Optimise DicomImage

[alanphys]

Hi James

I was looking through DicomImage in image.py and I saw that DicomImage.__init__ had

        self.metadata = retrieve_dicom_file(path)
        self._original_dtype = self.metadata.pixel_array.dtype
        self._raw_pixels = raw_pixels
        # read a second time to get pixel data
        try:
            path.seek(0)
        except AttributeError:
            pass
        ds = retrieve_dicom_file(path)
        if dtype is not None:
            self.array = ds.pixel_array.astype(dtype)
        else:
            self.array = ds.pixel_array.copy()
        # convert values to HU or CU
        self.array = _rescale_dicom_values(self.array, ds, raw_pixels=raw_pixels)

This seems a bit redundant to me. The old adage "If it aint broke doan fix it" probably applies and I'm sure there are good reasons why it is this way, but if I remove the second file load giving:

        self.metadata = retrieve_dicom_file(path)
        self._original_dtype = self.metadata.pixel_array.dtype
        self._raw_pixels = raw_pixels
        if dtype is not None:
            self.array = self.metadata.pixel_array.astype(dtype)
        else:
            self.array = self.metadata.pixel_array.copy()
        # convert values to HU or CU
        self.array = _rescale_dicom_values(self.array, self.metadata, raw_pixels=raw_pixels)

I get quite a significant performance increase. I tested using:

from pylinac import CatPhan604
import time

for I in range(5):
    start = time.time()
    ct = CatPhan604('../CatPhan604/')
    end = time.time()
    print(end - start)
    del ct

I get for the original function
0.37560391426086426
0.3352365493774414
0.33795595169067383
0.3667294979095459
0.33728504180908203

and for the modified function
0.30944371223449707
0.26961445808410645
0.2696726322174072
0.29987263679504395
0.2696547508239746

for an 88 slice CBCT.

Unfortunately I was not able to run the unit tests due to issue #543 to double check this does not affect anything down stream, but my test sets loaded and analyzed correctly. I realise this is quite a fundamental change but I thought I would put it out there.

Regards
Alan