def write_extraction_mask(self):
""" write both the .roi file and the tif pages
ROI file format specification: each row a ROI,
first col: kw for roi type
if circle: label, layer, pos x, pos y, diameter
if poly: label, layer, pos x_1, pos_y1, ... pos x_n, pos y_n
"""
outpath = self.SaveFileDialog(
title='saving ROIs',
default_dir=self.Main.Options.general['cwd'],
extension='*.roi')
outpath = self.append_extension(outpath, '.roi')
fh = open(outpath, 'w')
# iterate over ROIs
for i, ROI in enumerate(self.Main.ROIs.ROI_list):
label = str(ROI.label)
if type(ROI) == myCircleROI:
# pos = sp.array([ROI.pos().x(),ROI.pos().y()])
# pos = self.get_ROI_position(ROI)
x = str(sp.around(ROI.center[0], decimals=2))
y = str(sp.around(ROI.center[1], decimals=2))
d = str(sp.around(ROI.diameter, decimals=2))
fh.write('\t'.join(['circle', label, x, y, d, '\n']))
if type(ROI) == myPolyLineROI:
fh.write('\t'.join(['polygon', label]))
fh.write('\t')
handle_pos = [tup[1] for tup in ROI.getSceneHandlePositions()]
pos_mapped = [ROI.ViewBox.mapToView(pos) for pos in handle_pos]
for pos in (pos_mapped):
x = pos.x()
y = pos.y()
fh.write('\t'.join([
str(sp.around(x, decimals=2)),
str(sp.around(y, decimals=2))
]))
fh.write('\t')
fh.write('\n')
fh.close()
print "saved ROIs in .roi format to", outpath
# outpath = os.path.splitext(outpath)[0] + '_mask.tif'
# outpath = self.MainWindow.SaveFileDialog(title='saving ROIs',defaultdir=self.path,extension='.tif')
# extraction mask
self.Main.Processing.calc_extraction_mask()
io.save_tstack(self.Main.Data.extraction_mask.astype('uint16'),
os.path.splitext(outpath)[0] + '_mask.tif')
print "saved ROIs in .tif format to", outpath
pass
def write_extraction_mask(self):
""" write both the .roi file and the tif pages
ROI file format specification: each row a ROI,
first col: kw for roi type
if circle: label, layer, pos x, pos y, diameter
if poly: label, layer, pos x_1, pos_y1, ... pos x_n, pos y_n
"""
outpath = self.SaveFileDialog(title='saving ROIs',default_dir = self.Main.Options.general['cwd'], extension='*.roi')
outpath = self.append_extension(outpath, '.roi')
fh = open(outpath,'w')
# iterate over ROIs
for i,ROI in enumerate(self.Main.ROIs.ROI_list):
label = str(ROI.label)
if type(ROI) == myCircleROI:
# pos = sp.array([ROI.pos().x(),ROI.pos().y()])
# pos = self.get_ROI_position(ROI)
x = str(sp.around(ROI.center[0],decimals=2))
y = str(sp.around(ROI.center[1],decimals=2))
d = str(sp.around(ROI.diameter,decimals=2))
fh.write('\t'.join(['circle',label,x,y,d,'\n']))
if type(ROI) == myPolyLineROI:
fh.write('\t'.join(['polygon',label]))
fh.write('\t')
handle_pos = [tup[1] for tup in ROI.getSceneHandlePositions()]
pos_mapped = [ROI.ViewBox.mapToView(pos) for pos in handle_pos]
for pos in (pos_mapped):
x = pos.x()
y = pos.y()
fh.write('\t'.join([str(sp.around(x,decimals=2)),str(sp.around(y,decimals=2))]))
fh.write('\t')
fh.write('\n')
fh.close()
print("saved ROIs in .roi format to", outpath)
# outpath = os.path.splitext(outpath)[0] + '_mask.tif'
# outpath = self.MainWindow.SaveFileDialog(title='saving ROIs',defaultdir=self.path,extension='.tif')
# extraction mask
self.Main.Processing.calc_extraction_mask()
io.save_tstack(self.Main.Data.extraction_mask.astype('uint16'),os.path.splitext(outpath)[0] + '_mask.tif')
print("saved ROIs in .tif format to", outpath)
pass