retinotopic-maps/code/easyret_gui

#!/usr/bin/env python

import os
import wx
import wx.lib.filebrowsebutton as libtest
import wx.lib.agw.floatspin as FS
from os.path import join as opj

MAIN_WINDOW_DEFAULT_SIZE = (650,700)

class Frame(wx.Frame):
    
    def __init__(self, parent, id, title):
        style=wx.DEFAULT_FRAME_STYLE ^ (wx.RESIZE_BORDER) # XOR to remove the resizeable border        
        wx.Frame.__init__(self, parent, id, title=title, size=MAIN_WINDOW_DEFAULT_SIZE, style=style)
        self.Center() # open in the centre of the screen
        self.panel = wx.Panel(self)
        self.subject_id_label = wx.StaticText(self.panel, pos=(50, 45), size=(140,-1), label="Enter Subject ID:")
        self.subject_id = wx.TextCtrl(self.panel, pos=(200, 40), size=(60,-1))
        self.contract = libtest.FileBrowseButton(self.panel, pos=(50, 80), initialValue='Enter path to Contracting volume', toolTip='Enter/Browse path to Contracting volume', fileMask='*.nii.gz', size=(500,30), labelWidth=100)
        self.expand = libtest.FileBrowseButton(self.panel, pos=(50, 120), initialValue='Enter path to Expanding volume', toolTip='Enter/Browse path to Expanding volume', fileMask='*.nii.gz', size=(500,30), labelWidth=100)
        self.clock = libtest.FileBrowseButton(self.panel, pos=(50, 160), initialValue='Enter path to Clockwise volume', toolTip='Enter/Browse path to Clockwise volume', fileMask='*.nii.gz', size=(500,30), labelWidth=100)
        self.counter = libtest.FileBrowseButton(self.panel, labelWidth=10, pos=(50, 200),  initialValue='Enter path to Counter clockwise volume', toolTip='Enter/Browse path to Counter clockwise volume', fileMask='*.nii.gz', size=(500,30))
        self.mask = libtest.FileBrowseButton(self.panel, labelWidth=10, pos=(50, 240),  initialValue='Enter path to mask', toolTip='Enter/Browse path to brain mask of the retmapping volumes', fileMask='*.nii.gz', size=(350,30))
        self.FWHM_label = wx.StaticText(self.panel, pos=(50, 285), size=(250,-1), label="Spatial Smoothing FWHM (mm):")
        self.FWHM = FS.FloatSpin(self.panel, value='4', pos=(300, 280), size=(45, -1), min_val=0, max_val=10, increment=1)
        self.FWHM.SetDigits(0) 
        self.output_folder_label = wx.StaticText(self.panel, pos=(50, 325), size=(250,-1), label="Select output folder:")
        self.output = wx.DirPickerCtrl(self.panel, pos=(250, 320))
        self.postprocessingshift = wx.CheckBox(self.panel, -1, 'Post Processing Shift', pos=(50, 385))
        self.Bind(wx.EVT_CHECKBOX, self.OnPostProcessShift, self.postprocessingshift)
        self.surfacemaps = wx.CheckBox(self.panel, -1, 'Surface Maps', pos=(50, 415))
        self.Bind(wx.EVT_CHECKBOX, self.OnSurfaceMaps, self.surfacemaps)
        self.debugmode = wx.CheckBox(self.panel, -1, 'Debug Mode', pos=(50, 580))      
        self.process_button = wx.Button(self.panel, pos=(470, 580), size=(80, 25), label="EasyRet")
        self.Bind(wx.EVT_BUTTON, self.OnProcess, self.process_button)
        self.CreateMenuBar()
        self.CreateStatusBar()
    
    
    
        
    def CreateMenuBar(self):

        menuBar = wx.MenuBar()
        # Tell our Frame about this MenuBar
        self.SetMenuBar(menuBar)
        menuFile = wx.Menu()

        # NOTE on wx ids - they're used everywhere, we don't care about them
        # Used to handle events and other things
        # An id can be -1 or wx.ID_ANY, wx.NewId(), your own id
        # Get the id using object.GetId()
        
        # add a Help menu with an About item
        menuHelp = wx.Menu()
        menuBar.Append(menuHelp, '&Help')
        helpMenuItem = menuHelp.Append(-1, '&About', 'About EasyRet')
        self.Bind(wx.EVT_MENU, self.OnAbout, helpMenuItem)        
        
        # create a menu item for Exit and bind it to the OnExit function       
        exitMenuItem = menuHelp.Append(-1, '&Exit', 'Exit EasyRet')        
        self.Bind(wx.EVT_MENU, self.OnExit, exitMenuItem)
        
    def OnAbout(self,e):
        # A message dialog box with an OK button. wx.OK is a standard ID in wxWidgets.
        
        help_text='I am working on it\n please bear with me'
        dlg = wx.MessageDialog( self, help_text, "About EasyRet", wx.OK)
        dlg.ShowModal() # Show it
        dlg.Destroy() # finally destroy it when finished.
        
    def OnPostProcessShift(self, event):   
        if self.postprocessingshift.GetValue(): 
            self.con_shift_text = wx.StaticText(self.panel, pos=(250, 360), size=(200,-1), label="Con")        
            self.con_shift = FS.FloatSpin(self.panel, value='22.5', pos=(250, 380), size=(70, -1), min_val=-360, max_val=360, increment=0.25)
            self.con_shift.SetDigits(2)
            self.exp_shift_text = wx.StaticText(self.panel, pos=(320, 360), size=(200,-1), label="Exp")        
            self.exp_shift = FS.FloatSpin(self.panel, value='22.5', pos=(320, 380), size=(70, -1), min_val=-360, max_val=360, increment=0.25)
            self.exp_shift.SetDigits(2)
            self.clw_shift_text = wx.StaticText(self.panel, pos=(390, 360), size=(200,-1), label="Clw")        
            self.clw_shift = FS.FloatSpin(self.panel, value='22.5', pos=(390, 380), size=(70, -1), min_val=-360, max_val=360, increment=0.25)
            self.clw_shift.SetDigits(2)
            self.ccw_shift_text = wx.StaticText(self.panel, pos=(460, 360), size=(200,-1), label="Ccw")        
            self.ccw_shift = FS.FloatSpin(self.panel, value='22.5', pos=(460, 380), size=(70, -1), min_val=-360, max_val=360, increment=0.25)
            self.ccw_shift.SetDigits(2)
         
        else:
            self.con_shift.Destroy()
            self.con_shift_text.Destroy()
            self.exp_shift.Destroy()
            self.exp_shift_text.Destroy()
            self.clw_shift.Destroy()
            self.clw_shift_text.Destroy()
            self.ccw_shift.Destroy()
            self.ccw_shift_text.Destroy()
            
    def OnSurfaceMaps(self, event):   
        if self.surfacemaps.GetValue(): 
            self.anatomy = libtest.FileBrowseButton(self.panel, labelWidth=10, pos=(150, 450),  initialValue='Enter path to anatomy', toolTip='Enter/Browse path to the anatomical volume that was used for Freesurfer recon-all analysis', fileMask='*.nii.gz', size=(400,30))
            self.transformation = libtest.FileBrowseButton(self.panel, labelWidth=10, pos=(150, 490),  initialValue='Enter transformation matrix', toolTip='Enter/Browse path to the fsl type transformation file for co-registering BOLD retmapping volumes to anatomical volumes', fileMask='*.mat', size=(400,30))
            self.ROI = libtest.FileBrowseButton(self.panel, labelWidth=10, pos=(150, 530),  initialValue='Enter path to ROI mask', fileMask='*.nii.gz',  toolTip='Enter/Browse path to the ROI mask if you want your surface maps to be restricted to Occipital lobe only', size=(400,30))

        else:
            self.anatomy.Destroy()
            self.transformation.Destroy()
            self.ROI.Destroy()
            
    def OnProcess(self, event):
        
        from subprocess import PIPE, CalledProcessError, check_call, Popen
        bash_processing_script=opj(os.path.dirname(os.path.realpath(__file__)), 'process_retmap')
        subject_id = str(self.subject_id.GetValue())
        contract_volume = str(self.contract.GetValue())
        expand_volume = str(self.expand.GetValue())
        clock_volume = str(self.clock.GetValue())
        counter_volume = str(self.counter.GetValue())
        mask = str(self.mask.GetValue())
        FWHM = str(self.FWHM.GetValue())
        output_folder = str(self.output.GetPath())
        contract_shift=expand_shift=clock_shift=counter_shift=anatomy_volume=transformation_matrix=ROI=''
        post_processing_shift=str(self.postprocessingshift.GetValue())
        if self.postprocessingshift.GetValue():
            contract_shift=str(self.con_shift.GetValue())
            expand_shift=str(self.exp_shift.GetValue())
            clock_shift=str(self.clw_shift.GetValue())
            counter_shift=str(self.ccw_shift.GetValue())
        
        surface_maps=str(self.surfacemaps.GetValue())  
        if self.surfacemaps.GetValue():
            anatomy_volume=str(self.anatomy.GetValue())
            transformation_matrix=str(self.transformation.GetValue())
            ROI=str(self.ROI.GetValue())
        debug_mode=str(self.debugmode.GetValue())
        error_log=opj(output_folder, subject_id+'_error.log')
        #scripts/pyretmap/code/processing_pipeline/process_retmap sub-16 /home/data/psyinf/forrest_gump/anondata/sub016/BOLD/task005_run001/bold_bold3Tp2_to_subjbold3Tp2.nii.gz /home/data/psyinf/forrest_gump/anondata/sub016/BOLD/task005_run003/bold_bold3Tp2_to_subjbold3Tp2.nii.gz /home/data/psyinf/forrest_gump/anondata/sub016/BOLD/task005_run004/bold_bold3Tp2_to_subjbold3Tp2.nii.gz /home/data/psyinf/forrest_gump/anondata/sub016/BOLD/task005_run002/bold_bold3Tp2_to_subjbold3Tp2.nii.gz /home/data/psyinf/forrest_gump/anondata/sub016/templates/bold3Tp2/brain_mask.nii.gz /home/data/exppsy/spark/Study_Forrest checked -337.5 0.0 101.25 -281.25 checked /home/data/psyinf/forrest_gump/anondata/sub016/templates/t1w/head.nii.gz /home/data/psyinf/forrest_gump/anondata/sub016/templates/bold3Tp2/in_t1w/xfm_6dof.mat ''

        arguments_list=[bash_processing_script, subject_id, contract_volume, expand_volume, clock_volume, counter_volume, mask, FWHM, output_folder, post_processing_shift, contract_shift, expand_shift, clock_shift, counter_shift, surface_maps, anatomy_volume, transformation_matrix, ROI, debug_mode]
        print '\n\n'
        print ' '.join(arguments_list)
        print '\n\n'
        print 'Processing Retmap'

        with open(error_log, "w") as f:
            try:
                check_call(arguments_list, stderr=f)
            except CalledProcessError as e:
                print(e)
                exit(1)
        print 'Done'
        
    def OnExit(self, event):
        "Close the application by Destroying the object"
        # TRY add in your own print call here
        self.Destroy() # SHOW HELP SIDEBAR
        
    
class App(wx.App):
    
    def OnInit(self):
        self.frame = Frame(parent=None, id=-1, title='EasyRet')
        self.frame.Show()
        self.SetTopWindow(self.frame)
        return True
    
if __name__ == "__main__":       
    # make an App object, set stdout to the console so we can see errors
    app = App(redirect=False)
        
    app.MainLoop()