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ivim_toolbox.py
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#!/usr/bin/env pythonw
"""Graphical User Interface for ivim-toolbox.
Created on Tue Jul 2 17:45:43 2019
@author: slevyrosetti
"""
import wx
import ivim_fitting
import ivim_simu_compute_required_snr
class FrameFitData(wx.Frame):
def __init__(self, parent, id, title):
wx.Frame.__init__(self, parent, id=id, title=title, size=(500, 500))
fgrid = wx.FlexGridSizer(6, 2, 5, 10)
# load path buttons
self.paths = ["None", "None", "None", "None"]
self.LoadpathDWIbutton = wx.Button(self, -1, "4D diffusion-weighted images (nifti file)")
self.LoadpathDWIbutton.Bind(wx.EVT_BUTTON, lambda evt: Loadpath(self, evt, 0, itemType="file"))
self.LoadpathBvalbutton = wx.Button(self, -1, "B-value file (text file)")
self.LoadpathBvalbutton.Bind(wx.EVT_BUTTON, lambda evt: Loadpath(self, evt, 1, itemType="file"))
self.LoadpathMaskbutton = wx.Button(self, -1, "Binary mask defining voxels to be fitted (nifti file)")
self.LoadpathMaskbutton.Bind(wx.EVT_BUTTON, lambda evt: Loadpath(self, evt, 2, itemType="file"))
self.p0 = wx.TextCtrl(self, value=self.paths[0], style=wx.TE_READONLY | wx.TE_CENTER)
self.p1 = wx.TextCtrl(self, value=self.paths[1], style=wx.TE_READONLY | wx.TE_CENTER)
self.p2 = wx.TextCtrl(self, value=self.paths[2], style=wx.TE_READONLY | wx.TE_CENTER)
# model list
ModelChoiceName = wx.StaticText(self, label='Fit approach', style=wx.ALIGN_LEFT)
self.ModelChoice = wx.Choice(self, choices=['two-step', 'one-step'])
self.ModelChoice.SetSelection(1)
# output folder
self.LoadpathOFolderbutton = wx.Button(self, -1, "Output folder (need to exist)")
self.LoadpathOFolderbutton.Bind(wx.EVT_BUTTON, lambda evt: Loadpath(self, evt, 3, itemType="dir"))
self.p3 = wx.TextCtrl(self, value=self.paths[3], style=wx.TE_READONLY | wx.TE_CENTER)
# multi-threading checkbox
self.MTCheckBox = wx.CheckBox(self, label='Multi-threading')
self.MTCheckBox.SetValue(True)
# Run button
self.RunButton = wx.Button(self, -1, "Run fit")
self.RunButton.Bind(wx.EVT_BUTTON, self.ClickedOnRun)
# adapt path display to window size (DO NOT WORK APPARENTLY)
fgrid.AddGrowableCol(1, 1)
fgrid.AddMany([(self.LoadpathDWIbutton), (self.p0, wx.EXPAND), (self.LoadpathBvalbutton), (self.p1, wx.EXPAND), (self.LoadpathMaskbutton), (self.p2, wx.EXPAND), (ModelChoiceName),
(self.ModelChoice), (self.LoadpathOFolderbutton), (self.p3, wx.EXPAND), (self.MTCheckBox), (self.RunButton)])
self.SetSizer(fgrid)
self.Fit()
self.Centre()
def ClickedOnRun(self, event):
print("\n\n\n======= PARAMETERS =======")
print("4D diffusion-weighted file: "+self.paths[0])
print("B-value file: "+self.paths[1])
print("Mask file: "+self.paths[2])
model_chosen_index = self.ModelChoice.GetSelection()
if model_chosen_index == -1:
return
model_chosen = self.ModelChoice.GetString(model_chosen_index)
print("Fit approach: "+model_chosen)
print("Output folder: "+self.paths[3])
MTcheckbox_value = self.MTCheckBox.GetValue()
print("Multi-threading: "+str(MTcheckbox_value))
print("==========================\n\n")
# run fit
# ivim_fitting.main(dwi_fname=self.paths[0], bval_fname=self.paths[1], mask_fname=self.paths[2], model=model_chosen, ofolder=self.paths[3], multithreading=MTcheckbox_value)
class FrameRequiredSNR(wx.Frame):
def __init__(self, parent, title):
super(FrameRequiredSNR, self).__init__(parent, title=title, size=(500, 500))
# fgrid = wx.FlexGridSizer(7, 2, 5, 10)
panel = wx.Panel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
# Title
hbox1 = wx.BoxSizer(wx.HORIZONTAL)
l1 = wx.StaticText(panel, -1, label="Compute required SNR")
hbox1.Add(l1, 1, wx.EXPAND | wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 5)
vbox.Add(hbox1)
# Fit approach
hbox2 = wx.BoxSizer(wx.HORIZONTAL)
# static text
l2 = wx.StaticText(panel, -1, "Fit approach")
hbox2.Add(l2, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# drop down menu
self.ApproachChoice = wx.Choice(panel, choices=['two-step', 'one-step'])
self.ApproachChoice.SetSelection(1)
hbox2.Add(self.ApproachChoice, 1, wx.EXPAND|wx.ALIGN_RIGHT|wx.ALL, 5)
vbox.Add(hbox2)
# output folder
hbox3 = wx.BoxSizer(wx.HORIZONTAL)
# static text
l3 = wx.StaticText(panel, -1, "Output folder (need to exist)")
hbox3.Add(l3, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# load button
self.LoadpathOFolderbutton = wx.Button(panel, -1, "Load")
self.LoadpathOFolderbutton.Bind(wx.EVT_BUTTON, lambda evt: Loadpath(panel, evt, 0, itemType="dir"))
hbox3.Add(self.LoadpathOFolderbutton, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# text showing path
self.paths = ["None"]
self.p0 = wx.TextCtrl(panel, value=self.paths[0], style=wx.TE_READONLY | wx.TE_CENTER)
hbox3.Add(self.p0, 1, wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL, 5)
vbox.Add(hbox3)
# B-value distribution
hbox4 = wx.BoxSizer(wx.HORIZONTAL)
# static text
l4 = wx.StaticText(panel, -1, "B-value distribution (e.g. 0,10,50,500,800)")
hbox4.Add(l4, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# field to write
self.bval_field = wx.TextCtrl(panel)
hbox4.Add(self.bval_field, 1, wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL, 5)
vbox.Add(hbox4)
# Fivim range
hbox5 = wx.BoxSizer(wx.HORIZONTAL)
# static text
l5 = wx.StaticText(panel, -1, "F values (e.g. 0.1,0.2,0.3 or 0.1:0.01:0.3)")
hbox5.Add(l5, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# field to write
self.F_field = wx.TextCtrl(panel)
hbox5.Add(self.F_field, 1, wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL, 5)
vbox.Add(hbox5)
# Dstar range
hbox6 = wx.BoxSizer(wx.HORIZONTAL)
# static text
l6 = wx.StaticText(panel, -1, "D* values (e.g. 11e-3,3e-3,35e-3 or 3e-3:1e-3:30e-3)")
hbox6.Add(l6, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# field to write
self.Dstar_field = wx.TextCtrl(panel)
hbox6.Add(self.Dstar_field, 1, wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL, 5)
vbox.Add(hbox6)
# D range
hbox7 = wx.BoxSizer(wx.HORIZONTAL)
# static text
l7 = wx.StaticText(panel, -1, "D values (e.g. 0.3e-3,0.4e-3,0.5e-3 or 0.3e-3:0.1e-3:10e-3)")
hbox7.Add(l7, 1, wx.EXPAND | wx.ALIGN_LEFT | wx.ALL, 5)
# field to write
self.D_field = wx.TextCtrl(panel)
hbox7.Add(self.D_field, 1, wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL, 5)
vbox.Add(hbox7)
# Button run calculation
hbox8 = wx.BoxSizer(wx.HORIZONTAL)
# static text
self.RunButton = wx.Button(self, -1, "Run calculation")
hbox8.Add(self.RunButton, 1, wx.EXPAND | wx.ALIGN_CENTER | wx.ALL, 5)
vbox.Add(hbox8)
self.RunButton.Bind(wx.EVT_BUTTON, self.ClickedOnRun)
panel.SetSizer(vbox)
panel.SetSize((500, 300))
self.Centre()
self.Fit()
# def OnKeyTyped(self, event):
# print event.GetString()
#
# def OnEnterPressed(self, event):
# print "Enter pressed"
#
# def OnMaxLen(self, event):
# print "Maximum length reached"
#
def ClickedOnRun(self, event):
# retrieve selected fit approach from drop down menu
selected_approach_idx = self.ApproachChoice.GetSelection()
if selected_approach_idx == -1:
return
selected_approach = self.ApproachChoice.GetString(selected_approach_idx)
print("\n\n\n======= PARAMETERS =======")
print("Fit approach: "+selected_approach)
print("Output folder: "+self.paths[0])
print("B-value distribution: "+self.bval_field.GetValue())
print("F true values: "+self.F_field.GetValue())
print("D* true values: "+self.Dstar_field.GetValue())
print("D true values: "+self.D_field.GetValue())
print("==========================\n\n")
# run SNR calculation
# ivim_simu_compute_required_snr.main(model=selected_approach, ofolder=self.paths[0], bvals=self.bval_field.GetValue(), condition='FDstar', snr_init=1500., F_range=self.F_field.GetValue(), Dstar_range=self.Dstar_field.GetValue(), D_range=self.D_field.GetValue())
def Loadpath(frame, event, index, itemType="file"):
if itemType == "file":
with wx.FileDialog(frame, "Export Result ", style=wx.FD_OPEN) as fileDialog:
if fileDialog.ShowModal() == wx.ID_CANCEL:
return # user changed his mind
pathname = fileDialog.GetPath()
else:
with wx.DirDialog(frame, "Export Result ", style=wx.FD_OPEN) as dirDialog:
if dirDialog.ShowModal() == wx.ID_CANCEL:
return # user changed his mind
pathname = dirDialog.GetPath()
# save the current contents in the file
frame.paths[index] = pathname
p=[frame.p0, frame.p1, frame.p2, frame.p3]
p[index].SetValue(pathname)
if __name__=='__main__':
# print citation
print('\n\n'
'\n****************************** <3 Thank you for using our toolbox! <3 ***********************************'
'\n********************************* PLEASE CITE THE FOLLOWING PAPER ***************************************'
'\nLévy S, Rapacchi S, Massire A, et al. Intravoxel Incoherent Motion at 7 Tesla to quantify human spinal '
'\ncord perfusion: limitations and promises. Magn Reson Med. 2020;00:1-20. https://doi.org/10.1002/mrm.28195'
'\n*********************************************************************************************************'
'\n\n')
app = wx.App()
# instance and show frame to fit data
frameFitData = FrameFitData(parent=None, id=-1, title='IVIM toolbox: fit data')
frameFitData.Show()
# instance and show frame to compute required SNR
frameRequiredSNR = FrameRequiredSNR(parent=None, title='IVIM toolbox: compute required SNR')
frameRequiredSNR.Show()
app.MainLoop()