abfconvert.py

#!/usr/bin/env python3
# coding: utf-8
# Version 1.2

import os
import sys
import numpy as np
import pandas as pd
import tkinter as tk
from neo.io import AxonIO
from tkinter import filedialog, messagebox, DISABLED, NORMAL


class getparams(tk.Tk):

    def __init__(self):
        tk.Tk.__init__(self)
        self.eval('tk::PlaceWindow %s center' % self.winfo_pathname(self.winfo_id()))
        self.wm_title('Export Parameters')

        self.button = tk.Button(self, text='Initialize', command=self.on_button)

        self.lab0 = tk.Label(self,text='Format:')
        self.form = tk.StringVar()
        self.form.set('HDF5')
        self.form0 = tk.OptionMenu(self, self.form, 'HDF5', 'CSV', 'TSV',command=self.format_sel)

        self.lab1 = tk.Label(self,text='Compression:')
        self.comp = tk.IntVar()
        self.comp.set(0)
        self.comp0 = tk.Radiobutton(self, text='None', variable=self.comp, value=0, state=DISABLED)
        self.comp1 = tk.Radiobutton(self, text='GZIP', variable=self.comp, value=1, state=DISABLED)
        self.comp0.select()
 
        self.lab2 = tk.Label(self,text='Decimal Separator:')
        self.sep = tk.Entry(self,width=5)
        self.sep.insert(0,'.')
        self.sep.config(state=DISABLED) #Can't insert value while disabled

        self.dvar = tk.StringVar()
        self.lab3 = tk.Label(self,text='Decimals:')
        self.decims = tk.Spinbox(self, values=(0,1,2,3,4,5,6,'All'), textvariable=self.dvar, width=4, state=DISABLED)
        self.decims.insert('end','All')
        self.dvar.set(6)

        self.lab0.grid(row=0,column=0, sticky='W')
        self.form0.grid(row=0,column=1,columnspan=2)

        self.lab1.grid(row=1,column=0, sticky='W')
        self.comp0.grid(row=1,column=1)
        self.comp1.grid(row=1,column=2)

        self.lab2.grid(row=2,column=0, sticky='W')
        self.sep.grid(row=2,column=1,columnspan=2)

        self.lab3.grid(row=3,column=0, sticky='W')
        self.decims.grid(row=3,column=1,columnspan=2)

        self.button.grid(row=4,column=0, columnspan=3)

        self.lift()

    def on_button(self):
        global decims, form, comp, dsep
        decims = self.decims.get()
        form = self.form.get().lower()
        comp = self.comp.get()
        dsep = self.sep.get()
        if form=='csv' and dsep==',':
            messagebox.showwarning('Warning', 'Using comma as a separator in a Comma Separated Values file is a dumb thing to do.')
        else:
            self.destroy()

    def format_sel(self,form):        
        if form == 'HDF5':
            self.comp0.config(state=DISABLED)
            self.comp1.config(state=DISABLED)
            self.decims.config(state=DISABLED)
            self.sep.config(state=DISABLED)
        else:
            self.comp0.config(state=NORMAL)
            self.comp1.config(state=NORMAL)
            self.decims.config(state=NORMAL)
            self.sep.config(state=NORMAL)

root = tk.Tk()
root.withdraw()
file_paths=filedialog.askopenfilenames(title='Files to Convert',
           filetypes =(('ABF Files', '*.abf'),('All Files','*.*')))
root.destroy()

if file_paths:
    file_names=['.'.join(file_path.split('.')[:-1]) for file_path in file_paths]
else:
    sys.exit()

getparams().mainloop()

try:
    if form == 'hdf5': form = 'h5'
    sep = '\t' if form=='tsv' else ','
    comp = None if comp==0 else 'gzip'
except NameError: #window closed without a selection
    sys.exit()

for f in range(len(file_paths)):
    filename = file_names[f].split('/')[-1]
    print('Reading file {}/{}: {}'.format(f+1, len(file_paths), filename) )
    try:
        fileout = file_names[f] + '.' + form
        print('Extracting data.')
        reader = AxonIO(filename = file_paths[f])
        blks = reader.read(cascade=True,lazy=False)
        seg = blks[0].segments
        f=np.transpose(np.array([seg[0].analogsignals])[0])[0]

        print('Writing...')
        df=pd.DataFrame(f)

        if form == 'h5':
            df.to_hdf(fileout,'data')
        else:
            if decims=='All':
                df.to_csv(fileout,sep=sep,decimal=dsep,compression=comp)
            else:
                dformat = '%.'+decims+'f'
                df.to_csv(fileout,float_format=dformat,sep=sep,decimal=dsep,compression=comp)
            if comp == 'gzip':
                os.rename(fileout,fileout + '.gzip')
        print('File {} written sucessfully.'.format(filename + '.' + form))
    except:
        print('Couldn\'t process file {} succesfully.'.format(file_names[f]) )

fini = tk.Tk()
fini.withdraw()
messagebox.showinfo('ABF Convert', 'Finished Converting files.')