170 lines
10 KiB
Python
Executable file
170 lines
10 KiB
Python
Executable file
#!/usr/bin/env python
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import os
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import wx
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import wx.lib.filebrowsebutton as libtest
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import wx.lib.agw.floatspin as FS
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from os.path import join as opj
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MAIN_WINDOW_DEFAULT_SIZE = (650,700)
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class Frame(wx.Frame):
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def __init__(self, parent, id, title):
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style=wx.DEFAULT_FRAME_STYLE ^ (wx.RESIZE_BORDER) # XOR to remove the resizeable border
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wx.Frame.__init__(self, parent, id, title=title, size=MAIN_WINDOW_DEFAULT_SIZE, style=style)
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self.Center() # open in the centre of the screen
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self.panel = wx.Panel(self)
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self.subject_id_label = wx.StaticText(self.panel, pos=(50, 45), size=(140,-1), label="Enter Subject ID:")
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self.subject_id = wx.TextCtrl(self.panel, pos=(200, 40), size=(60,-1))
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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)
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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)
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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)
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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))
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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))
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self.FWHM_label = wx.StaticText(self.panel, pos=(50, 285), size=(250,-1), label="Spatial Smoothing FWHM (mm):")
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self.FWHM = FS.FloatSpin(self.panel, value='4', pos=(300, 280), size=(45, -1), min_val=0, max_val=10, increment=1)
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self.FWHM.SetDigits(0)
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self.output_folder_label = wx.StaticText(self.panel, pos=(50, 325), size=(250,-1), label="Select output folder:")
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self.output = wx.DirPickerCtrl(self.panel, pos=(250, 320))
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self.postprocessingshift = wx.CheckBox(self.panel, -1, 'Post Processing Shift', pos=(50, 385))
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self.Bind(wx.EVT_CHECKBOX, self.OnPostProcessShift, self.postprocessingshift)
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self.surfacemaps = wx.CheckBox(self.panel, -1, 'Surface Maps', pos=(50, 415))
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self.Bind(wx.EVT_CHECKBOX, self.OnSurfaceMaps, self.surfacemaps)
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self.debugmode = wx.CheckBox(self.panel, -1, 'Debug Mode', pos=(50, 580))
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self.process_button = wx.Button(self.panel, pos=(470, 580), size=(80, 25), label="EasyRet")
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self.Bind(wx.EVT_BUTTON, self.OnProcess, self.process_button)
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self.CreateMenuBar()
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self.CreateStatusBar()
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def CreateMenuBar(self):
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menuBar = wx.MenuBar()
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# Tell our Frame about this MenuBar
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self.SetMenuBar(menuBar)
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menuFile = wx.Menu()
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# NOTE on wx ids - they're used everywhere, we don't care about them
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# Used to handle events and other things
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# An id can be -1 or wx.ID_ANY, wx.NewId(), your own id
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# Get the id using object.GetId()
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# add a Help menu with an About item
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menuHelp = wx.Menu()
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menuBar.Append(menuHelp, '&Help')
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helpMenuItem = menuHelp.Append(-1, '&About', 'About EasyRet')
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self.Bind(wx.EVT_MENU, self.OnAbout, helpMenuItem)
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# create a menu item for Exit and bind it to the OnExit function
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exitMenuItem = menuHelp.Append(-1, '&Exit', 'Exit EasyRet')
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self.Bind(wx.EVT_MENU, self.OnExit, exitMenuItem)
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def OnAbout(self,e):
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# A message dialog box with an OK button. wx.OK is a standard ID in wxWidgets.
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help_text='I am working on it\n please bear with me'
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dlg = wx.MessageDialog( self, help_text, "About EasyRet", wx.OK)
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dlg.ShowModal() # Show it
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dlg.Destroy() # finally destroy it when finished.
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def OnPostProcessShift(self, event):
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if self.postprocessingshift.GetValue():
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self.con_shift_text = wx.StaticText(self.panel, pos=(250, 360), size=(200,-1), label="Con")
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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)
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self.con_shift.SetDigits(2)
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self.exp_shift_text = wx.StaticText(self.panel, pos=(320, 360), size=(200,-1), label="Exp")
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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)
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self.exp_shift.SetDigits(2)
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self.clw_shift_text = wx.StaticText(self.panel, pos=(390, 360), size=(200,-1), label="Clw")
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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)
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self.clw_shift.SetDigits(2)
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self.ccw_shift_text = wx.StaticText(self.panel, pos=(460, 360), size=(200,-1), label="Ccw")
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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)
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self.ccw_shift.SetDigits(2)
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else:
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self.con_shift.Destroy()
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self.con_shift_text.Destroy()
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self.exp_shift.Destroy()
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self.exp_shift_text.Destroy()
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self.clw_shift.Destroy()
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self.clw_shift_text.Destroy()
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self.ccw_shift.Destroy()
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self.ccw_shift_text.Destroy()
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def OnSurfaceMaps(self, event):
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if self.surfacemaps.GetValue():
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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))
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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))
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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))
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else:
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self.anatomy.Destroy()
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self.transformation.Destroy()
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self.ROI.Destroy()
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def OnProcess(self, event):
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from subprocess import PIPE, CalledProcessError, check_call, Popen
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bash_processing_script=opj(os.path.dirname(os.path.realpath(__file__)), 'process_retmap')
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subject_id = str(self.subject_id.GetValue())
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contract_volume = str(self.contract.GetValue())
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expand_volume = str(self.expand.GetValue())
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clock_volume = str(self.clock.GetValue())
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counter_volume = str(self.counter.GetValue())
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mask = str(self.mask.GetValue())
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FWHM = str(self.FWHM.GetValue())
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output_folder = str(self.output.GetPath())
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contract_shift=expand_shift=clock_shift=counter_shift=anatomy_volume=transformation_matrix=ROI=''
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post_processing_shift=str(self.postprocessingshift.GetValue())
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if self.postprocessingshift.GetValue():
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contract_shift=str(self.con_shift.GetValue())
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expand_shift=str(self.exp_shift.GetValue())
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clock_shift=str(self.clw_shift.GetValue())
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counter_shift=str(self.ccw_shift.GetValue())
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surface_maps=str(self.surfacemaps.GetValue())
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if self.surfacemaps.GetValue():
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anatomy_volume=str(self.anatomy.GetValue())
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transformation_matrix=str(self.transformation.GetValue())
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ROI=str(self.ROI.GetValue())
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debug_mode=str(self.debugmode.GetValue())
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error_log=opj(output_folder, subject_id+'_error.log')
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#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 ''
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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]
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print '\n\n'
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print ' '.join(arguments_list)
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print '\n\n'
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print 'Processing Retmap'
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with open(error_log, "w") as f:
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try:
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check_call(arguments_list, stderr=f)
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except CalledProcessError as e:
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print(e)
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exit(1)
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print 'Done'
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def OnExit(self, event):
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"Close the application by Destroying the object"
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# TRY add in your own print call here
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self.Destroy() # SHOW HELP SIDEBAR
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class App(wx.App):
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def OnInit(self):
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self.frame = Frame(parent=None, id=-1, title='EasyRet')
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self.frame.Show()
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self.SetTopWindow(self.frame)
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return True
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if __name__ == "__main__":
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# make an App object, set stdout to the console so we can see errors
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app = App(redirect=False)
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app.MainLoop()
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