['textcolor'],
#background=guiParams['listbgcolor'])
self.dirlist.bind('<<ListboxSelect>>', self.on_select)
self.dirlist.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.btnframe = Frame(parent)
self.btnframe.grid(column=col+2, row=row, sticky=NW)
#self.btnframe.config(background=guiParams['bgcolor'])
self.lib_addbutton =Button(self.btnframe, text='Add Directory',
command= lambda: self.add_library(parent))
self.lib_addbutton.grid(column=col, row=row, padx=10, pady=2,
sticky=NW)
self.lib_delbutton = Button(self.btnframe, text='Remove Directory',
command=self.rm_library, state=DISABLED)
self.lib_delbutton.grid(column=col, row=row+1, padx=10, pady=2,
sticky=NW)
self.lib_clearbutton = Button(self.btnframe, text='Clear All',
command=self.clear_library)
self.lib_clearbutton.grid(column=col, row=row+2, padx=10, pady=2,
sticky=NW)
def on_select(self, selection):
""" Enable or disable based on a valid directory selection. """
if self.dirlist.curselection():
self.lib_delbutton.configure(state=NORMAL)
else:
self.lib_delbutton.configure(state=DISABLED)
def add_library(self,parent):
""" Insert every selected directory chosen from the dialog.
Prevent duplicate directories by checking existing items. """
dirlist = self.dirlist.get(0, END)
newdir = Expresso.get_dir(parent)
if newdir not in dirlist:
self.dirlist.insert(END, newdir)
def rm_library(self):
""" Remove selected items from listbox when button in remove mode. """
# Reverse sort the selected indexes to ensure all items are removed
selected = sorted(self.dirlist.curselection(), reverse=True)
for item in selected:
self.dirlist.delete(item)
def clear_library(self):
""" Remove all items from listbox when button pressed """
self.dirlist.delete(0,END)
#------------------------------------------------------------------------------
class FileDataFrame(Frame):
def __init__(self, parent, col=0, row=0):
Frame.__init__(self, parent)
self.list_label = Label(parent, text='Detected files:')
self.list_label.grid(column=col, row=row, padx=10, pady=2, sticky=NW)
self.filelistframe = Frame(parent)
self.filelistframe.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.filelist = Listbox(self.filelistframe, width=64, height=8,
selectmode=EXTENDED)
self.filelist.bind('<<ListboxSelect>>', self.on_select)
#self.filelist.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.hscroll = Scrollbar(self.filelistframe)
self.hscroll.pack(side=BOTTOM, fill=X)
self.vscroll = Scrollbar(self.filelistframe)
self.vscroll.pack(side=RIGHT, fill=Y)
self.filelist.config(xscrollcommand=self.hscroll.set,
yscrollcommand=self.vscroll.set)
self.filelist.pack(side=TOP, fill=BOTH)
self.hscroll.configure(orient=HORIZONTAL,
command=self.filelist.xview)
self.vscroll.configure(orient=VERTICAL,
command=self.filelist.yview)
self.btnframe = Frame(parent)
self.btnframe.grid(column=col+2, row=row, sticky=NW)
# button used to initiate the scan of the above directories
self.scan_btn =Button(self.btnframe, text='Get HDF5 Files',
command= lambda: self.add_files(parent))
#self.scan_btn['state'] = 'disabled'
self.scan_btn.grid(column=col, row=row, padx=10, pady=2,
sticky=NW)
# button used to remove the detected data
self.remove_button = Button(self.btnframe, text='Remove Files')
self.remove_button['state'] = 'disabled'
self.remove_button['command'] = self.rm_files
self.remove_button.grid(column=col, row=row+1, padx=10, pady=2,
sticky=NW)
self.clear_button = Button(self.btnframe, text='Clear All')
self.clear_button['command'] = self.clear_files
self.clear_button.grid(column=col, row=row+2, padx=10, pady=2,
sticky=NW)
# label to show total files found and their size
# this label is blank to hide it until required to be shown
#self.total_label = Label(parent)
#self.total_label.grid(column=col+1, row=row+2, padx=10, pady=2,
# sticky=E)
def on_select(self, selection):
""" Enable or disable based on a valid directory selection. """
if self.filelist.curselection():
self.remove_button.configure(state=NORMAL)
else:
self.remove_button.configure(state=DISABLED)
def add_files(self,parent):
newfiles = Expresso.scan_dirs(parent)
file_list = self.filelist.get(0,END)
if len(newfiles) > 0:
#file_list = self.filelist.get(0,END)
#Expresso.clear_xplist(parent)
#Expresso.clear_channellist(parent)
for file in tuple(newfiles):
if file not in file_list:
self.filelist.insert(END,file)
def rm_files(self):
selected = sorted(self.filelist.curselection(), reverse=True)
for item in selected:
self.filelist.delete(item)
def clear_files(self):
self.filelist.delete(0,END)
#------------------------------------------------------------------------------
class XPDataFrame(Frame):
def __init__(self, parent, col=0, row=0):
Frame.__init__(self, parent)
self.list_label = Label(parent, text='XP list:')
self.list_label.grid(column=col, row=row, padx=10, pady=2, sticky=NW)
self.xplistframe = Frame(parent)
self.xplistframe.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.xplist = Listbox(self.xplistframe, width=64, height=8,
selectmode=EXTENDED)
self.xplist.bind('<<ListboxSelect>>', self.on_select)
#self.filelist.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.hscroll = Scrollbar(self.xplistframe)
self.hscroll.pack(side=BOTTOM, fill=X)
self.vscroll = Scrollbar(self.xplistframe)
self.vscroll.pack(side=RIGHT, fill=Y)
self.xplist.config(xscrollcommand=self.hscroll.set,
yscrollcommand=self.vscroll.set)
self.xplist.pack(side=TOP, fill=BOTH)
self.hscroll.configure(orient=HORIZONTAL,
command=self.xplist.xview)
self.vscroll.configure(orient=VERTICAL,
command=self.xplist.yview)
self.btnframe = Frame(parent)
self.btnframe.grid(column=col+2, row=row, sticky=NW)
# button used to initiate the scan of the above directories
self.unpack_btn =Button(self.btnframe, text='Unpack HDF5 Files',
command= lambda: self.add_xp(parent))
self.unpack_btn.grid(column=col, row=row, padx=10, pady=2,
sticky=NW)
# button used to remove the detected data
self.remove_button = Button(self.btnframe, text='Remove Files')
self.remove_button['state'] = 'disabled'
self.remove_button['command'] = self.rm_xp
self.remove_button.grid(column=col, row=row+1, padx=10, pady=2,
sticky=NW)
self.clear_button = Button(self.btnframe, text='Clear All')
self.clear_button['command'] = self.clear_xp
self.clear_button.grid(column=col, row=row+2, padx=10, pady=2,
sticky=NW)
# label to show total files found and their size
# this label is blank to hide it until required to be shown
#self.total_label = Label(parent)
#self.total_label.grid(column=col+1, row=row+2, padx=10, pady=2,
# sticky=E)
def on_select(self, selection):
""" Enable or disable based on a valid directory selection. """
if self.xplist.curselection():
self.remove_button.configure(state=NORMAL)
else:
self.remove_button.configure(state=DISABLED)
def add_xp(self,parent):
xp_list = self.xplist.get(0,END)
#Expresso.clear_channellist(parent)
newxp = Expresso.unpack_files(parent)
for xp in tuple(newxp):
if xp not in xp_list:
self.xplist.insert(END,xp)
def rm_xp(self):
selected = sorted(self.xplist.curselection(), reverse=True)
for item in selected:
self.xplist.delete(item)
def clear_xp(self):
self.xplist.delete(0,END)
#------------------------------------------------------------------------------
class ChannelDataFrame(Frame):
def __init__(self, parent, col=0, row=0):
Frame.__init__(self, parent)
self.list_label = Label(parent, text='Channel list:')
self.list_label.grid(column=col, row=row, padx=10, pady=2, sticky=N)
self.channellistframe = Frame(parent)
self.channellistframe.grid(column=col+1, row=row, padx=10, pady=2, sticky=E)
self.channellist = Listbox(self.channellistframe, width=64, height=8,
selectmode=EXTENDED)
self.channellist.bind('<<ListboxSelect>>', self.on_select)
#self.filelist.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.hscroll = Scrollbar(self.channellistframe)
self.hscroll.pack(side=BOTTOM, fill=X)
self.vscroll = Scrollbar(self.channellistframe)
self.vscroll.pack(side=RIGHT, fill=Y)
self.channellist.config(xscrollcommand=self.hscroll.set,
yscrollcommand=self.vscroll.set)
self.channellist.pack(side=TOP, fill=BOTH)
self.hscroll.configure(orient=HORIZONTAL,
command=self.channellist.xview)
self.vscroll.configure(orient=VERTICAL,
command=self.channellist.yview)
self.btnframe = Frame(parent)
self.btnframe.grid(column=col+2, row=row, sticky=NW)
# button used to initiate the scan of the above directories
self.unpack_btn =Button(self.btnframe, text='Unpack XP',
command= lambda: self.add_channels(parent))
self.unpack_btn.grid(column=col, row=row, padx=10, pady=2,
sticky=NW)
# button used to remove the detected data
self.remove_button = Button(self.btnframe, text='Remove Files')
self.remove_button['state'] = 'disabled'
self.remove_button['command'] = self.rm_channel
self.remove_button.grid(column=col, row=row+1, padx=10, pady=2,
sticky=NW)
self.clear_button = Button(self.btnframe, text='Clear All')
self.clear_button['command'] = self.clear_channel
self.clear_button.grid(column=col, row=row+2, padx=10, pady=2,
sticky=NW)
self.plot_button = Button(self.btnframe, text='Plot Channel')
self.plot_button['state'] = 'disabled'
self.plot_button['command'] = lambda: self.plot_channel(parent)
self.plot_button.grid(column=col, row=row+3, padx=10, pady=2,
sticky=SW)
self.save_button = Button(self.btnframe, text='Save CSV')
self.save_button['state'] = 'disabled'
self.save_button['command'] = lambda: self.save_results(parent)
self.save_button.grid(column=col, row=row+4, padx=10, pady=2,
sticky=SW)
self.selection_ind = []
# label to show total files found and their size
# this label is blank to hide it until required to be shown
#self.total_label = Label(parent)
#self.total_label.grid(column=col+1, row=row+2, padx=10, pady=2,
# sticky=E)
def on_select(self, selection):
""" Enable or disable based on a valid directory selection. """
if self.channellist.curselection():
self.remove_button.configure(state=NORMAL)
self.plot_button.configure(state=NORMAL)
self.save_button.configure(state=NORMAL)
self.selection_ind = sorted(self.channellist.curselection(), reverse=True)
#print(self.selection_ind)
else:
self.remove_button.configure(state=DISABLED)
self.plot_button.configure(state=DISABLED)
self.save_button.configure(state=DISABLED)
def add_channels(self,parent):
channel_list = self.channellist.get(0,END)
newchannels = Expresso.unpack_xp(parent)
for channel in tuple(newchannels):
if channel not in channel_list:
self.channellist.insert(END,channel)
def rm_channel(self):
selected = sorted(self.channellist.curselection(), reverse=True)
for item in selected:
self.channellist.delete(item)
def clear_channel(self):
self.channellist.delete(0,END)
def plot_channel(self,parent):
selected_ind = self.selection_ind
if len(selected_ind) != 1:
tkMessageBox.showinfo(title='Error',
message='Please select only one channel for plotting individual traces')
return
channel_entry = self.channellist.get(selected_ind[0])
dset, frames, t, dset_smooth, bouts, volumes = Expresso.get_channel_data(parent,channel_entry)
if dset.size != 0:
(dset,frames)
self.bouts = bouts
self.dset_smooth = dset_smooth
self.volumes = volumes
self.t = t
#fig_window = Toplevel()
self.fig, (self.ax1, self.ax2) = plt.subplots(2, sharex=True,
sharey=True,figsize=(12, 7))
self.ax1.set_ylabel('Liquid [nL]')
self.ax2.set_ylabel('Liquid [nL]')
self.ax2.set_xlabel('Time [s]')
self.ax1.set_title('Raw Data')
self.ax2.set_title('Smoothed Data')
self.ax1.plot(t,dset)
self.ax2.plot(t, dset_smooth)
for i in np.arange(bouts.shape[1]):
self.ax2.plot(t[bouts[0,i]:bouts[1,i]], dset_smooth[bouts[0,i]:bouts[1,i]],'r-')
self.ax2.axvspan(t[bouts[0,i]],t[bouts[1,i]-1],
facecolor='grey', edgecolor='none', alpha=0.3)
self.ax1.axvspan(t[bouts[0,i]],t[bouts[1,i]-1],
facecolor='grey', edgecolor='none', alpha=0.3)
self.ax1.set_xlim([t[0],t[-1]])
self.ax1.set_ylim([np.amin(dset),np.amax(dset)])
#self.fig.set_tight_layout(True)
plt.subplots_adjust(bottom=0.2)
self.ax_xrange = plt.axes([0.25, 0.1, 0.65, 0.03])
self.ax_xmid = plt.axes([0.25, 0.06, 0.65, 0.03])
self.slider_xrange = Slider(self.ax_xrange, 't range',
-1.0*np.amax(self.t), -1.0*3.0,
valinit=-1.0*np.amax(self.t))
self.slider_xmid = Slider(self.ax_xmid, 't mid', 0.0,
np.amax(self.t),
valinit=np.amax(self.t)/2,
facecolor='white')
def update(val):
xrange_val = -1.0*self.slider_xrange.val
xmid_val = self.slider_xmid.val
xmin = int(np.rint(np.amax([0, xmid_val - xrange_val/2])))
xmax = int(np.rint(np.amin([self.dset_smooth.size, xmid_val + xrange_val/2])))
xlim = [xmin, xmax]
ymin = self.dset_smooth[xmin]+1
ymax = self.dset_smooth[xmax-1]-1
ylim = np.sort([ymin, ymax])
self.ax2.set_xlim(xlim)
self.ax2.set_ylim(ylim)
#ax2_lim = ((xmin, np.amin(self.dset_smooth)), (xmax,np.amax(self.dset_smooth)))
#self.ax2.update_datalim(ax2_lim)
#self.ax2.autoscale()
self.fig.canvas.draw_idle()
self.slider_xrange.on_changed(update)
self.slider_xmid.on_changed(update)
full_channellist_entry = self.channellist.get(self.selection_ind[0])
filepath, filekeyname, groupkeyname = full_channellist_entry.split(', ',2)
dirpath, filename = os.path.split(filepath)
self.channel_name_full = filename + ", " + filekeyname + ", " + groupkeyname
self.fig.canvas.set_window_title(self.channel_name_full)
#self.save_button['state'] = 'normal'
#self.cursor = matplotlib.widgets.MultiCursor(self.fig.canvas, (self.ax1, self.ax2),
# color='black', linewidth=1,
# horizOn=False,vertOn=True)
#plt.show()
#plt.show(self.fig)
else:
tkMessageBox.showinfo(title='Error',
message='Invalid channel selection--no data in channel')
def save_results(self,parent):
selected_ind = self.selection_ind
if len(selected_ind) != 1:
tkMessageBox.showinfo(title='Error',
message='Please select only one channel for plotting individual traces')
return
full_channellist_entry = self.channellist.get(selected_ind[0])
_, _, self.t, _, self.bouts, self.volumes = Expresso.get_channel_data(parent,full_channellist_entry)
#full_channellist_entry = self.channellist.get(self.selection_ind[0])
filepath, filekeyname, groupkeyname = full_channellist_entry.split(', ',2)
dirpath, filename = os.path.split(filepath)
self.channel_name_full = filename + ", " + filekeyname + ", " + groupkeyname
if self.bouts.size > 0 :
bouts_transpose = np.transpose(self.bouts)
volumes_col = self.volumes.reshape(self.volumes.size,1)
row_mat = np.hstack((bouts_transpose,self.t[bouts_transpose],volumes_col))
if sys.version_info[0] < 3:
save_file = tkFileDialog.asksaveasfile(mode='wb',
defaultextension=".csv")
save_writer = csv.writer(save_file)
else:
save_filename = tkFileDialog.asksaveasfilename(defaultextension=".csv")
save_file = open(save_filename, 'w', newline='')
save_writer = csv.writer(save_file)
save_writer.writerow([self.channel_name_full])
save_writer.writerow(['Bout Number'] + ['Bout Start [idx]'] + \
['Bout End [idx]'] + ['Bout Start [s]'] + ['Bout End [s]']+ ['Volume [nL]'])
cc = 1
for row in row_mat:
new_row = np.insert(row,0,cc)
save_writer.writerow(new_row)
cc += 1
else:
tkMessageBox.showinfo(title='Error',
message='No feeding bouts to save')
#------------------------------------------------------------------------------
class BatchFrame(Frame):
def __init__(self, parent,col=0,row=0):
Frame.__init__(self, parent)
self.list_label = Label(parent, text='Batch analyze list:')
self.list_label.grid(column=col, row=row, padx=10, pady=2, sticky=S)
self.batchlistframe = Frame(parent)
self.batchlistframe.grid(column=col, row=row+1, columnspan = 2, rowspan = 3, padx=10, pady=2, sticky=N)
self.batchlist = Listbox(self.batchlistframe, width=64, height=12,
selectmode=EXTENDED)
self.batchlist.bind('<<ListboxSelect>>', self.on_select)
#self.filelist.grid(column=col+1, row=row, padx=10, pady=2, sticky=W)
self.hscroll = Scrollbar(self.batchlistframe)
self.hscroll.pack(side=BOTTOM, fill=X)
self.vscroll = Scrollbar(self.batchlistframe)
self.vscroll.pack(side=RIGHT, fill=Y)
self.batchlist.config(xscrollcommand=self.hscroll.set,
yscrollcommand=self.vscroll.set)
self.batchlist.pack(side=TOP, fill=BOTH)
self.hscroll.configure(orient=HORIZONTAL,
command=self.batchlist.xview)
self.vscroll.configure(orient=VERTICAL,
command=self.batchlist.yview)
self.entryframe = Frame(parent)
self.entryframe.grid(column=col, row=row+2,columnspan = 3, rowspan = 2, pady=60, sticky=N)
self.tmin_entry_label = Label(self.entryframe, text='t_min')
self.tmin_entry_label.grid(column=col, row=0, padx=10, pady=2, sticky=N)
self.tmin_entry = Entry(self.entryframe, width=8)
self.tmin_entry.insert(END,'0')
self.tmin_entry.grid(column=col, row=1,padx=10, pady=2, sticky=S)
self.tmax_entry_label = Label(self.entryframe, text='t_max')
self.tmax_entry_label.grid(column=col+1, row=0, padx=10, pady=2, sticky=N)
self.tmax_entry = Entry(self.entryframe, width=8)
self.tmax_entry.insert(END,'2000')
self.tmax_entry.grid(column=col+1, row=1,padx=10, pady=2, sticky=S)
self.tbin_entry_label = Label(self.entryframe, text='t_bin')
self.tbin_entry_label.grid(column=col+2, row=0, padx=10, pady=2, sticky=N)
self.tbin_entry = Entry(self.entryframe, width=8)
self.tbin_entry.insert(END,'20')
self.tbin_entry.grid(column=col+2, row=1,padx=10, pady=2, sticky=S)
self.btnframe = Frame(parent)
self.btnframe.grid(column=col, row=row+3, columnspan = 2, rowspan = 2, sticky=N)
# button used to initiate the scan of the above directories
self.add_btn =Button(self.btnframe, text='Add Channel(s) to Batch',
command= lambda: self.add_to_batch(parent))
self.add_btn.grid(column=col, row=row, padx=10, pady=2,
sticky=N)
# button used to remove the detected data
self.remove_button = Button(self.btnframe, text='Remove Selected')
self.remove_button['state'] = 'disabled'
self.remove_button['command'] = self.rm_channel
self.remove_button.grid(column=col, row=row+1, padx=10, pady=2,
sticky=N)
# button used to clear all batch files
self.clear_button = Button(self.btnframe, text='Clear All')
self.clear_button['command'] = self.clear_batch
self.clear_button.grid(column=col, row=row+2, padx=10, pady=2,
sticky=N)
self.plot_button = Button(self.btnframe, text='Plot Batch Analysis')
#self.plot_button['state'] = 'disabled'
self.plot_button['command'] = self.plot_batch
self.plot_button.grid(column=col+1, row=row, padx=10, pady=2,
sticky=S)
self.save_button = Button(self.btnframe, text='Save Batch Results')
#self.save_button['state'] = 'disabled'
self.save_button['command'] = self.save_batch
self.save_button.grid(column=col+1, row=row+1, padx=10, pady=2,
sticky=S)
self.save_ts_button = Button(self.btnframe, text='Save Time Series')
#self.save_button['state'] = 'disabled'
self.save_ts_button['command'] = lambda: self.save_time_series(parent)
self.save_ts_button.grid(column=col+1, row=row+2, padx=10, pady=2,
sticky=S)
self.selection_ind = []
# label to show total files found and their size
# this label is blank to hide it until required to be shown
#self.total_label = Label(parent)
#self.total_label.grid(column=col+1, row=row+2, padx=10, pady=2,
# sticky=E)
def on_select(self, selection):
""" Enable or disable based on a valid directory selection. """
if self.batchlist.curselection():
self.remove_button.configure(state=NORMAL)
#self.plot_button.configure(state=NORMAL)
self.selection_ind = sorted(self.batchlist.curselection(), reverse=True)
#print(self.selection_ind)
else:
self.remove_button.configure(state=DISABLED)
#self.plot_button.configure(state=DISABLED)
def add_to_batch(self,parent):
batch_list = self.batchlist.get(0,END)
for_batch = Expresso.fetch_channels_for_batch(parent)
for channel in tuple(for_batch):
if channel not in batch_list:
self.batchlist.insert(END,channel)
def rm_channel(self):
selected = sorted(self.batchlist.curselection(), reverse=True)
for item in selected:
self.batchlist.delete(item)
def clear_batch(self):
self.batchlist.delete(0,END)
def plot_batch(self):
batch_list = self.batchlist.get(0,END)
if len(batch_list) < 1:
tkMessageBox.showinfo(title='Error',
message='Add data to batch box for batch analysis')
return
else:
try:
tmin = int(self.tmin_entry.get())
tmax = int(self.tmax_entry.get())
tbin = int(self.tbin_entry.get())
except:
tkMessageBox.showinfo(title='Error',
message='Set time range and bin size')
return
(self.bouts_list, self.name_list, self.volumes_list, self.consumption_per_fly,
self.duration_per_fly, self.latency_per_fly, self.fig_raster,
self.fig_hist) = batch_bout_analysis(batch_list, tmin, tmax, tbin,True)
#self.save_button['state'] = 'enabled'
def save_batch(self):
batch_list = self.batchlist.get(0,END)
if len(batch_list) < 1:
tkMessageBox.showinfo(title='Error',
message='Add data to batch box for batch analysis')
return
else:
try:
tmin = int(self.tmin_entry.get())
tmax = int(self.tmax_entry.get())
tbin = int(self.tbin_entry.get())
except:
tkMessageBox.showinfo(title='Error',
message='Set time range and bin size')
return
(self.bouts_list, self.name_list, self.volumes_list, self.consumption_per_fly,
self.duration_per_fly, self.latency_per_fly) = \
batch_bout_analysis(batch_list, tmin, tmax, tbin,False)
save_filename = tkFileDialog.asksaveasfilename(defaultextension=".xlsx")
save_batch_xlsx(save_filename, self.bouts_list,self.name_list,
self.volumes_list,self.consumption_per_fly,
self.duration_per_fly, self.latency_per_fly)
def save_time_series(self,parent):
batch_list = self.batchlist.get(0,END)
if len(batch_list) < 1:
tkMessageBox.showinfo(title='Error',
message='Add data to batch box for batch analysis')
return
else:
save_dir = Expresso.get_dir(parent)
for entry in batch_list:
dset, frames, t, dset_smooth, bouts, _ = Expresso.get_channel_data(parent,entry)
feeding_boolean = np.zeros([1,dset.size])
for i in np.arange(bouts.shape[1]):
feeding_boolean[0,bouts[0,i]:bouts[1,i]] = 1
row_mat = np.vstack((frames, t, dset, dset_smooth, feeding_boolean))
row_mat = np.transpose(row_mat)
filepath, filekeyname, groupkeyname = entry.split(', ',2)
dirpath, filename = os.path.split(filepath)
save_name = filename[:-5] + "_" + filekeyname + "_" + groupkeyname + ".csv"
save_path = os.path.join(save_dir,save_name)
if sys.version_info[0] < 3:
out_path = open(save_path,mode='wb')
else:
out_path = open(save_path, 'w', newline='')
save_writer = csv.writer(out_path)
save_writer.writerow(['Idx'] + ['Time [s]'] + \
['Data Raw [nL]'] + ['Data Smoothed [nL]'] + ['Feeding [bool]'])
#cc = 1
for row in row_mat:
#new_row = np.insert(row,0,cc)
save_writer.writerow(row)
#cc += 1
out_path.close()
#------------------------------------------------------------------------------
#class LogoFrame(Frame):
# def __init__(self, parent,col=0,row=0):
# Frame.__init__(self, parent)
# self.parent = parent
# self.initLogo()
#
# def initLogo(self):
# self.pack()
# #insert logo
# self.logo_canvas = Canvas(self.parent,width=1000,height=200)
# self.logo_canvas.pack()
# self.im = Image.open('C:\\Users\\Fruit Flies\\Documents\\Python Scripts\\Expresso GUI\\expresso_alpha.jpg')
# self.logo_canvas.image = ImageTk.PhotoImage(self.im)
# #self.photo = ImageTk.PhotoImage(self.im)
# self.logo_canvas.create_image(0,0, image=self.logo_canvas.image, anchor=NW)
#------------------------------------------------------------------------------
class Expresso(Tk):
"""The GUI and functions."""
def __init__(self):
Tk.__init__(self)
# initialize important fields for retaining where we are in data space
init_dirs = []
self.initdirs = init_dirs
datapath = []
self.datadir_curr = datapath
filename = []
self.filename_curr = filename
filekeyname = []
self.filekeyname_curr = filekeyname
grpnum = []
self.grpnum_curr = grpnum
grp = []
self.grp_curr = grp
# run gui presets. may be unecessary
self.init_gui()
# initialize instances of frames created above
self.dirframe = DirectoryFrame(self, col=0, row=0)
self.fdata_frame = FileDataFrame(self, col=0, row=1)
self.xpdata_frame = XPDataFrame(self, col=0, row=2)
self.channeldata_frame = ChannelDataFrame(self, col=0, row=3)
self.batchdata_frame = BatchFrame(self,col=3,row=0)
#self.logo_frame = LogoFrame(self,col=0,row=0)
for datadir in self.initdirs:
self.dirframe.dirlist.insert(END, datadir)
#self.rawdata_plot = FigureFrame(self, col=4, row=0)
self.make_topmost()
self.protocol("WM_DELETE_WINDOW", self.on_quit)
def on_quit(self):
"""Exits program."""
if tkMessageBox.askokcancel("Quit","Do you want to quit?"):
self.destroy()
self.quit()
def make_topmost(self):
"""Makes this window the topmost window"""
self.lift()
self.attributes("-topmost", 1)
self.attributes("-topmost", 0)
def init_gui(self):
"""Label for GUI"""
self.title('Expresso Data Analysis (rough version)')
""" Menu bar """
self.option_add('*tearOff', 'FALSE')
self.menubar = Menu(self)
self.menu_file = Menu(self.menubar)
self.menu_file.add_command(label='Exit', command=self.on_quit)
self.menu_edit = Menu(self.menubar)
self.menubar.add_cascade(menu=self.menu_file, label='File')
self.menubar.add_cascade(menu=self.menu_edit, label='Edit')
self.config(menu=self.menubar)
"""
parent.title('Expresso Data Analysis (rough version)')
parent.option_add('*tearOff', 'FALSE')
parent.menubar = Menu(parent)
parent.menu_file = Menu(parent.menubar)
parent.menu_file.add_command(label='Exit', command=self.on_quit)
parent.menu_edit = Menu(parent.menubar)
parent.menubar.add_cascade(menu=parent.menu_file, label='File')
parent.menubar.add_cascade(menu=parent.menu_edit, label='Edit')
parent.config(menu=parent.menubar)
#self.configure(background='dim gray')
#self.tk_setPalette(background=guiParams['bgcolor'],
# foreground=guiParams['textcolor'])
"""
@staticmethod
def get_dir(self):
""" Method to return the directory selected by the user which should
be scanned by the application. """
# get user specified directory and normalize path
seldir = tkFileDialog.askdirectory(initialdir=sys.path[0])
if seldir:
seldir = os.path.abspath(seldir)
self.datadir_curr = seldir
return seldir
@staticmethod
def scan_dirs(self):
# build list of detected files from selected paths
files = []
temp_dirlist = list(self.dirframe.dirlist.get(0, END))
selected_ind = sorted(self.dirframe.dirlist.curselection(), reverse=True)
if len(selected_ind) < 1:
tkMessageBox.showinfo(title='Error',
message='Please select directory from which to grab hdf5 files')
return files
for ind in selected_ind:
temp_dir = temp_dirlist[ind]
for file in os.listdir(temp_dir):
if file.endswith(".hdf5"):
files.append(os.path.join(temp_dir,file))
self.datadir_curr = temp_dir
if len(files) > 0:
return files
else:
tkMessageBox.showinfo(title='Error',
message='No HDF5 files found.')
files = []
return files
@staticmethod
def unpack_files(self):
selected_ind = sorted(self.fdata_frame.filelist.curselection(), reverse=True)
#print(selected_ind)
selected = []
for ind in selected_ind:
selected.append(self.fdata_frame.filelist.get(ind))
#temp_dirlist = list(self.dirframe.dirlist.get(0, END))
#for dir in temp_dirlist:
fileKeyNames = []
for filename in selected:
#filename = os.path.join(dir,selected[0])
#print(filename)
if os.path.isfile(filename):
self.filename_curr = filename
f = h5py.File(filename,'r')
for key in list(f.keys()):
if key.startswith('XP'):
fileKeyNames.append(filename + ", " + key)
return fileKeyNames
@staticmethod
def unpack_xp(self):
selected_ind = sorted(self.xpdata_frame.xplist.curselection(), reverse=True)
groupKeyNames = []
for ind in selected_ind:
xp_entry = self.xpdata_frame.xplist.get(ind)
filename, filekeyname = xp_entry.split(', ', 1)
f = h5py.File(filename,'r')
#fileKeyNames = list(f.keys())
grp = f[filekeyname]
for key in list(grp.keys()):
groupKeyNames.append(filename + ', ' + filekeyname + ', ' + key)
#if groupKeyNames:
# self.filekeyname_curr = fileKeyNames[selected_ind[0]]
# self.grp_curr = grp
# self.grpnum_curr = selected_ind[0]
return groupKeyNames
@staticmethod
def clear_xplist(self):
self.xpdata_frame.xplist.delete(0,END)
@staticmethod
def clear_channellist(self):
self.channeldata_frame.channellist.delete(0,END)
#@staticmethod
#def clear_plot(self):
#in progress
@staticmethod
def get_channel_data(self,channel_entry):
#selected_ind = self.channeldata_frame.selection_ind
#if len(selected_ind) != 1:
# tkMessageBox.showinfo(title='Error',
# message='Please select only one channel for plotting individual traces')
# return (dset,frames)
#
#channel_entry = self.channeldata_frame.channellist.get(selected_ind[0])
filename, filekeyname, groupkeyname = channel_entry.split(', ',2)
#print filename
#print filekeyname
#print groupkeyname
dset, t = load_hdf5(filename,filekeyname,groupkeyname)
dset_check = (dset != -1)
if (np.sum(dset_check) == 0):
dset = np.array([])
frames = np.array([])
t = np.array([])
dset_smooth = np.array([])
bouts = np.array([])
volumes = np.array([])
print('Problem with loading data - invalid data set')
return (dset, frames, t, dset_smooth, bouts, volumes)
frames = np.arange(0,dset.size)
dset = dset[dset_check]
frames = frames[np.squeeze(dset_check)]
t = t[dset_check]
new_frames = np.arange(0,np.max(frames)+1)
sp_raw = interpolate.InterpolatedUnivariateSpline(frames, dset)
sp_t = interpolate.InterpolatedUnivariateSpline(frames, t)
dset = sp_raw(new_frames)
t = sp_t(new_frames)
frames = new_frames
try:
dset_smooth, bouts, volumes = bout_analysis(dset,frames)
return (dset, frames, t, dset_smooth, bouts, volumes)
except NameError:
dset = np.array([])
frames = np.array([])
t = np.array([])
dset_smooth = np.array([])
bouts = np.array([])
volumes = np.array([])
print('Problem with loading data set--invalid name')
return (dset, frames, t, dset_smooth, bouts, volumes)
@staticmethod
def fetch_channels_for_batch(self):
selected_ind = self.channeldata_frame.selection_ind
for_batch = []
if len(selected_ind) < 1:
tkMessageBox.showinfo(title='Error',
message='Please select channels to move to batch')
return for_batch
for ind in selected_ind:
for_batch.append(self.channeldata_frame.channellist.get(ind))
return for_batch
#@staticmethod
#def get_batch_data(self):
#def main():
# root = Tk()
# root.geometry("300x280+300+300")
# app = Expresso(root)
# root.mainloop()
""" Run main loop """
if __name__ == '__main__':
Expresso().mainloop()
#main()
"""
root = Tk()
Expresso(root)
root.mainloop()
"""
