Example #1
0
    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
Example #2
0
    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