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55 lines
1.8 KiB
55 lines
1.8 KiB
4 years ago
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from pathlib import Path
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from collections import namedtuple
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from defusedxml import ElementTree
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ArrayParameters = namedtuple(
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"ArrayParameters", ["size_x", "size_y", "dist_x", "dist_y"]
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)
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SpotParameters = namedtuple(
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"SpotParameters",
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["radius_spot", "radius_bkg", "roi_x", "roi_y", "crop_x", "crop_y"],
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)
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def _to_micro_meters(value):
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as_float = float(value)
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return int(as_float * 1000)
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def array_parameters_from_xml(tree):
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layout = tree.find("Layout")
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sx = int(layout.attrib["NofSpotsX"])
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sy = int(layout.attrib["NofSpotsY"])
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dx = _to_micro_meters(layout.attrib["SpotDistMmX"])
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dy = _to_micro_meters(layout.attrib["SpotDistMmY"])
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return ArrayParameters(sx, sy, dx, dy)
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def spot_parameters_from_xml(tree, array_parameters):
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array = tree.find("MicroArrayAnalysis").find("Settings")
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reg = tree.find("Registration").find("Settings")
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rs = _to_micro_meters(array.attrib["MinSpotSizeMm"])
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rb = _to_micro_meters(array.attrib["MaxSpotSizeMm"])
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rx = array_parameters.dist_x
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ry = array_parameters.dist_y
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# ROI is strangely named in params file, it's actually the outside crop
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cx = _to_micro_meters(reg.attrib["ROIMarginWidth"])
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cy = _to_micro_meters(reg.attrib["ROIMarginHeight"])
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return SpotParameters(rs, rb, rx, ry, cx, cy)
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def get_array_parameters(params_file):
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svary_file = Path(params_file).with_suffix(".svary")
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with svary_file.open("r") as file_handle:
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tree = ElementTree.parse(file_handle)
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return array_parameters_from_xml(tree)
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def get_spot_parameters(params_file, array_parameters):
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svalg_file = Path(params_file).with_suffix(".svalg")
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with svalg_file.open("r") as file_handle:
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tree = ElementTree.parse(file_handle)
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return spot_parameters_from_xml(tree, array_parameters)
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