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@JohnWangDataAnalyst
JohnWangDataAnalyst committed Mar 10, 2016
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374 changes: 374 additions & 0 deletions GUI_wz_m.py
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#!/opt/python 3.3/bin/python3
# -*- coding: utf-8 -*-

import tkinter as tk
import os
import sys
import distutils.dir_util
import subprocess
import pprint
#import messagebox

WDprocessing_index = 0
Dataprocessing_index = 0
EnvironSet_index = 0
fields = ["Object ID", "T1 MRI Data Path", "dWMRI Data Path", "fMRI(Bold) Data Path", "Working Directory"]

curWD = os.getcwd()
EnvironVariablesDict = {"SGE_ROOT":"/usr/local/ge2011.11/",\
"FREESURFER_HOME":"/opt/freesurfer",\
"FSLDIR":"/opt/fsl",\
"scripts_path":"Scripts",\
"MRTrixDIR":"/opt/mrtrix2/bin",\
"MRTrix3DIR":"/home/jwang/local/MRtrix3bin",\
"FSLSUBALREADYRUN":"true"}

PathList = ["/home/jwang/codes/fsl/bin:/opt/afni:/usr/local/ge2011.11/bin/linux-x64:/sbin"]

SourceList = ["/opt/source/octave.sh", \
"/opt/source/afni_fsl.sh",\
"/opt/source/freesurfer.sh",\
"/opt/freesurfer/SetUpFreeSurfer.sh",\
"/opt/fsl/etc/fslconf/fsl.sh"]

fields_check =[ "T1 Prerocessing with FreeSurfer",\
"DWI Prerocessing with FreeSurfer", \
"DWI Prerocessing with MrTrix2", \
"fMRI Preprocessing", \
"Generate mask",\
"Tracking", \
"Compute SC matrix", \
"Aggregate SC matrix", \
"Convert to TVB format and clean up results"]



script_dict = {

"title": "#!/bin/bash\n\
echo \"*************************************************************\"\n \
echo \"*** TVB empirical data pipeline ***\" \n \
echo \"*************************************************************\"\n\
unset SGE_ROOT \n",

"T1 Prerocessing with FreeSurfer":"echo \"************ T1 preprocessing with FreeSurfer *******\"\n\
${scripts_path}/FreeSurfer_recon-all.sh \n ",


"DWI Prerocessing with FreeSurfer":"echo \"********** DWI preprocessing with FreeSurfer ********\"\n \
${rootPath}/${scripts_path}/FreeSurfer_dt-recon.sh\n",


"DWI Prerocessing with MrTrix2":"echo \"********** DWI preprocessing with MRtrix2 ***********\"\n\
${scripts_path}/MRtrix_prepro.sh\n",

"fMRI Preprocessing": "echo \"**************** fMRI preprocessing *****************\"\n \
${scripts_path}/fmriFC.sh\n",

"Generate mask": "echo \"****************** Generate mask ********************\"\n \
${scripts_path}/mask.sh\n",

"Tracking": "echo \"********************* Tracking **********************\"\n \
${scripts_path}/runTracking.sh\n",

"Compute SC matrix":"echo \"************** Compute SC matrix *******************\"\n\
${scripts_path}/computeSC.sh\n",

"Aggregate SC matrix":"echo \"************** Aggregate SC matrix *****************\"\n\
${scripts_path}/aggregateSC.sh\n",

"Convert to TVB format and clean up results":"echo \"**** Convert to TVB format and clean up results ****\"\n \
${scripts_path}/convert2TVB.sh\n"}

"""
files_prepare_scripts = ["#!/bin/bash", \
"cd /", \
"if [ ! -d "+entries["Working Directory"].get()+"]; then", \
"mkdir "+entries["Working Directory"].get(), \
"fi", \
"cd "+entries["Working Directory"].get() ]"""


"""
files_prepare_scripts = ["#!/bin/bash", \
"cd /", \
"if [ ! -d "+entries["Working Directory"].get()+"]; then", \
"mkdir "+entries["Working Directory"].get(), \
"fi", \
"cd "+entries["Working Directory"].get() ]"""

def fetch(entries):
for key in entries:

text = entries[key].get()
print('%s: "%s"' % (key, entries[key]))


def makeform(root, fields):
entries = {}
for field in fields:
row = tk.Frame(root)
lab = tk.Label(row, text = field, anchor = 'w')
ent = tk.Entry(row)
row.pack(side = tk.TOP, fill = tk.X, padx = 5, pady = 5)
lab.pack(side = tk.LEFT)
ent.pack(side = tk.RIGHT, expand = tk.YES, fill = tk.X)
entries[field] = ent
return entries


def makeform_check(root, fields):
checks = {}
for field in fields_check:
row = tk.Frame(root)
lab = tk.Label(row, text = "", anchor = 'w')
var = tk.IntVar()
ent = tk.Checkbutton(row,text = field, variable = var)
row.pack(side = tk.TOP, fill = tk.X, padx = 5, pady = 5)
lab.pack(side = tk.LEFT)
ent.pack(side = tk.LEFT)
checks[field] = var
return checks




def WDprocessing(entries):
global WDprocessing_index
if WDprocessing_index == 1:
ans_wd = input("changing working directory? y/n")
ans_sub = input("changing working subject? y/n")

Path_Check_Correct = True
# check if the inputs from users are empty
if WDprocessing_index == 0 or (WDprocessing_index == 1 and ans_wd.lower() in ["y", "yes"]):

for key in entries:
if entries[key].get() == " ":
print("please input"+" "+key)
Path_Check_Correct = False
elif key != "Object ID" and not os.path.exists(entries[key].get()):
if key == "Working Directory":
os.makedirs(entries[key].get())

else:
print("please input valid"+" "+ key)
Path_Check_Correct = False

if Path_Check_Correct and (WDprocessing_index == 0 or (WDprocessing_index == 1 and ans_wd.lower() in ["y", "yes"])):
#current_path = os.getcwd()
distutils.dir_util.copy_tree(curWD+"/TVB", entries["Working Directory"].get())

if Path_Check_Correct and (WDprocessing_index == 0 or \
(WDprocessing_index == 1 and (ans_sub.lower() in ["y", "yes"] or ans_wd.lower() in ["y", "yes"]))):

subjects_path = entries["Working Directory"].get()+"/subjects"
subjectid_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()
rawdata_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA"
dti_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA/DTI"
T1_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA/MPRAGE"
Bold_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA/BOLD-EPI"


if not os.path.exists(subjects_path):
os.makedirs(subjects_path)
if not os.path.exists(subjectid_path):
os.makedirs(subjectid_path)
if not os.path.exists(rawdata_path):
os.makedirs(rawdata_path)
if not os.path.exists(dti_path):
os.makedirs(dti_path)
if not os.path.exists(T1_path):
os.makedirs(T1_path)
if not os.path.exists(Bold_path):
os.makedirs(Bold_path)
WDprocessing_index = 1

def Dataprocessing(entries):
global Dataprocessing_index
dti_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA/DTI"
T1_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA/MPRAGE"
Bold_path = entries["Working Directory"].get()+"/subjects"+"/"+entries["Object ID"].get()+"/RAWDATA/BOLD-EPI"
if WDprocessing_index == 0:
ans_wd_re = input("need run working directory process? y/n")

if WDprocessing_index == 1 or (WDprocessing_index == 0 and ans_wd_re.lower() in ["n", "no"]):
if len(os.listdir(entries["dWMRI Data Path"].get())) > 0:
distutils.dir_util.copy_tree(entries["dWMRI Data Path"].get(), dti_path)
if len(os.listdir(entries["fMRI(Bold) Data Path"].get()))>0:
distutils.dir_util.copy_tree(entries["fMRI(Bold) Data Path"].get(), Bold_path)
if len(os.listdir(entries["T1 MRI Data Path"].get())) > 0:
distutils.dir_util.copy_tree(entries["T1 MRI Data Path"].get(), T1_path)
Dataprocessing_index = 1




def EnvironSet(entries):
global EnvironSet_index
if WDprocessing_index*Dataprocessing_index == 0:
ans_env_conf = input("are you sure you have done working directory and data process? y/n")
if WDprocessing_index == 1 & Dataprocessing_index == 1 or \
(WDprocessing_index*Dataprocessing_index == 0 and ans_env_conf.lower()in ["y", "yes"]):
#os.environ["PATH"] += os.pathsep + os.pathsep.join(PathList)
#os.environ["LD_LIBRARY_PATH"]+=os.pathsep+os.pathsep.join(["/opt/lib.exported"])
for key in EnvironVariablesDict:
os.environ[key] = EnvironVariablesDict[key]
os.environ["subID"] = entries["Object ID"].get()
os.environ["rootPath"] = entries["Working Directory"].get()

for source in SourceList:
command = ['bash', '-c', 'source '+source]
proc = subprocess.Popen(command, stdout=subprocess.PIPE)

for line in proc.stdout:
(key, _, value) = line.partition("=")
os.environ[key]=value

proc.communicate()

pprint.pprint(dict(os.environ))

EnvironSet_index = 1


def sh_file_generation(entries, checks):
open(entries["Working Directory"].get()+"/TVB_pipe.sh", "w")
f = open(entries["Working Directory"].get()+"/TVB_pipe.sh", "r+")
os.chmod(entries["Working Directory"].get()+"/TVB_pipe.sh", 0o755)
f.write(script_dict["title"])
for field in fields_check:
if checks[field].get() ==1:
f.write(script_dict[field])
f.close()
os.chdir(entries["Working Directory"].get())
qsub_call = "qsub -V -q bigmem_16.q -l h_vmem=16G -cwd %s"
#subprocess.call("unset SGE_ROOT", shell=True)
subprocess.call(qsub_call % "TVB_pipe.sh", shell=True)


"""
open("files_prepare_scripts", "a")
f = open("files_prepare_scripts", "r+")
for script in files_prepare_scripts:
f.write(script+"\n")
f.close()"""




# class Checkbar(tk.Frame):
# def __init__(self, parent=None, picks=[], side = tk.LEFT, anchor = tk.W):
# tk.Frame.__init__(self, parent)
# self.vars = []
# for pick in picks:
# var = tk.IntVar()
# self.row = tk.Frame(self)
# chk = tk.Checkbutton(self.row,text = pick, variable = var)
# chk.pack(side = side, anchor = anchor, expand = tk.YES)
# self.vars.append(var)

# def state(self):
# return map((lambda var: var.get()), self.vars)





def quit_process():
os.chdir(curWD)
top.quit



if __name__ == '__main__':
top = tk.Tk()
ents = makeform(top, fields)
#top.bind('<Return>', (lambda event, e=ents: fetch(e)))
row = tk.Frame(top)
title_check = tk.Label(row, text = "Choose the processes:")
row.pack(side = tk.TOP, fill = tk.X, padx = 5, pady = 5)
title_check.pack(side = tk.LEFT)
chks = makeform_check(top,fields_check)
b1 = tk.Button(top,text = 'Quit', command = top.quit)
b1.pack(side =tk.LEFT, padx = 5, pady = 5)
b2 = tk.Button(top,text = 'Run Working Directory Process', command = (lambda e=ents: WDprocessing(e)))
b2.pack(side =tk.LEFT, padx = 5, pady = 5)

b4 = tk.Button(top,text = 'Run Data Copy Process', command = (lambda e=ents: Dataprocessing(e)))
b4.pack(side =tk.LEFT, padx = 5, pady = 5)

b3 = tk.Button(top,text = 'Environ Set', command = (lambda e=ents: EnvironSet(e)))
b3.pack(side =tk.LEFT, padx = 5, pady = 5)

b5 = tk.Button(top,text = 'Sh Script', command = (lambda e1=ents, e2=chks: sh_file_generation(e1,e2)))
b5.pack(side =tk.LEFT, padx = 5, pady = 5)


top.mainloop()


# CheckVar1 = tk.IntVar()
# CheckVar2 = tk.IntVar()
# CheckVar3 = tk.IntVar()
# CheckVar4 = tk.IntVar()
# CheckVar5 = tk.IntVar()
# CheckVar6 = tk.IntVar()
# CheckVar7 = tk.IntVar()
# CheckVar8 = tk.IntVar()
# CheckVar9 = tk.IntVar()

# tk.Label(top, text = "Object ID").grid(row = 0)
# tk.Label(top, text = "T1 MRI Data Path").grid(row = 1)
# tk.Label(top, text = "dWMRI Data Path").grid(row = 2)
# tk.Label(top, text = "fMRI(Bolt) Data Path").grid(row = 3)

# tk.Label(top, text = "Working Directory").grid(row = 4)





# e1 = tk.Entry(top)
# e2 = tk.Entry(top)
# e3 = tk.Entry(top)
# e4 = tk.Entry(top)
# e5 = tk.Entry(top)

# e1.grid(row = 0, column = 1)
# e2.grid(row = 1, column = 1)
# e3.grid(row = 2, column = 1)
# e4.grid(row = 3, column = 1)
# e5.grid(row = 4, column = 1)

# tk.Label(top, text = "Choose the processes:").grid(row = 6, sticky = tk.W)

# k=7;

# ObjectId = e1.get()
# T1Path = e2.get()
# DtiPath = e3.get()
# BoltPath = e4.get（）
# WorkPath = e5.get ()


# tk.Checkbutton(top, text = "T1 Prerocessing with FreeSurfer", variable = CheckVar1).grid(row = 0+k, sticky = tk.W)

# tk.Checkbutton(top, text = "DWI Prerocessing with FreeSurfer", variable = CheckVar2).grid(row = 1+k, sticky = tk.W)

# tk.Checkbutton(top, text = "DWI Prerocessing with MrTrix2", variable = CheckVar3).grid(row = 2+k, sticky = tk.W)
# tk.Checkbutton(top, text = "fMRI Preprocessing ", variable = CheckVar4).grid(row = 3+k, sticky = tk.W)
# tk.Checkbutton(top, text = "Generate mask ", variable = CheckVar5).grid(row = 4+k, sticky = tk.W)
# tk.Checkbutton(top, text = "Tracking ", variable = CheckVar6).grid(row = 5+k, sticky = tk.W)
# tk.Checkbutton(top, text = "Compute SC matrix ", variable = CheckVar7).grid(row = 6+k, sticky = tk.W)
# tk.Checkbutton(top, text = "Aggregate SC matrix", variable = CheckVar8).grid(row = 7+k, sticky = tk.W)
# tk.Checkbutton(top, text = "Convert to TVB format and clean up results ", variable = CheckVar9).grid(row = 8+k, sticky = tk.W)






#top.mainloop()
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