def process_img(img_path):
IJ.log('Processing {} ...'.format(img_path))
# open image
imp = IJ.openImage(img_path)
imp.show()
w_big = imp.getWindow()
w_big.setLocationAndSize(1050, 400, 500, 500)
# read relative csv file rows (coordinates of centers)
img_name, img_extension = os.path.splitext(img_path)
marker_path = img_name + '.csv'
if not os.path.exists(marker_path):
root = os.path.dirname(marker_path)
IJ.log('Creating corrected CSV files in {}...'.format(root))
mrk.markers_to_csv(root, y_inv_height=imp.height)
markers = mrk.read_marker(marker_path, to_int=True)
for cs in gen_cell_stacks(imp, markers, cube_roi_dim, scaleZ):
# identify cell in original image
imp.setSlice(cs.seed[2] + 1)
point = PointRoi(cs.seed[0], cs.seed[1])
point.setSize(3)
point.setColor(Color.RED)
imp.setRoi(point)
if discard_margin_cells:
if not cs.onBorder:
process_cell(cs)
else:
IJ.log('Skipped on border cell in seed ' + str(cs.seed))
else:
process_cell(cs)
c = raw_input(
"Press enter to show the next cell or 'n' to go to the next image\n"
)
cs.close()
if c == 'n':
IJ.log("Skipped remaining cells")
break
