Instantiating Pylinac classes from Pydicom datasets issue #550

[alanphys]

As proof of concept I have this working. You can do:

from pydicom import dcmread
from pylinac.core.image import DicomImageStack, DicomImage, load
from pylinac import CatPhan604
import matplotlib
matplotlib.use('TkAgg')
from pathlib import Path
import os.path as osp

test_dir = r'/home/.../TestFiles/CatPhan604/'
ds_list =[dcmread(path) for path in Path(test_dir).iterdir()]
dis = DicomImageStack(ds_list, min_number=3)
ct = CatPhan604(dis)
ct.analyze()
ct.publish_pdf(osp.join(test_dir,'result.pdf'))

or

test_dir = r'/home/.../TestFiles/CatPhan604/'
ds_list =[dcmread(path) for path in Path(test_dir).iterdir()]
ct = CatPhan604.from_dataset(ds_list)
ct.analyze()
ct.publish_pdf(osp.join(test_dir,'result.pdf'))

There is still a lot of work to be done, but at this stage I need to know that I haven't broken something upstream. The tests, such as I've been able to run, are passing, but I can only 42 of the 702 tests are running. @jrkerns, again, when you have a gap please run the test suite on this PR. I've also incorporated the commits from PR 547 and 553 in this PR.

Regards
Alan

[jrkerns]

Tests are passing.