51 lines
1.7 KiB
Python
51 lines
1.7 KiB
Python
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"""
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Wrapper over bftools
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"""
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import os
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import subprocess
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def convert(input_path, output_path, tile_x=None, tile_y=None,
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channel=0, series=0, crop_indices = None, bigtiff=False):
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"""
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Convert an input image in ZEISS LSM or CZI format to an OME TIFF.
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Slice spacing information is lost in this operation for some reason.
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"""
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# Set up the command for bfconvert
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bf_tools_dir = os.getenv('BFTOOLS_DIR', os.getcwd()) + "/"
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command = bf_tools_dir + "/bfconvert "
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if not os.path.exists(output_path):
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os.makedirs(output_path)
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output_path += "/" + os.path.splitext(input_path)[0] + "_T%t"
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# Only one channel at a time
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command += " -channel " + str(channel) + " "
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output_path += "_C%c"
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# Only one series at a time
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command += " -series " + str(series) + " "
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output_path += "_S%s"
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# Set up tiles
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if tile_x is not None and tile_y is not None:
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command += " -tilex " + str(tile_x) + " -tiley " + str(tile_y) + " "
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output_path += "_tile_X%x_Y%y_ID_%m"
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# bigtiff
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if bigtiff:
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command += " -bigtiff "
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# crop
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if crop_indices is not None:
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command += " -crop " + str(int(crop_indices[4])) + "," + str(int(crop_indices[5]))
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command += "," + str(int(crop_indices[6])) + "," + str(int(crop_indices[7])) + " "
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global_index = crop_indices[0] + crop_indices[1]*crop_indices[2]
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output_path += "_x_"+ str(int(crop_indices[0])) + "_y_" + str(int(crop_indices[1])) + "_m_" + str(int(global_index))
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command += input_path + " " + output_path + ".tiff"
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# Do the conversion
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p = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
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p.wait()
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