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Merge branch 'fix/dont-kill-fiji'
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* fix/dont-kill-fiji:
  Catch SystemExit exceptions in CMTK Registration
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@jefferis
jefferis committed Apr 16, 2015
2 parents a7999ea + 61fc034 commit dc83659
Showing 1 changed file with 135 additions and 132 deletions.
267 changes: 135 additions & 132 deletions CMTK_Registration_GUI.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,136 +81,139 @@ def updateOuputFolders():
return

## START!

gd = GenericDialogPlus('CMTK Registration GUI')

# 0.1) Identify path to CMTK binaries
bindir=cmtkgui.install_dir()
print 'bindir is ' + bindir
# 0.1) Identify path to munger.pl script
#munger='/Users/jefferis/bin/munger.pl'
munger=cmtkgui.tool_path('munger')
print 'munger is ' + munger
gd.addHelp("http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui")

dirFieldWidth=50
gdMargin=130
gd.addDirectoryField("Registration Folder",None,dirFieldWidth)
regrootf = gd.getStringFields().get(0)
# reference brain
gd.addFileField("Reference Brain", "",dirFieldWidth)
# input directory/image
gd.addDirectoryOrFileField("Input Image or Image Directory",None,dirFieldWidth)
imgdirf = gd.getStringFields().get(2)

gd.setInsets(10,gdMargin,10)
gd.addMessage("Output folders:")
outputf=gd.getMessage()

# what to do: affine/warp/reformat
gd.setInsets(10,200,10)
gd.addCheckboxGroup(3,2,["affine","01","warp","02","reformat","03"],[True,True,True,True,True,True],["Registration Actions","Reformat Channels"])
#gd.addCheckboxGroup(1,3,["01","02","03"],[True,True,True],["Reformat Channels"])

# Registration options
# Jefferis,Potter 2007, Cachero,Ostrovsky 2010, Manual
gd.addChoice("Registration Params",["Jefferis, Potter 2007","Cachero, Ostrovsky 2010"],"Jefferis, Potter 2007")
choicef=gd.getChoices().get(0)
print choicef.getSelectedItem()

# final Action (Test, Run, Write Script)
gd.addChoice("Action",["Test","Write Script","Run"],"Write Script")
font=Font("SansSerif",Font.BOLD,12)

# Advanced options
gd.setInsets(25,100,10)
gd.addMessage("Advanced Options:",font)
advancedoptionsf=gd.getMessage()

ncores=Runtime.getRuntime().availableProcessors()
defaultCores=1
if ncores >=8:
defaultCores=4
elif ncores>=4:
defaultCores=2
gd.addSlider("Number of cpu cores to use",1,ncores,defaultCores)

gd.setInsets(0,230,10)
gd.addCheckbox("Verbose log messages",False)

gd.addStringField("Output folder suffix","",20)
outsuffixf = gd.getStringFields().get(3)

gd.addStringField("(Further) Registration Params","",50);
regparamf = gd.getStringFields().get(4)
gd.addStringField("Additional Arguments to munger.pl","",50);

regrootf.addTextListener(RegRootListener())
imgdirf.addTextListener(ImageDirListener())
outsuffixf.addTextListener(OuputSuffixListener())
choicef.addItemListener(RegParamListener())
# used for errors etc
gd.addMessage("Start by choosing a registration directory or images directory!")
statusf=gd.getMessage()
gd.showDialog()
if gd.wasCanceled():
sys.exit("User cancelled!")
# Process Dialog Choices
rootDir=gd.getNextString()
os.chdir(rootDir)
refBrain=gd.getNextString()
image=gd.getNextString()
image=relpath(image,rootDir)
print refBrain
refBrain=relpath(refBrain,rootDir)
print refBrain

affine=gd.getNextBoolean()
ch01=gd.getNextBoolean()
warp=gd.getNextBoolean()
ch02=gd.getNextBoolean()
reformat=gd.getNextBoolean()
ch03=gd.getNextBoolean()
munger_actions=""
if affine:
munger_actions+="-a "
if warp:
munger_actions+="-w "
if reformat:
channels=''
if ch01:
channels+='01'
if ch02:
channels+='02'
if ch03:
channels+='03'
if channels != '':
munger_actions+="-r "+channels+" "

verbose=gd.getNextBoolean()
corestouse=gd.getNextNumber()
outsuffix=gd.getNextString()
regparams=gd.getNextChoice()
print regparams
regparams=gd.getNextString()
mungeropts=gd.getNextString()
action=gd.getNextChoice()

if action == 'Test': mungeropts+=' -t'
if verbose: mungeropts+=' -v'
mungeropts+=' -T %d' % (int(corestouse))

if not outsuffix == '':
mungeropts += ' -d .'+outsuffix

cmd='"%s" -b "%s" %s %s %s -s "%s" %s' % (munger,bindir,munger_actions,regparams,mungeropts,refBrain,image)
print cmd

if action !='Test':
# make a script
script=makescript(cmd,rootDir,outdir=os.path.join(rootDir,'commands'))
print 'script is %s' % (script)
try:
gd = GenericDialogPlus('CMTK Registration GUI')

# 0.1) Identify path to CMTK binaries
bindir=cmtkgui.install_dir()
print 'bindir is ' + bindir
# 0.1) Identify path to munger.pl script
#munger='/Users/jefferis/bin/munger.pl'
munger=cmtkgui.tool_path('munger')
print 'munger is ' + munger
gd.addHelp("http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui")

dirFieldWidth=50
gdMargin=130
gd.addDirectoryField("Registration Folder",None,dirFieldWidth)
regrootf = gd.getStringFields().get(0)
# reference brain
gd.addFileField("Reference Brain", "",dirFieldWidth)
# input directory/image
gd.addDirectoryOrFileField("Input Image or Image Directory",None,dirFieldWidth)
imgdirf = gd.getStringFields().get(2)

gd.setInsets(10,gdMargin,10)
gd.addMessage("Output folders:")
outputf=gd.getMessage()

# what to do: affine/warp/reformat
gd.setInsets(10,200,10)
gd.addCheckboxGroup(3,2,["affine","01","warp","02","reformat","03"],[True,True,True,True,True,True],["Registration Actions","Reformat Channels"])
#gd.addCheckboxGroup(1,3,["01","02","03"],[True,True,True],["Reformat Channels"])

# Registration options
# Jefferis,Potter 2007, Cachero,Ostrovsky 2010, Manual
gd.addChoice("Registration Params",["Jefferis, Potter 2007","Cachero, Ostrovsky 2010"],"Jefferis, Potter 2007")
choicef=gd.getChoices().get(0)
print choicef.getSelectedItem()

# final Action (Test, Run, Write Script)
gd.addChoice("Action",["Test","Write Script","Run"],"Write Script")
font=Font("SansSerif",Font.BOLD,12)

# Advanced options
gd.setInsets(25,100,10)
gd.addMessage("Advanced Options:",font)
advancedoptionsf=gd.getMessage()

ncores=Runtime.getRuntime().availableProcessors()
defaultCores=1
if ncores >=8:
defaultCores=4
elif ncores>=4:
defaultCores=2
gd.addSlider("Number of cpu cores to use",1,ncores,defaultCores)

gd.setInsets(0,230,10)
gd.addCheckbox("Verbose log messages",False)

gd.addStringField("Output folder suffix","",20)
outsuffixf = gd.getStringFields().get(3)

gd.addStringField("(Further) Registration Params","",50);
regparamf = gd.getStringFields().get(4)
gd.addStringField("Additional Arguments to munger.pl","",50);

regrootf.addTextListener(RegRootListener())
imgdirf.addTextListener(ImageDirListener())
outsuffixf.addTextListener(OuputSuffixListener())
choicef.addItemListener(RegParamListener())
# used for errors etc
gd.addMessage("Start by choosing a registration directory or images directory!")
statusf=gd.getMessage()
gd.showDialog()
if gd.wasCanceled():
sys.exit("User cancelled!")
# Process Dialog Choices
rootDir=gd.getNextString()
os.chdir(rootDir)
refBrain=gd.getNextString()
image=gd.getNextString()
image=relpath(image,rootDir)
print refBrain
refBrain=relpath(refBrain,rootDir)
print refBrain

affine=gd.getNextBoolean()
ch01=gd.getNextBoolean()
warp=gd.getNextBoolean()
ch02=gd.getNextBoolean()
reformat=gd.getNextBoolean()
ch03=gd.getNextBoolean()
munger_actions=""
if affine:
munger_actions+="-a "
if warp:
munger_actions+="-w "
if reformat:
channels=''
if ch01:
channels+='01'
if ch02:
channels+='02'
if ch03:
channels+='03'
if channels != '':
munger_actions+="-r "+channels+" "

verbose=gd.getNextBoolean()
corestouse=gd.getNextNumber()
outsuffix=gd.getNextString()
regparams=gd.getNextChoice()
print regparams
regparams=gd.getNextString()
mungeropts=gd.getNextString()
action=gd.getNextChoice()

if action == 'Test': mungeropts+=' -t'
if verbose: mungeropts+=' -v'
mungeropts+=' -T %d' % (int(corestouse))

if not outsuffix == '':
mungeropts += ' -d .'+outsuffix

cmd='"%s" -b "%s" %s %s %s -s "%s" %s' % (munger,bindir,munger_actions,regparams,mungeropts,refBrain,image)
print cmd

if action !='Test':
# make a script
script=makescript(cmd,rootDir,outdir=os.path.join(rootDir,'commands'))
print 'script is %s' % (script)

if action != 'Write Script':
# Actually run the script
subprocess.call(script,shell=False)
if action != 'Write Script':
# Actually run the script
subprocess.call(script,shell=False)
except SystemExit, e:
from ij import IJ
IJ.showStatus(str(e))

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