0)
Win.addMessage("If more than 1 template expected :")
Win.addNumericField("Score_Threshold [0-1]",
prefs.getFloat("Score_Threshold", 0.5), 2)
#Win.addNumericField("Min_peak_height relative to neighborhood ([0-1], decrease to get more hits)", prefs.getFloat("Tolerance",0.1), 2)
Win.addNumericField("Maximal_overlap between Bounding boxes [0-1]",
prefs.getFloat("MaxOverlap", 0.4), 2)
Win.addMessage("Outputs")
Win.addCheckbox("Add_ROI detected to ROI manager",
prefs.getInt("AddRoi", True))
Win.addCheckbox("Show_result table", prefs.getInt("ShowTable", False))
Win.addMessage("""If you use this plugin please cite :
Laurent SV Thomas, Jochen Gehrig
bioRxiv 619338; doi: https://doi.org/10.1101/619338""")
Win.addHelp(
"https://github.com/multi-template-matching/MultiTemplateMatching-Fiji/wiki"
)
Win.showDialog()
if Win.wasOKed():
template = Win.getNextImage()
image = Win.getNextImage()
flipv = Win.getNextBoolean()
fliph = Win.getNextBoolean()
angles = Win.getNextString()
method = Win.getNextChoice()
n_hit = int(Win.getNextNumber())
score_threshold = Win.getNextNumber()
#tolerance = Win.getNextNumber()
tolerance = 0
prefs.getFloat("Score_Threshold", 0.5), 2)
#Win.addNumericField("Min_peak_height relative to neighborhood ([0-1], decrease to get more hits)", prefs.getFloat("Tolerance",0.1), 2)
Win.addNumericField("Maximal_overlap between Bounding boxes [0-1]",
prefs.getFloat("MaxOverlap", 0.4), 2)
# Outputs
Win.addMessage("Outputs")
Win.addCheckbox("Open_images as a stack (must have identical sizes)",
prefs.getInt("ShowImages", True))
Win.addCheckbox("Add_ROI detected to ROI Manager",
prefs.getInt("AddRoi", True))
Win.addCheckbox("Show_result table", prefs.getInt("ShowTable", False))
Win.addMessage("""If you use this plugin please cite :
Laurent SV Thomas, Jochen Gehrig
bioRxiv 619338; doi: https://doi.org/10.1101/619338""")
Win.addHelp("https://github.com/LauLauThom/MultiTemplateMatching/wiki")
Win.showDialog()
if Win.wasOKed():
TemplatePath = Win.getNextString()
ImagePath = Win.getNextString()
RoiPath = Win.getNextString()
flipv = Win.getNextBoolean()
fliph = Win.getNextBoolean()
angles = Win.getNextString()
method = Win.getNextChoice()
n_hit = int(Win.getNextNumber())
score_threshold = Win.getNextNumber()
#tolerance = Win.getNextNumber()
tolerance = 0
gdp.addCheckbox("Always Select Golgi", golgi_select_def)
gdp.addToSameRow()
gdp.addCheckbox("Always Auto-Detect Golgi", auto_golgi_def)
gdp.addCheckbox("Mean_Max Detection", mean_max_def)
gdp.addToSameRow()
gdp.addCheckbox("Manual Background Selection", man_bck_def)
gdp.addCheckbox("Auto Position Image Window (position x,y):", auto_pos_def)
gdp.addStringField("x: ", xpos_def, 5)
gdp.addStringField("y: ", ypos_def, 5)
gdp.addMessage("------------------------------------------------------------", italicFont)
progress = images_processed(dest)
gdp.addMessage(str(progress[0])+'% Images Assayed' + ' ' +
'(' + str(progress[2]) + '/' + str(progress[1]) + ')', italicFont)
gdp.addHelp("https://github.com/JohnSargeant-rgb")
gdp.showDialog()
if gdp.wasOKed():
dest = gdp.getNextString().strip()
ProFolder = gdp.getNextString().strip()
Quant = gdp.getNextString().strip()
Quant_MM = gdp.getNextString().strip()
transport_c = gdp.getNextChoice()
file_type = gdp.getNextString().strip()
golgi_c = gdp.getNextChoice()
extension = gdp.getNextString().strip()
zoom_to = int(gdp.getNextChoice())
radius = gdp.getNextString().strip()
color_scale = gdp.getNextChoice()
always_select = gdp.getNextBoolean()
always_auto = gdp.getNextBoolean()
ref="reformatted"
outputf.setText("Output Folders: "+reg+", "+ref)
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()
return
## START!
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:")
