def decode_roi(roi_file):
roi_obj = RoiDecoder(roi_file)
x = roi_obj.getRoi().getPolygon().getBounds().x
y = roi_obj.getRoi().getPolygon().getBounds().y
width = roi_obj.getRoi().getPolygon().getBounds().width
height = roi_obj.getRoi().getPolygon().getBounds().height
return x, y, width, height
def roisFromFile(filePath):
""" Get rois ROI[] from an roi file encoded by imagej """
rois = []
isZip = zipfile.is_zipfile(filePath)
if isZip:
print("It is a zip-file")
zf = zipfile.ZipFile(filePath, 'r')
print zf.namelist()
for filename in zf.namelist():
try:
roiFile = zf.read(filename)
rd = RoiDecoder(roiFile)
roi = rd.getRoi()
rois.append(roi)
except KeyError:
print 'ERROR: Did not find %s in zip file' % filename
else:
rd = RoiDecoder(filePath)
rois.append(rd.getRoi())
return(rois)
}
Method = Dico_Method[method]
# Initialise time
ListTime = []
# Initialise list of templates (rather than opening them for every image iteration)
List_Template = [
IJ.openImage(templ_file.getPath()) for templ_file in template_files
]
### Search ROI ? ###
# Check if there is a searchRoi
if roi_file:
from ij.io import RoiDecoder
searchRoi = RoiDecoder.open(roi_file.getPath())
else:
searchRoi = None
# Check if it is a rectangular one
if searchRoi and searchRoi.getTypeAsString() == "Rectangle":
Bool_SearchRoi = True
else:
Bool_SearchRoi = False
# Define Offset for BBox if proper searchRoi
if Bool_SearchRoi:
dX = searchRoi.getXBase()
dY = searchRoi.getYBase()
else:
dX = dY = 0
raise Exception('The expected number of object should be at least 1')
if score_threshold < 0 or score_threshold > 1:
raise Exception('The score threshold should be in range [0,1]')
#if tolerance<0 or tolerance>1:
# raise Exception('Tolerance should be in range [0,1]')
if max_overlap < 0 or max_overlap > 1:
raise Exception('The max overlap should be in range [0,1]')
### Search ROI ? ###
# Check if there is a searchRoi
if RoiPath:
from ij.io import RoiDecoder
searchRoi = RoiDecoder.open(RoiPath)
else:
searchRoi = None
# Check if it is a rectangular one
if searchRoi and searchRoi.getTypeAsString() == "Rectangle":
Bool_SearchRoi = True
dX = int(searchRoi.getXBase())
dY = int(searchRoi.getYBase())
else:
Bool_SearchRoi = False
dX = dY = 0
## File or Folder
# Template(s)